From f07f0fb605129f5536480607bf42c0b4e26f39e6 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 11 Feb 2015 20:46:17 +0000
Subject: [PATCH 001/211] Hidden switch for unscaled output in polysomy

---
 polysomy.c | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/polysomy.c b/polysomy.c
index e5a94dca1..3c9743164 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -59,7 +59,7 @@ dist_t;
 
 typedef struct
 {
-    int ndist, nbins;
+    int ndist, nbins, ra_rr_scaling;
     double *xvals;
     dist_t *dist;
     char **argv, *output_dir;
@@ -72,7 +72,7 @@ args_t;
 
 FILE *open_file(char **fname, const char *mode, const char *fmt, ...);
 
-static void init_dist(dist_t *dist, int verbose)
+static void init_dist(args_t *args, dist_t *dist, int verbose)
 {
     // isolate RR and AA peaks and rescale so that they are comparable to hets
     int i, irr, iaa, n = dist->nvals;
@@ -123,6 +123,7 @@ static void init_dist(dist_t *dist, int verbose)
     //  Y:  cn=0     ra/rr=0.008316      aa/ra=7.250000      nra=12
     //  MT: cn=0     ra/rr=0.013699      aa/ra=0.666667      nra=3
 
+    if ( !args->ra_rr_scaling ) max_ra = max_aa = max_rr;
     if ( !sra || (sra/srr<0.1 && saa/sra>1.0) )
     {
         max_ra = max_aa;
@@ -208,7 +209,7 @@ static void init_data(args_t *args)
     bcf_sr_destroy(files);
 
     for (idist=0; idist<args->ndist; idist++)
-        init_dist(&args->dist[idist],args->verbose);
+        init_dist(args, &args->dist[idist],args->verbose);
 
     args->dat_fp = open_file(&args->dat_fname,"w","%s/dist.dat", args->output_dir);
     fprintf(args->dat_fp, "# This file was produced by: bcftools polysomy(%s+htslib-%s), the command line was:\n", bcftools_version(),hts_version());
@@ -293,13 +294,18 @@ static void init_data(args_t *args)
         "   plt.savefig(outdir+'/copy-number.png')\n"
         "   plt.close()\n"
         "\n"
+        "class myParser(argparse.ArgumentParser):\n"
+        "   def error(self, message):\n"
+        "       self.print_help()\n"
+        "       sys.stderr.write('error: %%s\\n' %% message)\n"
+        "       sys.exit(2)\n"
+        "\n"
         "def main():\n"
-        "   parser = argparse.ArgumentParser()\n"
+        "   parser = myParser()\n"
         "   parser.add_argument('-a', '--all', action='store_true', help='Create all plots')\n"
         "   parser.add_argument('-c', '--copy-number', action='store_true', help='Create copy-number plot')\n"
         "   parser.add_argument('-d', '--distrib', metavar='CHR', help='Plot BAF distribution of a single chromosome')\n"
         "   args = parser.parse_args()\n"
-        "   if args.distrib==None and not args.all and not args.copy_number: parser.print_help()\n"
         "   dat = {}; fit = {}; cn = {}\n"
         "   read_dat(dat,fit,cn)\n"
         "   if args.distrib!=None:\n"
@@ -309,6 +315,8 @@ static void init_data(args_t *args)
         "       plot_copy_number(cn)\n"
         "   elif args.copy_number:\n"
         "       plot_copy_number(cn)\n"
+        "   else:\n"
+        "       for chr in dat: plot_dist(dat,fit,chr)\n"
         "\n"
         "if __name__ == '__main__':\n"
         "   main()\n",
@@ -611,9 +619,11 @@ int main_polysomy(int argc, char *argv[])
     args->fit_th = 3.0;
     args->cn_penalty = 0.7;
     args->peak_symmetry = 0.7;
+    args->ra_rr_scaling = 1;
 
     static struct option loptions[] = 
     {
+        {"ra-rr-scaling",0,0,1},    // hidden option
         {"verbose",0,0,'v'},
         {"fit-th",1,0,'f'},
         {"cn-penalty",1,0,'c'},
@@ -631,6 +641,7 @@ int main_polysomy(int argc, char *argv[])
     {
         switch (c) 
         {
+            case  1 : args->ra_rr_scaling = 0; break;
             case 'f': 
                 args->fit_th = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -f %s\n", optarg);

From 278cb3397e69cd922f2b2285240636802634818c Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 12 Mar 2015 13:30:10 +0000
Subject: [PATCH 002/211] polysomy: new options, large rewrites at mostly
 unchanged performance

- rewritten for greater experimental flexibility
- the AA peak can be included in the fit (the -i option)
- the minimum fraction of aberrant cells as a command line parameter (-m)
- control the minimum cn4 bump size (-b)
---
 Makefile   |   2 +-
 peakfit.c  | 595 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 peakfit.h  |  49 +++++
 polysomy.c | 512 ++++++++++++++++++++++-----------------------
 4 files changed, 887 insertions(+), 271 deletions(-)
 create mode 100644 peakfit.c
 create mode 100644 peakfit.h

diff --git a/Makefile b/Makefile
index 3cf92a21e..92139048f 100644
--- a/Makefile
+++ b/Makefile
@@ -56,7 +56,7 @@ GSL_LIBS       =
 # and LICENSE documents to understand license implications.
 ifdef USE_GPL
     EXTRA_CPPFLAGS += -DUSE_GPL
-    OBJS += polysomy.o
+    OBJS += polysomy.o peakfit.o
     GSL_LIBS = -lgsl -lcblas
 endif
 
diff --git a/peakfit.c b/peakfit.c
new file mode 100644
index 000000000..93f1acd60
--- /dev/null
+++ b/peakfit.c
@@ -0,0 +1,595 @@
+/* The MIT License
+
+   Copyright (c) 2013-2014 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include "peakfit.h"
+#include <stdio.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_multifit_nlin.h>
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <assert.h>
+#include <math.h>
+
+#define NPARAMS 5
+
+// gauss params: sqrt(scale), center, sigma
+typedef struct _peak_t
+{
+    int fit_mask;
+    double params[NPARAMS], ori_params[NPARAMS];    // current and input parameters
+    struct { int scan; double min, max, best; } mc[NPARAMS];    // monte-carlo settings and best parameter
+    void (*calc_f)  (int nvals, double *xvals, double *yvals, void *args);
+    void (*calc_df) (int nvals, double *xvals, double *yvals, double *dfvals, int idf, void *args);
+    void (*print_func) (struct _peak_t *pk, kstring_t *str);
+    void (*convert_get) (struct _peak_t *pk, double *params);
+    double (*convert_set) (struct _peak_t *pk, int iparam, double value);
+}
+peak_t;
+
+struct _peakfit_t
+{
+    int npeaks, mpeaks, nparams, mparams;
+    peak_t *peaks;
+    double *params;
+    int nvals, mvals;
+    double *xvals, *yvals, *vals;
+    kstring_t str;
+    int verbose, nmc_iter;
+};
+
+
+/*
+    Gaussian peak with the center bound in the interval <d,e>:
+        yi = scale^2 * exp(-(xi-z)^2/sigma^2)
+
+        dy/dscale  = 2*scale * EXP
+        dy/dcenter = -scale^2 * sin(center) * (e-d) * (xi - z) * EXP / sigma^2
+        dy/dsigma  = 2*scale^2 * (xi - z)^2 * EXP / sigma^3
+
+    where
+        z   = 0.5*(cos(center)+1)*(e-d) + d
+        EXP = exp(-(xi-z)^2/sigma^2)
+*/
+void bounded_gaussian_calc_f(int nvals, double *xvals, double *yvals, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale2 = pk->params[0] * pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+    double d = pk->params[3];
+    double e = pk->params[4];
+    double z = 0.5*(cos(center)+1)*(e-d) + d;
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double tmp = (xvals[i] - z)/sigma;
+        yvals[i] += scale2 * exp(-tmp*tmp);
+    }
+}
+void bounded_gaussian_calc_df(int nvals, double *xvals, double *yvals, double *dfvals, int idf, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale  = pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+    double d = pk->params[3];
+    double e = pk->params[4];
+    double z = 0.5*(cos(center)+1)*(e-d) + d;
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double EXP = exp(-(xvals[i]-z)*(xvals[i]-z)/sigma/sigma);
+        double zi  = xvals[i] - z;
+        if ( idf==0 )       // dscale
+            dfvals[i] += 2*scale*EXP;
+        else if ( idf==1 )  // dcenter
+            dfvals[i] -= scale*scale*sin(center)*(e-d)*zi*EXP/sigma/sigma;
+        else if ( idf==2 )  // dsigma
+            dfvals[i] += 2*scale*scale*zi*zi*EXP/sigma/sigma/sigma;
+    }
+}
+void bounded_gaussian_sprint_func(peak_t *pk, kstring_t *str)
+{
+    double center = pk->params[1];
+    double d = pk->params[3];
+    double e = pk->params[4];
+    double z = 0.5*(cos(center)+1)*(e-d) + d;
+    ksprintf(str,"%f**2 * exp(-(x-%f)**2/%f**2)",fabs(pk->params[0]),z,fabs(pk->params[2]));
+}
+double bounded_gaussian_convert_set(peak_t *pk, int iparam, double value)
+{
+    if ( iparam!=1 ) return value;
+    double d = pk->ori_params[3];
+    double e = pk->ori_params[4];
+    if ( value<d ) value = d;
+    else if ( value>e ) value = e;
+    return acos(2*(value-d)/(e-d) - 1);
+}
+void bounded_gaussian_convert_get(peak_t *pk, double *params)
+{
+    params[0] = fabs(params[0]);
+    params[2] = fabs(params[2]);
+    double b = params[1];
+    double d = params[3];
+    double e = params[4];
+    params[1] = 0.5*(cos(b)+1)*(e-d) + d;
+}
+
+void peakfit_add_bounded_gaussian(peakfit_t *pkf, double a, double b, double c, double d, double e, int fit_mask)
+{
+    pkf->npeaks++;
+    hts_expand0(peak_t,pkf->npeaks,pkf->mpeaks,pkf->peaks);
+
+    int i, nfit = 0;
+    for (i=0; i<NPARAMS; i++) 
+        if ( fit_mask & (1<<i) ) nfit++;
+
+    assert( d<e );
+
+    pkf->nparams += nfit;
+    hts_expand0(double,pkf->nparams,pkf->mparams,pkf->params);
+
+    peak_t *pk = &pkf->peaks[pkf->npeaks-1];
+    memset(pk, 0, sizeof(peak_t));
+
+    pk->calc_f      = bounded_gaussian_calc_f;
+    pk->calc_df     = bounded_gaussian_calc_df;
+    pk->print_func  = bounded_gaussian_sprint_func;
+    pk->convert_set = bounded_gaussian_convert_set;
+    pk->convert_get = bounded_gaussian_convert_get;
+    pk->fit_mask    = fit_mask;
+    pk->ori_params[0] = a;
+    pk->ori_params[2] = c;
+    pk->ori_params[3] = d;
+    pk->ori_params[4] = e;
+    pk->ori_params[1] = pk->convert_set(pk, 1, b);
+}
+
+
+/*
+    Gaussian peak:
+        yi = scale^2 * exp(-(x-center)^2/sigma^2)
+
+        dy/dscale  = 2 * scale * EXP
+        dy/dcenter = 2 * scale^2 * (x-center) * EXP / sigma^2
+        dy/dsigma  = 2 * scale^2 * (x-center)^2 * EXP / sigma^3
+
+    where 
+        EXP = exp(-(x-center)^2/sigma^2)
+*/
+void gaussian_calc_f(int nvals, double *xvals, double *yvals, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale2 = pk->params[0] * pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double tmp = (xvals[i] - center)/sigma;
+        yvals[i] += scale2 * exp(-tmp*tmp);
+    }
+}
+void gaussian_calc_df(int nvals, double *xvals, double *yvals, double *dfvals, int idf, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale  = pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double zi  = xvals[i] - center;
+        double EXP = exp(-zi*zi/(sigma*sigma));
+        if ( idf==0 )       // dscale
+            dfvals[i] += 2*scale*EXP;
+        else if ( idf==1 )  // dcenter
+            dfvals[i] += 2*scale*scale*zi*EXP/(sigma*sigma);
+        else if ( idf==2 )  // dsigma
+            dfvals[i] += 2*scale*scale*zi*zi*EXP/(sigma*sigma*sigma);
+    }
+}
+void gaussian_sprint_func(struct _peak_t *pk, kstring_t *str)
+{
+    ksprintf(str,"%f**2 * exp(-(x-%f)**2/%f**2)",fabs(pk->params[0]),pk->params[1],fabs(pk->params[2]));
+}
+void gaussian_convert_get(peak_t *pk, double *params)
+{
+    params[0] = fabs(params[0]);
+    params[2] = fabs(params[2]);
+}
+
+
+void peakfit_add_gaussian(peakfit_t *pkf, double a, double b, double c, int fit_mask)
+{
+    pkf->npeaks++;
+    hts_expand0(peak_t,pkf->npeaks,pkf->mpeaks,pkf->peaks);
+
+    int i, nfit = 0;
+    for (i=0; i<NPARAMS; i++) 
+        if ( fit_mask & (1<<i) ) nfit++;
+
+    pkf->nparams += nfit;
+    hts_expand0(double,pkf->nparams,pkf->mparams,pkf->params);
+
+    peak_t *pk = &pkf->peaks[pkf->npeaks-1];
+    memset(pk, 0, sizeof(peak_t));
+
+    pk->calc_f      = gaussian_calc_f;
+    pk->calc_df     = gaussian_calc_df;
+    pk->print_func  = gaussian_sprint_func;
+    pk->convert_get = gaussian_convert_get;
+    pk->fit_mask    = fit_mask;
+    pk->ori_params[0] = a;
+    pk->ori_params[1] = b;
+    pk->ori_params[2] = c;
+}
+
+
+/*
+    exp peak:
+        yi = scale^2 * exp((x-center)/sigma^2)
+
+        dy/dscale  = 2 * scale * EXP
+        dy/dcenter = -scale^2  * EXP / sigma^2
+        dy/dsigma  = -2 * scale^2 * (x-center) * EXP / sigma^3
+
+    where 
+        EXP = exp((x-center)/sigma^2)
+*/
+void exp_calc_f(int nvals, double *xvals, double *yvals, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale2 = pk->params[0] * pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        yvals[i] += scale2 * exp((xvals[i]-center)/sigma/sigma);
+    }
+}
+void exp_calc_df(int nvals, double *xvals, double *yvals, double *dfvals, int idf, void *args)
+{
+    peak_t *pk = (peak_t*) args;
+
+    double scale  = pk->params[0];
+    double center = pk->params[1];
+    double sigma  = pk->params[2];
+
+    int i;
+    for (i=0; i<nvals; i++)
+    {
+        double EXP = exp((xvals[i]-center)/sigma/sigma);
+        if ( idf==0 )       // dscale
+            dfvals[i] += 2*scale*EXP;
+        else if ( idf==2 )  // dsigma
+            dfvals[i] -= 2*scale*scale*(xvals[i]-center)*EXP/sigma/sigma/sigma;
+    }
+}
+void exp_sprint_func(struct _peak_t *pk, kstring_t *str)
+{
+    ksprintf(str,"%f**2 * exp((x-%f)/%f**2)",fabs(pk->params[0]),pk->params[1],fabs(pk->params[2]));
+}
+void exp_convert_get(peak_t *pk, double *params)
+{
+    params[0] = fabs(params[0]);
+    params[1] = fabs(params[1]);
+    params[2] = fabs(params[2]);
+}
+
+void peakfit_add_exp(peakfit_t *pkf, double a, double b, double c, int fit_mask)
+{
+    pkf->npeaks++;
+    hts_expand0(peak_t,pkf->npeaks,pkf->mpeaks,pkf->peaks);
+
+    int i, nfit = 0;
+    for (i=0; i<NPARAMS; i++) 
+        if ( fit_mask & (1<<i) ) nfit++;
+
+    assert( !(fit_mask&2) );
+
+    pkf->nparams += nfit;
+    hts_expand0(double,pkf->nparams,pkf->mparams,pkf->params);
+
+    peak_t *pk = &pkf->peaks[pkf->npeaks-1];
+    memset(pk, 0, sizeof(peak_t));
+
+    pk->calc_f      = exp_calc_f;
+    pk->calc_df     = exp_calc_df;
+    pk->print_func  = exp_sprint_func;
+    pk->convert_get = exp_convert_get;
+    pk->fit_mask    = fit_mask;
+    pk->ori_params[0] = a;
+    pk->ori_params[1] = b;
+    pk->ori_params[2] = c;
+}
+
+
+void peakfit_set_params(peakfit_t *pkf, int ipk, double *params, int nparams)
+{
+    peak_t *pk = &pkf->peaks[ipk];
+    int i;
+    if ( pk->convert_set )
+        for (i=0; i<nparams; i++) pk->params[i] = pk->convert_set(pk, i, params[i]);
+    else
+        for (i=0; i<nparams; i++) pk->params[i] = params[i];
+}
+
+void peakfit_get_params(peakfit_t *pkf, int ipk, double *params, int nparams)
+{
+    peak_t *pk = &pkf->peaks[ipk];
+    int i;
+    for (i=0; i<nparams; i++) params[i] = pk->params[i];
+    if ( pk->convert_get ) pk->convert_get(pk, params);
+}
+
+peakfit_t *peakfit_init(void)
+{
+    return (peakfit_t*)calloc(1,sizeof(peakfit_t));
+}
+
+void peakfit_reset(peakfit_t *pkf)
+{
+    pkf->npeaks = pkf->nparams = 0;
+    memset(pkf->peaks,0,sizeof(peak_t)*pkf->mpeaks);
+}
+
+void peakfit_destroy(peakfit_t *pkf)
+{
+    free(pkf->str.s);
+    free(pkf->vals);
+    free(pkf->params);
+    free(pkf->peaks);
+    free(pkf);
+}
+
+int peakfit_calc_f(const gsl_vector *params, void *data, gsl_vector *yvals)
+{
+    peakfit_t *pkf = (peakfit_t *) data;
+
+    int i,j;
+    for (i=0; i<pkf->nvals; i++)
+        pkf->vals[i] = 0;
+
+    int iparam = 0;
+    for (i=0; i<pkf->npeaks; i++)
+    {
+        peak_t *pk = &pkf->peaks[i];
+        for (j=0; j<NPARAMS; j++)
+        {
+            if ( !(pk->fit_mask & (1<<j)) ) continue;
+            pk->params[j] = gsl_vector_get(params,iparam);
+            iparam++;
+        }
+        pk->calc_f(pkf->nvals, pkf->xvals, pkf->vals, pk);
+    }
+
+    for (i=0; i<pkf->nvals; i++)
+        gsl_vector_set(yvals, i, (pkf->vals[i] - pkf->yvals[i])/0.01);
+
+    return GSL_SUCCESS;
+}
+int peakfit_calc_df(const gsl_vector *params, void *data, gsl_matrix *jacobian)
+{
+    peakfit_t *pkf = (peakfit_t *) data;
+
+    int i,j,k,iparam = 0;
+    for (i=0; i<pkf->npeaks; i++)
+    {
+        peak_t *pk = &pkf->peaks[i];
+        int iparam_prev = iparam;
+        for (j=0; j<NPARAMS; j++)
+        {
+            if ( !(pk->fit_mask & (1<<j)) ) continue;
+            pk->params[j] = gsl_vector_get(params,iparam);
+            iparam++;
+        }
+        iparam = iparam_prev;
+        for (j=0; j<NPARAMS; j++)
+        {
+            if ( !(pk->fit_mask & (1<<j)) ) continue;
+            for (k=0; k<pkf->nvals; k++) pkf->vals[k] = 0;
+            pk->calc_df(pkf->nvals, pkf->xvals, pkf->yvals, pkf->vals, j, pk);
+            for (k=0; k<pkf->nvals; k++) gsl_matrix_set(jacobian, k, iparam, pkf->vals[k]);
+            iparam++;
+        }
+    }
+    return GSL_SUCCESS;
+}
+int peakfit_calc_fdf(const gsl_vector *params, void *data, gsl_vector *yvals, gsl_matrix *jacobian)
+{
+    peakfit_calc_f(params, data, yvals);
+    peakfit_calc_df(params, data, jacobian);
+    return GSL_SUCCESS;
+}
+
+double peakfit_evaluate(peakfit_t *pkf)
+{
+    int i;
+    for (i=0; i<pkf->nvals; i++)
+        pkf->vals[i] = 0;
+
+    for (i=0; i<pkf->npeaks; i++)
+        pkf->peaks[i].calc_f(pkf->nvals, pkf->xvals, pkf->vals, &pkf->peaks[i]);
+
+    double sum = 0;
+    for (i=0; i<pkf->nvals; i++)
+        sum += fabs(pkf->vals[i] - pkf->yvals[i]);
+
+    return sum;
+}
+
+const char *peakfit_sprint_func(peakfit_t *pkf)
+{
+    pkf->str.l = 0;
+    int i;
+    for (i=0; i<pkf->npeaks; i++)
+    {
+        if ( i>0 ) kputs(" + ", &pkf->str);
+        pkf->peaks[i].print_func(&pkf->peaks[i], &pkf->str);
+    }
+    return (const char*)pkf->str.s;
+}
+
+void peakfit_verbose(peakfit_t *pkf, int level)
+{
+    pkf->verbose = level;
+}
+
+void peakfit_set_mc(peakfit_t *pkf, double xmin, double xmax, int iparam, int niter)
+{
+    peak_t *pk = &pkf->peaks[ pkf->npeaks-1 ];
+    pk->mc[iparam].scan = 1;
+    pk->mc[iparam].min  = xmin;
+    pk->mc[iparam].max  = xmax;
+    pkf->nmc_iter = niter;
+}
+
+double peakfit_run(peakfit_t *pkf, int nvals, double *xvals, double *yvals)
+{
+    srand(0);   // for reproducibility
+
+    pkf->nvals = nvals;
+    pkf->xvals = xvals;
+    pkf->yvals = yvals;
+    hts_expand0(double,pkf->nvals,pkf->mvals,pkf->vals);
+    if ( !pkf->nparams ) return peakfit_evaluate(pkf);
+
+    gsl_multifit_function_fdf mfunc;
+    mfunc.f   = &peakfit_calc_f;
+    mfunc.df  = &peakfit_calc_df;
+    mfunc.fdf = &peakfit_calc_fdf;
+    mfunc.n   = nvals;
+    mfunc.p   = pkf->nparams;
+    mfunc.params = pkf;
+
+    const gsl_multifit_fdfsolver_type *solver_type;
+    gsl_multifit_fdfsolver *solver;
+    solver_type = gsl_multifit_fdfsolver_lmsder;
+    solver = gsl_multifit_fdfsolver_alloc(solver_type, nvals, mfunc.p);
+    gsl_vector *grad = gsl_vector_alloc(pkf->nparams);
+
+    int imc_iter, i,j, iparam;
+    double best_fit = HUGE_VAL;
+    for (imc_iter=0; imc_iter<=pkf->nmc_iter; imc_iter++)   // possibly multiple monte-carlo iterations
+    {
+        // set GSL parameters
+        iparam = 0;
+        for (i=0; i<pkf->npeaks; i++)
+        {
+            peak_t *pk = &pkf->peaks[i];
+            for (j=0; j<NPARAMS; j++)
+            {
+                pk->params[j] = pk->ori_params[j];
+                if ( pk->mc[j].scan )
+                {
+                    pk->params[j] = rand()*(pk->mc[j].max - pk->mc[j].min)/RAND_MAX + pk->mc[j].min;
+                    if ( pk->convert_set ) pk->params[j] = pk->convert_set(pk, j, pk->params[j]);
+                }
+                if ( !(pk->fit_mask & (1<<j)) ) continue;
+                pkf->params[iparam] = pk->params[j];
+                iparam++;
+            }
+        }
+
+        gsl_vector_view vview = gsl_vector_view_array(pkf->params, mfunc.p);
+        gsl_multifit_fdfsolver_set(solver, &mfunc, &vview.vector);
+
+        // iterate until convergence (or lack of it)
+        int ret, test1 = 0, test2 = 0, niter = 0, niter_max = 500;
+        do
+        {
+            ret = gsl_multifit_fdfsolver_iterate(solver);
+            if ( pkf->verbose >1 )
+            {
+                fprintf(stderr, "%d: ", niter);
+                for (i=0; i<pkf->npeaks; i++)
+                {
+                    peak_t *pk = &pkf->peaks[i];
+                    fprintf(stderr,"\t%f %f %f", pk->params[0],pk->params[1],pk->params[2]);
+                }
+                fprintf(stderr, "\t.. %s\n", gsl_strerror(ret));
+            }
+            if ( ret ) break;
+
+            gsl_multifit_gradient(solver->J, solver->f, grad);
+            test1 = gsl_multifit_test_gradient(grad, 1e-8);
+            test2 = gsl_multifit_test_delta(solver->dx, solver->x, 1e-8, 1e-8);
+        }
+        while ((test1==GSL_CONTINUE || test2==GSL_CONTINUE) && ++niter<niter_max);
+        if ( pkf->verbose >1 )
+        {
+            fprintf(stderr,"test1=%s\n", gsl_strerror(test1));
+            fprintf(stderr,"test2=%s\n", gsl_strerror(test2));
+        }
+
+        // recover parameters
+        iparam = 0;
+        for (i=0; i<pkf->npeaks; i++)
+        {
+            peak_t *pk = &pkf->peaks[i];
+            for (j=0; j<NPARAMS; j++)
+            {
+                if ( !(pk->fit_mask & (1<<j)) ) continue;
+                pk->params[j] = gsl_vector_get(solver->x, iparam++);
+            }
+        }
+
+        // evaluate fit, update best parameters
+        double fit = peakfit_evaluate(pkf);
+        if ( fit<best_fit )
+        {
+            for (i=0; i<pkf->npeaks; i++)
+            {
+                peak_t *pk = &pkf->peaks[i];
+                for (j=0; j<NPARAMS; j++) pk->mc[j].best = pk->params[j];
+            }
+        }
+        if ( fit<best_fit ) best_fit = fit;
+    }
+    gsl_multifit_fdfsolver_free(solver);
+    gsl_vector_free(grad);
+
+    for (i=0; i<pkf->npeaks; i++)
+    {
+        peak_t *pk = &pkf->peaks[i];
+        for (j=0; j<NPARAMS; j++) pk->params[j] = pk->mc[j].best;
+    }
+    return best_fit;
+}
+
+
diff --git a/peakfit.h b/peakfit.h
new file mode 100644
index 000000000..de497cd75
--- /dev/null
+++ b/peakfit.h
@@ -0,0 +1,49 @@
+/* The MIT License
+
+   Copyright (c) 2013-2014 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#ifndef PEAKFIT_H
+#define PEAKFIT_H
+
+typedef struct _peakfit_t peakfit_t;
+
+peakfit_t *peakfit_init(void);
+void peakfit_reset(peakfit_t *pkf);
+void peakfit_destroy(peakfit_t *pkf);
+
+void peakfit_add_gaussian(peakfit_t *pkf, double a, double b, double c, int fit_mask);
+void peakfit_add_bounded_gaussian(peakfit_t *pkf, double a, double b, double c, double d, double e, int fit_mask);
+void peakfit_add_exp(peakfit_t *pkf, double a, double b, double c, int fit_mask);
+void peakfit_set_mc(peakfit_t *pkf, double xmin, double xmax, int iparam, int niter);
+double peakfit_run(peakfit_t *pkf, int nvals, double *xvals, double *yvals);
+double peakfit_evaluate(peakfit_t *pkf);
+
+void peakfit_verbose(peakfit_t *pkf, int level);
+void peakfit_get_params(peakfit_t *pkf, int ipk, double *params, int nparams);
+void peakfit_set_params(peakfit_t *pkf, int ipk, double *params, int nparams);
+const char *peakfit_sprint_func(peakfit_t *pkf);
+
+#endif
+
diff --git a/polysomy.c b/polysomy.c
index 3c9743164..2f06af07a 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -35,24 +35,15 @@
 #include <htslib/vcf.h>
 #include <htslib/synced_bcf_reader.h>
 #include "bcftools.h"
+#include "peakfit.h"
 
 typedef struct
 {
-    int nvals;      // number of data points to fit against (excluding RR,AA peaks)
-    double *xvals;  // xvalues, pointer to dist_t.xvals
-    double *yvals;  // yvalues, pointer to dist_t.yvals
-    int ngauss;     // number of gaussian functions
-}
-data_t;
-
-typedef struct
-{
-    data_t dat;
     int nvals;          // all values, including RR,AA peaks
     double *xvals;      // pointer to args_t.xvals
     double *yvals;   
     int copy_number;    // heuristics to skip futile CN1 fits when no het peak is detected
-    int irr, iaa;       // chop off RR and AA peaks
+    int irr, ira, iaa;  // chop off RR and AA peaks
     char *chr;
 }
 dist_t;
@@ -63,8 +54,8 @@ typedef struct
     double *xvals;
     dist_t *dist;
     char **argv, *output_dir;
-    double fit_th, peak_symmetry, cn_penalty;
-    int argc, plot, verbose, regions_is_file, targets_is_file;
+    double fit_th, peak_symmetry, cn_penalty, bump_size, min_fraction;
+    int argc, plot, verbose, regions_is_file, targets_is_file, include_aa;
     char *dat_fname, *fname, *regions_list, *targets_list, *sample;
     FILE *dat_fp;
 }
@@ -77,9 +68,9 @@ static void init_dist(args_t *args, dist_t *dist, int verbose)
     // isolate RR and AA peaks and rescale so that they are comparable to hets
     int i, irr, iaa, n = dist->nvals;
 
-    // smooth the distribution
+    // smooth the distribution, this is just to find the peaks
     double *tmp = (double*) malloc(sizeof(double)*n);
-    int win = 0.02*n < 1 ? 1 : 0.02*n;
+    int win = 0.04*n < 1 ? 1 : 0.04*n;
     double avg = 0;
     for (i=0; i<win; i++) avg += dist->yvals[i];
     for (i=0; i<n-win; i++)
@@ -94,9 +85,17 @@ static void init_dist(args_t *args, dist_t *dist, int verbose)
     for (iaa=n-1,i=n-1; i>=n/2; i--) if ( tmp[i] < tmp[iaa] ) iaa = i;
     irr += win*0.5;
     iaa += win*0.5;
+    if ( iaa>=n ) iaa = n-1;
     if ( irr>=iaa ) error("FIXME: oops, dist normalization failed for %s: %d vs %d\n", dist->chr,irr,iaa); // we may need to be smarter
     free(tmp);
 
+    // clean the data: the AA peak is occasionally not centered at 1.0 but is closer to the center, chop off
+    int imax_aa = iaa;
+    for (i=iaa; i<n; i++)
+        if ( dist->yvals[imax_aa] < dist->yvals[i] ) imax_aa = i;
+    dist->nvals = imax_aa+1;
+    if ( iaa>=dist->nvals ) iaa = dist->nvals-1;
+
     // find the maximum and scale the peaks (first draft: no attempt to join the segments smootly)
     double max_rr = 0, max_aa = 0, max_ra = 0, srr = 0, saa = 0, sra = 0;
     for (i=0; i<irr; i++)
@@ -124,7 +123,7 @@ static void init_dist(args_t *args, dist_t *dist, int verbose)
     //  MT: cn=0     ra/rr=0.013699      aa/ra=0.666667      nra=3
 
     if ( !args->ra_rr_scaling ) max_ra = max_aa = max_rr;
-    if ( !sra || (sra/srr<0.1 && saa/sra>1.0) )
+    if ( !sra || (sra/srr<0.1 && saa/sra>1.0) ) // too few hets, CN1
     {
         max_ra = max_aa;
         dist->copy_number = 1;
@@ -138,12 +137,14 @@ static void init_dist(args_t *args, dist_t *dist, int verbose)
     if ( max_ra ) for (i=irr; i<=iaa; i++) dist->yvals[i] /= max_ra;
     if ( max_aa ) for (i=iaa+1; i<n; i++) dist->yvals[i] /= max_aa;
 
-    dist->dat.yvals = &dist->yvals[irr];
-    dist->dat.xvals = &dist->xvals[irr];
-    dist->dat.nvals = iaa - irr + 1;
+    dist->irr = irr;
+    dist->iaa = iaa;
+    dist->ira = n*0.5;
 
     if ( verbose )
-        fprintf(stderr,"%s:\t cn=%2d \t ra/rr=%f \t aa/ra=%f \t nra=%d\n", dist->chr,dist->copy_number,sra/srr,saa/sra, (int)sra);
+        fprintf(stderr,"%s:\t irr,ira,iaa=%.2f,%.2f,%.2f \t cn=%2d \t ra/rr=%f \t aa/ra=%f \t nra=%d\n", 
+            dist->chr, dist->xvals[irr],dist->xvals[dist->ira],dist->xvals[iaa],
+            dist->copy_number,sra/srr,saa/sra, (int)sra);
 }
 
 static void init_data(args_t *args)
@@ -209,7 +210,17 @@ static void init_data(args_t *args)
     bcf_sr_destroy(files);
 
     for (idist=0; idist<args->ndist; idist++)
+    {
+        #if 0
+            int j;
+            for (j=0; j<args->nbins; j++)
+            {
+                double x = args->dist[idist].xvals[j];
+                args->dist[idist].yvals[j] = exp(-(x-0.5)*(x-0.5)/1e-3);
+            }
+        #endif
         init_dist(args, &args->dist[idist],args->verbose);
+    }
 
     args->dat_fp = open_file(&args->dat_fname,"w","%s/dist.dat", args->output_dir);
     fprintf(args->dat_fp, "# This file was produced by: bcftools polysomy(%s+htslib-%s), the command line was:\n", bcftools_version(),hts_version());
@@ -218,7 +229,7 @@ static void init_data(args_t *args)
         fprintf(args->dat_fp, " %s",args->argv[i]);
     fprintf(args->dat_fp,"\n#\n");
     fprintf(args->dat_fp,"# DIST\t[2]Chrom\t[3]BAF\t[4]Normalized Count\n");
-    fprintf(args->dat_fp,"# FIT\t[2]Chrom\t[3]Mean of fitted Gaussian\t[4]Scale\t[5]Sigma[6]\tMean etc.\n");
+    fprintf(args->dat_fp,"# FIT\t[2]Goodness of Fit\t[3]iFrom\t[4]iTo\t[5]The Fitted Function\n");
     fprintf(args->dat_fp,"# CN\t[2]Chrom\t[3]Estimated Copy Number\t[4]Absolute fit deviation\n");
 
     char *fname = NULL;
@@ -230,7 +241,8 @@ static void init_data(args_t *args)
         "import matplotlib as mpl\n"
         "mpl.use('Agg')\n"
         "import matplotlib.pyplot as plt\n"
-        "import csv,math,sys,argparse\n"
+        "import csv,sys,argparse\n"
+        "from math import exp\n"
         "\n"
         "outdir = '%s'\n"
         "\n"
@@ -247,27 +259,25 @@ static void init_data(args_t *args)
         "              dat[chr].append(row)\n"
         "          elif type=='FIT':\n"
         "              if chr not in fit: fit[chr] = []\n"
-        "              fit[chr] = row[2:]\n"
+        "              fit[chr].append(row)\n"
         "          elif type=='CN':\n"
         "              cn[chr] = row[2]\n"
         "\n"
-        "def fitted_func(xvals,params):\n"
-        "   n = len(params)/3\n"
-        "   out = []\n"
-        "   for x in xvals:\n"
-        "       y = 0\n"
-        "       for i in range(n):\n"
-        "           mean  = float(params[i*3+0])\n"
-        "           scale = float(params[i*3+1])\n"
-        "           sigma = float(params[i*3+2])\n"
-        "           y += scale * math.exp(-(float(x)-mean)**2/sigma**2)\n"
-        "       out.append(y)\n"
-        "   return out\n"
-        "\n"
         "def plot_dist(dat,fit,chr):\n"
         "   fig, ax = plt.subplots(1, 1, figsize=(7,5))\n"
-        "   ax.plot([x[2] for x in dat[chr]],[x[3] for x in dat[chr]],'-',label='Distribution')\n"
-        "   ax.plot([x[2] for x in dat[chr]],fitted_func([x[2] for x in dat[chr]], fit[chr]),'-',label='Best Fit')\n"
+        "   ax.plot([x[2] for x in dat[chr]],[x[3] for x in dat[chr]],'k-',label='Distribution')\n"
+        "   if chr in fit:\n"
+        "       for i in range(len(fit[chr])):\n"
+        "           pfit = fit[chr][i]\n"
+        "           exec('def xfit(x): return '+pfit[5])\n"
+        "           istart = int(pfit[3])\n"
+        "           iend   = int(pfit[4])+1\n"
+        "           vals   = dat[chr][istart:iend]\n"
+        "           args   = {}\n"
+        "           if i==0: args = {'label':'Target to Fit'}\n"
+        "           ax.plot([x[2] for x in vals],[x[3] for x in vals],'r-',**args)\n"
+        "           if i==0: args = {'label':'Best Fit'}\n"
+        "           ax.plot([x[2] for x in vals],[xfit(float(x[2])) for x in vals],'g-',**args)\n"
         "   ax.set_title('BAF distribution, chr'+chr)\n"
         "   ax.set_xlabel('BAF')\n"
         "   ax.set_ylabel('Frequency')\n"
@@ -341,253 +351,202 @@ static void destroy_data(args_t *args)
     fclose(args->dat_fp);
 }
 
-static void save_dist(args_t *args, int idist, int ngauss, double *params)
+static void save_dist(args_t *args, dist_t *dist)
 {
     int i;
     for (i=0; i<args->nbins; i++)
-        fprintf(args->dat_fp,"DIST\t%s\t%f\t%f\n",args->dist[idist].chr,args->dist[idist].xvals[i],args->dist[idist].yvals[i]);
-    fprintf(args->dat_fp,"FIT\t%s", args->dist[idist].chr);
-    for (i=0; i<ngauss*3; i++) fprintf(args->dat_fp,"\t%f", params[i]);
-    fprintf(args->dat_fp,"\n");
+        fprintf(args->dat_fp,"DIST\t%s\t%f\t%f\n",dist->chr,dist->xvals[i],dist->yvals[i]);
 }
-
-int func_f(const gsl_vector *params, void *data, gsl_vector *yvals)
+static void fit_curves(args_t *args)
 {
-    data_t *dat = (data_t *) data;
+    peakfit_t *pkf = peakfit_init();
+    peakfit_verbose(pkf,args->verbose);
 
-    int i, j;
-    for (i=0; i<dat->nvals; i++)
+    int i, nmc = 50;
+    for (i=0; i<args->ndist; i++)
     {
-        double xi = dat->xvals[i];
-        double yi = 0;
-        for (j=0; j<dat->ngauss; j++)
-        {
-            double center = gsl_vector_get(params,j*3 + 0);
-            double scale  = gsl_vector_get(params,j*3 + 1);
-            double sigma  = gsl_vector_get(params,j*3 + 2);
+        dist_t *dist = &args->dist[i];
+        save_dist(args, &args->dist[i]);
 
-            double zi = (xi - center) / sigma;
-            yi += scale*scale * exp(-zi*zi);
+        if ( dist->copy_number!=0 )
+        {
+            fprintf(args->dat_fp,"CN\t%s\t%.2f\n", dist->chr,(float)dist->copy_number);
+            continue;
         }
-        gsl_vector_set(yvals, i, (yi - dat->yvals[i])/0.1);
-    }
-    return GSL_SUCCESS;
-}
 
-int func_df(const gsl_vector *params, void *data, gsl_matrix *jacobian)
-{
-    data_t *dat = (data_t *) data;
-
-    int i, j;
-    for (i=0; i<dat->nvals; i++)
-    {
-        // Jacobian matrix J(i,j) = dfi / dxj,
-        // where fi = (Yi - yi),
-        //       Yi = scale^2 * exp(-(center - xi)^2/sigma^2)
-        //
-
-        double xi = dat->xvals[i];
-        for (j=0; j<dat->ngauss; j++)
+        if ( args->verbose )
+            fprintf(stderr,"%s:\n", dist->chr);
+
+        int nrr_aa  = dist->iaa - dist->irr + 1;
+        int nrr_ra  = dist->ira - dist->irr + 1;
+        int naa_max = dist->nvals - dist->iaa;
+        double xrr  = dist->xvals[dist->irr], *xrr_vals = &dist->xvals[dist->irr], *yrr_vals = &dist->yvals[dist->irr];
+        double xaa  = dist->xvals[dist->iaa], *xaa_vals = &dist->xvals[dist->iaa], *yaa_vals = &dist->yvals[dist->iaa];
+        double xra  = dist->xvals[dist->ira];
+        double xmax = dist->xvals[dist->nvals-1];
+
+        // cn2: cn2a=AA peak, cn2b=RA peak
+        double cn2a_fit = 0;
+        char *cn2a_func = 0;
+        double cn2_params1[3] = {1,1,1} ,cn2_params2[3];
+        if ( args->include_aa )
         {
-            double center = gsl_vector_get(params,j*3 + 0);
-            double scale  = gsl_vector_get(params,j*3 + 1);
-            double sigma  = gsl_vector_get(params,j*3 + 2);
-
-            double zi = (xi - center) / sigma;
-            double ei = exp(-zi*zi);
-
-            gsl_matrix_set(jacobian, i, j*3 + 0, 2*scale*scale*(xi-center)/(sigma*sigma)*ei);
-            gsl_matrix_set(jacobian, i, j*3 + 1, 2*scale*ei);
-            gsl_matrix_set(jacobian, i, j*3 + 2, 2*scale*scale*(xi-center)*(xi-center)/(sigma*sigma*sigma)*ei);
+            peakfit_reset(pkf);
+            peakfit_add_exp(pkf, 1.0,1.0,0.2, 5);
+            peakfit_set_mc(pkf, 0.01,0.3,2,nmc);
+            peakfit_set_mc(pkf, 0.05,1.0,0,nmc);
+            cn2a_fit  = peakfit_run(pkf, naa_max, xaa_vals, yaa_vals);
+            cn2a_func = strdup(peakfit_sprint_func(pkf));
+            peakfit_get_params(pkf,0,cn2_params1,3);
         }
-    }
-    return GSL_SUCCESS;
-}
-
-int func_set(const gsl_vector *params, void *data, gsl_vector *yvals, gsl_matrix *jacobian)
-{
-    func_f(params, data, yvals);
-    func_df(params, data, jacobian);
-    return GSL_SUCCESS;
-}
-static double eval_fit(int nvals, double *xvals, double *yvals, int ngauss, double *params)
-{
-    double sum = 0;
-    int i, j;
-    for (i=0; i<nvals; i++)
-    {
-        double yval = 0;
-        for (j=0; j<ngauss; j++)
+        peakfit_reset(pkf);
+        peakfit_add_gaussian(pkf, 1.0,0.5,0.03, 5);
+        double cn2b_fit = peakfit_run(pkf, nrr_aa,xrr_vals,yrr_vals);
+        char *cn2b_func = strdup(peakfit_sprint_func(pkf));
+        peakfit_get_params(pkf,0,cn2_params2,3);
+        double cn2_fit = cn2a_fit + cn2b_fit;
+
+        // cn3: cn3a=AA peak, cn3b=RA peaks
+        double cn3a_fit = cn2a_fit;
+        char *cn3a_func = cn2a_func;
+        double cn3_params1[5], cn3_params2[5], *cn3_params3 = cn2_params1;
+        double min_dx3 = 0.5 - 1./(args->min_fraction+2);
+        peakfit_reset(pkf);
+        peakfit_add_bounded_gaussian(pkf, 1.0,1/3.,0.03, xrr,xra-min_dx3, 7);
+        peakfit_set_mc(pkf, xrr,xra-min_dx3, 1,nmc);
+        peakfit_add_bounded_gaussian(pkf, 1.0,2/3.,0.03, xra+min_dx3,xaa, 7);
+        peakfit_set_mc(pkf, xra+min_dx3,xaa, 1,nmc);
+        peakfit_run(pkf, nrr_aa, xrr_vals, yrr_vals);
+        peakfit_get_params(pkf,0,cn3_params1,5);
+        peakfit_get_params(pkf,1,cn3_params2,5);
+        double cn3_dx = (0.5-cn3_params1[1] + cn3_params2[1]-0.5)*0.5;
+        peakfit_reset(pkf);
+        peakfit_add_gaussian(pkf, cn3_params1[0],0.5-cn3_dx,cn3_params1[2], 5);
+        peakfit_add_gaussian(pkf, cn3_params2[0],0.5+cn3_dx,cn3_params1[3], 5);
+        double cn3b_fit = peakfit_run(pkf, nrr_aa, xrr_vals, yrr_vals);
+        char *cn3b_func = strdup(peakfit_sprint_func(pkf));
+        double a1 = cn3_params1[0]*cn3_params1[0];
+        double a2 = cn3_params2[0]*cn3_params2[0];
+        double dy_cn3    = a1 > a2 ? a2/a1 : a1/a2;
+        double b1 = cn3_params1[1], b2 = cn3_params2[1];
+        double cn3_frac1 = (1 - 2*b1) / b1;
+        double cn3_frac2 = (2*b2 - 1) / (1 - b2);
+        double cn3_frac  = 0.5*(cn3_frac1 + cn3_frac2);
+        double cn3_fit   = cn3a_fit + cn3b_fit;
+
+        // cn4 (contaminations): cn4a=AA bump, cn4b=RA bump, params1=big peak, params2=small peak
+        // min_frac=1 is interpreted as 50-50 contamination
+        double min_dx4  = 0.25*args->min_fraction;
+        double cn4a_fit = 0;
+        char *cn4a_func = 0;
+        double cn4a_params1[3] = {1,1,1} ,cn4a_params2[3] = {1,1,1}, cn4b_params1[3], cn4b_params2[5];
+        if ( args->include_aa )
         {
-            double center = params[j*3 + 0];
-            double scale  = params[j*3 + 1];
-            double sigma  = params[j*3 + 2];
-            
-            double zi = (xvals[i] - center) / sigma;
-            yval += scale * exp(-zi*zi);
+            peakfit_reset(pkf);
+            peakfit_add_exp(pkf, 0.5,1.0,0.2, 5);
+            peakfit_set_mc(pkf, 0.01,0.3,2,nmc);
+            peakfit_add_bounded_gaussian(pkf, 0.4,(xaa+xmax)*0.5,2e-2, xaa,xmax, 7);
+            peakfit_set_mc(pkf, xaa,xmax, 1,nmc);
+            cn4a_fit  = peakfit_run(pkf, naa_max, xaa_vals,yaa_vals);
+            cn4a_func = strdup(peakfit_sprint_func(pkf));
+            peakfit_get_params(pkf,0,cn4a_params1,3);
+            peakfit_get_params(pkf,1,cn4a_params2,5);
         }
-        sum += fabs(yval - yvals[i]);
-    }
-    return sum;
-}
-
-static int gauss_fit(dist_t *dist, int ngauss, double *params)
-{
-    data_t *dat = &dist->dat;
-    dat->ngauss = ngauss;
-
-    gsl_multifit_function_fdf mfunc;
-    mfunc.f   = &func_f;
-    mfunc.df  = &func_df;
-    mfunc.fdf = &func_set;
-    mfunc.n   = dat->nvals;
-    mfunc.p   = ngauss*3;      // number of fitting parameters
-    mfunc.params = dat;
-
-    const gsl_multifit_fdfsolver_type *solver_type;
-    gsl_multifit_fdfsolver *solver;
-    gsl_vector_view vview = gsl_vector_view_array(params, mfunc.p);
-    solver_type = gsl_multifit_fdfsolver_lmsder;
-    solver = gsl_multifit_fdfsolver_alloc(solver_type, dat->nvals, mfunc.p);
-    gsl_multifit_fdfsolver_set(solver, &mfunc, &vview.vector);
-
-    int i, status;
-    size_t iter = 0;
-    do
-    {
-        status = gsl_multifit_fdfsolver_iterate(solver);
-        if ( status ) break;
-        status = gsl_multifit_test_delta(solver->dx, solver->x, 1e-4, 1e-4);
-    }
-    while (status == GSL_CONTINUE && iter++ < 500);
-
-    for (i=0; i<mfunc.p; i++)
-        params[i] = gsl_vector_get(solver->x, i);
-
-    gsl_multifit_fdfsolver_free(solver);
-    return iter>500 ? -1 : 0;
-}
-
-static double best_fit(args_t *args, dist_t *dist, int ngauss, double *params)
-{
-    if ( ngauss==1 )
-    {
-        gauss_fit(dist,ngauss,params);
-        params[1] *= params[1];
-        return eval_fit(dist->dat.nvals, dist->dat.xvals, dist->dat.yvals, ngauss,params);
-    }
-
-    int i, j, n = 3;
-    int ipk = 3*(ngauss-1);
-    double delta = 0.5 * (params[ipk] - params[0]) / n;
-    double best_params[9], tmp_params[9], best_fit = HUGE_VAL;
-    for (i=0; i<n; i++)
-    {
-        memcpy(tmp_params,params,sizeof(double)*ngauss*3);
-        tmp_params[0]   += delta*i;
-        tmp_params[ipk] -= delta*i;
-        if ( gauss_fit(dist,ngauss,tmp_params)<0 ) continue;    // did not converge
-
-        for (j=0; j<ngauss; j++) tmp_params[j*3+1] *= tmp_params[j*3+1];
-
-        // From the nature of the data, we can assume that in presence of
-        // multiple peaks they will be placed symmetrically around 0.5. Also
-        // their size should be about the same. We evaluate the fit with this
-        // in mind.
-        double dx = fabs(0.5 - tmp_params[0]) + fabs(tmp_params[ipk] - 0.5);
-        tmp_params[0] = 0.5 - dx*0.5;
-        tmp_params[ipk] = 0.5 + dx*0.5;
-        double fit = eval_fit(dist->dat.nvals, dist->dat.xvals, dist->dat.yvals, ngauss, tmp_params);
-
-        if ( best_fit < fit ) continue;     // worse than previous
-        best_fit = fit;
-        memcpy(best_params,tmp_params,sizeof(double)*ngauss*3);
-    }
-    memcpy(params,best_params,sizeof(double)*ngauss*3);
-    return best_fit;
-}
-
-static void print_params(data_t *dat, int ngauss, double *params, float fit, float frac, char fail, char comment)
-{
-    int i, j;
-    printf("\t%c%c fit=%f frac=%.2f .. center,scale,sigma = ", comment,fail?fail:'o',fit,frac);
-    for (i=0; i<ngauss; i++)
-    {
-        if ( i!=0 ) printf("\t");
-        for (j=0; j<3; j++) printf(" %f", params[i*3+j]);
-    }
-    printf("\n");
-}
-static void fit_curves(args_t *args)
-{
-    int i;
-    for (i=0; i<args->ndist; i++)
-    {
-        dist_t *dist = &args->dist[i];
-        if ( dist->copy_number!=0 )
+        peakfit_reset(pkf);
+        peakfit_add_gaussian(pkf, 1.0,0.5,0.03, 5);
+        peakfit_add_bounded_gaussian(pkf, 0.6,0.3,0.03, xrr,xra-min_dx4, 7);
+        peakfit_set_mc(pkf, xrr,xra-min_dx4,1,nmc);
+        double cn4b_fit = peakfit_run(pkf, nrr_ra , xrr_vals, yrr_vals);
+        double cn4_fit = cn4a_fit + 2*cn4b_fit;
+        char *cn4b_func = strdup(peakfit_sprint_func(pkf));
+        peakfit_get_params(pkf,0,cn4b_params1,3);
+        peakfit_get_params(pkf,1,cn4b_params2,5);
+        double cn4b_frac = 1 - 2*cn4b_params2[1];
+        double cn4a_frac = !args->include_aa ? cn4b_frac : 2*(1 - cn4a_params2[1]);
+        double cn4_frac  = (cn4a_frac + cn4b_frac)*0.5;
+        // cn4a_params1: big AA exp peak
+        // cn4a_params2: small AA exp^2 peak
+        // cn4b_params1: big RA exp^2 peak
+        // cn4b_params2: small RA exp^2 peak
+        double bump1a = cn4a_params1[0]*cn4a_params1[0];
+        double bump2a = cn4a_params2[0]*cn4a_params2[0];
+        double bump1b = cn4b_params1[0]*cn4b_params1[0];
+        double bump2b = cn4b_params2[0]*cn4b_params2[0];
+        double dy_cn4a =  args->include_aa ? (bump1a < bump2a ? bump1a/bump2a : bump2a/bump1a) : 1;
+        double dy_cn4b =  bump1b < bump2b ? bump1b/bump2b : bump2b/bump1b;
+
+        char cn2_fail = '*', cn3_fail = '*', cn4_fail = '*';
+        if ( cn2_fit > args->fit_th ) cn2_fail = 'f';
+
+        if ( cn3_fit > args->fit_th ) cn3_fail = 'f';
+        else if ( dy_cn3 < args->peak_symmetry ) cn3_fail = 'y';    // size difference is too big
+
+        if ( cn4_fit > args->fit_th ) cn4_fail = 'f';
+        else if ( 10*dy_cn4a < args->bump_size || dy_cn4b < args->bump_size ) cn4_fail = 'y';   // bump size too small (10x: the AA peak is always smaller)
+
+        double cn = -1, fit = cn2_fit;
+        if ( cn2_fail == '*' ) { cn = 2; fit = cn2_fit; }
+        if ( cn3_fail == '*' )
         {
-            fprintf(args->dat_fp,"CN\t%s\t%.2f\n", dist->chr,(float)dist->copy_number);
-            save_dist(args, i, 0, NULL);
-            continue;
+            // use cn_penalty as a tiebreaker
+            if ( (cn<0 && cn3_fit<fit) || (cn3_fit < args->cn_penalty * fit) )
+            { 
+                cn = 2 + cn3_frac; 
+                fit = cn3_fit; 
+                if ( cn2_fail=='*' ) cn2_fail = 'p';
+            }
+            else cn3_fail = 'p';
+        }
+        if ( cn4_fail == '*' )
+        {
+            if ( (cn<0 && cn4_fit<fit) || (cn4_fit < args->cn_penalty * fit) )
+            { 
+                cn = 3 + cn4b_frac; 
+                fit = cn4_fit; 
+                if ( cn2_fail=='*' ) cn2_fail = 'p';
+                if ( cn3_fail=='*' ) cn3_fail = 'p';
+            }
+            else cn4_fail = 'p';
         }
-
-        // Parameters (center,scale,sigma) for gaussian peaks.
-        double params_cn2[] = { 1/2.,0.5,0.05 };
-        double params_cn3[] = { 1/3.,0.5,0.05, 2/3.,0.5,0.05 };
-        double params_cn4[] = { 1/4.,0.5,0.05, 1/2.,0.5,0.05, 3/4.,0.5,0.05 };
-
-        double fit_cn2 = best_fit(args,&args->dist[i],1,params_cn2);
-        double fit_cn3 = best_fit(args,&args->dist[i],2,params_cn3);
-        double fit_cn4 = best_fit(args,&args->dist[i],3,params_cn4);
-
-        double dx_cn3  = fabs(params_cn3[0] - params_cn3[3]);
-        double dx_cn4  = fabs(params_cn4[0] - params_cn4[6]);
-        double dy_cn3  = params_cn3[1] > params_cn3[4] ? params_cn3[4]/params_cn3[1] : params_cn3[1]/params_cn3[4];
-        double dy_cn4a = params_cn4[1] > params_cn4[7] ? params_cn4[7]/params_cn4[1] : params_cn4[1]/params_cn4[7]; // side peaks
-        double ymax = params_cn4[1] > params_cn4[7] ? params_cn4[1] : params_cn4[7];
-        double dy_cn4b = ymax > params_cn4[4] ? params_cn4[4]/ymax : ymax/params_cn4[4];    // middle peak
-
-        // Three peaks (CN4) are always a better fit than two (CN3) or one (CN2). Therefore
-        // check that peaks are well separated and that the peak sizes are reasonable
-        char cn2_fail = 0, cn3_fail = 0, cn4_fail = 0;
-        if ( fit_cn2 > args->fit_th ) cn2_fail = 'f';
-
-        if ( fit_cn3 > args->fit_th ) cn3_fail = 'f';
-        else if ( dx_cn3 < 0.05 ) cn3_fail = 'x';         // peak separation: at least ~10% of cells
-        else if ( dy_cn3 < args->peak_symmetry ) cn3_fail = 'y';    
-
-        if ( fit_cn4 > args->fit_th ) cn4_fail = 'f';
-        else if ( dx_cn4 < 0.1 ) cn4_fail = 'x';            // peak separation
-        else if ( dy_cn4a < args->peak_symmetry ) cn4_fail = 'y';
-        else if ( dy_cn4b < args->peak_symmetry ) cn4_fail = 'Y';
-
-        // Estimate fraction of affected cells. For CN4 we estimate
-        // contamination (the fraction of foreign cells), which is more
-        // common than CN4; hence the value is from the interval [0,0.5].
-        //      CN3 .. f = 2*dx/(1-dx)
-        //      CN4 .. f = dx
-        dx_cn3 = 2*dx_cn3 / (1-dx_cn3);
-
-        double cn = -1, fit = fit_cn2;
-        if ( !cn2_fail ) { cn = 2; fit = fit_cn2; }
-        if ( !cn3_fail && fit_cn3 < args->cn_penalty * fit ) { cn = 3; fit = fit_cn3; }
-        if ( !cn4_fail && fit_cn4 < args->cn_penalty * fit ) { cn = 4; fit = fit_cn4; }
-
-        if ( cn==-1 ) save_dist(args, i, 0, NULL);
-        else if ( cn==2 ) save_dist(args, i, 1, params_cn2);
-        else if ( cn==3 ) { save_dist(args, i, 2, params_cn3); cn = 2 + dx_cn3; }
-        else if ( cn==4 ) { save_dist(args, i, 3, params_cn4); cn = 3 + dx_cn4; }
 
         if ( args->verbose )
         {
-            printf("%s: \n", args->dist[i].chr);
-            print_params(&args->dist[i].dat, 1, params_cn2, fit_cn2, 1.0,    cn2_fail, cn==2 ? '*' : ' ');
-            print_params(&args->dist[i].dat, 2, params_cn3, fit_cn3, dx_cn3, cn3_fail, cn>2 && cn<=3 ? '*' : ' ');
-            print_params(&args->dist[i].dat, 3, params_cn4, fit_cn4, dx_cn4, cn4_fail, cn>3 ? '*' : ' ');
-            printf("\n");
+            fprintf(stderr,"\tcn2 %c fit=%e\n", cn2_fail, cn2_fit);
+            fprintf(stderr,"\t       .. %e\t%f %f %f\n", cn2b_fit, cn2_params2[0],cn2_params2[1],cn2_params2[2]);
+            fprintf(stderr,"\t       .. %e\t%f %f %f\n", cn2a_fit, cn2_params1[0],cn2_params1[1],cn2_params1[2]);
+            fprintf(stderr,"\tcn3 %c fit=%e  frac=%f  symmetry=%f (%f %f)\n", cn3_fail, cn3_fit, cn3_frac, dy_cn3,a1,a2);
+            fprintf(stderr,"\t       .. %e\t%f %f %f\t%f %f %f\n", cn3b_fit, cn3_params1[0],cn3_params1[1],cn3_params1[2], cn3_params2[0],cn3_params2[1],cn3_params2[2]);
+            fprintf(stderr,"\t       .. %e\t%f %f %f\n",           cn3a_fit, cn3_params3[0],cn3_params3[1],cn3_params3[2]);
+            fprintf(stderr,"\tcn4 %c fit=%e  frac=%f (%f+%f)/2  bumps=%f %f\n", cn4_fail, cn4_fit, cn4_frac, cn4b_frac,cn4a_frac,dy_cn4b,dy_cn4a);
+            fprintf(stderr,"\t       .. %e\t%f %f %f\t%f %f %f\n", cn4b_fit, cn4b_params1[0],cn4b_params1[1],cn4b_params1[2], cn4b_params2[0],cn4b_params2[1],cn4b_params2[2]);
+            fprintf(stderr,"\t       .. %e\t%f %f %f\t%f %f %f\n", cn4a_fit, cn4a_params1[0],cn4a_params1[1],cn4a_params1[2], cn4a_params2[0],cn4a_params2[1],cn4a_params2[2]);
+        }
+
+        if ( cn2_fail == '*' )
+        {
+            if ( cn2a_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2a_fit,dist->iaa,dist->nvals-1,cn2a_func);
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2b_fit,dist->irr,dist->iaa,cn2b_func);
+        }
+        if ( cn3_fail == '*' )
+        {
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3b_fit,dist->irr,dist->iaa,cn3b_func);
+            if ( cn3a_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3a_fit,dist->iaa,dist->nvals-1,cn3a_func);
+        }
+        if ( cn4_fail == '*' )
+        {
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4b_fit,dist->irr,dist->ira,cn4b_func);
+            if ( cn4a_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4a_fit,dist->iaa,dist->nvals-1,cn4a_func);
         }
         fprintf(args->dat_fp,"CN\t%s\t%.2f\t%f\n", dist->chr, cn, fit);
+
+        free(cn2a_func);
+        free(cn2b_func);
+        free(cn3b_func);
+        free(cn4a_func);
+        free(cn4b_func);
     }
+
+    peakfit_destroy(pkf);
 }
 
 static void usage(args_t *args)
@@ -604,9 +563,12 @@ static void usage(args_t *args)
     fprintf(stderr, "    -T, --targets-file <file>      similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "    -v, --verbose                  \n");
     fprintf(stderr, "Algorithm options:\n");
-    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (smaller more strict) [0.7]\n");
-    fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (smaller more strict) [3.0]\n");
-    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (bigger more strict) [0.7]\n");
+    fprintf(stderr, "    -b, --bump-size <float>        minimum bump difference (bigger more strict) [0.2]\n");
+    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (smaller more strict) [0.25]\n");
+    fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (smaller more strict) [3.3]\n");
+    fprintf(stderr, "    -i, --include-aa               include the AA peak also in CN2 and CN3 evaluation\n");
+    fprintf(stderr, "    -m, --min-fraction <float>     minimum distinguishable fraction of aberrant cells [0.1]\n");
+    fprintf(stderr, "    -p, --peak-symmetry <float>    CN3 peak symmetry threshold (bigger more strict) [0.7]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -616,14 +578,18 @@ int main_polysomy(int argc, char *argv[])
     args_t *args = (args_t*) calloc(1,sizeof(args_t));
     args->argc   = argc; args->argv = argv;
     args->nbins  = 150;
-    args->fit_th = 3.0;
-    args->cn_penalty = 0.7;
+    args->fit_th = 3.3;
+    args->cn_penalty = 0.25;
     args->peak_symmetry = 0.7;
+    args->bump_size = 0.2;
     args->ra_rr_scaling = 1;
+    args->min_fraction = 0.1;
 
     static struct option loptions[] = 
     {
         {"ra-rr-scaling",0,0,1},    // hidden option
+        {"include-aa",0,0,'i'},
+        {"min-fraction",1,0,'m'},
         {"verbose",0,0,'v'},
         {"fit-th",1,0,'f'},
         {"cn-penalty",1,0,'c'},
@@ -637,11 +603,17 @@ int main_polysomy(int argc, char *argv[])
         {0,0,0,0}
     };
     char c, *tmp;
-    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:",loptions,NULL)) >= 0) 
+    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:",loptions,NULL)) >= 0) 
     {
         switch (c) 
         {
             case  1 : args->ra_rr_scaling = 0; break;
+            case 'i': args->include_aa = 1; break;
+            case 'm': 
+                args->min_fraction = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -n %s\n", optarg);
+                if ( args->min_fraction<0 || args->min_fraction>1 ) error("Range error: -n %s\n", optarg);
+                break;
             case 'f': 
                 args->fit_th = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -f %s\n", optarg);
@@ -660,7 +632,7 @@ int main_polysomy(int argc, char *argv[])
             case 'r': args->regions_list = optarg; break;
             case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
             case 'o': args->output_dir = optarg; break;
-            case 'v': args->verbose = 1; break;
+            case 'v': args->verbose++; break;
             default: usage(args); break;
         }
     }

From 62764c0a12ac6f38355091c036a2f9cd1670eccb Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 16 Mar 2015 14:44:47 +0000
Subject: [PATCH 003/211] Tuning the parameters and fitting procedure, all RA
 peaks included for CN4

---
 polysomy.c | 218 ++++++++++++++++++++++++++++++-----------------------
 1 file changed, 122 insertions(+), 96 deletions(-)

diff --git a/polysomy.c b/polysomy.c
index 2f06af07a..ed8f3f897 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -385,61 +385,68 @@ static void fit_curves(args_t *args)
         double xra  = dist->xvals[dist->ira];
         double xmax = dist->xvals[dist->nvals-1];
 
-        // cn2: cn2a=AA peak, cn2b=RA peak
-        double cn2a_fit = 0;
-        char *cn2a_func = 0;
-        double cn2_params1[3] = {1,1,1} ,cn2_params2[3];
+
+        // CN2
+        double cn2aa_fit = 0, cn2ra_fit, cn2_fit;
+        char *cn2aa_func = 0, *cn2ra_func;
+        double cn2aa_params[3] = {1,1,1} ,cn2ra_params[3];
         if ( args->include_aa )
         {
             peakfit_reset(pkf);
             peakfit_add_exp(pkf, 1.0,1.0,0.2, 5);
             peakfit_set_mc(pkf, 0.01,0.3,2,nmc);
             peakfit_set_mc(pkf, 0.05,1.0,0,nmc);
-            cn2a_fit  = peakfit_run(pkf, naa_max, xaa_vals, yaa_vals);
-            cn2a_func = strdup(peakfit_sprint_func(pkf));
-            peakfit_get_params(pkf,0,cn2_params1,3);
+            cn2aa_fit  = peakfit_run(pkf, naa_max, xaa_vals, yaa_vals);
+            cn2aa_func = strdup(peakfit_sprint_func(pkf));
+            peakfit_get_params(pkf,0,cn2aa_params,3);
         }
         peakfit_reset(pkf);
-        peakfit_add_gaussian(pkf, 1.0,0.5,0.03, 5);
-        double cn2b_fit = peakfit_run(pkf, nrr_aa,xrr_vals,yrr_vals);
-        char *cn2b_func = strdup(peakfit_sprint_func(pkf));
-        peakfit_get_params(pkf,0,cn2_params2,3);
-        double cn2_fit = cn2a_fit + cn2b_fit;
-
-        // cn3: cn3a=AA peak, cn3b=RA peaks
-        double cn3a_fit = cn2a_fit;
-        char *cn3a_func = cn2a_func;
-        double cn3_params1[5], cn3_params2[5], *cn3_params3 = cn2_params1;
-        double min_dx3 = 0.5 - 1./(args->min_fraction+2);
+        peakfit_add_bounded_gaussian(pkf, 1.0,0.5,0.03, 0.45,0.55, 7);
+        peakfit_set_mc(pkf, 0.01,0.3,2,nmc);
+        peakfit_set_mc(pkf, 0.05,1.0,0,nmc);
+        cn2ra_fit  = peakfit_run(pkf, nrr_aa,xrr_vals,yrr_vals);
+        cn2ra_func = strdup(peakfit_sprint_func(pkf));
+        cn2_fit    = cn2ra_fit + cn2aa_fit;
+        peakfit_get_params(pkf,0,cn2ra_params,3);
+
+
+        // CN3: fit two peaks, then enforce the symmetry and fit again
+        double cn3rra_params[5], cn3raa_params[5], *cn3aa_params = cn2aa_params;
+        double cn3aa_fit = cn2aa_fit, cn3ra_fit;
+        char *cn3aa_func = cn2aa_func, *cn3ra_func;
+        double min_dx3   = 0.5 - 1./(args->min_fraction+2);
         peakfit_reset(pkf);
         peakfit_add_bounded_gaussian(pkf, 1.0,1/3.,0.03, xrr,xra-min_dx3, 7);
         peakfit_set_mc(pkf, xrr,xra-min_dx3, 1,nmc);
         peakfit_add_bounded_gaussian(pkf, 1.0,2/3.,0.03, xra+min_dx3,xaa, 7);
         peakfit_set_mc(pkf, xra+min_dx3,xaa, 1,nmc);
         peakfit_run(pkf, nrr_aa, xrr_vals, yrr_vals);
-        peakfit_get_params(pkf,0,cn3_params1,5);
-        peakfit_get_params(pkf,1,cn3_params2,5);
-        double cn3_dx = (0.5-cn3_params1[1] + cn3_params2[1]-0.5)*0.5;
+        // force symmetry around x=0.5
+        peakfit_get_params(pkf,0,cn3rra_params,5);
+        peakfit_get_params(pkf,1,cn3raa_params,5);
+        double cn3_dx = (0.5-cn3rra_params[1] + cn3raa_params[1]-0.5)*0.5;
         peakfit_reset(pkf);
-        peakfit_add_gaussian(pkf, cn3_params1[0],0.5-cn3_dx,cn3_params1[2], 5);
-        peakfit_add_gaussian(pkf, cn3_params2[0],0.5+cn3_dx,cn3_params1[3], 5);
-        double cn3b_fit = peakfit_run(pkf, nrr_aa, xrr_vals, yrr_vals);
-        char *cn3b_func = strdup(peakfit_sprint_func(pkf));
-        double a1 = cn3_params1[0]*cn3_params1[0];
-        double a2 = cn3_params2[0]*cn3_params2[0];
-        double dy_cn3    = a1 > a2 ? a2/a1 : a1/a2;
-        double b1 = cn3_params1[1], b2 = cn3_params2[1];
-        double cn3_frac1 = (1 - 2*b1) / b1;
-        double cn3_frac2 = (2*b2 - 1) / (1 - b2);
-        double cn3_frac  = 0.5*(cn3_frac1 + cn3_frac2);
-        double cn3_fit   = cn3a_fit + cn3b_fit;
-
-        // cn4 (contaminations): cn4a=AA bump, cn4b=RA bump, params1=big peak, params2=small peak
-        // min_frac=1 is interpreted as 50-50 contamination
-        double min_dx4  = 0.25*args->min_fraction;
-        double cn4a_fit = 0;
-        char *cn4a_func = 0;
-        double cn4a_params1[3] = {1,1,1} ,cn4a_params2[3] = {1,1,1}, cn4b_params1[3], cn4b_params2[5];
+        peakfit_add_gaussian(pkf, cn3rra_params[0],0.5-cn3_dx,cn3rra_params[2], 5);
+        peakfit_add_gaussian(pkf, cn3raa_params[0],0.5+cn3_dx,cn3raa_params[2], 5);
+        cn3ra_fit  = peakfit_run(pkf, nrr_aa, xrr_vals, yrr_vals);
+        cn3ra_func = strdup(peakfit_sprint_func(pkf));
+        // compare peak sizes
+        peakfit_get_params(pkf,0,cn3rra_params,3);
+        peakfit_get_params(pkf,1,cn3raa_params,3);
+        double cn3rra_size = cn3rra_params[0]*cn3rra_params[0];
+        double cn3raa_size = cn3raa_params[0]*cn3raa_params[0];
+        double cn3_dy      = cn3rra_size > cn3raa_size ? cn3raa_size/cn3rra_size : cn3rra_size/cn3raa_size;
+        double cn3_frac    = (1 - 2*cn3rra_params[1]) / cn3rra_params[1];
+        double cn3_fit     = cn3ra_fit + cn3aa_fit;
+
+
+        // CN4 (contaminations)
+        // - similarly to CN3, fit three peaks, then enforce the symmetry and fit again
+        // - min_frac=1 (resp. 0.5) is interpreted as 50:50% (rep. 75:25%) contamination
+        double cn4AAaa_params[3] = {1,1,1} ,cn4AAra_params[3] = {1,1,1}, cn4RAra_params[3], cn4RArr_params[5], cn4RAaa_params[5];
+        double cn4aa_fit = 0, cn4ra_fit;
+        char *cn4aa_func = 0, *cn4ra_func;
+        double min_dx4   = 0.25*args->min_fraction;
         if ( args->include_aa )
         {
             peakfit_reset(pkf);
@@ -447,50 +454,60 @@ static void fit_curves(args_t *args)
             peakfit_set_mc(pkf, 0.01,0.3,2,nmc);
             peakfit_add_bounded_gaussian(pkf, 0.4,(xaa+xmax)*0.5,2e-2, xaa,xmax, 7);
             peakfit_set_mc(pkf, xaa,xmax, 1,nmc);
-            cn4a_fit  = peakfit_run(pkf, naa_max, xaa_vals,yaa_vals);
-            cn4a_func = strdup(peakfit_sprint_func(pkf));
-            peakfit_get_params(pkf,0,cn4a_params1,3);
-            peakfit_get_params(pkf,1,cn4a_params2,5);
+            cn4aa_fit  = peakfit_run(pkf, naa_max, xaa_vals,yaa_vals);
+            cn4aa_func = strdup(peakfit_sprint_func(pkf));
+            peakfit_get_params(pkf,0,cn4AAaa_params,3);
+            peakfit_get_params(pkf,1,cn4AAra_params,5);
         }
         peakfit_reset(pkf);
         peakfit_add_gaussian(pkf, 1.0,0.5,0.03, 5);
         peakfit_add_bounded_gaussian(pkf, 0.6,0.3,0.03, xrr,xra-min_dx4, 7);
-        peakfit_set_mc(pkf, xrr,xra-min_dx4,1,nmc);
-        double cn4b_fit = peakfit_run(pkf, nrr_ra , xrr_vals, yrr_vals);
-        double cn4_fit = cn4a_fit + 2*cn4b_fit;
-        char *cn4b_func = strdup(peakfit_sprint_func(pkf));
-        peakfit_get_params(pkf,0,cn4b_params1,3);
-        peakfit_get_params(pkf,1,cn4b_params2,5);
-        double cn4b_frac = 1 - 2*cn4b_params2[1];
-        double cn4a_frac = !args->include_aa ? cn4b_frac : 2*(1 - cn4a_params2[1]);
-        double cn4_frac  = (cn4a_frac + cn4b_frac)*0.5;
-        // cn4a_params1: big AA exp peak
-        // cn4a_params2: small AA exp^2 peak
-        // cn4b_params1: big RA exp^2 peak
-        // cn4b_params2: small RA exp^2 peak
-        double bump1a = cn4a_params1[0]*cn4a_params1[0];
-        double bump2a = cn4a_params2[0]*cn4a_params2[0];
-        double bump1b = cn4b_params1[0]*cn4b_params1[0];
-        double bump2b = cn4b_params2[0]*cn4b_params2[0];
-        double dy_cn4a =  args->include_aa ? (bump1a < bump2a ? bump1a/bump2a : bump2a/bump1a) : 1;
-        double dy_cn4b =  bump1b < bump2b ? bump1b/bump2b : bump2b/bump1b;
-
+        peakfit_set_mc(pkf, xrr,xra-min_dx4,2,nmc);
+        peakfit_run(pkf, nrr_ra , xrr_vals, yrr_vals);
+        // suggest symmetry around x=0.5
+        peakfit_get_params(pkf,0,cn4RAra_params,3);
+        peakfit_get_params(pkf,1,cn4RArr_params,5);
+        double cn4_dx = 0.5-cn4RArr_params[1];
+        peakfit_reset(pkf);
+        peakfit_add_gaussian(pkf, cn4RAra_params[0],0.5,cn4RAra_params[2], 5);
+        peakfit_add_gaussian(pkf, cn4RArr_params[0],0.5-cn4_dx,cn4RArr_params[2], 7);
+        peakfit_add_gaussian(pkf, cn4RArr_params[0],0.5+cn4_dx,cn4RArr_params[2], 7);
+        peakfit_set_mc(pkf, 0.1,cn4RAra_params[0],0,nmc);
+        peakfit_set_mc(pkf, 0.01,0.1,2,nmc);
+        cn4ra_fit  = peakfit_run(pkf, nrr_aa , xrr_vals, yrr_vals);
+        cn4ra_func = strdup(peakfit_sprint_func(pkf));
+        peakfit_get_params(pkf,0,cn4RAra_params,3);
+        peakfit_get_params(pkf,1,cn4RArr_params,3);
+        peakfit_get_params(pkf,2,cn4RAaa_params,3);
+        double cn4RAra_size = cn4RAra_params[0]==0 ? HUGE_VAL : cn4RAra_params[0]*cn4RAra_params[0];
+        double cn4RArr_size = cn4RArr_params[0]*cn4RArr_params[0];
+        double cn4RAaa_size = cn4RAaa_params[0]*cn4RAaa_params[0];
+        double cn4_dy       = cn4RArr_size < cn4RAaa_size ? cn4RArr_size/cn4RAaa_size : cn4RAaa_size/cn4RArr_size;
+        double cn4_ymin     = cn4RArr_size < cn4RAaa_size ? cn4RArr_size/cn4RAra_size : cn4RAaa_size/cn4RAra_size;
+        cn4_dx              = (cn4RAaa_params[1]-0.5) - (0.5-cn4RArr_params[1]);
+        double cn4_frac     = cn4RAaa_params[1] - cn4RArr_params[1];
+        double cn4_fit      = cn4ra_fit + cn4aa_fit;
+
+
+        // Choose the best match
         char cn2_fail = '*', cn3_fail = '*', cn4_fail = '*';
         if ( cn2_fit > args->fit_th ) cn2_fail = 'f';
 
         if ( cn3_fit > args->fit_th ) cn3_fail = 'f';
-        else if ( dy_cn3 < args->peak_symmetry ) cn3_fail = 'y';    // size difference is too big
+        else if ( cn3_dy < args->peak_symmetry ) cn3_fail = 'y';    // size difference is too big
 
         if ( cn4_fit > args->fit_th ) cn4_fail = 'f';
-        else if ( 10*dy_cn4a < args->bump_size || dy_cn4b < args->bump_size ) cn4_fail = 'y';   // bump size too small (10x: the AA peak is always smaller)
+        else if ( cn4_ymin < args->bump_size ) cn4_fail = 'y';      // side peak is too small
+        else if ( cn4_dy < args->peak_symmetry ) cn4_fail = 'Y';    // size difference is too big
+        else if ( cn4_dx > 0.1 ) cn4_fail = 'x';                    // side peaks placed assymetrically
 
         double cn = -1, fit = cn2_fit;
         if ( cn2_fail == '*' ) { cn = 2; fit = cn2_fit; }
         if ( cn3_fail == '*' )
         {
             // use cn_penalty as a tiebreaker
-            if ( (cn<0 && cn3_fit<fit) || (cn3_fit < args->cn_penalty * fit) )
-            { 
+            if ( cn<0 || cn3_fit < args->cn_penalty * fit )
+            {
                 cn = 2 + cn3_frac; 
                 fit = cn3_fit; 
                 if ( cn2_fail=='*' ) cn2_fail = 'p';
@@ -499,9 +516,9 @@ static void fit_curves(args_t *args)
         }
         if ( cn4_fail == '*' )
         {
-            if ( (cn<0 && cn4_fit<fit) || (cn4_fit < args->cn_penalty * fit) )
-            { 
-                cn = 3 + cn4b_frac; 
+            if ( cn<0 || cn4_fit < args->cn_penalty * fit )
+            {
+                cn = 3 + cn4_frac; 
                 fit = cn4_fit; 
                 if ( cn2_fail=='*' ) cn2_fail = 'p';
                 if ( cn3_fail=='*' ) cn3_fail = 'p';
@@ -512,38 +529,47 @@ static void fit_curves(args_t *args)
         if ( args->verbose )
         {
             fprintf(stderr,"\tcn2 %c fit=%e\n", cn2_fail, cn2_fit);
-            fprintf(stderr,"\t       .. %e\t%f %f %f\n", cn2b_fit, cn2_params2[0],cn2_params2[1],cn2_params2[2]);
-            fprintf(stderr,"\t       .. %e\t%f %f %f\n", cn2a_fit, cn2_params1[0],cn2_params1[1],cn2_params1[2]);
-            fprintf(stderr,"\tcn3 %c fit=%e  frac=%f  symmetry=%f (%f %f)\n", cn3_fail, cn3_fit, cn3_frac, dy_cn3,a1,a2);
-            fprintf(stderr,"\t       .. %e\t%f %f %f\t%f %f %f\n", cn3b_fit, cn3_params1[0],cn3_params1[1],cn3_params1[2], cn3_params2[0],cn3_params2[1],cn3_params2[2]);
-            fprintf(stderr,"\t       .. %e\t%f %f %f\n",           cn3a_fit, cn3_params3[0],cn3_params3[1],cn3_params3[2]);
-            fprintf(stderr,"\tcn4 %c fit=%e  frac=%f (%f+%f)/2  bumps=%f %f\n", cn4_fail, cn4_fit, cn4_frac, cn4b_frac,cn4a_frac,dy_cn4b,dy_cn4a);
-            fprintf(stderr,"\t       .. %e\t%f %f %f\t%f %f %f\n", cn4b_fit, cn4b_params1[0],cn4b_params1[1],cn4b_params1[2], cn4b_params2[0],cn4b_params2[1],cn4b_params2[2]);
-            fprintf(stderr,"\t       .. %e\t%f %f %f\t%f %f %f\n", cn4a_fit, cn4a_params1[0],cn4a_params1[1],cn4a_params1[2], cn4a_params2[0],cn4a_params2[1],cn4a_params2[2]);
+            fprintf(stderr,"\t       .. %e\n", cn2ra_fit);
+            fprintf(stderr,"\t            RA:   %f %f %f\n", cn2ra_params[0],cn2ra_params[1],cn2ra_params[2]);
+            fprintf(stderr,"\t       .. %e\n", cn2aa_fit);
+            fprintf(stderr,"\t            AA:   %f %f %f\n", cn2aa_params[0],cn2aa_params[1],cn2aa_params[2]);
+            fprintf(stderr,"\tcn3 %c fit=%e  frac=%f  symmetry=%f\n", cn3_fail, cn3_fit, cn3_frac, cn3_dy);
+            fprintf(stderr,"\t       .. %e\n", cn3ra_fit);
+            fprintf(stderr,"\t            RRA:  %f %f %f\n", cn3rra_params[0],cn3rra_params[1],cn3rra_params[2]);
+            fprintf(stderr,"\t            RAA:  %f %f %f\n", cn3raa_params[0],cn3raa_params[1],cn3raa_params[2]);
+            fprintf(stderr,"\t       .. %e\n", cn3aa_fit);
+            fprintf(stderr,"\t            AAA:  %f %f %f\n", cn3aa_params[0],cn3aa_params[1],cn3aa_params[2]);
+            fprintf(stderr,"\tcn4 %c fit=%e  frac=%f  symmetry=%f ymin=%f\n", cn4_fail, cn4_fit, cn4_frac, cn4_dy, cn4_ymin);
+            fprintf(stderr,"\t       .. %e\n", cn4ra_fit);
+            fprintf(stderr,"\t            RArr:  %f %f %f\n", cn4RArr_params[0],cn4RArr_params[1],cn4RArr_params[2]);
+            fprintf(stderr,"\t            RAra:  %f %f %f\n", cn4RAra_params[0],cn4RAra_params[1],cn4RAra_params[2]);
+            fprintf(stderr,"\t            RAaa:  %f %f %f\n", cn4RAaa_params[0],cn4RAaa_params[1],cn4RAaa_params[2]);
+            fprintf(stderr,"\t       .. %e\n", cn4aa_fit);
+            fprintf(stderr,"\t            AAaa:  %f %f %f\n", cn4AAaa_params[0],cn4AAaa_params[1],cn4AAaa_params[2]);
         }
 
         if ( cn2_fail == '*' )
         {
-            if ( cn2a_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2a_fit,dist->iaa,dist->nvals-1,cn2a_func);
-            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2b_fit,dist->irr,dist->iaa,cn2b_func);
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2ra_fit,dist->irr,dist->iaa,cn2ra_func);
+            if ( cn2aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2aa_fit,dist->iaa,dist->nvals-1,cn2aa_func);
         }
         if ( cn3_fail == '*' )
         {
-            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3b_fit,dist->irr,dist->iaa,cn3b_func);
-            if ( cn3a_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3a_fit,dist->iaa,dist->nvals-1,cn3a_func);
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3ra_fit,dist->irr,dist->iaa,cn3ra_func);
+            if ( cn3aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3aa_fit,dist->iaa,dist->nvals-1,cn3aa_func);
         }
         if ( cn4_fail == '*' )
         {
-            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4b_fit,dist->irr,dist->ira,cn4b_func);
-            if ( cn4a_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4a_fit,dist->iaa,dist->nvals-1,cn4a_func);
+            fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4ra_fit,dist->irr,dist->iaa,cn4ra_func);
+            if ( cn4aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4aa_fit,dist->iaa,dist->nvals-1,cn4aa_func);
         }
         fprintf(args->dat_fp,"CN\t%s\t%.2f\t%f\n", dist->chr, cn, fit);
 
-        free(cn2a_func);
-        free(cn2b_func);
-        free(cn3b_func);
-        free(cn4a_func);
-        free(cn4b_func);
+        free(cn2aa_func);
+        free(cn2ra_func);
+        free(cn3ra_func);
+        free(cn4ra_func);
+        free(cn4aa_func);
     }
 
     peakfit_destroy(pkf);
@@ -563,12 +589,12 @@ static void usage(args_t *args)
     fprintf(stderr, "    -T, --targets-file <file>      similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "    -v, --verbose                  \n");
     fprintf(stderr, "Algorithm options:\n");
-    fprintf(stderr, "    -b, --bump-size <float>        minimum bump difference (bigger more strict) [0.2]\n");
-    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (smaller more strict) [0.25]\n");
+    fprintf(stderr, "    -b, --bump-size <float>        minimum bump size (bigger more strict) [0.1]\n");
+    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (smaller more strict) [0.3]\n");
     fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (smaller more strict) [3.3]\n");
     fprintf(stderr, "    -i, --include-aa               include the AA peak also in CN2 and CN3 evaluation\n");
     fprintf(stderr, "    -m, --min-fraction <float>     minimum distinguishable fraction of aberrant cells [0.1]\n");
-    fprintf(stderr, "    -p, --peak-symmetry <float>    CN3 peak symmetry threshold (bigger more strict) [0.7]\n");
+    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (bigger more strict) [0.6]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -579,9 +605,9 @@ int main_polysomy(int argc, char *argv[])
     args->argc   = argc; args->argv = argv;
     args->nbins  = 150;
     args->fit_th = 3.3;
-    args->cn_penalty = 0.25;
-    args->peak_symmetry = 0.7;
-    args->bump_size = 0.2;
+    args->cn_penalty = 0.3;
+    args->peak_symmetry = 0.6;
+    args->bump_size = 0.1;
     args->ra_rr_scaling = 1;
     args->min_fraction = 0.1;
 

From 983bea456fd48801eee528303546eec087efb975 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 17 Mar 2015 16:06:49 +0000
Subject: [PATCH 004/211] polysomy: CN4 side peaks symmetry check now relative
 rather than absolute; hidden --force-cn option for debugging

---
 polysomy.c | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/polysomy.c b/polysomy.c
index ed8f3f897..5c808acdd 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -55,7 +55,7 @@ typedef struct
     dist_t *dist;
     char **argv, *output_dir;
     double fit_th, peak_symmetry, cn_penalty, bump_size, min_fraction;
-    int argc, plot, verbose, regions_is_file, targets_is_file, include_aa;
+    int argc, plot, verbose, regions_is_file, targets_is_file, include_aa, force_cn;
     char *dat_fname, *fname, *regions_list, *targets_list, *sample;
     FILE *dat_fp;
 }
@@ -482,7 +482,9 @@ static void fit_curves(args_t *args)
         double cn4RAra_size = cn4RAra_params[0]==0 ? HUGE_VAL : cn4RAra_params[0]*cn4RAra_params[0];
         double cn4RArr_size = cn4RArr_params[0]*cn4RArr_params[0];
         double cn4RAaa_size = cn4RAaa_params[0]*cn4RAaa_params[0];
-        double cn4_dy       = cn4RArr_size < cn4RAaa_size ? cn4RArr_size/cn4RAaa_size : cn4RAaa_size/cn4RArr_size;
+        double cn4RArr_dy   = cn4RArr_size < cn4RAra_size ? cn4RArr_size/cn4RAra_size : cn4RAra_size/cn4RArr_size;
+        double cn4RAaa_dy   = cn4RAaa_size < cn4RAra_size ? cn4RAaa_size/cn4RAra_size : cn4RAra_size/cn4RAaa_size;
+        double cn4_dy       = cn4RArr_dy < cn4RAaa_dy ? cn4RArr_dy/cn4RAaa_dy : cn4RAaa_dy/cn4RArr_dy;
         double cn4_ymin     = cn4RArr_size < cn4RAaa_size ? cn4RArr_size/cn4RAra_size : cn4RAaa_size/cn4RAra_size;
         cn4_dx              = (cn4RAaa_params[1]-0.5) - (0.5-cn4RArr_params[1]);
         double cn4_frac     = cn4RAaa_params[1] - cn4RArr_params[1];
@@ -548,17 +550,17 @@ static void fit_curves(args_t *args)
             fprintf(stderr,"\t            AAaa:  %f %f %f\n", cn4AAaa_params[0],cn4AAaa_params[1],cn4AAaa_params[2]);
         }
 
-        if ( cn2_fail == '*' )
+        if ( args->force_cn==2 || cn2_fail == '*' )
         {
             fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2ra_fit,dist->irr,dist->iaa,cn2ra_func);
             if ( cn2aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn2aa_fit,dist->iaa,dist->nvals-1,cn2aa_func);
         }
-        if ( cn3_fail == '*' )
+        if ( args->force_cn==3 || cn3_fail == '*' )
         {
             fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3ra_fit,dist->irr,dist->iaa,cn3ra_func);
             if ( cn3aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn3aa_fit,dist->iaa,dist->nvals-1,cn3aa_func);
         }
-        if ( cn4_fail == '*' )
+        if ( args->force_cn==4 || cn4_fail == '*' )
         {
             fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4ra_fit,dist->irr,dist->iaa,cn4ra_func);
             if ( cn4aa_func ) fprintf(args->dat_fp,"FIT\t%s\t%e\t%d\t%d\t%s\n", dist->chr,cn4aa_fit,dist->iaa,dist->nvals-1,cn4aa_func);
@@ -594,7 +596,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (smaller more strict) [3.3]\n");
     fprintf(stderr, "    -i, --include-aa               include the AA peak also in CN2 and CN3 evaluation\n");
     fprintf(stderr, "    -m, --min-fraction <float>     minimum distinguishable fraction of aberrant cells [0.1]\n");
-    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (bigger more strict) [0.6]\n");
+    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (bigger more strict) [0.5]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -606,7 +608,7 @@ int main_polysomy(int argc, char *argv[])
     args->nbins  = 150;
     args->fit_th = 3.3;
     args->cn_penalty = 0.3;
-    args->peak_symmetry = 0.6;
+    args->peak_symmetry = 0.5;
     args->bump_size = 0.1;
     args->ra_rr_scaling = 1;
     args->min_fraction = 0.1;
@@ -614,6 +616,7 @@ int main_polysomy(int argc, char *argv[])
     static struct option loptions[] = 
     {
         {"ra-rr-scaling",0,0,1},    // hidden option
+        {"force-cn",1,0,2},         // hidden option
         {"include-aa",0,0,'i'},
         {"min-fraction",1,0,'m'},
         {"verbose",0,0,'v'},
@@ -634,6 +637,7 @@ int main_polysomy(int argc, char *argv[])
         switch (c) 
         {
             case  1 : args->ra_rr_scaling = 0; break;
+            case  2 : args->force_cn = atoi(optarg); break;
             case 'i': args->include_aa = 1; break;
             case 'm': 
                 args->min_fraction = strtod(optarg,&tmp);

From 57edcaba051b7d736fa815ba2bc2e10e56c574ce Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 29 Jun 2015 15:13:01 +0100
Subject: [PATCH 005/211] minor wording and whitespace changes to polysomy.c

---
 polysomy.c | 40 +++++++++++++++++++++-------------------
 1 file changed, 21 insertions(+), 19 deletions(-)

diff --git a/polysomy.c b/polysomy.c
index 5c808acdd..3962cf8a1 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -1,19 +1,19 @@
 /* The MIT License
 
-   Copyright (c) 2013-2014 Genome Research Ltd.
+   Copyright (c) 2013-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3@sanger.ac.uk>
-   
+
    Permission is hereby granted, free of charge, to any person obtaining a copy
    of this software and associated documentation files (the "Software"), to deal
    in the Software without restriction, including without limitation the rights
    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
    copies of the Software, and to permit persons to whom the Software is
    furnished to do so, subject to the following conditions:
-   
+
    The above copyright notice and this permission notice shall be included in
    all copies or substantial portions of the Software.
-   
+
    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
@@ -41,7 +41,7 @@ typedef struct
 {
     int nvals;          // all values, including RR,AA peaks
     double *xvals;      // pointer to args_t.xvals
-    double *yvals;   
+    double *yvals;
     int copy_number;    // heuristics to skip futile CN1 fits when no het peak is detected
     int irr, ira, iaa;  // chop off RR and AA peaks
     char *chr;
@@ -520,8 +520,8 @@ static void fit_curves(args_t *args)
         {
             if ( cn<0 || cn4_fit < args->cn_penalty * fit )
             {
-                cn = 3 + cn4_frac; 
-                fit = cn4_fit; 
+                cn = 3 + cn4_frac;
+                fit = cn4_fit;
                 if ( cn2_fail=='*' ) cn2_fail = 'p';
                 if ( cn3_fail=='*' ) cn3_fail = 'p';
             }
@@ -582,6 +582,7 @@ static void usage(args_t *args)
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Detect number of chromosomal copies from Illumina's B-allele frequency (BAF)\n");
     fprintf(stderr, "Usage:   bcftools polysomy [OPTIONS] <file.vcf>\n");
+    fprintf(stderr, "\n");
     fprintf(stderr, "General options:\n");
     fprintf(stderr, "    -o, --output-dir <path>        \n");
     fprintf(stderr, "    -r, --regions <region>         restrict to comma-separated list of regions\n");
@@ -590,13 +591,14 @@ static void usage(args_t *args)
     fprintf(stderr, "    -t, --targets <region>         similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>      similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "    -v, --verbose                  \n");
+    fprintf(stderr, "\n");
     fprintf(stderr, "Algorithm options:\n");
-    fprintf(stderr, "    -b, --bump-size <float>        minimum bump size (bigger more strict) [0.1]\n");
-    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (smaller more strict) [0.3]\n");
-    fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (smaller more strict) [3.3]\n");
-    fprintf(stderr, "    -i, --include-aa               include the AA peak also in CN2 and CN3 evaluation\n");
+    fprintf(stderr, "    -b, --bump-size <float>        minimum bump size (larger is stricter) [0.1]\n");
+    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (smaller is stricter) [0.3]\n");
+    fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (smaller is stricter) [3.3]\n");
+    fprintf(stderr, "    -i, --include-aa               include the AA peak in CN2 and CN3 evaluation\n");
     fprintf(stderr, "    -m, --min-fraction <float>     minimum distinguishable fraction of aberrant cells [0.1]\n");
-    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (bigger more strict) [0.5]\n");
+    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (larger is stricter) [0.5]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -613,7 +615,7 @@ int main_polysomy(int argc, char *argv[])
     args->ra_rr_scaling = 1;
     args->min_fraction = 0.1;
 
-    static struct option loptions[] = 
+    static struct option loptions[] =
     {
         {"ra-rr-scaling",0,0,1},    // hidden option
         {"force-cn",1,0,2},         // hidden option
@@ -632,27 +634,27 @@ int main_polysomy(int argc, char *argv[])
         {0,0,0,0}
     };
     char c, *tmp;
-    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:",loptions,NULL)) >= 0) 
+    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:",loptions,NULL)) >= 0)
     {
-        switch (c) 
+        switch (c)
         {
             case  1 : args->ra_rr_scaling = 0; break;
             case  2 : args->force_cn = atoi(optarg); break;
             case 'i': args->include_aa = 1; break;
-            case 'm': 
+            case 'm':
                 args->min_fraction = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -n %s\n", optarg);
                 if ( args->min_fraction<0 || args->min_fraction>1 ) error("Range error: -n %s\n", optarg);
                 break;
-            case 'f': 
+            case 'f':
                 args->fit_th = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -f %s\n", optarg);
                 break;
-            case 'p': 
+            case 'p':
                 args->peak_symmetry = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -p %s\n", optarg);
                 break;
-            case 'c': 
+            case 'c':
                 args->cn_penalty = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -c %s\n", optarg);
                 break;

From 9480a5458250c72d380d9302e9f99a4c5b6fc1bb Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 29 Jun 2015 15:13:41 +0100
Subject: [PATCH 006/211] show polysomy command in help message

This was hidden as it was/is experimental, but with the licensing
additions, users are explicitly requesting the command by compiling
with USE_GPL=1, so we might as well display in the help message.

Closes #280
---
 main.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.c b/main.c
index 98d8ee1b6..0130e39b2 100644
--- a/main.c
+++ b/main.c
@@ -151,7 +151,7 @@ static cmd_t cmds[] =
 #if USE_GPL
     { .func  = main_polysomy,
       .alias = "polysomy",
-      .help  = "-detect number of chromosomal copies",
+      .help  = "detect number of chromosomal copies",
     },
 #endif
     { .func  = main_vcfroh,

From 68b06b708753496c1c886b2778c214d6f196bd97 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 6 Jul 2015 10:28:47 +0100
Subject: [PATCH 007/211] update copyright dates for peakfit

---
 peakfit.c | 2 +-
 peakfit.h | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/peakfit.c b/peakfit.c
index 93f1acd60..89bdcb0c4 100644
--- a/peakfit.c
+++ b/peakfit.c
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2013-2014 Genome Research Ltd.
+   Copyright (c) 2013-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3@sanger.ac.uk>
    
diff --git a/peakfit.h b/peakfit.h
index de497cd75..8a9e4fab2 100644
--- a/peakfit.h
+++ b/peakfit.h
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2013-2014 Genome Research Ltd.
+   Copyright (c) 2013-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3@sanger.ac.uk>
    

From baa24a8fa1fc4739e4b5a10a220ad971a2fbeeed Mon Sep 17 00:00:00 2001
From: "Warren W. Kretzschmar" <wkretzsch@gmail.com>
Date: Tue, 28 Apr 2015 10:24:49 +0100
Subject: [PATCH 008/211] Implements "bcftools view -G removes all format
 header lines"

Resolves #248
---
 test/test.pl                |  1 +
 test/view.9.out             |  4 ----
 test/view.dropgenotypes.out | 12 ++++++++++++
 vcfview.c                   |  4 +++-
 4 files changed, 16 insertions(+), 5 deletions(-)
 create mode 100644 test/view.dropgenotypes.out

diff --git a/test/test.pl b/test/test.pl
index 621b8ec6a..71d80418c 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -107,6 +107,7 @@
 test_vcf_view($opts,in=>'view',out=>'view.10.out',args=>q[-ne 'INDEL=1 || PV4[0]<0.006'],reg=>'');
 test_vcf_view($opts,in=>'view',out=>'view.exclude.out',args=>'-s ^NA00003',reg=>'');
 test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.omitgenotypes.out',args=>'',reg=>'');
+test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.dropgenotypes.out',args=>'-G',reg=>'');
 test_vcf_view($opts,in=>'view.vectors',out=>'view.vectors.A.out',args=>'-asA',reg=>'');
 test_vcf_view($opts,in=>'view.vectors',out=>'view.vectors.B.out',args=>'-asB',reg=>'');
 test_vcf_view($opts,in=>'view.filter',out=>'view.filter.1.out',args=>q[-H -i'FMT/FGS[0]="AAAAAA"'],reg=>'');    # test expressions
diff --git a/test/view.9.out b/test/view.9.out
index b5b13bdb6..35292102c 100644
--- a/test/view.9.out
+++ b/test/view.9.out
@@ -20,10 +20,6 @@
 ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth">
 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
 ##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
 ##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
 ##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
diff --git a/test/view.dropgenotypes.out b/test/view.dropgenotypes.out
new file mode 100644
index 000000000..8e983f62b
--- /dev/null
+++ b/test/view.dropgenotypes.out
@@ -0,0 +1,12 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta
+##contig=<ID=20,length=62435964,assembly=B36,md5=f126cdf8a6e0c7f379d618ff66beb2da,species="Homo sapiens",taxonomy=x>
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14
+20	17330	.	T	A	3	PASS	NS=3;DP=11
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10
+20	1230237	.	T	.	47	PASS	NS=3;DP=13
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9
diff --git a/vcfview.c b/vcfview.c
index d89882430..ed888c7c1 100644
--- a/vcfview.c
+++ b/vcfview.c
@@ -220,8 +220,10 @@ static void init_data(args_t *args)
     if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
 
     // headers: hdr=full header, hsub=subset header, hnull=sites only header
-    if (args->sites_only)
+    if (args->sites_only){
         args->hnull = bcf_hdr_subset(args->hdr, 0, 0, 0);
+        bcf_hdr_remove(args->hnull, BCF_HL_FMT, NULL);
+    }
     if (args->n_samples > 0)
     {
         args->hsub = bcf_hdr_subset(args->hdr, args->n_samples, args->samples, args->imap);

From 8fdd4985d45969d188161b260fe4c1b94a322e18 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 26 Mar 2015 16:53:25 +0100
Subject: [PATCH 009/211] The HMM structure becomes opaque for future
 flexibility

---
 HMM.c    | 36 +++++++++++++++++++++++++++++++-----
 HMM.h    | 47 ++++++++++++++++++++++-------------------------
 vcfcnv.c | 23 +++++++++++++----------
 vcfroh.c | 49 ++++++++++++++++++++++++++++---------------------
 4 files changed, 94 insertions(+), 61 deletions(-)

diff --git a/HMM.c b/HMM.c
index 2d2a4021f..f20f91797 100644
--- a/HMM.c
+++ b/HMM.c
@@ -31,6 +31,32 @@
 #include <htslib/hts.h>
 #include "HMM.h"
 
+struct _hmm_t
+{
+    int nstates;    // number of states
+
+    double *vprob, *vprob_tmp;  // viterbi probs [nstates]
+    uint8_t *vpath;             // viterbi path [nstates*nvpath]
+    double *bwd, *bwd_tmp;      // bwd probs [nstates]
+    double *fwd;                // fwd probs [nstates*(nfwd+1)]
+    int nvpath, nfwd;
+
+    int ntprob_arr;             // number of pre-calculated tprob matrices
+    double *curr_tprob, *tmp;   // Temporary arrays; curr_tprob is short lived, valid only for
+                                //  one site (that is, one step of Viterbi algorithm)
+    double *tprob_arr;          // Array of transition matrices, precalculated to ntprob_arr
+                                //  positions. The first matrix is the initial tprob matrix
+                                //  set by hmm_init() or hmm_set_tprob()
+    set_tprob_f set_tprob;      // Optional user function to set / modify transition probabilities
+                                //  at each site (one step of Viterbi algorithm)
+    void *set_tprob_data;
+};
+
+uint8_t *hmm_get_viterbi_path(hmm_t *hmm) { return hmm->vpath; }
+double *hmm_get_tprob(hmm_t *hmm) { return hmm->tprob_arr; }
+int hmm_get_nstates(hmm_t *hmm) { return hmm->nstates; }
+double *hmm_get_fwd_bwd_prob(hmm_t *hmm) { return hmm->fwd; }
+
 static inline void multiply_matrix(int n, double *a, double *b, double *dst, double *tmp)
 {
     double *out = dst;
@@ -130,7 +156,7 @@ void hmm_run_viterbi(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[i];
 
         double vnorm = 0;
@@ -196,7 +222,7 @@ void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[i];
 
         double norm = 0;
@@ -222,7 +248,7 @@ void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[n-i-1];
 
         double bwd_norm = 0;
@@ -281,7 +307,7 @@ void hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[i] == prev_pos ? 0 : sites[i] - prev_pos - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, prev_pos, sites[i], hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[i];
 
         double norm = 0;
@@ -307,7 +333,7 @@ void hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
         int pos_diff = sites[n-i-1] == prev_pos ? 0 : prev_pos - sites[n-i-1] - 1;
 
         _set_tprob(hmm, pos_diff);
-        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data);
+        if ( hmm->set_tprob ) hmm->set_tprob(hmm, sites[n-i-1], prev_pos, hmm->set_tprob_data, hmm->curr_tprob);
         prev_pos = sites[n-i-1];
 
         double bwd_norm = 0;
diff --git a/HMM.h b/HMM.h
index 2fb141242..5d21e64da 100644
--- a/HMM.h
+++ b/HMM.h
@@ -31,28 +31,7 @@
 
 typedef struct _hmm_t hmm_t;
 
-typedef void (*set_tprob_f) (hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data);
-
-struct _hmm_t
-{
-    int nstates;    // number of states
-
-    double *vprob, *vprob_tmp;  // viterbi probs [nstates]
-    uint8_t *vpath;             // viterbi path [nstates*nvpath]
-    double *bwd, *bwd_tmp;      // bwd probs [nstates]
-    double *fwd;                // fwd probs [nstates*(nfwd+1)]
-    int nvpath, nfwd;
-
-    int ntprob_arr;             // number of pre-calculated tprob matrices
-    double *curr_tprob, *tmp;   // Temporary arrays; curr_tprob is short lived, valid only for
-                                //  one site (that is, one step of Viterbi algorithm)
-    double *tprob_arr;          // Array of transition matrices, precalculated to ntprob_arr
-                                //  positions. The first matrix is the initial tprob matrix
-                                //  set by hmm_init() or hmm_set_tprob()
-    set_tprob_f set_tprob;      // Optional user function to set / modify transition probabilities
-                                //  at each site (one step of Viterbi algorithm)
-    void *set_tprob_data;
-};
+typedef void (*set_tprob_f) (hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
 
 /**
  *   hmm_init() - initialize HMM
@@ -65,6 +44,14 @@ struct _hmm_t
 hmm_t *hmm_init(int nstates, double *tprob, int ntprob);
 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob);
 
+/**
+ *   hmm_get_tprob() - return the array of transition matrices, precalculated
+ *      to ntprob positions. The first matrix is the initial tprob matrix
+ *      set by hmm_init() or hmm_set_tprob()
+ */
+double *hmm_get_tprob(hmm_t *hmm);
+int hmm_get_nstates(hmm_t *hmm);
+
 /**
  *   hmm_set_tprob_func() - custom setter of transition probabilities
  */
@@ -82,17 +69,26 @@ void hmm_set_tprob_func(hmm_t *hmm, set_tprob_f set_tprob, void *data);
  */
 void hmm_run_viterbi(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
 
+/**
+ *   hmm_get_viterbi_path() - the viterbi path: state at ith site is the
+ *      (nstates*isite)-th element
+ */
+uint8_t *hmm_get_viterbi_path(hmm_t *hmm);
+
 /**
  *   hmm_run_fwd_bwd() - run the forward-backward algorithm
  *   @nsites:   number of sites 
  *   @eprob:    emission probabilities for each site and state (nsites x nstates)
  *   @sites:    list of positions
- *
- *   When done, hmm->fwd[] contains the calculated fwd*bwd probabilities. The
- *   probability of i-th state at j-th site can be accessed as fwd[j*nstates+i].
  */
 void hmm_run_fwd_bwd(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
 
+/**
+ *   hmm_get_fwd_bwd_prob() - the probability of i-th state at j-th site can
+ *      be accessed as fwd_bwd[j*nstates+i].
+ */
+double *hmm_get_fwd_bwd_prob(hmm_t *hmm);
+
 /**
  *   hmm_run_baum_welch() - run one iteration of Baum-Welch algorithm
  *   @nsites:   number of sites 
@@ -104,6 +100,7 @@ void hmm_run_fwd_bwd(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
  *   are not updated.
  */
 void hmm_run_baum_welch(hmm_t *hmm, int nsites, double *eprob, uint32_t *sites);
+
 void hmm_destroy(hmm_t *hmm);
 
 #endif
diff --git a/vcfcnv.c b/vcfcnv.c
index 7011795c3..5c82a3433 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -541,21 +541,23 @@ static void cnv_flush_viterbi(args_t *args)
     hmm_set_tprob(args->hmm, args->tprob, 10000);
     while ( args->baum_welch_th!=0 )
     {
-        double ori_ii = avg_ii_prob(hmm->nstates,hmm->tprob_arr);
+        int nstates = hmm_get_nstates(hmm);
+        double ori_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm));
         hmm_run_baum_welch(hmm, args->nsites, args->eprob, args->sites);
-        double new_ii = avg_ii_prob(hmm->nstates,hmm->tprob_arr);
+        double new_ii = avg_ii_prob(nstates,hmm_get_tprob(hmm));
         fprintf(stderr,"%e\t%e\t%e\n", ori_ii,new_ii,new_ii-ori_ii);
-        double *tprob = init_tprob_matrix(hmm->nstates, 1-new_ii, args->same_prob);
+        double *tprob = init_tprob_matrix(nstates, 1-new_ii, args->same_prob);
         hmm_set_tprob(args->hmm, tprob, 10000);
+        double *tprob_arr = hmm_get_tprob(hmm);
         free(tprob);
         if ( fabs(new_ii - ori_ii) < args->baum_welch_th )
         {
             int i,j;
-            for (i=0; i<hmm->nstates; i++)
+            for (i=0; i<nstates; i++)
             {
-                for (j=0; j<hmm->nstates; j++)
+                for (j=0; j<nstates; j++)
                 {
-                    printf(" %.15f", MAT(hmm->tprob_arr,hmm->nstates,j,i));
+                    printf(" %.15f", MAT(tprob_arr,nstates,j,i));
                 }
                 printf("\n");
             }
@@ -567,12 +569,13 @@ static void cnv_flush_viterbi(args_t *args)
 
 
     // Output the results
-    double qual = 0;
-    int i,j, isite, start_cn = hmm->vpath[0], start_pos = args->sites[0], istart_pos = 0;
+    uint8_t *vpath = hmm_get_viterbi_path(hmm);
+    double qual = 0, *fwd = hmm_get_fwd_bwd_prob(hmm);
+    int i,j, isite, start_cn = vpath[0], start_pos = args->sites[0], istart_pos = 0;
     for (isite=0; isite<args->nsites; isite++)
     {
-        int state = hmm->vpath[args->nstates*isite];
-        double *pval = hmm->fwd + isite*args->nstates;
+        int state = vpath[args->nstates*isite];
+        double *pval = fwd + isite*args->nstates;
 
         qual += pval[start_cn];
 
diff --git a/vcfroh.c b/vcfroh.c
index 6ab2fc024..bb7653705 100644
--- a/vcfroh.c
+++ b/vcfroh.c
@@ -78,8 +78,8 @@ typedef struct _args_t
 }
 args_t;
 
-void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data);
-void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data);
+void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
+void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob);
 
 void *smalloc(size_t size)
 {
@@ -268,24 +268,24 @@ static double get_genmap_rate(args_t *args, int start, int end)
     return rate;
 }
 
-void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data)
+void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
 {
     args_t *args = (args_t*) data;
     double ci = get_genmap_rate(args, pos - prev_pos, pos);
-    MAT(hmm->curr_tprob,2,STATE_HW,STATE_HW) *= 1-ci;
-    MAT(hmm->curr_tprob,2,STATE_HW,STATE_AZ) *= ci;
-    MAT(hmm->curr_tprob,2,STATE_AZ,STATE_HW) *= ci;
-    MAT(hmm->curr_tprob,2,STATE_AZ,STATE_AZ) *= 1-ci;
+    MAT(tprob,2,STATE_HW,STATE_HW) *= 1-ci;
+    MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ) *= 1-ci;
 }
 
-void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data)
+void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
 {
     args_t *args = (args_t*) data;
     double ci = (pos - prev_pos) * args->rec_rate;
-    MAT(hmm->curr_tprob,2,STATE_HW,STATE_HW) *= 1-ci;
-    MAT(hmm->curr_tprob,2,STATE_HW,STATE_AZ) *= ci;
-    MAT(hmm->curr_tprob,2,STATE_AZ,STATE_HW) *= ci;
-    MAT(hmm->curr_tprob,2,STATE_AZ,STATE_AZ) *= 1-ci;
+    MAT(tprob,2,STATE_HW,STATE_HW) *= 1-ci;
+    MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ) *= 1-ci;
 }
 
 
@@ -328,9 +328,10 @@ static void flush_viterbi(args_t *args)
         hmm_run_viterbi(args->hmm, args->nsites, args->eprob, args->sites);
 
         const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid);
+        uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
         for (i=0; i<args->nsites; i++)
         {
-            printf("%s\t%d\t%d\t..\n", chr,args->sites[i]+1,args->hmm->vpath[i*2]==STATE_AZ ? 1 : 0);
+            printf("%s\t%d\t%d\t..\n", chr,args->sites[i]+1,vpath[i*2]==STATE_AZ ? 1 : 0);
         }
         return;
     }
@@ -341,8 +342,9 @@ static void flush_viterbi(args_t *args)
     int niter = 0;
     do
     {
-        t2az_prev = MAT(args->hmm->tprob_arr,2,1,0); //args->t2AZ;
-        t2hw_prev = MAT(args->hmm->tprob_arr,2,0,1); //args->t2HW;
+        double *tprob_arr = hmm_get_tprob(args->hmm);
+        t2az_prev = MAT(tprob_arr,2,1,0); //args->t2AZ;
+        t2hw_prev = MAT(tprob_arr,2,0,1); //args->t2HW;
         double tcounts[] = { 0,0,0,0 };
         for (i=0; i<args->nrids; i++)
         {
@@ -353,15 +355,17 @@ static void flush_viterbi(args_t *args)
             hmm_run_viterbi(args->hmm, nsites, args->eprob+ioff*2, args->sites+ioff);
 
             // what transitions were observed: add to the total counts
+            uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
             for (j=1; j<nsites; j++)
             {
                 // count the number of transitions
-                int prev_state = args->hmm->vpath[2*(j-1)];
-                int curr_state = args->hmm->vpath[2*j];
+                int prev_state = vpath[2*(j-1)];
+                int curr_state = vpath[2*j];
                 MAT(tcounts,2,curr_state,prev_state) += 1;
             }
         }
 
+
         // update the transition matrix tprob
         for (i=0; i<2; i++)
         {
@@ -375,15 +379,17 @@ static void flush_viterbi(args_t *args)
         else
             hmm_set_tprob(args->hmm, tcounts, 10000);
 
-        deltaz = fabs(MAT(args->hmm->tprob_arr,2,1,0)-t2az_prev);
-        delthw = fabs(MAT(args->hmm->tprob_arr,2,0,1)-t2hw_prev);
+        tprob_arr = hmm_get_tprob(args->hmm);
+        deltaz = fabs(MAT(tprob_arr,2,1,0)-t2az_prev);
+        delthw = fabs(MAT(tprob_arr,2,0,1)-t2hw_prev);
         niter++;
 
         fprintf(stderr,"%d: %f %f\n", niter,deltaz,delthw);
     }
     while ( deltaz > 0.0 || delthw > 0.0 );
     fprintf(stderr, "Viterbi training converged in %d iterations to", niter);
-    for (i=0; i<2; i++) for (j=0; j<2; j++) fprintf(stderr, " %f", MAT(args->hmm->tprob_arr,2,i,j));
+    double *tprob_arr = hmm_get_tprob(args->hmm);
+    for (i=0; i<2; i++) for (j=0; j<2; j++) fprintf(stderr, " %f", MAT(tprob_arr,2,i,j));
     fprintf(stderr, "\n");
     
     // output the results
@@ -392,11 +398,12 @@ static void flush_viterbi(args_t *args)
         int ioff = args->rid_offs[i];
         int nsites = (i+1==args->nrids ? args->nsites : args->rid_offs[i+1]) - ioff;
         hmm_run_viterbi(args->hmm, nsites, args->eprob+ioff*2, args->sites+ioff);
+        uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
 
         const char *chr = bcf_hdr_id2name(args->hdr,args->rids[i]);
         for (j=0; j<nsites; j++)
         {
-            printf("%s\t%d\t%d\t..\n", chr,args->sites[ioff+j]+1,args->hmm->vpath[j*2]==STATE_AZ ? 1 : 0);
+            printf("%s\t%d\t%d\t..\n", chr,args->sites[ioff+j]+1,vpath[j*2]==STATE_AZ ? 1 : 0);
         }
     }
 }

From f506244ff159856ba03f327a34b5830b0b8d4401 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 29 Jun 2015 14:42:14 +0100
Subject: [PATCH 010/211] RoH bugfix: Transition probabilities must scale to 1

---
 HMM.c    |  2 +-
 HMM.h    |  2 +-
 vcfcnv.c |  2 +-
 vcfroh.c | 22 ++++++++++------------
 4 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/HMM.c b/HMM.c
index f20f91797..78501ca55 100644
--- a/HMM.c
+++ b/HMM.c
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2014 Genome Research Ltd.
+   Copyright (c) 2014-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3@sanger.ac.uk>
 
diff --git a/HMM.h b/HMM.h
index 5d21e64da..3f5e0f10a 100644
--- a/HMM.h
+++ b/HMM.h
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2014 Genome Research Ltd.
+   Copyright (c) 2014-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3@sanger.ac.uk>
 
diff --git a/vcfcnv.c b/vcfcnv.c
index 5c82a3433..d3d777b26 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -1,6 +1,6 @@
 /* The MIT License
 
-   Copyright (c) 2014 Genome Research Ltd.
+   Copyright (c) 2014-2015 Genome Research Ltd.
 
    Author: Petr Danecek <pd3@sanger.ac.uk>
    
diff --git a/vcfroh.c b/vcfroh.c
index bb7653705..69a1727c8 100644
--- a/vcfroh.c
+++ b/vcfroh.c
@@ -1,6 +1,6 @@
 /*  vcfroh.c -- HMM model for detecting runs of autozygosity.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -272,20 +272,20 @@ void set_tprob_genmap(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, d
 {
     args_t *args = (args_t*) data;
     double ci = get_genmap_rate(args, pos - prev_pos, pos);
-    MAT(tprob,2,STATE_HW,STATE_HW) *= 1-ci;
     MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
     MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
-    MAT(tprob,2,STATE_AZ,STATE_AZ) *= 1-ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ)  = 1 - MAT(tprob,2,STATE_HW,STATE_AZ);
+    MAT(tprob,2,STATE_HW,STATE_HW)  = 1 - MAT(tprob,2,STATE_AZ,STATE_HW);
 }
 
 void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data, double *tprob)
 {
     args_t *args = (args_t*) data;
     double ci = (pos - prev_pos) * args->rec_rate;
-    MAT(tprob,2,STATE_HW,STATE_HW) *= 1-ci;
     MAT(tprob,2,STATE_HW,STATE_AZ) *= ci;
     MAT(tprob,2,STATE_AZ,STATE_HW) *= ci;
-    MAT(tprob,2,STATE_AZ,STATE_AZ) *= 1-ci;
+    MAT(tprob,2,STATE_AZ,STATE_AZ)  = 1 - MAT(tprob,2,STATE_HW,STATE_AZ);
+    MAT(tprob,2,STATE_HW,STATE_HW)  = 1 - MAT(tprob,2,STATE_AZ,STATE_HW);
 }
 
 
@@ -301,19 +301,17 @@ void set_tprob_recrate(hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *data,
  *  Transition probabilities:
  *    tAZ = P(AZ|HW)  .. parameter
  *    tHW = P(HW|AZ)  .. parameter
- *    P(AZ|AZ) = 1 - P(HW|AZ) = 1 - tHW
- *    P(HW|HW) = 1 - P(AZ|HW) = 1 - tAZ
  *
  *    ci  = P_i(C)    .. probability of cross-over at site i, from genetic map
  *
  *    AZi = P_i(AZ)   .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
  *    HWi = P_i(HW)
  *
- *    P_i(AZ|AZ) = P(AZ|AZ) * (1-ci) * AZ{i-1} = (1-tHW) * (1-ci) * AZ{i-1}
  *    P_i(AZ|HW) = P(AZ|HW) * ci * HW{i-1}     = tAZ * ci * (1 - AZ{i-1})
- *
- *    P_i(HW|HW) = P(HW|HW) * (1-ci) * HW{i-1} = (1-tAZ) * (1-ci) * (1 - AZ{i-1})
  *    P_i(HW|AZ) = P(HW|AZ) * ci * AZ{i-1}     = tHW * ci * AZ{i-1}
+ *    P_i(AZ|AZ) = 1 - P_i(HW|AZ)
+ *    P_i(HW|HW) = 1 - P_i(AZ|HW)
+ *
  */
 
 static void flush_viterbi(args_t *args)
@@ -668,8 +666,8 @@ static void usage(args_t *args)
     fprintf(stderr, "    -T, --targets-file <file>          similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "HMM Options:\n");
-    fprintf(stderr, "    -a, --hw-to-az <float>             P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy-Weinberg) state [1e-8]\n");
-    fprintf(stderr, "    -H, --az-to-hw <float>             P(HW|AZ) transition probability from HW to AZ state [1e-7]\n");
+    fprintf(stderr, "    -a, --hw-to-az <float>             P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state [1e-1]\n");
+    fprintf(stderr, "    -H, --az-to-hw <float>             P(HW|AZ) transition probability from AZ to HW state [1e-1]\n");
     fprintf(stderr, "    -V, --viterbi-training             perform Viterbi training to estimate transition probabilities\n");
     fprintf(stderr, "\n");
     exit(1);

From 3ba5f38ced4e3938348fa231a2f3d794ee43bc5a Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 30 Jun 2015 16:41:02 +0100
Subject: [PATCH 011/211] New bcftools roh --AF-dflt option; changed -a,-H
 defaults; fixed a bug in -e -

---
 bcftools.h       |  8 ++++++++
 doc/bcftools.txt | 10 ++++++----
 vcfcnv.c         |  7 -------
 vcfroh.c         | 46 ++++++++++++++++++++++++++++++----------------
 4 files changed, 44 insertions(+), 27 deletions(-)

diff --git a/bcftools.h b/bcftools.h
index 7d3936ad7..6f22272b9 100644
--- a/bcftools.h
+++ b/bcftools.h
@@ -27,6 +27,7 @@ THE SOFTWARE.  */
 
 #include <stdarg.h>
 #include <htslib/vcf.h>
+#include <math.h>
 
 #define FT_GZ 1
 #define FT_VCF 2
@@ -60,4 +61,11 @@ static inline char gt2iupac(char a, char b)
     return iupac[(int)a][(int)b];
 }
 
+static inline double phred_score(double prob)
+{
+    if ( prob==0 ) return 99;
+    prob = -4.3429*log(prob);
+    return prob>99 ? 99 : prob;
+}
+
 #endif
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 6c2cde83e..1dca046f8 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1332,20 +1332,22 @@ Emission probabilities:
 Transition probabilities:
   tAZ = P(AZ|HW)  .. from HW to AZ, the -a parameter
   tHW = P(HW|AZ)  .. from AZ to HW, the -H parameter
-  P(AZ|AZ) = 1 - P(HW|AZ) = 1 - tHW
-  P(HW|HW) = 1 - P(AZ|HW) = 1 - tAZ
 
   ci  = P_i(C)  .. probability of cross-over at site i, from genetic map
   AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
   HWi = P_i(HW) 
 
-  P_{i+1}(AZ) = oAZ * max[(1-tHW) * (1-ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
-  P_{i+1}(HW) = oHW * max[(1-tAZ) * (1-ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]
+  P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
+  P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]
 
 --------------------------------------
 
 ==== General Options:
 
+*--AF-dflt* 'FLOAT'::
+    in case allele frequency is not known, use the 'FLOAT'. By default, sites where
+    allele frequency cannot be determined, or is 0, are skipped.
+
 *--AF-tag* 'TAG'::
     use the specified INFO tag 'TAG' as an allele frequency estimate
     instead of the defaul AC and AN tags. Sites which do not have 'TAG'
diff --git a/vcfcnv.c b/vcfcnv.c
index d3d777b26..08b980c6b 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -518,13 +518,6 @@ static inline char copy_number_state(args_t *args, int istate, int ismpl)
     return code[idx];
 }
 
-static double phred_score(double prob)
-{
-    if ( prob==0 ) return 99;
-    prob = -4.3429*log(prob);
-    return prob>99 ? 99 : prob;
-}
-
 static double avg_ii_prob(int n, double *mat)
 {
     int i;
diff --git a/vcfroh.c b/vcfroh.c
index 69a1727c8..fa64b798e 100644
--- a/vcfroh.c
+++ b/vcfroh.c
@@ -49,7 +49,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr;
     double t2AZ, t2HW;      // P(AZ|HW) and P(HW|AZ) parameters
-    double unseen_PL;
+    double unseen_PL, dflt_AF;
 
     char *genmap_fname;
     genmap_t *genmap;
@@ -122,20 +122,21 @@ static void init_data(args_t *args)
         }
         free(smpls);
     }
-    else
+    else if ( !args->estimate_AF )
         kputs(args->sample, &str);
 
-    int ret = bcf_hdr_set_samples(args->hdr, str.s, 0);
-    if ( ret<0 ) error("Error parsing the list of samples: %s\n", str.s);
-    else if ( ret>0 ) error("The %d-th sample not found in the VCF\n", ret);
+    if ( str.l )
+    {
+        int ret = bcf_hdr_set_samples(args->hdr, str.s, 0);
+        if ( ret<0 ) error("Error parsing the list of samples: %s\n", str.s);
+        else if ( ret>0 ) error("The %d-th sample not found in the VCF\n", ret);
+    }
 
     if ( args->af_tag )
         if ( !bcf_hdr_idinfo_exists(args->hdr,BCF_HL_INFO,bcf_hdr_id2int(args->hdr,BCF_DT_ID,args->af_tag)) )
             error("No such INFO tag in the VCF: %s\n", args->af_tag);
 
-    if ( !bcf_sr_set_samples(args->files, str.s, 0) )
-        error("Error: could not set the samples %s\n", str.s);
-    args->nsmpl = args->files->n_smpl;
+    args->nsmpl = bcf_hdr_nsamples(args->hdr);
     args->ismpl = bcf_hdr_id2int(args->hdr, BCF_DT_SAMPLE, args->sample);
     free(str.s);
 
@@ -324,12 +325,16 @@ static void flush_viterbi(args_t *args)
     {
         // single viterbi pass, one chromsome
         hmm_run_viterbi(args->hmm, args->nsites, args->eprob, args->sites);
+        hmm_run_fwd_bwd(args->hmm, args->nsites, args->eprob, args->sites);
+        double *fwd = hmm_get_fwd_bwd_prob(args->hmm);
 
         const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid);
         uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
         for (i=0; i<args->nsites; i++)
         {
-            printf("%s\t%d\t%d\t..\n", chr,args->sites[i]+1,vpath[i*2]==STATE_AZ ? 1 : 0);
+            int state = vpath[i*2]==STATE_AZ ? 1 : 0;
+            double *pval = fwd + i*2;
+            printf("%s\t%d\t%d\t%.1f\n", chr,args->sites[i]+1, state, phred_score(1.0-pval[state]));
         }
         return;
     }
@@ -363,13 +368,12 @@ static void flush_viterbi(args_t *args)
             }
         }
 
-
         // update the transition matrix tprob
         for (i=0; i<2; i++)
         {
             int n = 0;
             for (j=0; j<2; j++) n += MAT(tcounts,2,i,j);
-            error("fixme: state %d not observed\n", i+1);
+            if ( !n) error("fixme: state %d not observed\n", i+1);
             for (j=0; j<2; j++) MAT(tcounts,2,i,j) /= n;
         }
         if ( args->genmap_fname || args->rec_rate > 0 )
@@ -515,7 +519,11 @@ int parse_line(args_t *args, bcf1_t *line, double *alt_freq, double *pdg)
     }
 
     if ( ret<0 ) return ret;
-
+    if ( *alt_freq==0.0 )
+    {
+        if ( args->dflt_AF==0 ) return -1;       // we skip sites with AF=0
+        *alt_freq = args->dflt_AF;
+    }
 
     // Set P(D|G)
     if ( args->fake_PLs )
@@ -652,6 +660,7 @@ static void usage(args_t *args)
     fprintf(stderr, "Usage:   bcftools roh [options] <in.vcf.gz>\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "General Options:\n");
+    fprintf(stderr, "        --AF-dflt <float>              if AF is not known, use this allele frequency [skip]\n");
     fprintf(stderr, "        --AF-tag <TAG>                 use TAG for allele frequency\n");
     fprintf(stderr, "        --AF-file <file>               read allele frequencies from file (CHR\\tPOS\\tREF,ALT\\tAF)\n");
     fprintf(stderr, "    -e, --estimate-AF <file>           calculate AC,AN counts on the fly, using either all samples (\"-\") or samples listed in <file>\n");
@@ -666,8 +675,8 @@ static void usage(args_t *args)
     fprintf(stderr, "    -T, --targets-file <file>          similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "HMM Options:\n");
-    fprintf(stderr, "    -a, --hw-to-az <float>             P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state [1e-1]\n");
-    fprintf(stderr, "    -H, --az-to-hw <float>             P(HW|AZ) transition probability from AZ to HW state [1e-1]\n");
+    fprintf(stderr, "    -a, --hw-to-az <float>             P(AZ|HW) transition probability from HW (Hardy-Weinberg) to AZ (autozygous) state [6.7e-8]\n");
+    fprintf(stderr, "    -H, --az-to-hw <float>             P(HW|AZ) transition probability from AZ to HW state [5e-9]\n");
     fprintf(stderr, "    -V, --viterbi-training             perform Viterbi training to estimate transition probabilities\n");
     fprintf(stderr, "\n");
     exit(1);
@@ -679,8 +688,8 @@ int main_vcfroh(int argc, char *argv[])
     args_t *args  = (args_t*) calloc(1,sizeof(args_t));
     args->argc    = argc; args->argv = argv;
     args->files   = bcf_sr_init();
-    args->t2AZ    = 1e-1;
-    args->t2HW    = 1e-1;
+    args->t2AZ    = 6.7e-8;
+    args->t2HW    = 5e-9;
     args->rec_rate = 0;
     int regions_is_file = 0, targets_is_file = 0;
 
@@ -688,6 +697,7 @@ int main_vcfroh(int argc, char *argv[])
     {
         {"AF-tag",1,0,0},
         {"AF-file",1,0,1},
+        {"AF-dflt",1,0,2},
         {"estimate-AF",1,0,'e'},
         {"GTs-only",1,0,'G'},
         {"sample",1,0,'s'},
@@ -710,6 +720,10 @@ int main_vcfroh(int argc, char *argv[])
         switch (c) {
             case 0: args->af_tag = optarg; naf_opts++; break;
             case 1: args->af_fname = optarg; naf_opts++; break;
+            case 2: 
+                args->dflt_AF = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: --AF-dflt %s\n", optarg);
+                break;
             case 'e': args->estimate_AF = optarg; naf_opts++; break;
             case 'I': args->snps_only = 1; break;
             case 'G':

From aea4cf9bc605f2172769754fd7bd11e19487afa3 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Mon, 6 Jul 2015 11:25:45 +0100
Subject: [PATCH 012/211] Fix polysomy dependencies [minor]

---
 Makefile | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 92139048f..bb75b8503 100644
--- a/Makefile
+++ b/Makefile
@@ -159,7 +159,8 @@ kmin.o: kmin.c kmin.h
 mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h)
 prob1.o: prob1.c $(prob1_h)
 vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h
-polysomy.o: polysomy.c $(htslib_hts_h)
+polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h
+peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
 consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h
 version.o: version.h version.c
 

From da26c063287397535e82e3b3a6ef3328eedf0c49 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 29 Jun 2015 07:27:03 +0100
Subject: [PATCH 013/211] plot-vcfstats: Fix edge case in tstv_by_qual plot,
 see #229

---
 plot-vcfstats | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plot-vcfstats b/plot-vcfstats
index 38d93355c..2ed9ec7f5 100755
--- a/plot-vcfstats
+++ b/plot-vcfstats
@@ -1281,7 +1281,7 @@ sub plot_tstv_by_QUAL
             \\tfor row in reader:
             \\t\\tif row[0][0] != '#': dat.append([float(x) for x in row])
 
-            if plot_tstv_by_qual:
+            if plot_tstv_by_qual and len(dat)>2:
             \\tfig = plt.figure(figsize=($$opts{img_width},$$opts{img_height}))
             \\tax1 = fig.add_subplot(111)
             \\tax1.plot([row[1] for row in dat], [row[2] for row in dat], '^-', ms=3, mec='$$opts{id2col}[$id]', color='$$opts{id2col}[$id]')

From 4eec7d5f82e677a0d4f4d75e20c1184fb9adb5f6 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 16 Mar 2015 13:30:16 +0000
Subject: [PATCH 014/211] concat: new --compact-PS switch

---
 vcfconcat.c | 43 +++++++++++++++++++++++++++++++++----------
 1 file changed, 33 insertions(+), 10 deletions(-)

diff --git a/vcfconcat.c b/vcfconcat.c
index aa46b1032..ec46fc5fa 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -50,6 +50,7 @@ typedef struct _args_t
 
     char **argv, *output_fname, *file_list, **fnames, *regions_list;
     int argc, nfnames, allow_overlaps, phased_concat, remove_dups, regions_is_file;
+    int compact_PS, phase_set_changed;
 }
 args_t;
 
@@ -246,7 +247,11 @@ static void phased_flush(args_t *args)
         bcf_translate(args->out_hdr, args->files->readers[0].header, arec);
         if ( args->nswap )
             phase_update(args, args->out_hdr, arec);
-        bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
         bcf_write(args->out_fh, args->out_hdr, arec);
 
         if ( arec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%d vs %d  [1]\n", bcf_seqname(args->files->readers[0].header,arec),arec->pos+1,args->prev_pos_check+1);
@@ -283,11 +288,20 @@ static void phased_flush(args_t *args)
             bcf_update_format_int32(args->out_hdr,brec,"PQ",args->phase_qual,nsmpl);
             PQ_printed = 1;
             for (j=0; j<nsmpl; j++)
-                if ( args->phase_qual[j] < args->min_PQ ) args->phase_set[j] = brec->pos+1;
+                if ( args->phase_qual[j] < args->min_PQ ) 
+                {
+                    args->phase_set[j] = brec->pos+1;
+                    args->phase_set_changed = 1;
+                }
+                else if ( args->compact_PS ) args->phase_set[j] = bcf_int32_missing;
         }
         if ( args->nswap )
             phase_update(args, args->out_hdr, brec);
-        bcf_update_format_int32(args->out_hdr,brec,"PS",args->phase_set,nsmpl);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,brec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
         bcf_write(args->out_fh, args->out_hdr, brec);
 
         if ( brec->pos < args->prev_pos_check ) error("FIXME, disorder: %s:%d vs %d  [2]\n", bcf_seqname(args->files->readers[1].header,brec),brec->pos+1,args->prev_pos_check+1);
@@ -311,6 +325,7 @@ static void phased_push(args_t *args, bcf1_t *arec, bcf1_t *brec)
 
         for (i=0; i<nsmpl; i++)
             args->phase_set[i] = arec->pos+1;
+        args->phase_set_changed = 1;
 
         if ( args->seen_seq[chr_id] ) error("The chromosome block %s is not contiguous\n", bcf_seqname(args->files->readers[0].header,arec));
         args->seen_seq[chr_id] = 1;
@@ -323,7 +338,11 @@ static void phased_push(args_t *args, bcf1_t *arec, bcf1_t *brec)
         bcf_translate(args->out_hdr, args->files->readers[0].header, arec);
         if ( args->nswap )
             phase_update(args, args->out_hdr, arec);
-        bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+        if ( !args->compact_PS || args->phase_set_changed )
+        {
+            bcf_update_format_int32(args->out_hdr,arec,"PS",args->phase_set,nsmpl);
+            args->phase_set_changed = 0;
+        }
         bcf_write(args->out_fh, args->out_hdr, arec);
 
         if ( arec->pos < args->prev_pos_check )
@@ -511,7 +530,7 @@ static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Concatenate or combine VCF/BCF files. All source files must have the same sample\n");
-    fprintf(stderr, "         columns appearing in the same order. Can be used, for example, to\n");
+    fprintf(stderr, "         columns appearing in the same order. The program can be used, for example, to\n");
     fprintf(stderr, "         concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\n");
     fprintf(stderr, "         VCF into one. The input files must be sorted by chr and position. The files\n");
     fprintf(stderr, "         must be given in the correct order to produce sorted VCF on output unless\n");
@@ -520,14 +539,15 @@ static void usage(args_t *args)
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "   -a, --allow-overlaps           First coordinate of the next file can precede last record of the current file.\n");
-    fprintf(stderr, "   -D, --remove-duplicates        Output only once records present in multiple files.\n");
+    fprintf(stderr, "   -c, --compact-PS               Do not output PS tag at each site, only at the start of a new phase set block.\n");
+    fprintf(stderr, "   -D, --remove-duplicates        Output records present in multiple files only once.\n");
     fprintf(stderr, "   -f, --file-list <file>         Read the list of files from a file.\n");
     fprintf(stderr, "   -l, --ligate                   Ligate phased VCFs by matching phase at overlapping haplotypes\n");
-    fprintf(stderr, "   -q, --min-PQ <int>             Break phase set if phasing quality is lower than <int> [30]\n");
     fprintf(stderr, "   -o, --output <file>            Write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
-    fprintf(stderr, "   -r, --regions <region>         restrict to comma-separated list of regions\n");
-    fprintf(stderr, "   -R, --regions-file <file>      restrict to regions listed in a file\n");
+    fprintf(stderr, "   -q, --min-PQ <int>             Break phase set if phasing quality is lower than <int> [30]\n");
+    fprintf(stderr, "   -r, --regions <region>         Restrict to comma-separated list of regions\n");
+    fprintf(stderr, "   -R, --regions-file <file>      Restrict to regions listed in a file\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -543,6 +563,7 @@ int main_vcfconcat(int argc, char *argv[])
 
     static struct option loptions[] =
     {
+        {"compact-PS",0,0,'c'},
         {"regions",1,0,'r'},
         {"regions-file",1,0,'R'},
         {"remove-duplicates",0,0,'D'},
@@ -555,9 +576,10 @@ int main_vcfconcat(int argc, char *argv[])
         {0,0,0,0}
     };
     char *tmp;
-    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dr:R:",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dr:R:c",loptions,NULL)) >= 0)
     {
         switch (c) {
+            case 'c': args->compact_PS = 1; break;
             case 'r': args->regions_list = optarg; break;
             case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
             case 'D': args->remove_dups = 1; break;
@@ -591,6 +613,7 @@ int main_vcfconcat(int argc, char *argv[])
         optind++;
     }
     if ( args->allow_overlaps && args->phased_concat ) args->allow_overlaps = 0;
+    if ( args->compact_PS && !args->phased_concat ) error("The -c option is intended only with -l\n");
     if ( args->file_list )
     {
         if ( args->nfnames ) error("Cannot combine -l with file names on command line.\n");

From 4abc0f289f1f650d5d620cd4c7d4288edaaf8e75 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 29 Apr 2015 11:43:08 +0100
Subject: [PATCH 015/211] concat -d option to remove duplicates based on one of
 the collapse srings: <snps|indels|both|all|none>

---
 vcfconcat.c | 23 ++++++++++++++++++-----
 1 file changed, 18 insertions(+), 5 deletions(-)

diff --git a/vcfconcat.c b/vcfconcat.c
index ec46fc5fa..c6db1d7d9 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -48,8 +48,8 @@ typedef struct _args_t
     int nbuf, mbuf, prev_chr, min_PQ, prev_pos_check;
     int32_t *GTa, *GTb, mGTa, mGTb, *phase_qual, *phase_set;
 
-    char **argv, *output_fname, *file_list, **fnames, *regions_list;
-    int argc, nfnames, allow_overlaps, phased_concat, remove_dups, regions_is_file;
+    char **argv, *output_fname, *file_list, **fnames, *remove_dups, *regions_list;
+    int argc, nfnames, allow_overlaps, phased_concat, regions_is_file;
     int compact_PS, phase_set_changed;
 }
 args_t;
@@ -126,6 +126,16 @@ static void init_data(args_t *args)
             if ( bcf_sr_set_regions(args->files, args->regions_list, args->regions_is_file)<0 )
                 error("Failed to read the regions: %s\n", args->regions_list);
         }
+        if ( args->remove_dups )
+        {
+            if ( !strcmp(args->remove_dups,"snps") ) args->files->collapse |= COLLAPSE_SNPS;
+            else if ( !strcmp(args->remove_dups,"indels") ) args->files->collapse |= COLLAPSE_INDELS;
+            else if ( !strcmp(args->remove_dups,"both") ) args->files->collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
+            else if ( !strcmp(args->remove_dups,"any") ) args->files->collapse |= COLLAPSE_ANY;
+            else if ( !strcmp(args->remove_dups,"all") ) args->files->collapse |= COLLAPSE_ANY;
+            else if ( !strcmp(args->remove_dups,"none") ) args->files->collapse = COLLAPSE_NONE;
+            else error("The -D string \"%s\" not recognised.\n", args->remove_dups);
+        }
         for (i=0; i<args->nfnames; i++)
             if ( !bcf_sr_add_reader(args->files,args->fnames[i]) ) error("Failed to open %s: %s\n", args->fnames[i],bcf_sr_strerror(args->files->errnum));
     }
@@ -540,7 +550,8 @@ static void usage(args_t *args)
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "   -a, --allow-overlaps           First coordinate of the next file can precede last record of the current file.\n");
     fprintf(stderr, "   -c, --compact-PS               Do not output PS tag at each site, only at the start of a new phase set block.\n");
-    fprintf(stderr, "   -D, --remove-duplicates        Output records present in multiple files only once.\n");
+    fprintf(stderr, "   -d, --rm-dups <string>         Output duplicate records present in multiple files only once: <snps|indels|both|all|none>\n");
+    fprintf(stderr, "   -D, --remove-duplicates        Alias for -d none\n");
     fprintf(stderr, "   -f, --file-list <file>         Read the list of files from a file.\n");
     fprintf(stderr, "   -l, --ligate                   Ligate phased VCFs by matching phase at overlapping haplotypes\n");
     fprintf(stderr, "   -o, --output <file>            Write output to a file [standard output]\n");
@@ -567,6 +578,7 @@ int main_vcfconcat(int argc, char *argv[])
         {"regions",1,0,'r'},
         {"regions-file",1,0,'R'},
         {"remove-duplicates",0,0,'D'},
+        {"rm-dups",1,0,'d'},
         {"allow-overlaps",0,0,'a'},
         {"ligate",0,0,'l'},
         {"output",1,0,'o'},
@@ -576,13 +588,14 @@ int main_vcfconcat(int argc, char *argv[])
         {0,0,0,0}
     };
     char *tmp;
-    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dr:R:c",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:r:R:c",loptions,NULL)) >= 0)
     {
         switch (c) {
             case 'c': args->compact_PS = 1; break;
             case 'r': args->regions_list = optarg; break;
             case 'R': args->regions_list = optarg; args->regions_is_file = 1; break;
-            case 'D': args->remove_dups = 1; break;
+            case 'd': args->remove_dups = optarg; break;
+            case 'D': args->remove_dups = "none"; break;
             case 'q': 
                 args->min_PQ = strtol(optarg,&tmp,10);
                 if ( *tmp ) error("Could not parse argument: --min-PQ %s\n", optarg);

From 566df3cccb86b5677dbb75c8acc9f69e34469746 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 29 Apr 2015 13:22:50 +0100
Subject: [PATCH 016/211] concat -l: Print warning and proceed if GT not
 present

---
 vcfconcat.c | 24 +++++++++++++++++++++---
 1 file changed, 21 insertions(+), 3 deletions(-)

diff --git a/vcfconcat.c b/vcfconcat.c
index c6db1d7d9..d480279e7 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -1,6 +1,6 @@
 /*  vcfconcat.c -- Concatenate or combine VCF/BCF files.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -201,6 +201,7 @@ int vcf_write_line(htsFile *fp, kstring_t *line);
 static void phase_update(args_t *args, bcf_hdr_t *hdr, bcf1_t *rec)
 {
     int i, nGTs = bcf_get_genotypes(hdr, rec, &args->GTa, &args->mGTa);
+    if ( nGTs <= 0 ) return;    // GT field is not present
     for (i=0; i<bcf_hdr_nsamples(hdr); i++)
     {
         if ( !args->swap_phase[i] ) continue;
@@ -220,6 +221,7 @@ static void phased_flush(args_t *args)
     bcf_hdr_t *bhdr = args->files->readers[1].header;
 
     int i, j, nsmpl = bcf_hdr_nsamples(args->out_hdr);
+    static int gt_absent_warned = 0;
 
     for (i=0; i<args->nbuf; i+=2)
     {
@@ -227,10 +229,26 @@ static void phased_flush(args_t *args)
         bcf1_t *brec = args->buf[i+1];
 
         int nGTs = bcf_get_genotypes(ahdr, arec, &args->GTa, &args->mGTa);
-        if ( nGTs < 0 ) error("GT is not present at %s:%d\n", bcf_seqname(ahdr,arec), arec->pos+1);
+        if ( nGTs < 0 ) 
+        {
+            if ( !gt_absent_warned )
+            {
+                fprintf(stderr,"GT is not present at %s:%d. (This warning is printed only once.)\n", bcf_seqname(ahdr,arec), arec->pos+1);
+                gt_absent_warned = 1;
+            }
+            continue;
+        }
         if ( nGTs != 2*nsmpl ) continue;    // not diploid
         nGTs = bcf_get_genotypes(bhdr, brec, &args->GTb, &args->mGTb);
-        if ( nGTs < 0 ) error("GT is not present at %s:%d\n", bcf_seqname(bhdr,brec), brec->pos+1);
+        if ( nGTs < 0 )
+        {
+            if ( !gt_absent_warned )
+            {
+                fprintf(stderr,"GT is not present at %s:%d. (This warning is printed only once.)\n", bcf_seqname(bhdr,brec), brec->pos+1);
+                gt_absent_warned = 1;
+            }
+            continue;
+        }
         if ( nGTs != 2*nsmpl ) continue;    // not diploid
 
         for (j=0; j<nsmpl; j++)

From 0f15ea86de1e17040ffed10841bef40e185e2da3 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 6 Jul 2015 16:47:20 +0100
Subject: [PATCH 017/211] bcf_hdr_combine replaced by bcf_hdr_merge

bcf_hdr_combine deprecated and replaced by bcf_hdr_merge in htslib
(2bb9370f5a24938d8a2dc56f404e584661bf413f).

Fixes #208
---
 vcfconcat.c | 19 +++++++------------
 vcfmerge.c  |  7 +++----
 2 files changed, 10 insertions(+), 16 deletions(-)

diff --git a/vcfconcat.c b/vcfconcat.c
index d480279e7..f5370f1ba 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -73,20 +73,15 @@ static void init_data(args_t *args)
     {
         htsFile *fp = hts_open(args->fnames[i], "r"); if ( !fp ) error("Failed to open: %s\n", args->fnames[i]);
         bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to parse header: %s\n", args->fnames[i]);
-        if ( !args->out_hdr )
-            args->out_hdr = bcf_hdr_dup(hdr);
-        else
-        {
-            bcf_hdr_combine(args->out_hdr, hdr);
+        args->out_hdr = bcf_hdr_merge(args->out_hdr,hdr);
+        if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) )
+            error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
 
-            if ( bcf_hdr_nsamples(hdr) != bcf_hdr_nsamples(args->out_hdr) )
-                error("Different number of samples in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
+        int j;
+        for (j=0; j<bcf_hdr_nsamples(hdr); j++)
+            if ( strcmp(args->out_hdr->samples[j],hdr->samples[j]) )
+                error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
 
-            int j;
-            for (j=0; j<bcf_hdr_nsamples(hdr); j++)
-                if ( strcmp(args->out_hdr->samples[j],hdr->samples[j]) )
-                    error("Different sample names in %s. Perhaps \"bcftools merge\" is what you are looking for?\n", args->fnames[i]);
-        }
         if ( args->phased_concat )
         {
             int ret = bcf_read(fp, hdr, line);
diff --git a/vcfmerge.c b/vcfmerge.c
index ea26903d3..c2d3c0880 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -421,11 +421,10 @@ static int info_rules_add_values(args_t *args, bcf_hdr_t *hdr, bcf1_t *line, inf
 
 int bcf_hdr_sync(bcf_hdr_t *h);
 
-void bcf_hdr_merge(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples)
+void merge_headers(bcf_hdr_t *hw, const bcf_hdr_t *hr, const char *clash_prefix, int force_samples)
 {
     // header lines
-    int ret = bcf_hdr_combine(hw, hr);
-    if ( ret!=0 ) error("Error occurred while merging the headers.\n");
+    hw = bcf_hdr_merge(hw, hr);
 
     // samples
     int i;
@@ -1911,7 +1910,7 @@ void merge_vcf(args_t *args)
         for (i=0; i<args->files->nreaders; i++)
         {
             char buf[10]; snprintf(buf,10,"%d",i+1);
-            bcf_hdr_merge(args->out_hdr, args->files->readers[i].header,buf,args->force_samples);
+            merge_headers(args->out_hdr, args->files->readers[i].header,buf,args->force_samples);
         }
         bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_merge");
         bcf_hdr_sync(args->out_hdr);

From 7e7a7dbfcd0a65bae14c02299cb4ce1a243544aa Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 13 May 2015 14:01:42 +0100
Subject: [PATCH 018/211] More control duplicate lines removal with norm (REF
 still not treated well)

---
 vcfnorm.c | 46 +++++++++++++++++++++++++++++++++-------------
 1 file changed, 33 insertions(+), 13 deletions(-)

diff --git a/vcfnorm.c b/vcfnorm.c
index d2dd7aeed..613888002 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -1396,7 +1396,7 @@ static bcf1_t *mrows_flush(args_t *args)
 static void flush_buffer(args_t *args, htsFile *file, int n)
 {
     bcf1_t *line;
-    int i, k, prev_rid = -1, prev_pos = 0, prev_type = 0;
+    int i, k;
     for (i=0; i<n; i++)
     {
         k = rbuf_shift(&args->rbuf);
@@ -1417,16 +1417,6 @@ static void flush_buffer(args_t *args, htsFile *file, int n)
                 continue;
             }
         }
-        // todo: merge with next record if POS and the type are same. For now, just discard if asked to do so.
-        if ( args->rmdup )
-        {
-            int line_type = bcf_get_variant_types(args->lines[k]);
-            if ( prev_rid>=0 && prev_rid==args->lines[k]->rid && prev_pos==args->lines[k]->pos && prev_type==line_type )
-                continue;
-            prev_rid  = args->lines[k]->rid;
-            prev_pos  = args->lines[k]->pos;
-            prev_type = line_type;
-        }
         bcf_write1(file, args->hdr, args->lines[k]);
     }
     if ( args->mrows_op==MROWS_MERGE && !args->rbuf.n )
@@ -1537,11 +1527,29 @@ static void normalize_vcf(args_t *args)
     bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_norm");
     bcf_hdr_write(out, args->hdr);
 
+    int prev_rid = -1, prev_pos = -1, prev_type = 0;
     while ( bcf_sr_next_line(args->files) )
     {
         args->ntotal++;
 
         bcf1_t *line = args->files->readers[0].buffer[0];
+        if ( args->rmdup )
+        {
+            int line_type = bcf_get_variant_types(line);
+            if ( prev_rid>=0 && prev_rid==line->rid && prev_pos==line->pos )
+            {
+                if ( (args->rmdup>>1)&COLLAPSE_ANY ) continue;
+                if ( (args->rmdup>>1)&COLLAPSE_SNPS && line_type&(VCF_SNP|VCF_MNP) && prev_type&(VCF_SNP|VCF_MNP) ) continue;
+                if ( (args->rmdup>>1)&COLLAPSE_INDELS && line_type&(VCF_INDEL) && prev_type&(VCF_INDEL) ) continue;
+            }
+            else
+            {
+                prev_rid  = line->rid;
+                prev_pos  = line->pos;
+                prev_type = 0;
+            }
+            prev_type |= line_type;
+        }
 
         // still on the same chromosome?
         int i,j,ilast = rbuf_last(&args->rbuf);
@@ -1597,6 +1605,7 @@ static void usage(void)
     fprintf(stderr, "Options:\n");
     fprintf(stderr, "    -c, --check-ref <e|w|x|s>         check REF alleles and exit (e), warn (w), exclude (x), or set (s) bad sites [e]\n");
     fprintf(stderr, "    -D, --remove-duplicates           remove duplicate lines of the same type.\n");
+    fprintf(stderr, "    -d, --rm-dup <type>               remove duplicate snps|indels|both|any\n");
     fprintf(stderr, "    -f, --fasta-ref <file>            reference sequence\n");
     fprintf(stderr, "    -m, --multiallelics <-|+>[type]   split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n");
     fprintf(stderr, "    -N, --do-not-normalize            do not normalize indels (with -m or -c s)\n");
@@ -1639,6 +1648,7 @@ int main_vcfnorm(int argc, char *argv[])
         {"targets-file",1,0,'T'},
         {"site-win",1,0,'w'},
         {"remove-duplicates",0,0,'D'},
+        {"rm-dup",1,0,'d'},
         {"output",1,0,'o'},
         {"output-type",1,0,'O'},
         {"check-ref",1,0,'c'},
@@ -1646,9 +1656,16 @@ int main_vcfnorm(int argc, char *argv[])
         {0,0,0,0}
     };
     char *tmp;
-    while ((c = getopt_long(argc, argv, "hr:R:f:w:Do:O:c:m:t:T:sN",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sN",loptions,NULL)) >= 0) {
         switch (c) {
             case 'N': args->do_indels = 0; break;
+            case 'd':
+                if ( !strcmp("snps",optarg) ) args->rmdup = COLLAPSE_SNPS<<1;
+                else if ( !strcmp("indels",optarg) ) args->rmdup = COLLAPSE_INDELS<<1;
+                else if ( !strcmp("both",optarg) ) args->rmdup = COLLAPSE_BOTH<<1;
+                else if ( !strcmp("any",optarg) ) args->rmdup = COLLAPSE_ANY<<1;
+                else error("The argument to -d not recognised: %s\n", optarg);
+                break;
             case 'm':
                 if ( optarg[0]=='-' ) args->mrows_op = MROWS_SPLIT;
                 else if ( optarg[0]=='+' ) args->mrows_op = MROWS_MERGE;
@@ -1678,7 +1695,10 @@ int main_vcfnorm(int argc, char *argv[])
                 }
                 break;
             case 'o': args->output_fname = optarg; break;
-            case 'D': args->rmdup = 1; break;
+            case 'D':
+                fprintf(stderr,"Warning: `-D` is functional but deprecated, replaced by `-d both`.\n"); 
+                args->rmdup = COLLAPSE_NONE<<1;
+                break;
             case 's': args->strict_filter = 1; break;
             case 'f': args->ref_fname = optarg; break;
             case 'r': args->region = optarg; break;

From 4bfe242e9cf28091f5fb097f8ecece6d26d3e17a Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 25 Jun 2015 15:24:52 +0100
Subject: [PATCH 019/211] Output missing FMT fields as "." rather than negative
 integer when querying FMT vectors, such as PL{0}

---
 convert.c | 36 +++++++++++++++++++++++++++++++-----
 1 file changed, 31 insertions(+), 5 deletions(-)

diff --git a/convert.c b/convert.c
index ab7aefe7d..3e289f025 100644
--- a/convert.c
+++ b/convert.c
@@ -140,10 +140,22 @@ static void process_filter(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isa
     }
     else kputc('.', str);
 }
-static inline int bcf_array_ivalue(void *bcf_array, int type, int idx)
+static inline int32_t bcf_array_ivalue(void *bcf_array, int type, int idx)
 {
-    if ( type==BCF_BT_INT8 ) return ((int8_t*)bcf_array)[idx];
-    if ( type==BCF_BT_INT16 ) return ((int16_t*)bcf_array)[idx];
+    if ( type==BCF_BT_INT8 )
+    {
+        int8_t val = ((int8_t*)bcf_array)[idx];
+        if ( val==bcf_int8_missing ) return bcf_int32_missing;
+        if ( val==bcf_int8_vector_end ) return bcf_int32_vector_end;
+        return val;
+    }
+    if ( type==BCF_BT_INT16 )
+    {
+        int16_t val = ((int16_t*)bcf_array)[idx];
+        if ( val==bcf_int16_missing ) return bcf_int32_missing;
+        if ( val==bcf_int16_vector_end ) return bcf_int32_vector_end;
+        return val;
+    }
     return ((int32_t*)bcf_array)[idx];
 }
 static void process_info(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isample, kstring_t *str)
@@ -243,8 +255,22 @@ static void process_format(convert_t *convert, bcf1_t *line, fmt_t *fmt, int isa
             kputc('.', str);
             return;
         }
-        if ( fmt->fmt->type == BCF_BT_FLOAT ) ksprintf(str, "%g", ((float*)(fmt->fmt->p + isample*fmt->fmt->size))[fmt->subscript]);
-        else if ( fmt->fmt->type != BCF_BT_CHAR ) kputw(bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript), str);
+        if ( fmt->fmt->type == BCF_BT_FLOAT )
+        {
+            float *ptr = (float*)(fmt->fmt->p + isample*fmt->fmt->size);
+            if ( bcf_float_is_missing(ptr[fmt->subscript]) || bcf_float_is_vector_end(ptr[fmt->subscript]) )
+                kputc('.', str);
+            else
+                ksprintf(str, "%g", ptr[fmt->subscript]);
+        }
+        else if ( fmt->fmt->type != BCF_BT_CHAR )
+        {
+            int32_t ival = bcf_array_ivalue(fmt->fmt->p+isample*fmt->fmt->size,fmt->fmt->type,fmt->subscript);
+            if ( ival==bcf_int32_missing || ival==bcf_int32_vector_end )
+                kputc('.', str);
+            else
+                kputw(ival, str);
+        }
         else error("TODO: %s:%d .. fmt->type=%d\n", __FILE__,__LINE__, fmt->fmt->type);
     }
     else

From ddc0bef5b6c1db86ad6f4dd7715db9ba74ccaa70 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 27 Feb 2015 14:18:02 +0000
Subject: [PATCH 020/211] Updated cnv command:

- CNx state removed
- automatic optimization of parameters to increase sensitivity when
only a fraction of cells is aberrant (at the cose of decreased specificity)
- LRR smoothing
---
 vcfcnv.c | 629 +++++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 493 insertions(+), 136 deletions(-)

diff --git a/vcfcnv.c b/vcfcnv.c
index 08b980c6b..6287f5bde 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -35,20 +35,29 @@
 #include <htslib/khash_str2int.h>
 #include "bcftools.h"
 #include "HMM.h"
+#include "rbuf.h"
 
-#define DBG_HMM_PRN 0
+#define DBG0 0
 
-#define N_STATES 5
+#define N_STATES 4
 #define CN0 0
 #define CN1 1
 #define CN2 2
 #define CN3 3
-#define CNx 4
+
+typedef struct
+{
+    float mean, dev2, norm;
+}
+gauss_param_t;
 
 typedef struct
 {
     char *name;
-    int idx;
+    int idx;    // VCF sample index
+    float *lrr,*baf, baf_dev2, baf_dev2_dflt;
+    float cell_frac, cell_frac_dflt;
+    gauss_param_t gauss_param[18];
     double pobs[N_STATES];
     FILE *dat_fh, *cn_fh, *summary_fh;
     char *dat_fname, *cn_fname, *summary_fname;
@@ -63,11 +72,12 @@ typedef struct _args_t
     sample_t query_sample, control_sample;
 
     int nstates;    // number of states: N_STATES for one sample, N_STATES^2 for two samples
-    double baf_sigma2, lrr_sigma2;          // squared std dev of B-allele frequency and LRR distribution
+    double lrr_dev2;                        // squared std dev of LRR distribution
     double lrr_bias, baf_bias;              // LRR/BAF weights
     double same_prob, ij_prob;              // prior of both samples being the same and the transition probability P(i|j)
     double err_prob;                        // constant probability of erroneous measurement
-    double pRR, pRA, pAA, pRR_dflt, pRA_dflt, pAA_dflt;
+    float *nonref_afs, nonref_af, nonref_af_dflt, fRR, fRA, fAA;
+    unsigned long int nRR, nRA, nAA;
 
     double *tprob, *tprob_arr;  // array of transition matrices, precalculated up to ntprob_arr positions
     int ntprob_arr;
@@ -77,18 +87,17 @@ typedef struct _args_t
     uint32_t *sites;        // positions [nsites,msites]
     int nsites, msites;
 
-    double baum_welch_th;
+    double baum_welch_th, optimize_frac; 
     float plot_th;
     FILE *summary_fh;
     char **argv, *regions_list, *summary_fname, *output_dir;
     char *targets_list, *af_fname;
-    int argc;
+    int argc, verbose, lrr_smooth_win;
 }
 args_t;
 
 FILE *open_file(char **fname, const char *mode, const char *fmt, ...);
 
-
 static inline void hmm2cn_state(int nstates, int i, int *a, int *b)
 {
     *a = i / N_STATES;
@@ -100,10 +109,10 @@ static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
     double *mat = (double*) malloc(sizeof(double)*ndim*ndim);
 
     assert( ndim==N_STATES || ndim==N_STATES*N_STATES);
-    double pii = 1 - ij_prob*(N_STATES-1);
 
     if ( ndim==N_STATES )   // one sample
     {
+        double pii = 1 - ij_prob*(N_STATES-1);
         if ( pii < ij_prob ) error("Error: -x set a bit too high, P(x|x) < P(x|y): %e vs %e\n", pii,ij_prob);
         for (j=0; j<ndim; j++)
         {
@@ -115,6 +124,7 @@ static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
                     MAT(mat,ndim,i,j) = pii;
                 else
                     MAT(mat,ndim,i,j) = ij_prob;
+
                 sum += MAT(mat,ndim,i,j);
             }
             assert( fabs(sum - 1.0)<1e-15 );
@@ -122,6 +132,11 @@ static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
     }
     else    // two samples
     {
+        // interpret ij_prob differently, as ii_prob in fact, so that for two
+        // samples the behaviour is somewhat closer to single sample calling
+        // with s=0. 
+        double pii = 1 - ij_prob*(N_STATES-1);
+        ij_prob = (1 - pii) / (ndim - 1);
         for (j=0; j<ndim; j++)
         {
             int ja,jb;
@@ -158,7 +173,7 @@ static void init_sample_files(sample_t *smpl, char *dir)
     smpl->cn_fh  = open_file(&smpl->cn_fname,"w","%s/cn.%s.tab",dir,smpl->name);
     smpl->summary_fh = open_file(&smpl->summary_fname,"w","%s/summary.%s.tab",dir,smpl->name);
     fprintf(smpl->dat_fh,"# [1]Chromosome\t[2]Position\t[3]BAF\t[4]LRR\n");
-    fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\t[8]P(CNx)\n");
+    fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\n");
     fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\n");
 }
 static void close_sample_files(sample_t *smpl)
@@ -168,6 +183,7 @@ static void close_sample_files(sample_t *smpl)
     fclose(smpl->summary_fh);
 }
 
+static double norm_cdf(double mean, double dev);
 static void init_data(args_t *args)
 {
     args->prev_rid = -1;
@@ -292,7 +308,6 @@ static void plot_sample(args_t *args, sample_t *smpl)
             "       heat[1][x] = cn_dat[x][3]\n"
             "       heat[2][x] = cn_dat[x][4]\n"
             "       heat[3][x] = cn_dat[x][5]\n"
-            "       heat[4][x] = cn_dat[x][6]\n"
             "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n"
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'.-',ms=3,color='black')\n"
@@ -304,9 +319,9 @@ static void plot_sample(args_t *args, sample_t *smpl)
             "    ax2.set_ylabel('BAF')\n"
             "    ax3.set_ylabel('CN')\n"
             "    ax3.set_xlabel('Coordinate (chrom '+chr+')',fontsize=10)\n"
-            "    ax3.set_ylim(-0.1,5.1)\n"
-            "    ax3.set_yticks([0.5,1.5,2.5,3.5,4.5])\n"
-            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3','CN4'])\n"
+            "    ax3.set_ylim(-0.1,4.1)\n"
+            "    ax3.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
             "    plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92)\n"
             "    plt.savefig('%s/plot.%s.chr'+chr+'.png')\n"
             "    plt.close()\n"
@@ -428,7 +443,6 @@ static void create_plots(args_t *args)
             "       heat[1][x] = cn_dat[x][3]\n"
             "       heat[2][x] = cn_dat[x][4]\n"
             "       heat[3][x] = cn_dat[x][5]\n"
-            "       heat[4][x] = cn_dat[x][6]\n"
             "    mesh = ax3.pcolormesh(xgrid, ygrid, heat, cmap='bwr')\n"
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
@@ -445,7 +459,6 @@ static void create_plots(args_t *args)
             "       heat[1][x] = cn_dat[x][3]\n"
             "       heat[2][x] = cn_dat[x][4]\n"
             "       heat[3][x] = cn_dat[x][5]\n"
-            "       heat[4][x] = cn_dat[x][6]\n"
             "    mesh = ax4.pcolormesh(xgrid, ygrid, heat, cmap='bwr_r')\n"
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax4.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
@@ -471,12 +484,12 @@ static void create_plots(args_t *args)
             "    ax6.set_ylabel('LRR')\n"
             "    ax5.set_ylabel('BAF')\n"
             "    ax4.set_ylabel('CN')\n"
-            "    ax3.set_ylim(-0.1,5.1)\n"
-            "    ax3.set_yticks([0.5,1.5,2.5,3.5,4.5])\n"
-            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3','CN4'])\n"
-            "    ax4.set_ylim(-0.1,5.1)\n"
-            "    ax4.set_yticks([0.5,1.5,2.5,3.5,4.5])\n"
-            "    ax4.set_yticklabels(['CN0','CN1','CN2','CN3','CN4'])\n"
+            "    ax3.set_ylim(-0.1,4.1)\n"
+            "    ax3.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax3.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
+            "    ax4.set_ylim(-0.1,4.1)\n"
+            "    ax4.set_yticks([0.5,1.5,2.5,3.5])\n"
+            "    ax4.set_yticklabels(['CN0','CN1','CN2','CN3'])\n"
             "    plt.subplots_adjust(left=0.08,right=0.95,bottom=0.08,top=0.92,hspace=0)\n"
             "    plt.savefig('%s/plot.%s.%s.chr'+chr+'.png')\n"
             "    plt.close()\n"
@@ -501,6 +514,11 @@ static void destroy_data(args_t *args)
     free(args->eprob);
     free(args->tprob);
     free(args->summary_fname);
+    free(args->nonref_afs);
+    free(args->query_sample.baf);
+    free(args->query_sample.lrr);
+    free(args->control_sample.baf);
+    free(args->control_sample.lrr);
     free(args->query_sample.name);
     free(args->query_sample.dat_fname);
     free(args->query_sample.cn_fname);
@@ -526,12 +544,372 @@ static double avg_ii_prob(int n, double *mat)
     return avg/n;
 }
 
+#define GAUSS_CN1_PK_R(smpl)    (&((smpl)->gauss_param[0]))
+#define GAUSS_CN1_PK_A(smpl)    (&((smpl)->gauss_param[1]))
+#define GAUSS_CN2_PK_RR(smpl)   (&((smpl)->gauss_param[2]))
+#define GAUSS_CN2_PK_RA(smpl)   (&((smpl)->gauss_param[3]))
+#define GAUSS_CN2_PK_AA(smpl)   (&((smpl)->gauss_param[4]))
+#define GAUSS_CN3_PK_RRR(smpl)  (&((smpl)->gauss_param[5]))
+#define GAUSS_CN3_PK_RRA(smpl)  (&((smpl)->gauss_param[6]))
+#define GAUSS_CN3_PK_RAA(smpl)  (&((smpl)->gauss_param[7]))
+#define GAUSS_CN3_PK_AAA(smpl)  (&((smpl)->gauss_param[8]))
+
+static inline double norm_prob(double baf, gauss_param_t *param)
+{
+    return exp(-(baf-param->mean)*(baf-param->mean)*0.5/param->dev2) / param->norm / sqrt(2*M_PI*param->dev2);
+}
+
+static int set_observed_prob(args_t *args, sample_t *smpl, int isite)
+{
+    float baf = smpl->baf[isite];
+    float lrr = smpl->lrr[isite];
+
+    float fRR = args->fRR;
+    float fRA = args->fRA;
+    float fAA = args->fAA;
+
+    if ( baf<0 )
+    {
+        // no call: either some technical issue or the call could not be made because it is CN0
+        int i;
+        smpl->pobs[CN0] = 0.5;
+        for (i=1; i<N_STATES; i++) smpl->pobs[i] = (1.0-smpl->pobs[CN0])/(N_STATES-1);
+        return 0;
+    }
+
+    double cn1_baf = 
+        norm_prob(baf,GAUSS_CN1_PK_R(smpl)) * (fRR + fRA*0.5) +
+        norm_prob(baf,GAUSS_CN1_PK_A(smpl)) * (fAA + fRA*0.5) ;
+    double cn2_baf = 
+        norm_prob(baf,GAUSS_CN2_PK_RR(smpl)) * fRR + 
+        norm_prob(baf,GAUSS_CN2_PK_RA(smpl)) * fRA + 
+        norm_prob(baf,GAUSS_CN2_PK_AA(smpl)) * fAA;
+    double cn3_baf = 
+        norm_prob(baf,GAUSS_CN3_PK_RRR(smpl)) * fRR + 
+        norm_prob(baf,GAUSS_CN3_PK_RRA(smpl)) * fRA*0.5 + 
+        norm_prob(baf,GAUSS_CN3_PK_RAA(smpl)) * fRA*0.5 + 
+        norm_prob(baf,GAUSS_CN3_PK_AAA(smpl)) * fAA;
+
+    double norm = cn1_baf + cn2_baf + cn3_baf;
+    cn1_baf /= norm;
+    cn2_baf /= norm;
+    cn3_baf /= norm;
+
+    #if DBG0
+    if ( args->verbose ) fprintf(stderr,"%f\t%f %f %f\n", baf,cn1_baf,cn2_baf,cn3_baf);
+    #endif
+
+    double cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/args->lrr_dev2);
+    double cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/args->lrr_dev2);
+    double cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/args->lrr_dev2);
+
+    smpl->pobs[CN0] = 0;
+    smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr);
+    smpl->pobs[CN2] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn2_baf)*(1 - args->lrr_bias + args->lrr_bias*cn2_lrr);
+    smpl->pobs[CN3] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn3_baf)*(1 - args->lrr_bias + args->lrr_bias*cn3_lrr);
+
+    return 0;
+}
+
+static void set_emission_prob(args_t *args, int isite)
+{
+    double *eprob = &args->eprob[args->nstates*isite];
+    int i;
+    for (i=0; i<N_STATES; i++)
+        eprob[i] = args->query_sample.pobs[i];
+}
+
+static void set_emission_prob2(args_t *args, int isite)
+{
+    double *eprob = &args->eprob[args->nstates*isite];
+    int i, j;
+    for (i=0; i<N_STATES; i++)
+    {
+        for (j=0; j<N_STATES; j++)
+        {
+            eprob[i*N_STATES+j] = args->query_sample.pobs[i]*args->control_sample.pobs[j];
+        }
+    }
+}
+
+static void set_gauss_params(args_t *args, sample_t *smpl);
+static double norm_cdf(double mean, double dev)
+{
+    double bot = 0, top = 1;
+    top = 1 - 0.5*erfc((top-mean)/(dev*sqrt(2)));
+    bot = 1 - 0.5*erfc((bot-mean)/(dev*sqrt(2)));
+    return top-bot;
+}
+
+static void set_emission_probs(args_t *args)
+{
+    if ( !args->af_fname )
+    {
+        args->fRR = 0.76;
+        args->fRA = 0.14;
+        args->fAA = 0.098;
+    }
+
+    set_gauss_params(args, &args->query_sample);
+    if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+
+    #if DBG0
+    args->verbose = 1;
+    args->query_sample.baf[0] = 0; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1/3.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1/2.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 2/3.; set_observed_prob(args,&args->query_sample,0);
+    args->query_sample.baf[0] = 1; set_observed_prob(args,&args->query_sample,0);
+    args->verbose = 0;
+    #endif
+
+    int i;
+    for (i=0; i<args->nsites; i++)
+    {
+        if ( args->af_fname )
+        {
+            args->fRR = (1-args->nonref_afs[i])*(1-args->nonref_afs[i]);
+            args->fRA = 2*args->nonref_afs[i]*(1-args->nonref_afs[i]);
+            args->fAA = args->nonref_afs[i]*args->nonref_afs[i];
+        }
+        set_observed_prob(args,&args->query_sample,i);
+        if ( args->control_sample.name )
+        {
+            set_observed_prob(args,&args->control_sample,i);
+            set_emission_prob2(args,i);
+        }
+        else
+            set_emission_prob(args,i);
+    }
+}
+
+static void smooth_data(float *dat, int ndat, int win)
+{
+    if ( win<=1 ) return;
+
+    int i,j, k1 = win/2, k2 = win-k1;
+    rbuf_t rbuf;
+    rbuf_init(&rbuf,win);
+    float sum = 0, *buf = (float*)malloc(sizeof(float)*win);
+    for (i=0; i<k2; i++)
+    {
+        sum += dat[i];
+        int j = rbuf_append(&rbuf);
+        buf[j] = dat[i];
+    }
+    for (i=0; i<ndat; i++)
+    {
+        dat[i] = sum/rbuf.n;
+        if ( i>=k1 )
+        {
+            j = rbuf_shift(&rbuf);
+            sum -= buf[j];
+        }
+        if ( i+k2<ndat )
+        {
+            sum += dat[i+k2];
+            j = rbuf_append(&rbuf);
+            buf[j] = dat[i+k2];
+        }
+    }
+    free(buf);
+}
+
+static void set_gauss_params(args_t *args, sample_t *smpl)
+{
+    int i;
+    for (i=0; i<18; i++) smpl->gauss_param[i].dev2 = smpl->baf_dev2;
+
+    double dev = sqrt(smpl->baf_dev2);
+
+    GAUSS_CN1_PK_R(smpl)->mean = 0;
+    GAUSS_CN1_PK_A(smpl)->mean = 1;
+    GAUSS_CN1_PK_R(smpl)->norm = norm_cdf(GAUSS_CN1_PK_R(smpl)->mean,dev);
+    GAUSS_CN1_PK_A(smpl)->norm = norm_cdf(GAUSS_CN1_PK_A(smpl)->mean,dev);
+
+    GAUSS_CN2_PK_RR(smpl)->mean = 0;
+    GAUSS_CN2_PK_RA(smpl)->mean = 0.5;
+    GAUSS_CN2_PK_AA(smpl)->mean = 1;
+    GAUSS_CN2_PK_RR(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RR(smpl)->mean,dev);
+    GAUSS_CN2_PK_RA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_RA(smpl)->mean,dev);
+    GAUSS_CN2_PK_AA(smpl)->norm = norm_cdf(GAUSS_CN2_PK_AA(smpl)->mean,dev);
+
+    GAUSS_CN3_PK_RRR(smpl)->mean = 0;
+    GAUSS_CN3_PK_RRA(smpl)->mean = 1.0/(2+smpl->cell_frac);
+    GAUSS_CN3_PK_RAA(smpl)->mean = (1.0+smpl->cell_frac)/(2+smpl->cell_frac);
+    GAUSS_CN3_PK_AAA(smpl)->mean = 1;
+    GAUSS_CN3_PK_RRR(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRR(smpl)->mean,dev);
+    GAUSS_CN3_PK_RRA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RRA(smpl)->mean,dev);
+    GAUSS_CN3_PK_RAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_RAA(smpl)->mean,dev);
+    GAUSS_CN3_PK_AAA(smpl)->norm = norm_cdf(GAUSS_CN3_PK_AAA(smpl)->mean,dev);
+}
+
+static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
+{
+    hmm_t *hmm = args->hmm;
+
+    // estimate the BAF mean and deviation for CN3
+    double mean_cn3 = 0, norm_cn3 = 0;
+    double baf_dev2 = 0, baf_AA_dev2 = 0, norm_baf_AA_dev2 = 0;
+
+    int i, j;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>4/5.) { baf_AA_dev2 += (1.0-baf)*(1.0-baf); norm_baf_AA_dev2++; continue; }       // skip AA genotypes
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR genotypes
+
+        double prob_cn3 = 0, *probs = hmm->fwd + i*hmm->nstates;
+        if ( !args->control_sample.name )
+        {
+            prob_cn3 = probs[CN3];
+        }
+        else if ( ismpl==0 )
+        {
+            // query sample: CN3 probability must be recovered from all states of the control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3*N_STATES+j];
+        }
+        else
+        {
+            // same as above but for control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3+j*N_STATES];
+        }
+        mean_cn3 += prob_cn3 * baf;
+        norm_cn3 += prob_cn3;
+    }
+    if ( !norm_cn3 )
+    {
+        smpl->cell_frac = 1.0;
+        return 1;
+    }
+    mean_cn3 /= norm_cn3;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR,AA genotypes
+
+        double prob_cn3 = 0, *probs = hmm->fwd + i*hmm->nstates;
+        if ( !args->control_sample.name )
+        {
+            prob_cn3 = probs[CN3];
+        }
+        else if ( ismpl==0 )
+        {
+            // query sample: CN3 probability must be recovered from all states of the control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3*N_STATES+j];
+        }
+        else
+        {
+            // same as above but for control sample
+            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3+j*N_STATES];
+        }
+        baf_dev2 += prob_cn3 * (baf - mean_cn3)*(baf - mean_cn3);
+    }
+
+    /*
+        A noisy CN2 band is hard to distinguish from two CN3 bands which are
+        close to each other. Set a treshold on the minimum separation based
+        on the BAF deviation at p=0.95
+    */
+    baf_dev2 /= norm_cn3;
+    baf_AA_dev2 /= norm_baf_AA_dev2;
+    if ( baf_dev2 < baf_AA_dev2 )  baf_dev2 = baf_AA_dev2;
+    double max_mean_cn3 = 0.5 - sqrt(baf_dev2)*1.644854;    // R: qnorm(0.95)=1.644854
+    //fprintf(stderr,"dev=%f  AA_dev=%f  max_mean_cn3=%f  mean_cn3=%f\n", baf_dev2,baf_AA_dev2,max_mean_cn3,mean_cn3);
+    assert( max_mean_cn3>0 );
+
+    double new_frac = 1./mean_cn3 - 2;
+    if ( mean_cn3 > max_mean_cn3 || new_frac < args->optimize_frac )
+    {
+        // out of bounds, beyond our detection limits. Give up and say it converged
+        smpl->cell_frac = 1.0;
+        return 1;
+    }
+    if ( new_frac>1 ) new_frac = 1;
+    int converged = fabs(new_frac - smpl->cell_frac) < 1e-1 ? 1 : 0;
+
+    // Update dev2, but stay within safe limits
+    if ( baf_dev2 > 3*smpl->baf_dev2_dflt ) baf_dev2 = 3*smpl->baf_dev2_dflt;
+    else if ( baf_dev2 < 0.5*smpl->baf_dev2_dflt ) baf_dev2 = 0.5*smpl->baf_dev2_dflt;
+
+    smpl->cell_frac = new_frac;
+    smpl->baf_dev2  = baf_dev2;
+
+    return converged;
+}
+
+// Update parameters which depend on the estimated fraction of aberrant cells
+// in CN3.  Returns 0 if the current estimate did not need to be updated or 1
+// if there was a change.
+static int update_args(args_t *args)
+{
+    int converged = update_sample_args(args, &args->query_sample, 0);
+    if ( args->control_sample.name )
+    {
+        converged += update_sample_args(args, &args->control_sample, 1);
+        return converged==2 ? 0 : 1;
+    }
+    return converged ? 0 : 1;
+}
+
 static void cnv_flush_viterbi(args_t *args)
 {
     if ( !args->nsites ) return;
 
+    // Set HMM transition matrix for the new chromsome again. This is for case
+    // Baum-Welch was used, which is experimental, largerly unsupported and not
+    // done by default.
     hmm_t *hmm = args->hmm;
     hmm_set_tprob(args->hmm, args->tprob, 10000);
+
+    // Smooth LRR values to reduce noise
+    smooth_data(args->query_sample.lrr,args->nsites, args->lrr_smooth_win);
+    if ( args->control_sample.name ) smooth_data(args->control_sample.lrr,args->nsites, args->lrr_smooth_win);
+
+    // Set the BAF peak likelihoods, such as P(RRR|CN3), taking account the
+    // estimated fraction of aberrant cells in the mixture. With the new chromosome,
+    // reset the fraction to the default value.
+    args->query_sample.cell_frac   = args->query_sample.cell_frac_dflt;
+    args->control_sample.cell_frac = args->control_sample.cell_frac_dflt;
+    args->query_sample.baf_dev2    = args->query_sample.baf_dev2_dflt;
+    args->control_sample.baf_dev2  = args->control_sample.baf_dev2_dflt;
+    set_gauss_params(args, &args->query_sample);
+    if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+
+    if ( args->optimize_frac )
+    {
+        int niter = 0;
+        fprintf(stderr,"Attempting to estimate the fraction of aberrant cells (chr %s):\n", bcf_hdr_id2name(args->hdr,args->prev_rid));
+        do
+        {
+            fprintf(stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2);
+            if ( args->control_sample.name )
+                fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
+            fprintf(stderr,"\n");
+            set_emission_probs(args);
+            hmm_run_fwd_bwd(hmm, args->nsites, args->eprob, args->sites);
+        }
+        while ( update_args(args) && ++niter<20 );
+        if ( niter>=20 )
+        {
+            // no convergence
+            args->query_sample.cell_frac   = args->query_sample.cell_frac_dflt;
+            args->control_sample.cell_frac = args->control_sample.cell_frac_dflt;
+            args->query_sample.baf_dev2    = args->query_sample.baf_dev2_dflt;
+            args->control_sample.baf_dev2  = args->control_sample.baf_dev2_dflt;
+            set_gauss_params(args, &args->query_sample);
+            if ( args->control_sample.name ) set_gauss_params(args, &args->control_sample);
+        }
+
+        fprintf(stderr,"\t.. %f %f", args->query_sample.cell_frac,args->query_sample.baf_dev2);
+        if ( args->control_sample.name )
+            fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
+        fprintf(stderr,"\n");
+    }
+    set_emission_probs(args);
+
     while ( args->baum_welch_th!=0 )
     {
         int nstates = hmm_get_nstates(hmm);
@@ -630,76 +1008,15 @@ static void cnv_flush_viterbi(args_t *args)
     }
 }
 
-static int set_observed_prob(args_t *args, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt, sample_t *smpl)
+static int parse_lrr_baf(sample_t *smpl, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt, float *baf, float *lrr)
 {
-    float baf, lrr;
-    baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0];
-    if ( bcf_float_is_missing(baf) || isnan(baf) ) baf = -0.1;    // arbitrary negative value == missing value
-
-    lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0];
-    if ( bcf_float_is_missing(lrr) || isnan(lrr) ) baf = -0.1;
+    *baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0];
+    if ( bcf_float_is_missing(*baf) || isnan(*baf) ) *baf = -0.1;    // arbitrary negative value == missing value
 
-    if ( baf>=0 )    // skip missing values
-        fprintf(smpl->dat_fh,"%s\t%d\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), args->sites[args->nsites-1]+1,baf,lrr);
+    *lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0];
+    if ( bcf_float_is_missing(*lrr) || isnan(*lrr) ) { *lrr = 0; *baf = -0.1; }
 
-    if ( baf<0 )
-    {
-        // no call: either some technical issue or the call could not be made because it is CN0
-        int i;
-        smpl->pobs[CN0] = 0.5;
-        for (i=1; i<N_STATES; i++) smpl->pobs[i] = (1.0-smpl->pobs[CN0])/(N_STATES-1);
-        return 0;
-    }
-
-    double pk0, pk14, pk13, pk12, pk23, pk34, pk1;
-    pk0  = exp(-baf*baf/args->baf_sigma2);
-    pk14 = exp(-(baf-1/4.)*(baf-1/4.)/args->baf_sigma2);
-    pk13 = exp(-(baf-1/3.)*(baf-1/3.)/args->baf_sigma2);
-    pk12 = exp(-(baf-1/2.)*(baf-1/2.)/args->baf_sigma2);
-    pk23 = exp(-(baf-2/3.)*(baf-2/3.)/args->baf_sigma2);
-    pk34 = exp(-(baf-3/4.)*(baf-3/4.)/args->baf_sigma2);
-    pk1  = exp(-(baf-1.0)*(baf-1.0)/args->baf_sigma2);
-
-    double cn1_baf, cn2_baf, cn3_baf, cn4_baf;
-    cn1_baf = pk0*(args->pRR+args->pRA/2.)  + pk1*(args->pAA+args->pRA/2.);
-    cn2_baf = pk0*args->pRR + pk1*args->pAA + pk12*args->pRA;
-    cn3_baf = pk0*args->pRR + pk1*args->pAA + (pk13 + pk23)*args->pRA/2.;
-    cn4_baf = pk0*args->pRR + pk1*args->pAA + (pk14 + pk12 + pk34)*args->pRA/3.;
-
-    double cn1_lrr, cn2_lrr, cn3_lrr, cn4_lrr;
-    cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/args->lrr_sigma2);
-    cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/args->lrr_sigma2);
-    cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/args->lrr_sigma2);
-    cn4_lrr = exp(-(lrr - 0.75)*(lrr - 0.75)/args->lrr_sigma2);
-
-    smpl->pobs[CN0] = 0;
-    smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr);
-    smpl->pobs[CN2] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn2_baf)*(1 - args->lrr_bias + args->lrr_bias*cn2_lrr);
-    smpl->pobs[CN3] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn3_baf)*(1 - args->lrr_bias + args->lrr_bias*cn3_lrr);
-    smpl->pobs[CNx] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn4_baf)*(1 - args->lrr_bias + args->lrr_bias*cn4_lrr);
-
-    return 0;
-}
-
-static void set_emission_prob(args_t *args)
-{
-    double *eprob = &args->eprob[args->nstates*(args->nsites-1)];
-    int i;
-    for (i=0; i<N_STATES; i++)
-        eprob[i] = args->query_sample.pobs[i];
-}
-
-static void set_emission_prob2(args_t *args)
-{
-    double *eprob = &args->eprob[args->nstates*(args->nsites-1)];
-    int i, j;
-    for (i=0; i<N_STATES; i++)
-    {
-        for (j=0; j<N_STATES; j++)
-        {
-            eprob[i*N_STATES+j] = args->query_sample.pobs[i]*args->control_sample.pobs[j];
-        }
-    }
+    return *baf<0 ? 0 : 1;
 }
 
 int read_AF(bcf_sr_regions_t *tgt, bcf1_t *line, double *alt_freq);
@@ -719,6 +1036,7 @@ static void cnv_next_line(args_t *args, bcf1_t *line)
         cnv_flush_viterbi(args);
         args->prev_rid = line->rid;
         args->nsites = 0;
+        args->nRR = args->nAA = args->nRA = 0;
     }
 
     // Process line
@@ -728,49 +1046,53 @@ static void cnv_next_line(args_t *args, bcf1_t *line)
     if ( !(baf_fmt = bcf_get_fmt(args->hdr, line, "BAF")) ) return; 
     if ( !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return;
 
-    // Realloc buffers needed by viterbi and fwd-bwd
+    float baf1,lrr1,baf2,lrr2;
+    int ret = 0;
+    ret += parse_lrr_baf(&args->query_sample,  baf_fmt,lrr_fmt,&baf1,&lrr1);
+    ret += parse_lrr_baf(&args->control_sample,baf_fmt,lrr_fmt,&baf2,&lrr2);
+    if ( !ret ) return;
+
+    // Realloc buffers needed to store observed data and used by viterbi and fwd-bwd
     args->nsites++;
     int m = args->msites;
     hts_expand(uint32_t,args->nsites,args->msites,args->sites);
     if ( args->msites!=m )
+    {
         args->eprob = (double*) realloc(args->eprob,sizeof(double)*args->msites*args->nstates);
+        if ( args->control_sample.name )
+        {
+            args->control_sample.lrr = (float*) realloc(args->control_sample.lrr,sizeof(float)*args->msites);
+            args->control_sample.baf = (float*) realloc(args->control_sample.baf,sizeof(float)*args->msites);
+        }
+        args->query_sample.lrr = (float*) realloc(args->query_sample.lrr,sizeof(float)*args->msites);
+        args->query_sample.baf = (float*) realloc(args->query_sample.baf,sizeof(float)*args->msites);
+        if ( args->af_fname )
+            args->nonref_afs = (float*) realloc(args->nonref_afs,sizeof(float)*args->msites);
+    }
     args->sites[args->nsites-1] = line->pos;
-
-    double alt_freq;
-    if ( !args->af_fname || read_AF(args->files->targets, line, &alt_freq) < 0 )
+    args->query_sample.lrr[args->nsites-1] = lrr1;
+    args->query_sample.baf[args->nsites-1] = baf1;
+    if ( args->af_fname )
     {
-        args->pRR = args->pRR_dflt;
-        args->pRA = args->pRA_dflt;
-        args->pAA = args->pAA_dflt;
+        double alt_freq;
+        args->nonref_afs[args->nsites-1] = read_AF(args->files->targets,line,&alt_freq)<0 ? args->nonref_af_dflt : alt_freq;
     }
-    else
+    if ( args->control_sample.name )
     {
-        args->pRR = (1 - alt_freq)*(1 - alt_freq);
-        args->pRA = 2*(1 - alt_freq)*alt_freq;
-        args->pAA = alt_freq*alt_freq;
+        args->control_sample.lrr[args->nsites-1] = lrr2;
+        args->control_sample.baf[args->nsites-1] = baf2;
+        if ( baf2>=0 )  // skip missing values
+            fprintf(args->control_sample.dat_fh,"%s\t%d\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), line->pos+1,baf2,lrr2);
     }
+    if ( baf1>=0 )  // skip missing values
+        fprintf(args->query_sample.dat_fh,"%s\t%d\t%.3f\t%.3f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), line->pos+1,baf1,lrr1);
 
-    int ret = set_observed_prob(args, baf_fmt,lrr_fmt, &args->query_sample);
-    if ( ret<0 ) 
+    if ( baf1>=0 )
     {
-        args->nsites--;
-        return;
+        if ( baf1<1/5. ) args->nRR++;
+        else if ( baf1>4/5. ) args->nAA++;
+        else args->nRA++;
     }
-    if ( args->control_sample.name )
-    {
-        ret = set_observed_prob(args, baf_fmt,lrr_fmt, &args->control_sample);
-        if ( ret<0 )
-        {
-            args->nsites--;
-            return;
-        }
-    }
-
-    if ( args->control_sample.name )
-        set_emission_prob2(args);
-    else
-        set_emission_prob(args);
-
     args->nused++;
 }
 
@@ -779,7 +1101,7 @@ static void usage(args_t *args)
     fprintf(stderr, "\n");
     fprintf(stderr, "About:   Copy number variation caller, requires Illumina's B-allele frequency (BAF) and Log R\n");
     fprintf(stderr, "         Ratio intensity (LRR). The HMM considers the following copy number states: CN 2\n");
-    fprintf(stderr, "         (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain), x (other)\n");
+    fprintf(stderr, "         (normal), 1 (single-copy loss), 0 (complete loss), 3 (single-copy gain)\n");
     fprintf(stderr, "Usage:   bcftools cnv [OPTIONS] <file.vcf>\n");
     fprintf(stderr, "General Options:\n");
     fprintf(stderr, "    -c, --control-sample <string>      optional control sample name to highlight differences\n");
@@ -792,11 +1114,15 @@ static void usage(args_t *args)
     fprintf(stderr, "    -t, --targets <region>             similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>          similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "HMM Options:\n");
+    fprintf(stderr, "    -a, --aberrant <float[,float]>     fraction of aberrant cells in query and control [1.0,1.0]\n");
     fprintf(stderr, "    -b, --BAF-weight <float>           relative contribution from BAF [1]\n");
-    fprintf(stderr, "    -e, --err-prob <float>             probability of error [1e-4]\n");
+    fprintf(stderr, "    -d, --BAF-dev <float[,float]>      expected BAF deviation in query and control [0.04,0.04]\n"); // experimental
+    fprintf(stderr, "    -e, --err-prob <float>             uniform error probability [1e-4]\n");
     fprintf(stderr, "    -l, --LRR-weight <float>           relative contribution from LRR [0.2]\n");
+    fprintf(stderr, "    -L, --LRR-smooth-win <int>         window of LRR moving average smoothing [10]\n");
+    fprintf(stderr, "    -O, --optimize <float>             estimate fraction of aberrant cells down to <float> [1.0]\n");
     fprintf(stderr, "    -P, --same-prob <float>            prior probability of -s/-c being same [1e-1]\n");
-    fprintf(stderr, "    -x, --xy-prob <float>              P(x|y) transition probability [1e-8]\n");
+    fprintf(stderr, "    -x, --xy-prob <float>              P(x|y) transition probability [1e-9]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -808,6 +1134,11 @@ int main_vcfcnv(int argc, char *argv[])
     args->argc      = argc; args->argv = argv;
     args->files     = bcf_sr_init();
     args->plot_th   = 1e9;   // by default plot none
+    args->nonref_af_dflt = 0.1;
+    args->lrr_smooth_win = 10;
+
+    args->query_sample.cell_frac_dflt = 1;
+    args->control_sample.cell_frac_dflt = 1;
 
     // How much FORMAT/LRR and FORMAT/BAF matter
     args->lrr_bias  = 0.2;
@@ -815,26 +1146,22 @@ int main_vcfcnv(int argc, char *argv[])
     args->err_prob  = 1e-4;
 
     // Transition probability to a different state and the prior of both samples being the same
-    args->ij_prob   = 1e-8;
+    args->ij_prob   = 1e-9;
     args->same_prob = 1e-1;
 
     // Squared std dev of BAF and LRR values (gaussian noise), estimated from real data (hets, one sample, one chr)
-    args->baf_sigma2 = 0.08*0.08;   // illumina: 0.03
-    args->lrr_sigma2 = 0.4*0.4; //0.20*0.20;   // illumina: 0.18
-
-    // Priors for RR, RA, AA genotypes
-    args->pRR_dflt = 0.76;
-    args->pRA_dflt = 0.14;
-    args->pAA_dflt = 0.098;
-    // args->pRR = 0.69;
-    // args->pRA = 0.18;
-    // args->pAA = 0.11;
+    args->query_sample.baf_dev2_dflt = args->control_sample.baf_dev2_dflt = 0.04*0.04; // illumina: 0.03
+    args->lrr_dev2 = 0.1*0.1; //0.20*0.20;   // illumina: 0.18
 
     int regions_is_file = 0, targets_is_file = 0;
     static struct option loptions[] = 
     {
+        {"BAF-dev",1,0,'d'},
+        {"LRR-smooth-win",1,0,'L'},
         {"AF-file",1,0,'f'},
-        {"baum-welch",1,0,'W'},
+        {"baum-welch",1,0,'W'}, // hidden
+        {"optimize",1,0,'O'},
+        {"aberrant",1,0,'a'},
         {"err-prob",1,0,'e'},
         {"BAF-weight",1,0,'b'},
         {"LRR-weight",1,0,'l'},
@@ -851,9 +1178,39 @@ int main_vcfcnv(int argc, char *argv[])
         {0,0,0,0}
     };
     char *tmp = NULL;
-    while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:W:f:",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W:f:a:L:d:",loptions,NULL)) >= 0) {
         switch (c) {
+            case 'L': 
+                args->lrr_smooth_win = strtol(optarg,&tmp,10);
+                if ( *tmp ) error("Could not parse: --LRR-smooth-win %s\n", optarg);
+                break;
             case 'f': args->af_fname = optarg; break;
+            case 'O': 
+                args->optimize_frac = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -O %s\n", optarg);
+                break;
+            case 'd':
+                args->query_sample.baf_dev2_dflt = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -d %s\n", optarg);
+                    args->control_sample.baf_dev2_dflt = strtod(optarg,&tmp);
+                    if ( *tmp ) error("Could not parse: -a %s\n", optarg);
+                }
+                else
+                    args->control_sample.baf_dev2_dflt = args->query_sample.baf_dev2_dflt;
+                args->query_sample.baf_dev2_dflt   *= args->query_sample.baf_dev2_dflt;
+                args->control_sample.baf_dev2_dflt *= args->control_sample.baf_dev2_dflt;
+                break;
+            case 'a':
+                args->query_sample.cell_frac_dflt = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -a %s\n", optarg);
+                    args->control_sample.cell_frac_dflt = strtod(optarg,&tmp);
+                    if ( *tmp ) error("Could not parse: -a %s\n", optarg);
+                }
+                break;
             case 'W':
                 args->baum_welch_th = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -W %s\n", optarg);

From d2b012f483756089a795f88c84317578d48f23e5 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 26 Mar 2015 15:59:28 +0000
Subject: [PATCH 021/211] cnv -O: Increase robustness by smoothing HMM lks
 before updating the mean

---
 vcfcnv.c | 46 ++++++++++++++++++++++++++++------------------
 1 file changed, 28 insertions(+), 18 deletions(-)

diff --git a/vcfcnv.c b/vcfcnv.c
index 6287f5bde..1f0e56aba 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -24,6 +24,12 @@
 
  */
 
+/*
+    Known issues:
+    - The --AF-file option behaves like --targets-file, sites not listed in the AFs
+      are skipped.
+*/
+
 #include <stdio.h>
 #include <unistd.h>
 #include <getopt.h>
@@ -76,8 +82,9 @@ typedef struct _args_t
     double lrr_bias, baf_bias;              // LRR/BAF weights
     double same_prob, ij_prob;              // prior of both samples being the same and the transition probability P(i|j)
     double err_prob;                        // constant probability of erroneous measurement
-    float *nonref_afs, nonref_af, nonref_af_dflt, fRR, fRA, fAA;
+    float *nonref_afs, nonref_af, nonref_af_dflt, fRR, fRA, fAA, *tmpf;
     unsigned long int nRR, nRA, nAA;
+    int mtmpf;
 
     double *tprob, *tprob_arr;  // array of transition matrices, precalculated up to ntprob_arr positions
     int ntprob_arr;
@@ -510,6 +517,7 @@ static void destroy_data(args_t *args)
 {
     bcf_sr_destroy(args->files);
     hmm_destroy(args->hmm);
+    free(args->tmpf);
     free(args->sites);
     free(args->eprob);
     free(args->tprob);
@@ -752,11 +760,14 @@ static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
     double mean_cn3 = 0, norm_cn3 = 0;
     double baf_dev2 = 0, baf_AA_dev2 = 0, norm_baf_AA_dev2 = 0;
 
-    int i, j;
+    // experimental: smooth CN3 probs to bias toward bigger events, this lowers
+    // the FP rate when the data is noisy
+    hts_expand(float,args->nsites,args->mtmpf,args->tmpf);
+    int i, j, k = 0;
     for (i=0; i<args->nsites; i++)
     {
         float baf = smpl->baf[i];
-        if ( baf>4/5.) { baf_AA_dev2 += (1.0-baf)*(1.0-baf); norm_baf_AA_dev2++; continue; }       // skip AA genotypes
+        if ( baf>4/5.) continue;        // skip AA genotypes
         if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
         if ( baf<1/5.) continue;        // skip RR genotypes
 
@@ -775,6 +786,18 @@ static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
             // same as above but for control sample
             for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3+j*N_STATES];
         }
+        args->tmpf[k++] = prob_cn3;
+    }
+    smooth_data(args->tmpf, k, 50);
+    k = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        float baf = smpl->baf[i];
+        if ( baf>4/5.) { baf_AA_dev2 += (1.0-baf)*(1.0-baf); norm_baf_AA_dev2++; continue; }       // skip AA genotypes
+        if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
+        if ( baf<1/5.) continue;        // skip RR genotypes
+
+        double prob_cn3 = args->tmpf[k++];
         mean_cn3 += prob_cn3 * baf;
         norm_cn3 += prob_cn3;
     }
@@ -784,27 +807,14 @@ static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
         return 1;
     }
     mean_cn3 /= norm_cn3;
+    k = 0;
     for (i=0; i<args->nsites; i++)
     {
         float baf = smpl->baf[i];
         if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
         if ( baf<1/5.) continue;        // skip RR,AA genotypes
 
-        double prob_cn3 = 0, *probs = hmm->fwd + i*hmm->nstates;
-        if ( !args->control_sample.name )
-        {
-            prob_cn3 = probs[CN3];
-        }
-        else if ( ismpl==0 )
-        {
-            // query sample: CN3 probability must be recovered from all states of the control sample
-            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3*N_STATES+j];
-        }
-        else
-        {
-            // same as above but for control sample
-            for (j=0; j<N_STATES; j++) prob_cn3 += probs[CN3+j*N_STATES];
-        }
+        double prob_cn3 = args->tmpf[k++];
         baf_dev2 += prob_cn3 * (baf - mean_cn3)*(baf - mean_cn3);
     }
 

From 2b50604dc60b3dca2e87ec763b62110092240ae3 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 26 Mar 2015 16:04:20 +0000
Subject: [PATCH 022/211] cnv: Update to the modified HMM API

---
 vcfcnv.c | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/vcfcnv.c b/vcfcnv.c
index 1f0e56aba..bec54dd6e 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -755,6 +755,8 @@ static void set_gauss_params(args_t *args, sample_t *smpl)
 static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
 {
     hmm_t *hmm = args->hmm;
+    double *fwd = hmm_get_fwd_bwd_prob(hmm);
+    int nstates = hmm_get_nstates(hmm);
 
     // estimate the BAF mean and deviation for CN3
     double mean_cn3 = 0, norm_cn3 = 0;
@@ -771,7 +773,7 @@ static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
         if ( baf>0.5 ) baf = 1 - baf;   // the bands should be symmetric
         if ( baf<1/5.) continue;        // skip RR genotypes
 
-        double prob_cn3 = 0, *probs = hmm->fwd + i*hmm->nstates;
+        double prob_cn3 = 0, *probs = fwd + i*nstates;
         if ( !args->control_sample.name )
         {
             prob_cn3 = probs[CN3];

From d3f9fe45c6f491f7dc9b5cdabe3c30a8e0006b69 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 27 Apr 2015 10:15:55 +0100
Subject: [PATCH 023/211] cnv: Prior on CN2; changed the default -P to be more
 strict (0.5)

---
 HMM.c    | 43 ++++++++++++++++++++++++++++++++++++++-----
 HMM.h    |  8 ++++++++
 vcfcnv.c | 44 +++++++++++++++++++++++++++++++++++++++++---
 3 files changed, 87 insertions(+), 8 deletions(-)

diff --git a/HMM.c b/HMM.c
index 78501ca55..91965449f 100644
--- a/HMM.c
+++ b/HMM.c
@@ -50,6 +50,7 @@ struct _hmm_t
     set_tprob_f set_tprob;      // Optional user function to set / modify transition probabilities
                                 //  at each site (one step of Viterbi algorithm)
     void *set_tprob_data;
+    double *init_probs;         // Initial state probabilities, NULL for uniform probs
 };
 
 uint8_t *hmm_get_viterbi_path(hmm_t *hmm) { return hmm->vpath; }
@@ -89,6 +90,18 @@ hmm_t *hmm_init(int nstates, double *tprob, int ntprob)
     return hmm;
 }
 
+void hmm_init_states(hmm_t *hmm, double *probs)
+{
+    if ( !probs )
+    {
+        free(hmm->init_probs);
+        hmm->init_probs = NULL;
+    }
+
+    if ( !hmm->init_probs ) hmm->init_probs = (double*) malloc(sizeof(double)*hmm->nstates);
+    memcpy(hmm->init_probs,probs,sizeof(double)*hmm->nstates);
+}
+
 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob)
 {
     hmm->ntprob_arr = ntprob;
@@ -144,7 +157,10 @@ void hmm_run_viterbi(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
 
     // Init all states with equal likelihood
     int i,j, nstates = hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->vprob[i] = 1./nstates;
+    if ( hmm->init_probs )
+        for (i=0; i<nstates; i++) hmm->vprob[i] = hmm->init_probs[i];
+    else
+        for (i=0; i<nstates; i++) hmm->vprob[i] = 1./nstates;
 
     // Run Viterbi
     uint32_t prev_pos = sites[0];
@@ -208,8 +224,16 @@ void hmm_run_fwd_bwd(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
 
     // Init all states with equal likelihood
     int i,j,k, nstates = hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->fwd[i] = 1./hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->bwd[i] = 1./hmm->nstates;
+    if ( hmm->init_probs )
+    {
+        for (i=0; i<nstates; i++) hmm->fwd[i] = hmm->init_probs[i];
+        for (i=0; i<nstates; i++) hmm->bwd[i] = hmm->init_probs[i];
+    }
+    else
+    {
+        for (i=0; i<nstates; i++) hmm->fwd[i] = 1./hmm->nstates;
+        for (i=0; i<nstates; i++) hmm->bwd[i] = 1./hmm->nstates;
+    }
 
     // Run fwd 
     uint32_t prev_pos = sites[0];
@@ -288,8 +312,16 @@ void hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
 
     // Init all states with equal likelihood
     int i,j,k, nstates = hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->fwd[i] = 1./hmm->nstates;
-    for (i=0; i<nstates; i++) hmm->bwd[i] = 1./hmm->nstates;
+    if ( hmm->init_probs )
+    {
+        for (i=0; i<nstates; i++) hmm->fwd[i] = hmm->init_probs[i];
+        for (i=0; i<nstates; i++) hmm->bwd[i] = hmm->init_probs[i];
+    }
+    else
+    {
+        for (i=0; i<nstates; i++) hmm->fwd[i] = 1./hmm->nstates;
+        for (i=0; i<nstates; i++) hmm->bwd[i] = 1./hmm->nstates;
+    }
 
     // New transition matrix: temporary values
     double *tmp_xi = (double*) calloc(nstates*nstates,sizeof(double));
@@ -388,6 +420,7 @@ void hmm_run_baum_welch(hmm_t *hmm, int n, double *eprobs, uint32_t *sites)
 
 void hmm_destroy(hmm_t *hmm)
 {
+    free(hmm->init_probs);
     free(hmm->vprob);
     free(hmm->vprob_tmp);
     free(hmm->vpath);
diff --git a/HMM.h b/HMM.h
index 3f5e0f10a..7f01245ed 100644
--- a/HMM.h
+++ b/HMM.h
@@ -44,6 +44,14 @@ typedef void (*set_tprob_f) (hmm_t *hmm, uint32_t prev_pos, uint32_t pos, void *
 hmm_t *hmm_init(int nstates, double *tprob, int ntprob);
 void hmm_set_tprob(hmm_t *hmm, double *tprob, int ntprob);
 
+/**
+ *   hmm_init_states() - initial state probabilities
+ *   @probs:  initial state probabilities or NULL to reset to default
+ *
+ *   If uncalled, all states are initialized with the same likelihood
+ */
+void hmm_init_states(hmm_t *hmm, double *probs);
+
 /**
  *   hmm_get_tprob() - return the array of transition matrices, precalculated
  *      to ntprob positions. The first matrix is the initial tprob matrix
diff --git a/vcfcnv.c b/vcfcnv.c
index bec54dd6e..a9dfb7fb0 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -87,6 +87,7 @@ typedef struct _args_t
     int mtmpf;
 
     double *tprob, *tprob_arr;  // array of transition matrices, precalculated up to ntprob_arr positions
+    double *iprobs;             // states' initial probabilities
     int ntprob_arr;
 
     hmm_t *hmm;
@@ -174,6 +175,41 @@ static double *init_tprob_matrix(int ndim, double ij_prob, double same_prob)
     return mat;
 }
 
+static double *init_iprobs(int ndim, double same_prob)
+{
+    int i;
+    double *probs = (double*) malloc(sizeof(double)*ndim);
+
+    assert( ndim==N_STATES || ndim==N_STATES*N_STATES);
+
+    if ( ndim==N_STATES )   
+    {
+        // one sample: prior on CN2
+        for (i=0; i<ndim; i++) 
+            probs[i] = i==CN2 ? 0.5 : 0.5/3;
+    }
+    else
+    {
+        // two samples
+        double norm = 0;
+        for (i=0; i<ndim; i++) 
+        {
+            int ia,ib;
+            hmm2cn_state(ndim, i, &ia, &ib);
+
+            double pa = ia==CN2 ? 0.5 : 0.5/3;
+            double pb = ib==CN2 ? 0.5 : 0.5/3;
+
+            probs[i] = pa*pb;
+            if ( ia!=ib ) probs[i] *= 1-same_prob;
+
+            norm += probs[i];
+        }
+        for (i=0; i<ndim; i++) probs[i] /= norm;
+    }
+    return probs;
+}
+
 static void init_sample_files(sample_t *smpl, char *dir)
 {
     smpl->dat_fh = open_file(&smpl->dat_fname,"w","%s/dat.%s.tab",dir,smpl->name);
@@ -225,8 +261,10 @@ static void init_data(args_t *args)
     args->query_sample.idx = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->query_sample.name);
     args->control_sample.idx = args->control_sample.name ? bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,args->control_sample.name) : -1;
     args->nstates = args->control_sample.name ? N_STATES*N_STATES : N_STATES;
-    args->tprob = init_tprob_matrix(args->nstates, args->ij_prob, args->same_prob);
+    args->tprob  = init_tprob_matrix(args->nstates, args->ij_prob, args->same_prob);
+    args->iprobs = init_iprobs(args->nstates, args->same_prob);
     args->hmm = hmm_init(args->nstates, args->tprob, 10000);
+    hmm_init_states(args->hmm, args->iprobs);
 
     args->summary_fh = stdout;
     if ( args->output_dir )
@@ -1133,7 +1171,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -l, --LRR-weight <float>           relative contribution from LRR [0.2]\n");
     fprintf(stderr, "    -L, --LRR-smooth-win <int>         window of LRR moving average smoothing [10]\n");
     fprintf(stderr, "    -O, --optimize <float>             estimate fraction of aberrant cells down to <float> [1.0]\n");
-    fprintf(stderr, "    -P, --same-prob <float>            prior probability of -s/-c being same [1e-1]\n");
+    fprintf(stderr, "    -P, --same-prob <float>            prior probability of -s/-c being the same [0.5]\n");
     fprintf(stderr, "    -x, --xy-prob <float>              P(x|y) transition probability [1e-9]\n");
     fprintf(stderr, "\n");
     exit(1);
@@ -1159,7 +1197,7 @@ int main_vcfcnv(int argc, char *argv[])
 
     // Transition probability to a different state and the prior of both samples being the same
     args->ij_prob   = 1e-9;
-    args->same_prob = 1e-1;
+    args->same_prob = 0.5;
 
     // Squared std dev of BAF and LRR values (gaussian noise), estimated from real data (hets, one sample, one chr)
     args->query_sample.baf_dev2_dflt = args->control_sample.baf_dev2_dflt = 0.04*0.04; // illumina: 0.03

From 733f25770a8d1318818d1e53e989abb8eaee212c Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 17 Jul 2015 13:13:32 +0100
Subject: [PATCH 024/211] Further support for case-insensitive REF,ALT allele
 merging

See also 1f81d259b9e970f1aacac136f78f1bec6898238b and samtools/htslib@3fcf7c9026b3dff17ab20893b8019eaf4f3bb675

Fixes #285

Petentially fixes #284
---
 test/merge.2.b.vcf |  2 +-
 vcfmerge.c         |  2 +-
 vcmp.c             | 13 +++++++------
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/test/merge.2.b.vcf b/test/merge.2.b.vcf
index fab439f78..8700f1c79 100644
--- a/test/merge.2.b.vcf
+++ b/test/merge.2.b.vcf
@@ -26,5 +26,5 @@
 1	3106154	.	C	CCC	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
 1	3106154	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
 1	3200000	.	C	T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
-1	3200010	.	C	A,T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
+1	3200010	.	c	A,T	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
 1	3200020	.	C	T,G	59.2	PASS	AN=4;AC=2	GT:GL	./.:1,4,6,2,5,3	.:1,3,2
diff --git a/vcfmerge.c b/vcfmerge.c
index ea26903d3..c98c285c2 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -578,7 +578,7 @@ char **merge_alleles(char **a, int na, int *map, char **b, int *nb, int *mb)
             ai = a[i];
 
         for (j=1; j<*nb; j++)
-            if ( !strcmp(ai,b[j]) ) break;
+            if ( !strcasecmp(ai,b[j]) ) break;
 
         if ( j<*nb ) // $b already has the same allele
         {
diff --git a/vcmp.c b/vcmp.c
index a117cd344..da0be3024 100644
--- a/vcmp.c
+++ b/vcmp.c
@@ -53,17 +53,18 @@ int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2)
     vcmp->ndref = 0;
 
     char *a = ref1, *b = ref2;
-    while ( *a && *b && *a==*b ) { a++; b++; }
+    while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
     if ( !*a && !*b ) return 0;
     if ( *a && *b ) return -1;  // refs not compatible
 
+    int i;
     if ( *a )   // ref1 is longer
     {
         vcmp->nmatch = b-ref2;
         while ( *a ) a++;
         vcmp->ndref = (a-ref1) - vcmp->nmatch;
         hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
-        memcpy(vcmp->dref,ref1+vcmp->nmatch,vcmp->ndref);
+        for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch+i]);
         vcmp->dref[vcmp->ndref] = 0;
         return 0;
     }
@@ -73,7 +74,7 @@ int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2)
     while ( *b ) b++;
     vcmp->ndref = (b-ref2) - vcmp->nmatch;
     hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
-    memcpy(vcmp->dref,ref2+vcmp->nmatch,vcmp->ndref);
+    for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref2[vcmp->nmatch+i]);
     vcmp->dref[vcmp->ndref] = 0;
     vcmp->ndref *= -1;
     return 0;
@@ -85,7 +86,7 @@ int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2)
     for (i=0; i<nals1; i++)
     {
         char *a = als1[i], *b = al2;
-        while ( *a && *b && *a==*b ) { a++; b++; }
+        while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
         if ( *a && *b ) continue;   // mismatch
         if ( !vcmp->ndref )
         {
@@ -98,14 +99,14 @@ int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2)
         {
             if ( vcmp->ndref<0 ) continue;
             for (j=0; j<vcmp->ndref; j++)
-                if ( !a[j] || a[j]!=vcmp->dref[j] ) break;
+                if ( !a[j] || toupper(a[j])!=vcmp->dref[j] ) break;
             if ( j!=vcmp->ndref || a[j] ) continue;
             break;  // found
         }
 
         if ( vcmp->ndref>0 ) continue;
         for (j=0; j<-vcmp->ndref; j++)
-            if ( !b[j] || b[j]!=vcmp->dref[j] ) break;
+            if ( !b[j] || toupper(b[j])!=vcmp->dref[j] ) break;
         if ( j!=-vcmp->ndref || b[j] ) continue;
         break;  // found
     }

From cecff77a83c1b76a9edc7e4e7ae6692e0517d5d3 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 17 Jul 2015 08:39:49 +0100
Subject: [PATCH 025/211] more informative error message: annotate supports FMT
 fields only from a VCF

Closes #294
---
 vcfannotate.c | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/vcfannotate.c b/vcfannotate.c
index 00630a58b..b7ba548be 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -1240,8 +1240,11 @@ static void init_columns(args_t *args)
                     }
             }
         }
-        else if ( args->tgts_is_vcf && (!strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4)) )
+        else if ( !strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4) )
         {
+            if ( !args->tgts_is_vcf )
+                error("Error: FORMAT fields can be carried over from a VCF file only.\n");
+
             char *key = str.s + (!strncasecmp("FMT/",str.s,4) ? 4 : 7);
             if ( force_samples<0 ) force_samples = replace;
             if ( force_samples>=0 && replace!=REPLACE_ALL ) force_samples = replace;;

From ae5663dfc4542257813f73680e0f9cfa571526ba Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 28 Jul 2015 08:52:47 +0100
Subject: [PATCH 026/211] merge: More informative error message when FILTER is
 undefined

---
 vcfmerge.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcfmerge.c b/vcfmerge.c
index c98c285c2..881105aa0 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -789,7 +789,7 @@ void merge_filter(args_t *args, bcf1_t *out)
             if ( kitr == kh_end(tmph) )
             {
                 int id = bcf_hdr_id2int(out_hdr, BCF_DT_ID, flt);
-                if ( id==-1 ) error("The filter not defined: %s\n", flt);
+                if ( id==-1 ) error("Error: The filter is not defined in the header: %s\n", flt);
                 hts_expand(int,out->d.n_flt+1,ma->mflt,ma->flt);
                 ma->flt[out->d.n_flt] = id;
                 out->d.n_flt++;

From 58a1cf3a7cd473d31aef9ed0e1fc1669cffe47fe Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Sat, 11 Jul 2015 17:01:52 +0100
Subject: [PATCH 027/211] Resolved assert when comparing long GT strings

---
 filter.c | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/filter.c b/filter.c
index 20d570e8a..413946bd1 100644
--- a/filter.c
+++ b/filter.c
@@ -561,12 +561,22 @@ static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *to
         return;
     }
     int i, blen = 3, nsmpl = bcf_hdr_nsamples(flt->hdr);
-    kstring_t str; str.s = tok->str_value; str.m = tok->values[0] * nsmpl; str.l = 0;
+    kstring_t str;
+
+gt_length_too_big:
+    str.s = tok->str_value; str.m = tok->values[0] * nsmpl; str.l = 0;
     for (i=0; i<nsmpl; i++)
     {
         int plen = str.l;
         bcf_format_gt(fmt, i, &str);
-        assert( str.l - plen <= blen ); // increase blen if this fails
+        if ( str.l - plen > blen )
+        {
+            // too many alternate alleles or ploidy is too large, the genotype does not fit
+            // three characters ("0/0" vs "10/10").
+            tok->str_value = str.s;
+            blen *= 2;
+            goto gt_length_too_big;
+        }
         plen = str.l - plen;
         while ( plen<blen )
         {

From 0cf6efb012e797902a056b2284dccd311bdf8b5e Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 28 Jul 2015 09:04:32 +0100
Subject: [PATCH 028/211] plugin: new --version switch

---
 vcfplugin.c | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/vcfplugin.c b/vcfplugin.c
index a8bf5d34a..c3fac72d1 100644
--- a/vcfplugin.c
+++ b/vcfplugin.c
@@ -465,6 +465,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -h, --help                  list plugin's options\n");
     fprintf(stderr, "   -l, --list-plugins          list available plugins. See BCFTOOLS_PLUGINS environment variable and man page for details\n");
     fprintf(stderr, "   -v, --verbose               print debugging information on plugin failure\n");
+    fprintf(stderr, "   -V, --version               print version string and exit\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -477,7 +478,7 @@ int main_plugin(int argc, char *argv[])
     args->output_fname = "-";
     args->output_type = FT_VCF;
     args->nplugin_paths = -1;
-    int regions_is_file = 0, targets_is_file = 0, plist_only = 0, usage_only = 0;
+    int regions_is_file = 0, targets_is_file = 0, plist_only = 0, usage_only = 0, version_only = 0;
 
     if ( argc==1 ) usage(args);
     char *plugin_name = NULL;
@@ -485,6 +486,7 @@ int main_plugin(int argc, char *argv[])
 
     static struct option loptions[] =
     {
+        {"version",0,0,'V'},
         {"verbose",0,0,'v'},
         {"help",0,0,'h'},
         {"list-plugins",0,0,'l'},
@@ -498,9 +500,10 @@ int main_plugin(int argc, char *argv[])
         {"targets-file",1,0,'T'},
         {0,0,0,0}
     };
-    while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:v",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vV",loptions,NULL)) >= 0)
     {
         switch (c) {
+            case 'V': version_only = 1; break;
             case 'v': args->verbose = 1; break;
             case 'o': args->output_fname = optarg; break;
             case 'O':
@@ -528,6 +531,14 @@ int main_plugin(int argc, char *argv[])
     if ( usage_only && ! plugin_name ) usage(args);
 
     load_plugin(args, plugin_name, 1, &args->plugin);
+    if ( version_only )
+    {
+        const char *bver, *hver;
+        args->plugin.version(&bver, &hver);
+        printf("bcftools  %s using htslib %s\n", bcftools_version(), hts_version());
+        printf("plugin at %s using htslib %s\n\n", bver, hver);
+        return 0;
+    }
 
     if ( usage_only )
     {

From d8b82c3d9f769c6f75446d437a667d1dda521a03 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 28 Jul 2015 09:11:37 +0100
Subject: [PATCH 029/211] vcfplugin: header boilerplate mentioned the wrong
 file

---
 vcfplugin.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/vcfplugin.c b/vcfplugin.c
index c3fac72d1..437d40fc6 100644
--- a/vcfplugin.c
+++ b/vcfplugin.c
@@ -1,6 +1,6 @@
-/*  vcfannotate.c -- Annotate and edit VCF/BCF files.
+/*  vcfplugin.c -- plugin modules for operating on VCF/BCF files.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 

From 5653f1bc4a3a1ffe1e93bdd6d282d669a5f3a129 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 23 Jul 2015 19:58:25 +0100
Subject: [PATCH 030/211] Include ctype for toupper declaration in vcmp

---
 vcmp.c | 1 +
 1 file changed, 1 insertion(+)

diff --git a/vcmp.c b/vcmp.c
index da0be3024..8d04b8942 100644
--- a/vcmp.c
+++ b/vcmp.c
@@ -26,6 +26,7 @@ THE SOFTWARE.  */
 #include <string.h>
 #include <stdlib.h>
 #include <htslib/hts.h>
+#include <ctype.h>
 #include "vcmp.h"
 
 struct _vcmp_t

From 2962f5cdea669fdc122c133001be02d8b98dcbe5 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 23 Jul 2015 22:54:06 +0100
Subject: [PATCH 031/211] New fill-tags plugin to set INFO tags
 AN,AC,AC_Hom,AC_Het,AC_Hemi

---
 plugins/fill-tags.c | 262 ++++++++++++++++++++++++++++++++++++++++++++
 test/fill-tags.out  |  40 +++++++
 test/test.pl        |   4 +-
 3 files changed, 305 insertions(+), 1 deletion(-)
 create mode 100644 plugins/fill-tags.c
 create mode 100644 test/fill-tags.out

diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c
new file mode 100644
index 000000000..c7bd7fd24
--- /dev/null
+++ b/plugins/fill-tags.c
@@ -0,0 +1,262 @@
+/* The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include "bcftools.h"
+
+#define SET_AN      (1<<0)
+#define SET_AC      (1<<1)
+#define SET_AC_Hom  (1<<2)
+#define SET_AC_Het  (1<<3)
+#define SET_AC_Hemi (1<<4)
+
+typedef struct
+{
+    int nhom, nhet, nhemi, nac;
+}
+counts_t;
+
+typedef struct
+{
+    bcf_hdr_t *in_hdr, *out_hdr;
+    int tags, marr, mcounts, gt_id;
+    int32_t *arr;
+    counts_t *counts;
+}
+args_t;
+
+static args_t args;
+
+const char *about(void)
+{
+    return "Set INFO tags AN, AC, AC_Hom, AC_Het, AC_Hemi.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Set INFO tags AN, AC, AC_Hom, AC_Het, AC_Hemi.\n"
+        "Usage: bcftools +fill-tags [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -t, --tags LIST         list of output tags. By default, all tags are filled.\n"
+        "\n"
+        "Example:\n"
+        "   bcftools +fill-tags in.bcf -Ob -o out.bcf -- -t AN,AC\n"
+        "   bcftools +fill-tags in.bcf -Ob -o out.bcf\n"
+        "\n";
+}
+
+int parse_tags(args_t *args, const char *str)
+{
+    int i, flag = 0, n_tags;
+    char **tags = hts_readlist(str, 0, &n_tags);
+    for(i=0; i<n_tags; i++)
+    {
+        if ( !strcasecmp(tags[i],"AN") ) flag |= SET_AN;
+        else if ( !strcasecmp(tags[i],"AC") ) flag |= SET_AC;
+        else if ( !strcasecmp(tags[i],"AC_Hom") ) flag |= SET_AC_Hom;
+        else if ( !strcasecmp(tags[i],"AC_Het") ) flag |= SET_AC_Het;
+        else if ( !strcasecmp(tags[i],"AC_Hemi") ) flag |= SET_AC_Hemi;
+        else
+        {
+            fprintf(stderr,"Unknown tag \"%s\" in \"%s\"\n", tags[i], str);
+            exit(1);
+        }
+        free(tags[i]);
+    }
+    if (n_tags) free(tags);
+    return flag;
+}
+
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    memset(&args,0,sizeof(args_t));
+    args.in_hdr  = in;
+    args.out_hdr = out;
+
+    static struct option loptions[] =
+    {
+        {"tags",1,0,'t'},
+        {0,0,0,0}
+    };
+    char c;
+    while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 't': args.tags |= parse_tags(&args,optarg); break;
+            case 'h':
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( optind != argc ) error(usage());
+    if ( !args.tags ) args.tags |= SET_AN|SET_AC|SET_AC_Hom|SET_AC_Het|SET_AC_Hemi;
+    
+    args.gt_id = bcf_hdr_id2int(args.in_hdr,BCF_DT_ID,"GT");
+    if ( args.gt_id<0 ) error("Error: GT field is not present\n");
+
+    if ( args.tags&SET_AN ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
+    if ( args.tags&SET_AC ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">");
+    if ( args.tags&SET_AC_Hom ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Hom,Number=A,Type=Integer,Description=\"Allele counts in homozygous genotypes\">");
+    if ( args.tags&SET_AC_Het ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Het,Number=A,Type=Integer,Description=\"Allele counts in heterozygous genotypes\">");
+    if ( args.tags&SET_AC_Hemi ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Hemi,Number=A,Type=Integer,Description=\"Allele counts in hemizygous genotypes\">");
+
+    return 0;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    int i;
+
+    bcf_unpack(rec, BCF_UN_FMT);
+    bcf_fmt_t *fmt_gt = NULL;
+    for (i=0; i<rec->n_fmt; i++)
+        if ( rec->d.fmt[i].id==args.gt_id ) { fmt_gt = &rec->d.fmt[i]; break; }
+    if ( !fmt_gt ) return rec;    // no GT tag
+
+    hts_expand(int32_t,rec->n_allele,args.marr,args.arr);
+    hts_expand(counts_t,rec->n_allele,args.mcounts,args.counts);
+    memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+    memset(args.counts,0,sizeof(*args.counts)*rec->n_allele);
+
+    #define BRANCH_INT(type_t,vector_end) { \
+        for (i=0; i<rec->n_sample; i++) \
+        { \
+            type_t *p = (type_t*) (fmt_gt->p + i*fmt_gt->size); \
+            int ial, als = 0; \
+            for (ial=0; ial<fmt_gt->n; ial++) \
+            { \
+                if ( p[ial]==vector_end ) break; /* smaller ploidy */ \
+                if ( bcf_gt_is_missing(p[ial]) ) break; /* missing allele */ \
+                int idx = bcf_gt_allele(p[ial]); \
+                \
+                if ( idx >= rec->n_allele ) \
+                    error("Incorrect allele (\"%d\") in %s at %s:%d\n",idx,args.in_hdr->samples[i],bcf_seqname(args.in_hdr,rec),rec->pos+1); \
+                als |= (1<<idx);  /* this breaks with too many alleles */ \
+            } \
+            if ( ial==0 ) continue; /* missing alleles */ \
+            int is_hom  = als && !(als & (als-1)); /* only one bit is set */ \
+            int is_hemi = ial==1; \
+            for (ial=0; als; ial++) \
+            { \
+                if ( als&1 ) \
+                { \
+                    if ( !is_hom ) \
+                        args.counts[ial].nhet++; \
+                    else if ( !is_hemi ) \
+                        args.counts[ial].nhom += 2; \
+                    else \
+                        args.counts[ial].nhemi++; \
+                } \
+                als >>= 1; \
+            } \
+        } \
+    }
+    switch (fmt_gt->type) {
+        case BCF_BT_INT8:  BRANCH_INT(int8_t,  bcf_int8_vector_end); break;
+        case BCF_BT_INT16: BRANCH_INT(int16_t, bcf_int16_vector_end); break;
+        case BCF_BT_INT32: BRANCH_INT(int32_t, bcf_int32_vector_end); break;
+        default: error("The GT type is not recognised: %d at %s:%d\n",fmt_gt->type, bcf_seqname(args.in_hdr,rec),rec->pos+1); break;
+    }
+    #undef BRANCH_INT
+    if ( args.tags&SET_AN )
+    {
+        args.arr[0] = 0;
+        for (i=0; i<rec->n_allele; i++)
+            args.arr[0] += args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AN",args.arr,1)!=0 )
+            error("Error occurred while updating AN at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    if ( args.tags&SET_AC )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+            for (i=1; i<rec->n_allele; i++)
+                args.arr[i] += args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
+        }
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AC",args.arr+1,n)!=0 )
+            error("Error occurred while updating AC at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    if ( args.tags&SET_AC_Het )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+            for (i=1; i<rec->n_allele; i++)
+                args.arr[i] += args.counts[i].nhet;
+        }
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Het",args.arr+1,n)!=0 )
+            error("Error occurred while updating AC_Het at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    if ( args.tags&SET_AC_Hom )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+            for (i=1; i<rec->n_allele; i++)
+                args.arr[i] += args.counts[i].nhom;
+        }
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Hom",args.arr+1,n)!=0 )
+            error("Error occurred while updating AC_Hom at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    if ( args.tags&SET_AC_Hemi )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
+            for (i=1; i<rec->n_allele; i++)
+                args.arr[i] += args.counts[i].nhemi;
+        }
+        if ( bcf_update_info_int32(args.out_hdr,rec,"AC_Hemi",args.arr+1,n)!=0 )
+            error("Error occurred while updating AC_Hemi at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
+    return rec;
+}
+
+void destroy(void)
+{
+    free(args.counts);
+    free(args.arr);
+}
+
+
+
diff --git a/test/fill-tags.out b/test/fill-tags.out
new file mode 100644
index 000000000..eb8676f05
--- /dev/null
+++ b/test/fill-tags.out
@@ -0,0 +1,40 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
+##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=test,Description="Testing filter">
+##contig=<ID=1,assembly=b37,length=249250621>
+##contig=<ID=2,assembly=b37,length=249250621>
+##contig=<ID=3,assembly=b37,length=198022430>
+##contig=<ID=4,assembly=b37,length=191154276>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##readme=AAAAAA
+##readme=BBBBBB
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
+##INFO=<ID=AC_Hom,Number=A,Type=Integer,Description="Allele counts in homozygous genotypes">
+##INFO=<ID=AC_Het,Number=A,Type=Integer,Description="Allele counts in heterozygous genotypes">
+##INFO=<ID=AC_Hemi,Number=A,Type=Integer,Description="Allele counts in hemizygous genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	3000150	.	C	T	59.2	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ	0/1:245	0/1:245
+1	3000151	.	C	T	59.2	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1;AC_Het=1,0;AC_Hom=0,0;AC_Hemi=0,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP	0/1:245:32	0/1:245:32
+1	3106154	.	C	CT	59.2	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP	0/1:245:32	0/1:245:32
+1	3157410	.	GA	G	90.6	q10	AN=4;AC=4;AC_Het=0;AC_Hom=4;AC_Hemi=0	GT:GQ:DP	1/1:21:21	1/1:21:21
+1	3162006	.	GAA	G	60.2	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP	0/1:212:22	0/1:212:22
+1	3177144	.	G	T	45	PASS	AN=4;AC=2;AC_Het=0;AC_Hom=2;AC_Hemi=0	GT:GQ:DP	0/0:150:30	1/1:150:30
+1	3177144	.	G	.	45	PASS	AN=4	GT:GQ:DP	0/0:150:30	0/0:150:30
+1	3184885	.	TAAAA	TA,T	61.5	PASS	AN=4;AC=2,2;AC_Het=2,2;AC_Hom=0,0;AC_Hemi=0,0	GT:GQ:DP	1/2:12:10	1/2:12:10
+2	3199812	.	G	GTT,GT	82.7	PASS	AN=4;AC=2,2;AC_Het=2,2;AC_Hom=0,0;AC_Hemi=0,0	GT:GQ:DP	1/2:322:26	1/2:322:26
+3	3212016	.	CTT	C,CT	79	PASS	AN=4;AC=2,2;AC_Het=2,2;AC_Hom=0,0;AC_Hemi=0,0	GT:GQ:DP	1/2:91:26	1/2:91:26
+4	3258448	.	TACACACAC	T	.	PASS	AN=4;AC=2;AC_Het=2;AC_Hom=0;AC_Hemi=0	GT:GQ:DP	0/1:325:31	0/1:325:31
diff --git a/test/test.pl b/test/test.pl
index 71d80418c..cd9fbe462 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -158,8 +158,10 @@
 test_vcf_plugin($opts,in=>'plugin1',out=>'dosage.out',cmd=>'+dosage');
 test_vcf_plugin($opts,in=>'fixploidy',out=>'fixploidy.out',cmd=>'+fixploidy',args=>'-- -s {PATH}/fixploidy.samples -p {PATH}/fixploidy.ploidy');
 test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -n 5');
-test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -gn 5');
+test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -g GT');
+test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -g GT -n 5');
 test_vcf_plugin($opts,in=>'view.GL',out=>'view.PL.vcf',cmd=>'+tag2tag',args=>'-- -r --gl-to-pl');
+test_vcf_plugin($opts,in=>'merge.a',out=>'fill-tags.out',cmd=>'+fill-tags');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.vcf.out',do_bcf=>0,args=>'');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.bcf.out',do_bcf=>1,args=>'');
 test_vcf_concat($opts,in=>['concat.2.a','concat.2.b'],out=>'concat.2.vcf.out',do_bcf=>0,args=>'-a');

From 653c26ad111f97c18dda6eaad136cffbda5fb4d1 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 23 Jul 2015 20:34:19 +0100
Subject: [PATCH 032/211] Fix bcftools_pluginCommand=plugin header annotation.

---
 vcfplugin.c | 1 -
 1 file changed, 1 deletion(-)

diff --git a/vcfplugin.c b/vcfplugin.c
index 437d40fc6..1c2921c65 100644
--- a/vcfplugin.c
+++ b/vcfplugin.c
@@ -573,7 +573,6 @@ int main_plugin(int argc, char *argv[])
         args->plugin.argv = argv + optind;
     }
     optind = 0;
-    args->plugin.argv[0] = plugin_name;
 
     args->files = bcf_sr_init();
     if ( args->regions_list )

From 264745ee68c8bcb89b4302ced5f14c4c4336a10f Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 29 May 2015 14:58:47 +0100
Subject: [PATCH 033/211] New isec -n~BITMASK option

---
 doc/bcftools.txt | 11 ++++++++---
 vcfisec.c        | 25 ++++++++++++++++++++++---
 2 files changed, 30 insertions(+), 6 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 1dca046f8..56249f736 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -906,9 +906,9 @@ in the other files.
     include only sites for which 'EXPRESSION' is true. See discussion
     of *-e, --exclude* above.
 
-*-n, --nfiles* \[+-=]'INT'::
-    output positions present in this many (=), this many or more (+), or this
-    many or fewer (-) files
+*-n, --nfiles* \[+-=]'INT'|~'BITMAP'::
+    output positions present in this many (=), this many or more (+), this
+    many or fewer (-), or the exact same (~) files
 
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*.  When several files are being
@@ -958,6 +958,11 @@ Extract records private to A or B comparing by position only
     bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz
 ----
 
+Print a list of records which are present in A and B but not in C and D
+----
+    bcftools isec -n~1100 -c all A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz
+----
+
 
 [[merge]]
 === bcftools merge ['OPTIONS'] 'A.vcf.gz' 'B.vcf.gz' [...]
diff --git a/vcfisec.c b/vcfisec.c
index 27b812981..c86b0cdb3 100644
--- a/vcfisec.c
+++ b/vcfisec.c
@@ -41,6 +41,7 @@ THE SOFTWARE.  */
 #define OP_EQUAL 3
 #define OP_VENN 4
 #define OP_COMPLEMENT 5
+#define OP_EXACT 6
 
 // Logic of the filters: include or exclude sites which match the filters?
 #define FLT_INCLUDE 1
@@ -56,6 +57,7 @@ typedef struct
     FILE *fh_log, *fh_sites;
     htsFile **fh_out;
     char **argv, *prefix, *output_fname, **fnames, *write_files, *targets_list, *regions_list;
+    char *isec_exact;
     int argc;
 }
 args_t;
@@ -190,7 +192,12 @@ void isec_vcf(args_t *args)
             case OP_COMPLEMENT: if ( n!=1 || !bcf_sr_has_line(files,0) ) continue; break;
             case OP_EQUAL: if ( n != args->isec_n ) continue; break;
             case OP_PLUS: if ( n < args->isec_n ) continue; break;
-            case OP_MINUS: if ( n > args->isec_n ) continue;
+            case OP_MINUS: if ( n > args->isec_n ) continue; break;
+            case OP_EXACT:
+                for (i=0; i<files->nreaders; i++)
+                    if ( files->has_line[i] != args->isec_exact[i] ) break;
+                if ( i<files->nreaders ) continue;
+                break;
         }
 
         if ( out_std )
@@ -294,6 +301,16 @@ static void init_data(args_t *args)
         }
     }
 
+    if ( args->isec_op==OP_EXACT )
+    {
+        if ( strlen(args->isec_exact)!=args->files->nreaders )
+            error("The number of files does not match the bitmask: %d vs %s\n", args->files->nreaders,args->isec_exact);
+        for (i=0; i<args->files->nreaders; i++)
+            if ( args->isec_exact[i]!='0' && args->isec_exact[i]!='1' ) error("Unexpected bitmask: %s\n",args->isec_exact);
+        for (i=0; i<args->files->nreaders; i++)
+            args->isec_exact[i] -= '0';
+    }
+
     // Which files to write: parse the string passed with -w
     char *p = args->write_files;
     while (p && *p)
@@ -445,7 +462,7 @@ static void usage(void)
     fprintf(stderr, "    -e, --exclude <expr>          exclude sites for which the expression is true\n");
     fprintf(stderr, "    -f, --apply-filters <list>    require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
     fprintf(stderr, "    -i, --include <expr>          include only sites for which the expression is true\n");
-    fprintf(stderr, "    -n, --nfiles [+-=]<int>       output positions present in this many (=), this many or more (+), or this many or fewer (-) files\n");
+    fprintf(stderr, "    -n, --nfiles [+-=~]<int>      output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files\n");
     fprintf(stderr, "    -o, --output <file>           write output to a file [standard output]\n");
     fprintf(stderr, "    -O, --output-type <b|u|z|v>   b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
     fprintf(stderr, "    -p, --prefix <dir>            if given, subset each of the input files accordingly, see also -w\n");
@@ -538,9 +555,11 @@ int main_vcfisec(int argc, char *argv[])
                     if ( *p=='-' ) { args->isec_op = OP_MINUS; p++; }
                     else if ( *p=='+' ) { args->isec_op = OP_PLUS; p++; }
                     else if ( *p=='=' ) { args->isec_op = OP_EQUAL; p++; }
+                    else if ( *p=='~' ) { args->isec_op = OP_EXACT; p++; }
                     else if ( isdigit(*p) ) args->isec_op = OP_EQUAL;
                     else error("Could not parse --nfiles %s\n", optarg);
-                    if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg);
+                    if ( args->isec_op == OP_EXACT ) args->isec_exact = p;
+                    else if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg);
                 }
                 break;
             case 'h':

From 6ccecd140528e5c005934b1f8a6177de6ddda0dc Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 15 Jun 2015 09:50:24 +0100
Subject: [PATCH 034/211] New annotate -m option to mark sites present/absent
 in a file

---
 doc/bcftools.txt |  3 +++
 vcfannotate.c    | 36 +++++++++++++++++++++++++++++++++---
 2 files changed, 36 insertions(+), 3 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 56249f736..d7b68072a 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -291,6 +291,9 @@ This command allows to add or remove annotations.
     include only sites for which 'EXPRESSION' is true. For valid expressions see
     *<<expressions,EXPRESSIONS>>*.
 
+*-m, --mark-sites* [+-]'TAG'::
+    annotate sites which are present ("+") or absent ("-") in the *-a* file with a new INFO/TAG flag
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
diff --git a/vcfannotate.c b/vcfannotate.c
index b7ba548be..2723e7bc0 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -78,6 +78,9 @@ annot_col_t;
 #define FLT_INCLUDE 1
 #define FLT_EXCLUDE 2
 
+#define MARK_LISTED   1
+#define MARK_UNLISTED 2
+
 typedef struct _args_t
 {
     bcf_srs_t *files;
@@ -115,8 +118,8 @@ typedef struct _args_t
     kstring_t tmpks;
 
     char **argv, *output_fname, *targets_fname, *regions_list, *header_fname;
-    char *remove_annots, *columns, *rename_chrs, *sample_names;
-    int argc, drop_header, tgts_is_vcf;
+    char *remove_annots, *columns, *rename_chrs, *sample_names, *mark_sites;
+    int argc, drop_header, tgts_is_vcf, mark_sites_logic;
 }
 args_t;
 
@@ -1390,6 +1393,14 @@ static void init_data(args_t *args)
         args->set_ids = convert_init(args->hdr_out, NULL, 0, args->set_ids_fmt);
     }
 
+    if ( args->mark_sites )
+    {
+        if ( !args->targets_fname ) error("The -a option not given\n");
+        if ( args->tgts_is_vcf ) error("todo: -a is a VCF\n");  // very easy to add..
+        bcf_hdr_printf(args->hdr_out,"##INFO=<ID=%s,Number=0,Type=Flag,Description=\"Sites %slisted in %s\">",
+            args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites);
+    }
+
     bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_annotate");
     if ( !args->drop_header )
     {
@@ -1545,9 +1556,20 @@ static void annotate(args_t *args, bcf1_t *line)
 
         if ( i<args->nalines )
         {
+            // there is a matching line
             for (j=0; j<args->ncols; j++)
                 if ( args->cols[j].setter(args,line,&args->cols[j],&args->alines[i]) )
                     error("fixme: Could not set %s at %s:%d\n", args->cols[j].hdr_key,bcf_seqname(args->hdr,line),line->pos+1);
+
+        }
+
+        if ( args->mark_sites )
+        {
+            // ideally, we'd like to be far more general than this in future, see https://github.com/samtools/bcftools/issues/87
+            if ( args->mark_sites_logic==MARK_LISTED )
+                bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,i<args->nalines?1:0);
+            else
+                bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,i<args->nalines?0:1);
         }
     }
     else if ( args->files->nreaders == 2 && bcf_sr_has_line(args->files,1) )
@@ -1585,6 +1607,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -h, --header-lines <file>      lines which should be appended to the VCF header\n");
     fprintf(stderr, "   -I, --set-id [+]<format>       set ID column, see man pagee for details\n");
     fprintf(stderr, "   -i, --include <expr>           select sites for which the expression is true (see man pagee for details)\n");
+    fprintf(stderr, "   -m, --mark-sites [+-]<tag>     add INFO/tag flag to sites which are (\"+\") or are not (\"-\") listed in the -a file\n");
     fprintf(stderr, "   -o, --output <file>            write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
     fprintf(stderr, "   -r, --regions <region>         restrict to comma-separated list of regions\n");
@@ -1611,6 +1634,7 @@ int main_vcfannotate(int argc, char *argv[])
 
     static struct option loptions[] =
     {
+        {"mark-sites",1,0,'m'},
         {"set-id",1,0,'I'},
         {"output",1,0,'o'},
         {"output-type",1,0,'O'},
@@ -1627,9 +1651,15 @@ int main_vcfannotate(int argc, char *argv[])
         {"samples-file",1,0,'S'},
         {0,0,0,0}
     };
-    while ((c = getopt_long(argc, argv, "h:?o:O:r:R:a:x:c:i:e:S:s:I:",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h:?o:O:r:R:a:x:c:i:e:S:s:I:m:",loptions,NULL)) >= 0)
     {
         switch (c) {
+            case 'm': 
+                args->mark_sites_logic = MARK_LISTED;
+                if ( optarg[0]=='+' ) args->mark_sites = optarg+1;
+                else if ( optarg[0]=='-' ) { args->mark_sites = optarg+1; args->mark_sites_logic = MARK_UNLISTED; }
+                else args->mark_sites = optarg; 
+                break;
             case 'I': args->set_ids_fmt = optarg; break;
             case 's': args->sample_names = optarg; break;
             case 'S': args->sample_names = optarg; args->sample_is_file = 1; break;

From d0ff204878f6013a463c1b3641295eb79098a666 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 28 Jul 2015 09:51:53 +0100
Subject: [PATCH 035/211] docs update

include docs update from:

* 6ccecd140528e5c005934b1f8a6177de6ddda0dc
* 264745ee68c8bcb89b4302ced5f14c4c4336a10f
* 3ba5f38ced4e3938348fa231a2f3d794ee43bc5a
---
 doc/bcftools.1    | 41 ++++++++++++++++++++++++++++++++---------
 doc/bcftools.html | 27 +++++++++++++++++----------
 2 files changed, 49 insertions(+), 19 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index 8988447b7..a56a6b0ba 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-06-15 15:56 BST
+.\"      Date: 2015-07-28 09:49 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-06\-15 15:56 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-07\-28 09:49 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-06\-15 15:56 BST\fR and refers to bcftools git version \fB1\&.2\-45\-g3d18e21+\fR\&.
+This manual page was last updated \fB2015\-07\-28 09:49 BST\fR and refers to bcftools git version \fB1\&.2\-74\-g6ccecd1+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -549,6 +549,13 @@ is true\&. For valid expressions see
 \fBEXPRESSIONS\fR\&.
 .RE
 .PP
+\fB\-m, \-\-mark\-sites\fR \fITAG\fR
+.RS 4
+annotate sites which are present ("+") or absent ("\-") in the
+\fB\-a\fR
+file with a new INFO/TAG flag
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -1561,9 +1568,9 @@ is true\&. See discussion of
 above\&.
 .RE
 .PP
-\fB\-n, \-\-nfiles\fR [+\-=]\fIINT\fR
+\fB\-n, \-\-nfiles\fR [+\-=]\fIINT\fR|~\fIBITMAP\fR
 .RS 4
-output positions present in this many (=), this many or more (+), or this many or fewer (\-) files
+output positions present in this many (=), this many or more (+), this many or fewer (\-), or the exact same (~) files
 .RE
 .PP
 \fB\-o, \-\-output\fR \fIFILE\fR
@@ -1673,6 +1680,18 @@ Extract records private to A or B comparing by position only
 .if n \{\
 .RE
 .\}
+.sp
+Print a list of records which are present in A and B but not in C and D
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    bcftools isec \-n~1100 \-c all A\&.vcf\&.gz B\&.vcf\&.gz C\&.vcf\&.gz D\&.vcf\&.gz
+.fi
+.if n \{\
+.RE
+.\}
 .RE
 .SS "bcftools merge [\fIOPTIONS\fR] \fIA\&.vcf\&.gz\fR \fIB\&.vcf\&.gz\fR [\&...]"
 .sp
@@ -2355,15 +2374,13 @@ Emission probabilities:
 Transition probabilities:
   tAZ = P(AZ|HW)  \&.\&. from HW to AZ, the \-a parameter
   tHW = P(HW|AZ)  \&.\&. from AZ to HW, the \-H parameter
-  P(AZ|AZ) = 1 \- P(HW|AZ) = 1 \- tHW
-  P(HW|HW) = 1 \- P(AZ|HW) = 1 \- tAZ
 
   ci  = P_i(C)  \&.\&. probability of cross\-over at site i, from genetic map
   AZi = P_i(AZ) \&.\&. probability of site i being AZ/non\-AZ, scaled so that AZi+HWi = 1
   HWi = P_i(HW)
 
-  P_{i+1}(AZ) = oAZ * max[(1\-tHW) * (1\-ci) * AZ{i\-1} , tAZ * ci * (1\-AZ{i\-1})]
-  P_{i+1}(HW) = oHW * max[(1\-tAZ) * (1\-ci) * (1\-AZ{i\-1}) , tHW * ci * AZ{i\-1}]
+  P_{i+1}(AZ) = oAZ * max[(1 \- tAZ * ci) * AZ{i\-1} , tAZ * ci * (1\-AZ{i\-1})]
+  P_{i+1}(HW) = oHW * max[(1 \- tHW * ci) * (1\-AZ{i\-1}) , tHW * ci * AZ{i\-1}]
 .fi
 .if n \{\
 .RE
@@ -2378,6 +2395,12 @@ Transition probabilities:
 \fBGeneral Options:\fR
 .RS 4
 .PP
+\fB\-\-AF\-dflt\fR \fIFLOAT\fR
+.RS 4
+in case allele frequency is not known, use the
+\fIFLOAT\fR\&. By default, sites where allele frequency cannot be determined, or is 0, are skipped\&.
+.RE
+.PP
 \fB\-\-AF\-tag\fR \fITAG\fR
 .RS 4
 use the specified INFO tag
diff --git a/doc/bcftools.html b/doc/bcftools.html
index 28b8928c7..9919479fb 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp1764672"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25161584"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
 work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-06-15 15:56 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-45-g3d18e21+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-07-28 09:49 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-74-g6ccecd1+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -245,6 +245,10 @@
     include only sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see
     <span class="strong"><strong><a class="link" href="#expressions" title="EXPRESSIONS">EXPRESSIONS</a></strong></span>.
 </dd><dt><span class="term">
+<span class="strong"><strong>-m, --mark-sites</strong></span> <span class="emphasis"><em><span class="+-">TAG</span></em></span>
+</span></dt><dd>
+    annotate sites which are present ("+") or absent ("-") in the <span class="strong"><strong>-a</strong></span> file with a new INFO/TAG flag
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -874,10 +878,10 @@
     include only sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. See discussion
     of <span class="strong"><strong>-e, --exclude</strong></span> above.
 </dd><dt><span class="term">
-<span class="strong"><strong>-n, --nfiles</strong></span> [+-=]<span class="emphasis"><em>INT</em></span>
+<span class="strong"><strong>-n, --nfiles</strong></span> [+-=]<span class="emphasis"><em>INT</em></span>|~<span class="emphasis"><em>BITMAP</em></span>
 </span></dt><dd>
-    output positions present in this many (=), this many or more (+), or this
-    many or fewer (-) files
+    output positions present in this many (=), this many or more (+), this
+    many or fewer (-), or the exact same (~) files
 </dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
@@ -912,7 +916,7 @@
 </span></dt><dd>
     list of input files to output given as 1-based indices. With <span class="strong"><strong>-p</strong></span> and no
     <span class="strong"><strong>-w</strong></span>, all files are written.
-</dd></dl></div><div class="refsect3" title="Examples:"><a id="_examples"></a><h4>Examples:</h4><p>Create intersection and complements of two sets saving the output in dir/*</p><pre class="screen">    bcftools isec -p dir A.vcf.gz B.vcf.gz</pre><p>Filter sites in A and B (but not in C) and create intersection</p><pre class="screen">    bcftools isec -e'MAF&lt;0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -p dir</pre><p>Extract and write records from A shared by both A and B using exact allele match</p><pre class="screen">    bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz</pre><p>Extract records private to A or B comparing by position only</p><pre class="screen">    bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz</pre></div></div><div class="refsect2" title="bcftools merge [OPTIONS] A.vcf.gz B.vcf.gz […]"><a id="merge"></a><h3>bcftools merge [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>A.vcf.gz</em></span> <span class="emphasis"><em>B.vcf.gz</em></span> […]</h3><p>Merge multiple VCF/BCF files from non-overlapping sample sets to create one
+</dd></dl></div><div class="refsect3" title="Examples:"><a id="_examples"></a><h4>Examples:</h4><p>Create intersection and complements of two sets saving the output in dir/*</p><pre class="screen">    bcftools isec -p dir A.vcf.gz B.vcf.gz</pre><p>Filter sites in A and B (but not in C) and create intersection</p><pre class="screen">    bcftools isec -e'MAF&lt;0.01' -i'dbSNP=1' -e- A.vcf.gz B.vcf.gz C.vcf.gz -p dir</pre><p>Extract and write records from A shared by both A and B using exact allele match</p><pre class="screen">    bcftools isec -p dir -n=2 -w1 A.vcf.gz B.vcf.gz</pre><p>Extract records private to A or B comparing by position only</p><pre class="screen">    bcftools isec -p dir -n-1 -c all A.vcf.gz B.vcf.gz</pre><p>Print a list of records which are present in A and B but not in C and D</p><pre class="screen">    bcftools isec -n~1100 -c all A.vcf.gz B.vcf.gz C.vcf.gz D.vcf.gz</pre></div></div><div class="refsect2" title="bcftools merge [OPTIONS] A.vcf.gz B.vcf.gz […]"><a id="merge"></a><h3>bcftools merge [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>A.vcf.gz</em></span> <span class="emphasis"><em>B.vcf.gz</em></span> […]</h3><p>Merge multiple VCF/BCF files from non-overlapping sample sets to create one
 multi-sample file.  For example, when merging file <span class="emphasis"><em>A.vcf.gz</em></span> containing
 samples <span class="emphasis"><em>S1</em></span>, <span class="emphasis"><em>S2</em></span> and <span class="emphasis"><em>S3</em></span> and file <span class="emphasis"><em>B.vcf.gz</em></span> containing samples <span class="emphasis"><em>S3</em></span> and
 <span class="emphasis"><em>S4</em></span>, the output file will contain four samples named <span class="emphasis"><em>S1</em></span>, <span class="emphasis"><em>S2</em></span>, <span class="emphasis"><em>S3</em></span>, <span class="emphasis"><em>2:S3</em></span>
@@ -1274,15 +1278,18 @@
 Transition probabilities:
   tAZ = P(AZ|HW)  .. from HW to AZ, the -a parameter
   tHW = P(HW|AZ)  .. from AZ to HW, the -H parameter
-  P(AZ|AZ) = 1 - P(HW|AZ) = 1 - tHW
-  P(HW|HW) = 1 - P(AZ|HW) = 1 - tAZ
 
   ci  = P_i(C)  .. probability of cross-over at site i, from genetic map
   AZi = P_i(AZ) .. probability of site i being AZ/non-AZ, scaled so that AZi+HWi = 1
   HWi = P_i(HW)
 
-  P_{i+1}(AZ) = oAZ * max[(1-tHW) * (1-ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
-  P_{i+1}(HW) = oHW * max[(1-tAZ) * (1-ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]</pre></div><div class="refsect3" title="General Options:"><a id="_general_options"></a><h4>General Options:</h4><div class="variablelist"><dl><dt><span class="term">
+  P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
+  P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]</pre></div><div class="refsect3" title="General Options:"><a id="_general_options"></a><h4>General Options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--AF-dflt</strong></span> <span class="emphasis"><em>FLOAT</em></span>
+</span></dt><dd>
+    in case allele frequency is not known, use the <span class="emphasis"><em>FLOAT</em></span>. By default, sites where
+    allele frequency cannot be determined, or is 0, are skipped.
+</dd><dt><span class="term">
 <span class="strong"><strong>--AF-tag</strong></span> <span class="emphasis"><em>TAG</em></span>
 </span></dt><dd>
     use the specified INFO tag <span class="emphasis"><em>TAG</em></span> as an allele frequency estimate

From 40ee806a6f649a16d22f19f2c0755a28dce54f05 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 17 Jul 2015 10:09:53 +0100
Subject: [PATCH 036/211] Fix in -i/-e filtering in the convert command; query
 missing GT fields e.g. as GT="."

---
 doc/bcftools.txt |  5 +++++
 filter.c         | 31 ++++++++++++++++++++++++-------
 vcfconvert.c     |  5 +++--
 3 files changed, 32 insertions(+), 9 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index d7b68072a..574ac7ef5 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1678,6 +1678,11 @@ These filtering expressions are accepted by *<<annotate,annotate>>*,
 
         DP=".", DP!="."
 
+* missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".")
+using this expression
+
+        GT="."
+
 * TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
 
         TYPE="indel" | TYPE="snp"
diff --git a/filter.c b/filter.c
index 413946bd1..8c3d0837a 100644
--- a/filter.c
+++ b/filter.c
@@ -568,15 +568,32 @@ static void filters_set_genotype_string(filter_t *flt, bcf1_t *line, token_t *to
     for (i=0; i<nsmpl; i++)
     {
         int plen = str.l;
-        bcf_format_gt(fmt, i, &str);
-        if ( str.l - plen > blen )
+
+        #define BRANCH(type_t) { \
+            type_t *ptr = (type_t*) (fmt->p + i*fmt->size); \
+            if ( !(ptr[0]>>1) ) kputc('.',&str); \
+        }
+        switch (fmt->type) {
+            case BCF_BT_INT8:  BRANCH(int8_t); break;
+            case BCF_BT_INT16: BRANCH(int16_t); break;
+            case BCF_BT_INT32: BRANCH(int32_t); break;
+            default: fprintf(stderr,"FIXME: type %d in bcf_format_gt?\n", fmt->type); abort(); break;
+        }
+        #undef BRANCH
+
+        if ( plen==str.l )
         {
-            // too many alternate alleles or ploidy is too large, the genotype does not fit
-            // three characters ("0/0" vs "10/10").
-            tok->str_value = str.s;
-            blen *= 2;
-            goto gt_length_too_big;
+            bcf_format_gt(fmt, i, &str);
+            if ( str.l - plen > blen )
+            {
+                // too many alternate alleles or ploidy is too large, the genotype does not fit
+                // three characters ("0/0" vs "10/10").
+                tok->str_value = str.s;
+                blen *= 2;
+                goto gt_length_too_big;
+            }
         }
+
         plen = str.l - plen;
         while ( plen<blen )
         {
diff --git a/vcfconvert.c b/vcfconvert.c
index f4922a17c..c3d793e86 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -93,11 +93,12 @@ static void open_vcf(args_t *args, const char *format_str)
     }
     if ( !bcf_sr_add_reader(args->files, args->infname) )
         error("Failed to open %s: %s\n", args->infname,bcf_sr_strerror(args->files->errnum));
-    if ( args->filter_str )
-        args->filter = filter_init(args->header, args->filter_str);
 
     args->header = args->files->readers[0].header;
 
+    if ( args->filter_str )
+        args->filter = filter_init(args->header, args->filter_str);
+
     int i, nsamples = 0, *samples = NULL;
     if ( args->sample_list && strcmp("-",args->sample_list) )
     {

From b62ae45ba53ac1088424dab4a9f4b245e6994754 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 9 Mar 2015 21:37:12 +0000
Subject: [PATCH 037/211] bugfix in filtering expressions involving ALT=. sites

---
 filter.c | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/filter.c b/filter.c
index 8c3d0837a..ccc844568 100644
--- a/filter.c
+++ b/filter.c
@@ -664,7 +664,12 @@ static void filters_set_ac(filter_t *flt, bcf1_t *line, token_t *tok)
     if ( tok->idx>=0 )
     {
         tok->nvalues = 1;
-        tok->values[0] = flt->tmpi[tok->idx+1];
+        tok->values[0] = tok->idx+1<line->n_allele ? flt->tmpi[tok->idx+1] : 0;
+    }
+    else if ( line->n_allele==1 )   // no ALT
+    {
+        tok->nvalues = 1;
+        tok->values[0] = 0;
     }
     else
     {

From d3af7da5b4551cb0ff1c02950e32e2c334499047 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Sun, 3 May 2015 08:31:30 +0100
Subject: [PATCH 038/211] rbuf_expand0 macro made analogous to hts_expand0

---
 rbuf.h           | 25 +++++++++++++++----------
 test/test-rbuf.c |  2 +-
 vcffilter.c      |  2 +-
 3 files changed, 17 insertions(+), 12 deletions(-)

diff --git a/rbuf.h b/rbuf.h
index 89ff9aabd..3d2805c77 100644
--- a/rbuf.h
+++ b/rbuf.h
@@ -174,23 +174,28 @@ static inline void rbuf_shift_n(rbuf_t *rbuf, int n)
  *  rbuf_expand0() - expand round buffer and set the newly allocated elements to 0
  *  @rbuf:      the rbuf holder
  *  @type_t:    data type
+ *  @n:         requested number of elements
  *  @data:      data array to be realloced
  *
  *  Note: The new array is linearized and leaves the rbuf.f offset untouched,
  *  thus the size of the new buffer is determined by the current position.
  */
-#define rbuf_expand0(rbuf,type_t,data) { \
-    int m = (rbuf)->m + (rbuf)->f + 1; \
-    m--, m|=m>>1, m|=m>>2, m|=m>>4, m|=m>>8, m|=m>>16, m++; /* kroundup32 */ \
-    data = (type_t*) realloc(data, sizeof(type_t)*m); \
-    type_t *ptr = data; \
-    memset(ptr+(rbuf)->m,0,sizeof(type_t)*(m-(rbuf)->m)); \
-    if ( (rbuf)->f ) \
+#define rbuf_expand0(rbuf,type_t,n,data) \
+{ \
+    if ( n > (rbuf)->m ) \
     { \
-        memcpy(ptr+(rbuf)->m,ptr,sizeof(type_t)*(rbuf)->f); \
-        memset(ptr,0,sizeof(type_t)*(rbuf)->f); \
+        int m = n + (rbuf)->f; \
+        m--, m|=m>>1, m|=m>>2, m|=m>>4, m|=m>>8, m|=m>>16, m++; /* kroundup32 */ \
+        data = (type_t*) realloc(data, sizeof(type_t)*m); \
+        type_t *ptr = data; \
+        memset(ptr+(rbuf)->m,0,sizeof(type_t)*(m-(rbuf)->m)); \
+        if ( (rbuf)->f ) \
+        { \
+            memcpy(ptr+(rbuf)->m,ptr,sizeof(type_t)*(rbuf)->f); \
+            memset(ptr,0,sizeof(type_t)*(rbuf)->f); \
+        } \
+        (rbuf)->m = m; \
     } \
-    (rbuf)->m = m; \
 }
 
 #endif
diff --git a/test/test-rbuf.c b/test/test-rbuf.c
index c428339fc..bc8ebe92b 100644
--- a/test/test-rbuf.c
+++ b/test/test-rbuf.c
@@ -64,7 +64,7 @@ int main(int argc, char **argv)
     debug_print(&rbuf, dat);
 
     printf("Expanding:\n");
-    rbuf_expand0(&rbuf,int,dat);
+    rbuf_expand0(&rbuf,int,rbuf.n+1,dat);
     debug_print(&rbuf, dat);
 
     free(dat);
diff --git a/vcffilter.c b/vcffilter.c
index 481941c64..f2abf0f4b 100644
--- a/vcffilter.c
+++ b/vcffilter.c
@@ -227,7 +227,7 @@ static void buffered_filters(args_t *args, bcf1_t *line)
         if ( ilast>=0 && line->rid != args->rbuf_lines[ilast]->rid )
             flush_buffer(args, args->rbuf.n); // new chromosome, flush everything
 
-        if ( args->rbuf.n >= args->rbuf.m ) rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf_lines);
+        rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n,args->rbuf_lines);
 
         // Insert the new record in the buffer. The line would be overwritten in
         // the next bcf_sr_next_line call, therefore we need to swap it with an

From 33464ef77f4604f440cd10c6f0d6cd73a539ab05 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Sun, 3 May 2015 08:34:12 +0100
Subject: [PATCH 039/211] Moved hts_bcf_wmode to be accesible by plugins

---
 vcfisec.c | 8 --------
 version.c | 8 ++++++++
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/vcfisec.c b/vcfisec.c
index c86b0cdb3..c082d68d0 100644
--- a/vcfisec.c
+++ b/vcfisec.c
@@ -128,14 +128,6 @@ FILE *open_file(char **fname, const char *mode, const char *fmt, ...)
     return fp;
 }
 
-const char *hts_bcf_wmode(int file_type)
-{
-    if ( file_type == FT_BCF ) return "wbu";    // uncompressed BCF
-    if ( file_type & FT_BCF ) return "wb";      // compressed BCF
-    if ( file_type & FT_GZ ) return "wz";       // compressed VCF
-    return "w";                                 // uncompressed VCF
-}
-
 void isec_vcf(args_t *args)
 {
     bcf_srs_t *files = args->files;
diff --git a/version.c b/version.c
index 4a2ea7d35..00eeb5ab2 100644
--- a/version.c
+++ b/version.c
@@ -44,4 +44,12 @@ void error(const char *format, ...)
     exit(-1);
 }
 
+const char *hts_bcf_wmode(int file_type)
+{
+    if ( file_type == FT_BCF ) return "wbu";    // uncompressed BCF
+    if ( file_type & FT_BCF ) return "wb";      // compressed BCF
+    if ( file_type & FT_GZ ) return "wz";       // compressed VCF
+    return "w";                                 // uncompressed VCF
+}
+
 

From 0b8f0eaa67a4a4f73a566b739baddd9ac98d3959 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 20 May 2015 10:07:07 +0100
Subject: [PATCH 040/211] norm: Replace IUPAC ambiguity codes in fasta ref with
 Ns

---
 vcfnorm.c | 38 ++++++++++++++++++++++++++++++++++----
 1 file changed, 34 insertions(+), 4 deletions(-)

diff --git a/vcfnorm.c b/vcfnorm.c
index 613888002..b8a9ba30f 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -79,6 +79,18 @@ typedef struct
 }
 args_t;
 
+static inline int replace_iupac_codes(char *seq, int nseq)
+{
+    // Replace ambiguity codes with N for now, it awaits to be seen what the VCF spec codifies in the end
+    int i, n = 0;
+    for (i=0; i<nseq; i++)
+    {
+        char c = toupper(seq[i]);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' ) { seq[i] = 'N'; n++; }
+    }
+    return n;
+}
+
 static void fix_ref(args_t *args, bcf1_t *line)
 {
     int reflen = strlen(line->d.allele[0]);
@@ -91,9 +103,11 @@ static void fix_ref(args_t *args, bcf1_t *line)
 
     char *ref = faidx_fetch_seq(args->fai, (char*)bcf_seqname(args->hdr,line), line->pos, line->pos+maxlen-1, &len);
     if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", bcf_seqname(args->hdr,line),line->pos+1);
+    replace_iupac_codes(ref,len);
 
-    // is the REF different?
     args->nref.tot++;
+
+    // is the REF different?
     if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
 
     // is the REF allele missing or N?
@@ -106,6 +120,14 @@ static void fix_ref(args_t *args, bcf1_t *line)
         return;
     }
 
+    // does REF contain non-standard bases?
+    if ( replace_iupac_codes(line->d.allele[0],strlen(line->d.allele[0])) )
+    {
+        args->nref.set++;
+        bcf_update_alleles(args->hdr,line,(const char**)line->d.allele,line->n_allele);
+        if ( !strncasecmp(line->d.allele[0],ref,reflen) ) { free(ref); return; }
+    }
+
     // is it swapped?
     for (i=1; i<line->n_allele; i++)
     {
@@ -235,13 +257,21 @@ static int realign(args_t *args, bcf1_t *line)
     bcf_unpack(line, BCF_UN_STR);
 
     // Sanity check REF
-    int nref, reflen = strlen(line->d.allele[0]);
+    int i, nref, reflen = strlen(line->d.allele[0]);
     char *ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref);
     if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos+1);
+    replace_iupac_codes(ref,nref);
+
+    // does REF contain non-standard bases?
+    if ( replace_iupac_codes(line->d.allele[0],reflen) )
+    {
+        args->nchanged++;
+        bcf_update_alleles(args->hdr,line,(const char**)line->d.allele,line->n_allele);
+    }
     if ( strcasecmp(ref,line->d.allele[0]) )
     {
         if ( args->check_ref==CHECK_REF_EXIT )
-            error("Reference allele mismatch at %s:%d .. '%s' vs '%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[0]);
+            error("Reference allele mismatch at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[0]);
         if ( args->check_ref & CHECK_REF_WARN )
             fprintf(stderr,"REF_MISMATCH\t%s\t%d\t%s\n", bcf_seqname(args->hdr,line),line->pos+1,line->d.allele[0]);
         free(ref);
@@ -253,7 +283,6 @@ static int realign(args_t *args, bcf1_t *line)
     if ( line->n_allele == 1 ) return ERR_OK;    // a REF
 
     // make a copy of each allele for trimming
-    int i;
     hts_expand0(kstring_t,line->n_allele,args->ntmp_als,args->tmp_als);
     kstring_t *als = args->tmp_als;
     for (i=0; i<line->n_allele; i++)
@@ -290,6 +319,7 @@ static int realign(args_t *args, bcf1_t *line)
             free(ref);
             ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos-npad, line->pos-1, &nref);
             if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos-npad+1);
+            replace_iupac_codes(ref,nref);
             for (i=0; i<line->n_allele; i++)
             {
                 ks_resize(&als[i], als[i].l + npad);

From 1b485cee87c03ca06d36a902f394d105e0cdc5d2 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 24 Apr 2015 09:51:34 +0100
Subject: [PATCH 041/211] norm: Set freed alleles to NULL to prevent multiple
 free()s

---
 vcfnorm.c | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/vcfnorm.c b/vcfnorm.c
index b8a9ba30f..aa82e949d 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -1312,7 +1312,11 @@ static void merge_biallelics_to_multiallelic(args_t *args, bcf1_t *dst, bcf1_t *
         if ( !args->als ) error("Failed to merge alleles at %s:%d\n", bcf_seqname(args->hdr,dst),dst->pos+1);
     }
     bcf_update_alleles(args->hdr, dst, (const char**)args->als, args->nals);
-    for (i=0; i<args->nals; i++) free(args->als[i]);
+    for (i=0; i<args->nals; i++)
+    {
+        free(args->als[i]);
+        args->als[i] = NULL;
+    }
 
     if ( lines[0]->d.n_flt ) bcf_update_filter(args->hdr, dst, lines[0]->d.flt, lines[0]->d.n_flt);
     for (i=1; i<nlines; i++) {

From 5e1e930cebbe2b44f03ae16d44f8575869c96f01 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 9 Mar 2015 21:53:01 +0000
Subject: [PATCH 042/211] stats: previously omitted ALT=. sites now count as
 SNPs in per-sample stats (HomRR counts)

---
 test/check.chk | 5 +++--
 test/stats.chk | 3 +++
 vcfstats.c     | 7 +++++--
 3 files changed, 11 insertions(+), 4 deletions(-)

diff --git a/test/check.chk b/test/check.chk
index 1012e5c81..4ad6cf806 100644
--- a/test/check.chk
+++ b/test/check.chk
@@ -5,6 +5,7 @@
 # SN	[2]id	[3]key	[4]value
 SN	0	number of samples:	2
 SN	0	number of records:	18
+SN	0	number of no-ALTs:	1
 SN	0	number of SNPs:	5
 SN	0	number of MNPs:	1
 SN	0	number of indels:	9
@@ -70,8 +71,8 @@ DP	0	32	4	11.111111	0	0.000000
 DP	0	35	4	11.111111	0	0.000000
 # PSC, Per-sample counts
 # PSC	[2]id	[3]sample	[4]nRefHom	[5]nNonRefHom	[6]nHets	[7]nTransitions	[8]nTransversions	[9]nIndels	[10]average depth	[11]nSingletons
-PSC	0	A	0	2	3	3	2	9	28.7	1
-PSC	0	B	1	1	3	2	2	9	28.7	0
+PSC	0	A	0	2	4	3	2	9	28.7	1
+PSC	0	B	1	1	4	2	2	9	28.7	0
 # HWE
 # HWE	[2]id	[3]1st ALT allele frequency	[4]Number of observations	[5]25th percentile	[6]median	[7]75th percentile
 HWE	0	0.000000	2	0.490000	0.490000	0.990000
diff --git a/test/stats.chk b/test/stats.chk
index ea87209c1..6f603866d 100644
--- a/test/stats.chk
+++ b/test/stats.chk
@@ -1,6 +1,7 @@
 SN	0	number of samples:	3
 SN	1	number of samples:	3
 SN	0	number of records:	0
+SN	0	number of no-ALTs:	0
 SN	0	number of SNPs:	0
 SN	0	number of MNPs:	0
 SN	0	number of indels:	0
@@ -8,6 +9,7 @@ SN	0	number of others:	0
 SN	0	number of multiallelic sites:	0
 SN	0	number of multiallelic SNP sites:	0
 SN	1	number of records:	0
+SN	1	number of no-ALTs:	0
 SN	1	number of SNPs:	0
 SN	1	number of MNPs:	0
 SN	1	number of indels:	0
@@ -15,6 +17,7 @@ SN	1	number of others:	0
 SN	1	number of multiallelic sites:	0
 SN	1	number of multiallelic SNP sites:	0
 SN	2	number of records:	3
+SN	2	number of no-ALTs:	0
 SN	2	number of SNPs:	3
 SN	2	number of MNPs:	0
 SN	2	number of indels:	0
diff --git a/vcfstats.c b/vcfstats.c
index e0a0c2c83..8892f25fd 100644
--- a/vcfstats.c
+++ b/vcfstats.c
@@ -75,7 +75,7 @@ smpl_r_t;
 
 typedef struct
 {
-    int n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records;
+    int n_snps, n_indels, n_mnps, n_others, n_mals, n_snp_mals, n_records, n_noalts;
     int *af_ts, *af_tv, *af_snps;   // first bin of af_* stats are singletons
     #if HWE_STATS
         int *af_hwe;
@@ -809,7 +809,7 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
                     case GT_HOM_AA: nalt_tot++; break;
                 }
             #endif
-            if ( line_type&VCF_SNP )
+            if ( line_type&VCF_SNP || line_type==VCF_REF )  // count ALT=. as SNP
             {
                 if ( gt == GT_HET_RA ) stats->smpl_hets[is]++;
                 else if ( gt == GT_HET_AA ) stats->smpl_hets[is]++;
@@ -1019,6 +1019,8 @@ static void do_vcf_stats(args_t *args)
 
         stats->n_records++;
 
+        if ( line_type==VCF_REF )
+            stats->n_noalts++;
         if ( line_type&VCF_SNP )
             do_snp_stats(args, stats, reader);
         if ( line_type&VCF_INDEL )
@@ -1095,6 +1097,7 @@ static void print_stats(args_t *args)
     {
         stats_t *stats = &args->stats[id];
         printf("SN\t%d\tnumber of records:\t%d\n", id, stats->n_records);
+        printf("SN\t%d\tnumber of no-ALTs:\t%d\n", id, stats->n_noalts);
         printf("SN\t%d\tnumber of SNPs:\t%d\n", id, stats->n_snps);
         printf("SN\t%d\tnumber of MNPs:\t%d\n", id, stats->n_mnps);
         printf("SN\t%d\tnumber of indels:\t%d\n", id, stats->n_indels);

From 6fed5ac7a68a2cd0bc2121b99bcfbb3eacbec3e5 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 15 May 2015 09:35:43 +0100
Subject: [PATCH 043/211] stats: output also indel nHET and nAA in PSI stats

---
 test/check.chk |  4 ++++
 test/stats.chk |  9 +++++++++
 vcfstats.c     | 33 +++++++++++++++++++++++----------
 3 files changed, 36 insertions(+), 10 deletions(-)

diff --git a/test/check.chk b/test/check.chk
index 4ad6cf806..0f78e654e 100644
--- a/test/check.chk
+++ b/test/check.chk
@@ -73,6 +73,10 @@ DP	0	35	4	11.111111	0	0.000000
 # PSC	[2]id	[3]sample	[4]nRefHom	[5]nNonRefHom	[6]nHets	[7]nTransitions	[8]nTransversions	[9]nIndels	[10]average depth	[11]nSingletons
 PSC	0	A	0	2	4	3	2	9	28.7	1
 PSC	0	B	1	1	4	2	2	9	28.7	0
+# PSI, Per-Sample Indels
+# PSI	[2]id	[3]sample	[4]in-frame	[5]out-frame	[6]not applicable	[7]out/(in+out) ratio	[8]nHets	[9]nAA
+PSI	0	A	0	0	0	0.00	9	0
+PSI	0	B	0	0	0	0.00	9	0
 # HWE
 # HWE	[2]id	[3]1st ALT allele frequency	[4]Number of observations	[5]25th percentile	[6]median	[7]75th percentile
 HWE	0	0.000000	2	0.490000	0.490000	0.990000
diff --git a/test/stats.chk b/test/stats.chk
index 6f603866d..6b2dd3be2 100644
--- a/test/stats.chk
+++ b/test/stats.chk
@@ -87,4 +87,13 @@ PSC	1	C	0	0	0	0	0	0	0.0	0
 PSC	2	A	3	0	0	0	0	0	0.0	0
 PSC	2	B	0	0	3	3	0	0	0.0	0
 PSC	2	C	0	3	0	3	0	0	0.0	0
+PSI	0	A	0	0	0	0.00	0	0
+PSI	0	B	0	0	0	0.00	0	0
+PSI	0	C	0	0	0	0.00	0	0
+PSI	1	A	0	0	0	0.00	0	0
+PSI	1	B	0	0	0	0.00	0	0
+PSI	1	C	0	0	0	0.00	0	0
+PSI	2	A	0	0	0	0.00	0	0
+PSI	2	B	0	0	0	0.00	0	0
+PSI	2	C	0	0	0	0.00	0	0
 HWE	2	49.000000	3	0.330000	0.330000	0.330000
diff --git a/vcfstats.c b/vcfstats.c
index 8892f25fd..a207ccc53 100644
--- a/vcfstats.c
+++ b/vcfstats.c
@@ -92,6 +92,7 @@ typedef struct
     int in_frame, out_frame, na_frame, in_frame_alt1, out_frame_alt1, na_frame_alt1;
     int subst[15];
     int *smpl_hets, *smpl_homRR, *smpl_homAA, *smpl_ts, *smpl_tv, *smpl_indels, *smpl_ndp, *smpl_sngl;
+    int *smpl_indel_hets, *smpl_indel_homs;
     int *smpl_frm_shifts; // not-applicable, in-frame, out-frame
     unsigned long int *smpl_dp;
     idist_t dp, dp_sites;
@@ -437,6 +438,8 @@ static void init_stats(args_t *args)
             stats->smpl_hets   = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_homAA  = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_homRR  = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_indel_hets = (int *) calloc(args->files->n_smpl,sizeof(int));
+            stats->smpl_indel_homs = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_ts     = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_tv     = (int *) calloc(args->files->n_smpl,sizeof(int));
             stats->smpl_indels = (int *) calloc(args->files->n_smpl,sizeof(int));
@@ -514,6 +517,8 @@ static void destroy_stats(args_t *args)
         if (stats->smpl_hets) free(stats->smpl_hets);
         if (stats->smpl_homAA) free(stats->smpl_homAA);
         if (stats->smpl_homRR) free(stats->smpl_homRR);
+        if (stats->smpl_indel_homs) free(stats->smpl_indel_homs);
+        if (stats->smpl_indel_hets) free(stats->smpl_indel_hets);
         if (stats->smpl_ts) free(stats->smpl_ts);
         if (stats->smpl_tv) free(stats->smpl_tv);
         if (stats->smpl_indels) free(stats->smpl_indels);
@@ -827,7 +832,12 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
             }
             if ( line_type&VCF_INDEL )
             {
-                if ( gt != GT_HOM_RR ) stats->smpl_indels[is]++;
+                if ( gt != GT_HOM_RR )
+                {
+                    stats->smpl_indels[is]++;
+                    if ( gt==GT_HET_RA || gt==GT_HET_AA ) stats->smpl_indel_hets[is]++;
+                    else if ( gt==GT_HOM_AA ) stats->smpl_indel_homs[is]++;
+                }
                 if ( stats->smpl_frm_shifts )
                 {
                     assert( ial<line->n_allele && jal<line->n_allele );
@@ -1357,19 +1367,22 @@ static void print_stats(args_t *args)
         }
 
 
-        if ( args->exons )
+        printf("# PSI, Per-Sample Indels\n# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\t[8]nHets\t[9]nAA\n");
+        for (id=0; id<args->nstats; id++)
         {
-            printf("# PSI, Per-Sample Indels\n# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\n");
-            for (id=0; id<args->nstats; id++)
+            stats_t *stats = &args->stats[id];
+            for (i=0; i<args->files->n_smpl; i++)
             {
-                stats_t *stats = &args->stats[id];
-                for (i=0; i<args->files->n_smpl; i++)
+                int na = 0, in = 0, out = 0;
+                if ( args->exons )
                 {
-                    int na  = stats->smpl_frm_shifts[i*3 + 0];
-                    int in  = stats->smpl_frm_shifts[i*3 + 1];
-                    int out = stats->smpl_frm_shifts[i*3 + 2];
-                    printf("PSI\t%d\t%s\t%d\t%d\t%d\t%.2f\n", id,args->files->samples[i], in,out,na,in+out?1.0*out/(in+out):0);
+                    na  = stats->smpl_frm_shifts[i*3 + 0];
+                    in  = stats->smpl_frm_shifts[i*3 + 1];
+                    out = stats->smpl_frm_shifts[i*3 + 2];
                 }
+                int nhom = stats->smpl_indel_homs[i];
+                int nhet = stats->smpl_indel_hets[i];
+                printf("PSI\t%d\t%s\t%d\t%d\t%d\t%.2f\t%d\t%d\n", id,args->files->samples[i], in,out,na,in+out?1.0*out/(in+out):0,nhet,nhom);
             }
         }
 

From eee5780494c9716df2d99ec50bc4b347e638d843 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 10 Mar 2015 14:22:46 +0000
Subject: [PATCH 044/211] gtcheck: switch automatically to -G99 at ALT=. sites
 in absence of PLs

---
 vcfgtcheck.c | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/vcfgtcheck.c b/vcfgtcheck.c
index e3f03cc94..ac45e122f 100644
--- a/vcfgtcheck.c
+++ b/vcfgtcheck.c
@@ -408,8 +408,18 @@ static void check_gt(args_t *args)
         if ( !fake_pls )
         {
             if ( (npl=bcf_get_format_int32(args->sm_hdr, sm_line, "PL", &args->pl_arr, &args->npl_arr)) <= 0 )
-                error("PL not present at %s:%d?", args->sm_hdr->id[BCF_DT_CTG][sm_line->rid].key, sm_line->pos+1);
-            npl /= bcf_hdr_nsamples(args->sm_hdr);
+            {
+                if ( sm_line->n_allele==1 )
+                {
+                    // PL values may not be present when ALT=. (mpileup/bcftools output), in that case 
+                    // switch automatically to GT at these sites
+                    npl = fake_PLs(args, args->sm_hdr, sm_line);
+                }
+                else
+                    error("PL not present at %s:%d?\n", args->sm_hdr->id[BCF_DT_CTG][sm_line->rid].key, sm_line->pos+1);
+            }
+            else
+                npl /= bcf_hdr_nsamples(args->sm_hdr);
         }
         else
             npl = fake_PLs(args, args->sm_hdr, sm_line);

From 7e15f83ae728f71c87f32b3d68e231f16022d182 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 10 Mar 2015 14:31:37 +0000
Subject: [PATCH 045/211] gtcheck: more informative description of discordance
 per-site

---
 vcfgtcheck.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/vcfgtcheck.c b/vcfgtcheck.c
index ac45e122f..cbfba2510 100644
--- a/vcfgtcheck.c
+++ b/vcfgtcheck.c
@@ -99,7 +99,7 @@ static void plot_check(args_t *args, char *target_sample, char *query_sample)
             "fig,ax1 = plt.subplots(figsize=(8,5))\n"
             "ax2 = ax1.twinx()\n"
             "plots  = ax1.plot([x[0] for x in dat],'o-', ms=3, color='g', mec='g', label='Discordance (total)')\n"
-            "plots += ax1.plot([x[1] for x in dat], '^', ms=3, color='r', mec='r', label='Discordance (per site)')\n"
+            "plots += ax1.plot([x[1] for x in dat], '^', ms=3, color='r', mec='r', label='Discordance (avg per site)')\n"
             "plots += ax2.plot([x[2] for x in dat],'v', ms=3, color='k', label='Number of sites')\n"
             "if iq!=-1:\n"
             "   ax1.plot([iq],[dat[iq][0]],'o',color='orange', ms=9)\n"
@@ -496,7 +496,7 @@ static void check_gt(args_t *args)
     for (i=0; i<nsamples; i++) p[i] = &args->lks[i];
     qsort(p, nsamples, sizeof(int*), cmp_doubleptr);
 
-    fprintf(fp, "# [1]CN\t[2]Discordance with %s (total)\t[3]Discordance (score per site)\t[4]Number of sites compared\t[5]Sample\t[6]Sample ID\n", args->sm_hdr->samples[query_isample]);
+    fprintf(fp, "# [1]CN\t[2]Discordance with %s (total)\t[3]Discordance (avg score per site)\t[4]Number of sites compared\t[5]Sample\t[6]Sample ID\n", args->sm_hdr->samples[query_isample]);
     for (i=0; i<nsamples; i++)
     {
         int idx = p[i] - args->lks;

From 255ee9a151cf7ca23ff6cf6f294f2d89dac48ea6 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 13 May 2015 10:16:50 +0100
Subject: [PATCH 046/211] Support for -i/-e filtering in vcfstats

For consistency, changed existing -i/-e in vcfstats to -I/-E.

[NEWS]
* stats: -i/-e short options changed to -I/-E to accommodate the
  filtering -i/-e (--include/--exclude) options used in other tools
---
 doc/bcftools.txt | 12 ++++++++--
 vcfstats.c       | 60 ++++++++++++++++++++++++++++++++++++++----------
 2 files changed, 58 insertions(+), 14 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 574ac7ef5..027cb4b7e 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1439,7 +1439,11 @@ columns.
 *--debug*::
     produce verbose per-site and per-sample output
 
-*-e, --exons* 'file.gz'::
+*-e, --exclude* 'EXPRESSION'::
+    exclude sites for which 'EXPRESSION' is true. For valid expressions see
+    *<<expressions,EXPRESSIONS>>*.
+
+*-E, --exons* 'file.gz'::
     tab-delimited file with exons for indel frameshifts statistics. The columns
     of the file are CHR, FROM, TO, with 1-based, inclusive, positions. The file
     is BGZF-compressed and indexed with tabix
@@ -1453,7 +1457,11 @@ columns.
 *-F, --fasta-ref* 'ref.fa'::
     faidx indexed reference sequence file to determine INDEL context
 
-*-i, --split-by-ID*::
+*-i, --include* 'EXPRESSION'::
+    include only sites for which 'EXPRESSION' is true. For valid expressions see
+    *<<expressions,EXPRESSIONS>>*.
+
+*-I, --split-by-ID*::
     collect stats separately for sites which have the ID column set ("known
     sites") or which do not have the ID column set ("novel sites").
 
diff --git a/vcfstats.c b/vcfstats.c
index a207ccc53..578be7bce 100644
--- a/vcfstats.c
+++ b/vcfstats.c
@@ -1,6 +1,6 @@
 /*  vcfstats.c -- Produces stats which can be plotted using plot-vcfstats.
 
-    Copyright (C) 2012-2014 Genome Research Ltd.
+    Copyright (C) 2012-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -38,6 +38,11 @@ THE SOFTWARE.  */
 #include <htslib/faidx.h>
 #include <inttypes.h>
 #include "bcftools.h"
+#include "filter.h"
+
+// Logic of the filters: include or exclude sites which match the filters?
+#define FLT_INCLUDE 1
+#define FLT_EXCLUDE 2
 
 #define HWE_STATS 1
 #define QUAL_STATS 1
@@ -146,6 +151,11 @@ typedef struct
     char **argv, *exons_fname, *regions_list, *samples_list, *targets_list;
     int argc, verbose_sites, first_allele_only, samples_is_file;
     int split_by_id, nstats;
+
+    filter_t *filter[2];
+    char *filter_str;
+    int filter_logic;   // include or exclude sites which match the filters? One of FLT_INCLUDE/FLT_EXCLUDE
+
     // Per Sample r working data arrays of size equal to number of samples
     smpl_r_t* smpl_r_snps;
     smpl_r_t* smpl_r_indels;
@@ -388,6 +398,13 @@ static void init_stats(args_t *args)
     args->nstats = args->files->nreaders==1 ? 1 : 3;
     if ( args->split_by_id ) args->nstats = 2;
 
+    if ( args->filter_str )
+    {
+        args->filter[0] = filter_init(bcf_sr_get_header(args->files,0), args->filter_str);
+        if ( args->files->nreaders==2 )
+            args->filter[1] = filter_init(bcf_sr_get_header(args->files,1), args->filter_str);
+    }
+
     // AF corresponds to AC but is more robust for mixture of haploid and diploid GTs
     args->m_af = 101;
     for (i=0; i<args->files->nreaders; i++)
@@ -548,6 +565,8 @@ static void destroy_stats(args_t *args)
     free(args->smpl_r_snps);
     free(args->smpl_r_indels);
     if (args->indel_ctx) indel_ctx_destroy(args->indel_ctx);
+    if (args->filter[0]) filter_destroy(args->filter[0]);
+    if (args->filter[1]) filter_destroy(args->filter[1]);
 }
 
 static void init_iaf(args_t *args, bcf_sr_t *reader)
@@ -1011,15 +1030,26 @@ static void do_vcf_stats(args_t *args)
     {
         bcf_sr_t *reader = NULL;
         bcf1_t *line = NULL;
-        int ret = 0, i;
+        int ret = 0, i, pass = 1;
         for (i=0; i<files->nreaders; i++)
         {
             if ( !bcf_sr_has_line(files,i) ) continue;
+            if ( args->filter[i] )
+            {
+                int is_ok = filter_test(args->filter[i], bcf_sr_get_line(files,i), NULL);
+                if ( args->filter_logic & FLT_EXCLUDE ) is_ok = is_ok ? 0 : 1;
+                if ( !is_ok ) { pass = 0; break; }
+            }
             ret |= 1<<i;
-            if ( reader ) continue;
-            reader = &files->readers[i];
-            line = files->readers[i].buffer[0];
+            if ( !reader )
+            {
+                reader = &files->readers[i];
+                line = bcf_sr_get_line(files,i);
+            }
+
         }
+        if ( !pass ) continue;
+
         int line_type = bcf_get_variant_types(line);
         init_iaf(args, reader);
 
@@ -1441,10 +1471,12 @@ static void usage(void)
     fprintf(stderr, "    -1, --1st-allele-only              include only 1st allele at multiallelic sites\n");
     fprintf(stderr, "    -c, --collapse <string>            treat as identical records with <snps|indels|both|all|some|none>, see man page for details [none]\n");
     fprintf(stderr, "    -d, --depth <int,int,int>          depth distribution: min,max,bin size [0,500,1]\n");
-    fprintf(stderr, "    -e, --exons <file.gz>              tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)\n");
+    fprintf(stderr, "    -e, --exclude <expr>               exclude sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -E, --exons <file.gz>              tab-delimited file with exons for indel frameshifts (chr,from,to; 1-based, inclusive, bgzip compressed)\n");
     fprintf(stderr, "    -f, --apply-filters <list>         require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
     fprintf(stderr, "    -F, --fasta-ref <file>             faidx indexed reference sequence file to determine INDEL context\n");
-    fprintf(stderr, "    -i, --split-by-ID                  collect stats for sites with ID separately (known vs novel)\n");
+    fprintf(stderr, "    -i, --include <expr>               select sites for which the expression is true (see man page for details)\n");
+    fprintf(stderr, "    -I, --split-by-ID                  collect stats for sites with ID separately (known vs novel)\n");
     fprintf(stderr, "    -r, --regions <region>             restrict to comma-separated list of regions\n");
     fprintf(stderr, "    -R, --regions-file <file>          restrict to regions listed in a file\n");
     fprintf(stderr, "    -s, --samples <list>               list of samples for sample stats, \"-\" to include all samples\n");
@@ -1469,6 +1501,8 @@ int main_vcfstats(int argc, char *argv[])
     static struct option loptions[] =
     {
         {"1st-allele-only",0,0,'1'},
+        {"include",1,0,'i'},
+        {"exclude",1,0,'e'},
         {"help",0,0,'h'},
         {"collapse",1,0,'c'},
         {"regions",1,0,'r'},
@@ -1476,17 +1510,17 @@ int main_vcfstats(int argc, char *argv[])
         {"verbose",0,0,'v'},
         {"depth",1,0,'d'},
         {"apply-filters",1,0,'f'},
-        {"exons",1,0,'e'},
+        {"exons",1,0,'E'},
         {"samples",1,0,'s'},
         {"samples-file",1,0,'S'},
-        {"split-by-ID",0,0,'i'},
+        {"split-by-ID",0,0,'I'},
         {"targets",1,0,'t'},
         {"targets-file",1,0,'T'},
         {"fasta-ref",1,0,'F'},
         {"user-tstv",1,0,'u'},
         {0,0,0,0}
     };
-    while ((c = getopt_long(argc, argv, "hc:r:R:e:s:S:d:it:T:F:f:1u:v",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "hc:r:R:e:s:S:d:i:t:T:F:f:1u:vIE:",loptions,NULL)) >= 0) {
         switch (c) {
             case 'u': add_user_stats(args,optarg); break;
             case '1': args->first_allele_only = 1; break;
@@ -1513,10 +1547,12 @@ int main_vcfstats(int argc, char *argv[])
             case 'f': args->files->apply_filters = optarg; break;
             case 'r': args->regions_list = optarg; break;
             case 'R': args->regions_list = optarg; regions_is_file = 1; break;
-            case 'e': args->exons_fname = optarg; break;
+            case 'E': args->exons_fname = optarg; break;
             case 's': args->samples_list = optarg; break;
             case 'S': args->samples_list = optarg; args->samples_is_file = 1; break;
-            case 'i': args->split_by_id = 1; break;
+            case 'I': args->split_by_id = 1; break;
+            case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
+            case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);

From 0bde8e0eaa50c17614bcc2d54e28f279bdff2ae6 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 17 Jul 2015 13:34:18 +0100
Subject: [PATCH 047/211] remove install dependency on asciidoc

doc/bcftools.1 exists and is updated by the maintainers from the
bcftools.txt asciidoc, so there is no need to build this file
for installation

add some documentation to the Makefile to explain docs dependency
on asciidoc

Fixes #289
---
 Makefile | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index bb75b8503..15eef3c25 100644
--- a/Makefile
+++ b/Makefile
@@ -178,9 +178,15 @@ doc/bcftools.1: doc/bcftools.txt
 doc/bcftools.html: doc/bcftools.txt
 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format xhtml bcftools.txt
 
+# make docs target depends the a2x asciidoc program
 docs: doc/bcftools.1 doc/bcftools.html
 
-install: $(PROG) doc/bcftools.1
+# To avoid an install dependency on asciidoc, the make install target
+# does not depend on doc/bcftools.1
+# bcftools.1 is a generated file from the asciidoc bcftools.txt file.
+# Since there is no make dependency, bcftools.1 can be out-of-date and
+# make docs can be run to update if asciidoc is available
+install: $(PROG)
 	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
 	$(INSTALL_PROGRAM) $(PROG) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)
 	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)

From c4a53ac222735905e01f1ab0a6c22fc46de17c27 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 28 Jul 2015 16:01:11 +0100
Subject: [PATCH 048/211] update man docs

---
 doc/bcftools.1    | 51 ++++++++++++++++++++++++++++++++++++++++-------
 doc/bcftools.html | 25 +++++++++++++++++------
 doc/bcftools.txt  |  4 ++--
 3 files changed, 65 insertions(+), 15 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index a56a6b0ba..1269ac051 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-07-28 09:49 BST
+.\"      Date: 2015-07-28 16:00 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-07\-28 09:49 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-07\-28 16:00 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-07\-28 09:49 BST\fR and refers to bcftools git version \fB1\&.2\-74\-g6ccecd1+\fR\&.
+This manual page was last updated \fB2015\-07\-28 16:00 BST\fR and refers to bcftools git version \fB1\&.2\-96\-g5d52a36+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -2531,7 +2531,15 @@ ranges of depth distribution: min, max, and size of the bin
 produce verbose per\-site and per\-sample output
 .RE
 .PP
-\fB\-e, \-\-exons\fR \fIfile\&.gz\fR
+\fB\-e, \-\-exclude\fR \fIEXPRESSION\fR
+.RS 4
+exclude sites for which
+\fIEXPRESSION\fR
+is true\&. For valid expressions see
+\fBEXPRESSIONS\fR\&.
+.RE
+.PP
+\fB\-E, \-\-exons\fR \fIfile\&.gz\fR
 .RS 4
 tab\-delimited file with exons for indel frameshifts statistics\&. The columns of the file are CHR, FROM, TO, with 1\-based, inclusive, positions\&. The file is BGZF\-compressed and indexed with tabix
 .RE
@@ -2557,7 +2565,15 @@ see
 faidx indexed reference sequence file to determine INDEL context
 .RE
 .PP
-\fB\-i, \-\-split\-by\-ID\fR
+\fB\-i, \-\-include\fR \fIEXPRESSION\fR
+.RS 4
+include only sites for which
+\fIEXPRESSION\fR
+is true\&. For valid expressions see
+\fBEXPRESSIONS\fR\&.
+.RE
+.PP
+\fB\-I, \-\-split\-by\-ID\fR
 .RS 4
 collect stats separately for sites which have the ID column set ("known sites") or which do not have the ID column set ("novel sites")\&.
 .RE
@@ -3014,13 +3030,34 @@ FlagA=1 && FlagB=0
 .sp -1
 .IP \(bu 2.3
 .\}
-"\&." to test missing values in INFO tags
+"\&." to test missing values
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+DP="\&.", DP!="\&.", ALT="\&."
+.fi
+.if n \{\
+.RE
+.\}
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+missing genotypes can be matched regardless of phase and ploidy ("\&.|\&.", "\&./\&.", "\&.") using this expression
 .sp
 .if n \{\
 .RS 4
 .\}
 .nf
-DP="\&.", DP!="\&."
+GT="\&."
 .fi
 .if n \{\
 .RE
diff --git a/doc/bcftools.html b/doc/bcftools.html
index 9919479fb..2202b9f30 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25161584"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp205456"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
 work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-07-28 09:49 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-74-g6ccecd1+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-07-28 16:00 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-96-g5d52a36+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -1379,7 +1379,12 @@
 </span></dt><dd>
     produce verbose per-site and per-sample output
 </dd><dt><span class="term">
-<span class="strong"><strong>-e, --exons</strong></span> <span class="emphasis"><em>file.gz</em></span>
+<span class="strong"><strong>-e, --exclude</strong></span> <span class="emphasis"><em>EXPRESSION</em></span>
+</span></dt><dd>
+    exclude sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see
+    <span class="strong"><strong><a class="link" href="#expressions" title="EXPRESSIONS">EXPRESSIONS</a></strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>-E, --exons</strong></span> <span class="emphasis"><em>file.gz</em></span>
 </span></dt><dd>
     tab-delimited file with exons for indel frameshifts statistics. The columns
     of the file are CHR, FROM, TO, with 1-based, inclusive, positions. The file
@@ -1393,7 +1398,12 @@
 </span></dt><dd>
     faidx indexed reference sequence file to determine INDEL context
 </dd><dt><span class="term">
-<span class="strong"><strong>-i, --split-by-ID</strong></span>
+<span class="strong"><strong>-i, --include</strong></span> <span class="emphasis"><em>EXPRESSION</em></span>
+</span></dt><dd>
+    include only sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see
+    <span class="strong"><strong><a class="link" href="#expressions" title="EXPRESSIONS">EXPRESSIONS</a></strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>-I, --split-by-ID</strong></span>
 </span></dt><dd>
     collect stats separately for sites which have the ID column set ("known
     sites") or which do not have the ID column set ("novel sites").
@@ -1601,8 +1611,11 @@
 FILTER, QUAL, ID, REF, ALT[0]</pre></li><li class="listitem"><p class="simpara">
 1 (or 0) to test the presence (or absence) of a flag
 </p><pre class="literallayout">FlagA=1 &amp;&amp; FlagB=0</pre></li><li class="listitem"><p class="simpara">
-"." to test missing values in INFO tags
-</p><pre class="literallayout">DP=".", DP!="."</pre></li><li class="listitem"><p class="simpara">
+"." to test missing values
+</p><pre class="literallayout">DP=".", DP!=".", ALT="."</pre></li><li class="listitem"><p class="simpara">
+missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".")
+using this expression
+</p><pre class="literallayout">GT="."</pre></li><li class="listitem"><p class="simpara">
 TYPE for variant type in REF,ALT columns (indel,snp,mnp,ref,other)
 </p><pre class="literallayout">TYPE="indel" | TYPE="snp"</pre></li><li class="listitem"><p class="simpara">
 array subscripts, "*" for any field
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 027cb4b7e..7fa3361f3 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1682,9 +1682,9 @@ These filtering expressions are accepted by *<<annotate,annotate>>*,
 
         FlagA=1 && FlagB=0
 
-* "." to test missing values in INFO tags
+* "." to test missing values
 
-        DP=".", DP!="."
+        DP=".", DP!=".", ALT="."
 
 * missing genotypes can be matched regardless of phase and ploidy (".|.", "./.", ".")
 using this expression

From 21e745acd9fe61c5844d2c63bc1a1eee6f827ad5 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 28 May 2015 10:41:32 +0100
Subject: [PATCH 049/211] call: new ploidy handling

---
 doc/bcftools.txt |  47 +++++-
 ploidy.c         |  22 ++-
 ploidy.h         |  14 +-
 vcfcall.c        | 406 ++++++++++++++++++++++++++++++-----------------
 4 files changed, 329 insertions(+), 160 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 7fa3361f3..0f6b43efd 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -194,8 +194,29 @@ specific commands to see if they apply.
     File of sample names to include or exclude if prefixed with "&#94;".
     One sample per line.
     The command *<<call,bcftools call>>* accepts an optional second
-    column indicating ploidy (0, 1 or 2) and can parse also PED files.
-    With *<<call,bcftools call>> -C* 'trio', PED file is expected.
+    column indicating ploidy (0, 1 or 2) or sex (as defined by
+    *<<ploidy,--ploidy>>*, for example "F" or "M"), and can parse also PED
+    files. If the second column is not present,
+    the sex "F" is assumed.
+    With *<<call,bcftools call>> -C* 'trio', PED file is expected. File
+    formats examples:
+----
+    sample1    1
+    sample2    2
+    sample3    2
+
+  or
+
+    sample1    M
+    sample2    F
+    sample3    F
+
+  or a .ped file (here is shown a minimum working example, the first column is 
+  ignored and the last indicates sex: 1=male, 2=female)
+
+    ignored daughterA fatherA motherA 2
+    ignored sonB fatherB motherB 1
+----
 
 *-t, --targets* \[&#94;]'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
     Similar as *-r, --regions*, but the next position is accessed by streaming the
@@ -370,6 +391,28 @@ demand. The original calling model can be invoked with the *-c* option.
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
+*--ploidy* 'ASSEMBLY'['?'][[ploidy]]::
+    predefined ploidy, use 'list' (or any other unused word) to print a list
+    of all predefined assemblies. Append a question mark to print the actual
+    definition. See also *--ploidy-file*.
+
+*--ploidy-file* 'FILE'::
+    ploidy definition given as a space/tab-delimited list of
+    CHROM, FROM, TO, SEX, PLOIDY. The SEX codes are arbitrary and
+    correspond to the ones used by *<<samples_file,--samples-file>>*. 
+    The default ploidy can be given using the starred records (see
+    below), unlisted regions have ploidy 2. The default ploidy definition is
+----
+    X 1 60000 M 1
+    X 2699521 154931043 M 1
+    Y 1 59373566 M 1
+    Y 1 59373566 F 0
+    MT 1 16569 M 1
+    MT 1 16569 F 1
+    *  * *     M 2
+    *  * *     F 2
+----
+
 *-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
     see *<<common_options,Common Options>>*
 
diff --git a/ploidy.c b/ploidy.c
index 44dac77f8..3d3027aa2 100644
--- a/ploidy.c
+++ b/ploidy.c
@@ -33,12 +33,20 @@ struct _ploidy_t
 {
     int nsex, msex;     // number of genders, m:number of allocated elements in id2sex array
     int dflt, min, max; // ploidy: default, min and max (only explicitly listed)
+    int *sex2dflt;
     regidx_t *idx;
     void *sex2id;
     char **id2sex;
     kstring_t tmp_str;
 };
 
+typedef struct
+{
+    int sex, ploidy;
+}
+sex_ploidy_t;
+
+
 regidx_t *ploidy_regions(ploidy_t *ploidy)
 {
     return ploidy->idx;
@@ -78,6 +86,8 @@ int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, v
         hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex);
         ploidy->id2sex[ploidy->nsex-1] = strdup(ploidy->tmp_str.s);
         sp->sex = khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
+        ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
+        ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt;
     }
 
     ss = se;
@@ -88,6 +98,15 @@ int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, v
     if ( sp->ploidy < ploidy->min ) ploidy->min = sp->ploidy;
     if ( sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy;
 
+    // Special case, chr="*" stands for a default value
+    ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( ss[0]=='*' && (!ss[1] || isspace(ss[1])) ) 
+    {
+        ploidy->sex2dflt[ploidy->nsex-1] = sp->ploidy;
+        return -1;
+    }
+
     return 0;
 }
 
@@ -141,6 +160,7 @@ void ploidy_destroy(ploidy_t *ploidy)
     if ( ploidy->idx ) regidx_destroy(ploidy->idx);
     free(ploidy->id2sex);
     free(ploidy->tmp_str.s);
+    free(ploidy->sex2dflt);
     free(ploidy);
 }
 
@@ -157,7 +177,7 @@ int ploidy_query(ploidy_t *ploidy, char *seq, int pos, int *sex2ploidy, int *min
         if ( min ) *min = ploidy->dflt;
         if ( max ) *max = ploidy->dflt;
         if ( sex2ploidy )
-            for (i=0; i<ploidy->nsex; i++) sex2ploidy[i] = ploidy->dflt;
+            for (i=0; i<ploidy->nsex; i++) sex2ploidy[i] = ploidy->sex2dflt[i];
         return 0;
     }
 
diff --git a/ploidy.h b/ploidy.h
index b505eb95f..6deef737f 100644
--- a/ploidy.h
+++ b/ploidy.h
@@ -40,13 +40,16 @@
         ploidy_destroy(pld);
 
     An example of ploidy file format follows. The coordinates are 1-based and
-    inclusive:
+    inclusive. The "*" records define the default ploidy for each sex. If not
+    present, the default_ploidy passed to ploidy_init is used instead:
         X 1 60000 M 1
         X 2699521 154931043 M 1
         Y 1 59373566 M 1
         Y 1 59373566 F 0
         MT 1 16569 M 1
         MT 1 16569 F 1
+        *  * *     M 2
+        *  * *     F 2
 */
 
 #ifndef __PLOIDY_H__
@@ -56,17 +59,10 @@
 
 typedef struct _ploidy_t ploidy_t;
 
-typedef struct
-{
-    int sex, ploidy;
-}
-sex_ploidy_t;
-
-
 /*
  *  ploidy_init()
  *  @param fname:   input file name or NULL if default ploidy from example above should be used
- *  @param dflt:    default ploidy to use for unlisted regions
+ *  @param dflt:    default ploidy to use for unlisted regions (the '* * *' records have precedence).
  *
  *  Returns new structure on success or NULL on error.
  */
diff --git a/vcfcall.c b/vcfcall.c
index 1aad4662f..181f73ef5 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -34,10 +34,12 @@ THE SOFTWARE.  */
 #include <stdarg.h>
 #include <htslib/kfunc.h>
 #include <htslib/synced_bcf_reader.h>
+#include <htslib/khash_str2int.h>
 #include <ctype.h>
 #include "bcftools.h"
 #include "call.h"
 #include "prob1.h"
+#include "ploidy.h"
 
 void error(const char *format, ...);
 
@@ -73,6 +75,12 @@ typedef struct
     char *regions, *targets;    // regions to process
     int regions_is_file, targets_is_file;
 
+    char *samples_fname;
+    int samples_is_file;
+    int *sample2sex;    // mapping for ploidy. If negative, interpreted as -1*ploidy
+    int *sex2ploidy, *sex2ploidy_prev, nsex;
+    ploidy_t *ploidy;
+
     bcf1_t *missed_line;
     call_t aux;     // parameters and temporary data
     gvcf_t gvcf;
@@ -92,43 +100,96 @@ typedef struct
 }
 args_t;
 
-static family_t *get_family(family_t *fam, int nfam, char *name)
+static char **add_sample(void *name2idx, char **lines, int *nlines, int *mlines, char *name, char sex, int *ith)
 {
-    int i;
-    for (i=0; i<nfam; i++)
-    {
-        if ( !strcmp(fam[i].name, name) ) return &fam[i];
-    }
-    return NULL;
+    int ret = khash_str2int_get(name2idx, name, ith);
+    if ( ret==0 ) return lines;
+
+    hts_expand(char*,(*nlines+1),*mlines,lines);
+    int len = strlen(name);
+    lines[*nlines] = (char*) malloc(len+3);
+    memcpy(lines[*nlines],name,len);
+    lines[*nlines][len]   = ' ';
+    lines[*nlines][len+1] = sex;
+    lines[*nlines][len+2] = 0;
+    *ith = *nlines;
+    (*nlines)++;
+    khash_str2int_set(name2idx, strdup(name), *ith);
+    return lines;
 }
 
-static char **add_sample(char **sam, int *n, int *m, char *name, int ploidy, int *ith)
+typedef struct
 {
-    int i;
-    for (i=0; i<*n; i++)
+    const char *alias, *about, *ploidy;
+}
+ploidy_predef_t;
+
+static ploidy_predef_t ploidy_predefs[] =
+{
+    { .alias  = "GRCh37",
+      .about  = "Human Genome reference assembly GRCh37 / hg19",
+      .ploidy =
+          "X 1 60000 M 1\n"
+          "X 2699521 154931043 M 1\n"
+          "Y 1 59373566 M 1\n"
+          "Y 1 59373566 F 0\n"
+          "MT 1 16569 M 1\n"
+          "MT 1 16569 F 1\n"
+          "chrX 1 60000 M 1\n"
+          "chrX 2699521 154931043 M 1\n"
+          "chrY 1 59373566 M 1\n"
+          "chrY 1 59373566 F 0\n"
+          "chrM 1 16569 M 1\n"
+          "chrM 1 16569 F 1\n"
+          "*  * *     M 2\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "GRCh38",
+      .about  = "Human Genome reference assembly GRCh38 / hg38, plain chromosome naming (1,2,3,..)",
+      .ploidy =
+          "X 1 9999 M 1\n"
+          "X 2781480 155701381 M 1\n"
+          "Y 1 57227415 M 1\n"
+          "Y 1 57227415 F 0\n"
+          "MT 1 16569 M 1\n"
+          "MT 1 16569 F 1\n"
+          "chrX 1 9999 M 1\n"
+          "chrX 2781480 155701381 M 1\n"
+          "chrY 1 57227415 M 1\n"
+          "chrY 1 57227415 F 0\n"
+          "chrM 1 16569 M 1\n"
+          "chrM 1 16569 F 1\n"
+          "*  * *     M 2\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "X",
+      .about  = "Treat male samples as haploid and female as diploid regardless of the chromosome name",
+      .ploidy =
+          "*  * *     M 1\n"
+          "*  * *     F 2\n"
+    },
+    { .alias  = "Y",
+      .about  = "Treat male samples as haploid and female as no-copy, regardless of the chromosome name",
+      .ploidy =
+          "*  * *     M 1\n"
+          "*  * *     F 0\n"
+    },
     {
-        if ( !strcmp(sam[i], name) )
-        {
-            *ith = i;
-            return sam;
-        }
+        .alias  = NULL,
+        .about  = NULL,
+        .ploidy = NULL,
     }
-    hts_expand(char*,(*n+1),*m,sam);
-    int len = strlen(name);
-    sam[*n] = (char*) malloc(len+2);
-    memcpy(sam[*n],name,len+1);
-    sam[*n][len+1] = ploidy;
-    *ith = *n;
-    (*n)++;
-    return sam;
-}
+};
 
-static char **parse_ped_samples(call_t *call, char **vals, int _n)
+// only 5 columns are required and the first is ignored:
+//  ignored,sample,father(or 0),mother(or 0),sex(1=M,2=F)
+static char **parse_ped_samples(call_t *call, char **vals, int nvals, int *nsmpl)
 {
-    int i, j, max = 0, n = 0;
-    kstring_t str = {0,0,0};
-    char **sam = NULL;
-    for (i=0; i<_n; i++)
+    int i, j, mlines = 0, nlines = 0;
+    kstring_t str = {0,0,0}, fam_str = {0,0,0};
+    void *name2idx = khash_str2int_init();
+    char **lines = NULL;
+    for (i=0; i<nvals; i++)
     {
         str.l = 0;
         kputs(vals[i], &str);
@@ -149,52 +210,38 @@ static char **parse_ped_samples(call_t *call, char **vals, int _n)
         }
         if ( j!=5 ) break;
 
-        family_t *fam = get_family(call->fams, call->nfams, str.s);
-        if ( !fam )
+        char sex = col_ends[3][1]=='1' ? 'M' : 'F';
+        lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[0]+1, sex, &j);
+        if ( strcmp(col_ends[1]+1,"0") && strcmp(col_ends[2]+1,"0") )   // father and mother
         {
             call->nfams++;
             hts_expand(family_t, call->nfams, call->mfams, call->fams);
-            fam = &call->fams[call->nfams-1];
-            fam->name = strdup(str.s);
-            for (j=0; j<3; j++) fam->sample[j] = -1;
-        }
-
-        int ploidy = 2;
-        if ( call->flag & (CALL_CHR_X|CALL_CHR_Y) )
-        {
-            if ( col_ends[3][1]=='1' ) ploidy = 1; // male: one chrX and one chrY copy
-            else
-                ploidy = call->flag & CALL_CHR_X ? 2 : 0; // female: two chrX copies, no chrY
-        }
-        sam = add_sample(sam, &n, &max, col_ends[0]+1, ploidy, &j);
-        if ( strcmp(col_ends[1]+1,"0") )    // father
-        {
-            if ( fam->sample[CHILD]>=0 ) error("Multiple childs in %s [%s,%s]\n", str.s, sam[j],sam[fam->sample[CHILD]]);
-            fam->sample[CHILD] = j;
-            if ( fam->sample[FATHER]>=0 ) error("Two fathers in %s?\n", str.s);
-            sam = add_sample(sam, &n, &max, col_ends[1]+1, call->flag & (CALL_CHR_X|CALL_CHR_Y) ? 1 : 2, &fam->sample[FATHER]);
-        }
-        if ( strcmp(col_ends[2]+1,"0") )    // mother
-        {
-            if ( fam->sample[MOTHER]>=0 ) error("Two mothers in %s?\n", str.s);
-            sam = add_sample(sam, &n, &max, col_ends[2]+1, call->flag & CALL_CHR_Y ? 0 : 2, &fam->sample[MOTHER]);
+            family_t *fam = &call->fams[call->nfams-1];
+            fam_str.l = 0;
+            ksprintf(&fam_str,"father=%s, mother=%s, child=%s", col_ends[1]+1,col_ends[2]+1,col_ends[0]+1);
+            fam->name = strdup(fam_str.s);
+
+            if ( !khash_str2int_has_key(name2idx, col_ends[1]+1) )
+                lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[1]+1, 'M', &fam->sample[FATHER]);
+            if ( !khash_str2int_has_key(name2idx, col_ends[2]+1) )
+                lines = add_sample(name2idx, lines, &nlines, &mlines, col_ends[2]+1, 'F', &fam->sample[MOTHER]);
+
+            khash_str2int_get(name2idx, col_ends[0]+1, &fam->sample[CHILD]);
+            khash_str2int_get(name2idx, col_ends[1]+1, &fam->sample[FATHER]);
+            khash_str2int_get(name2idx, col_ends[2]+1, &fam->sample[MOTHER]);
         }
     }
     free(str.s);
+    free(fam_str.s);
+    khash_str2int_destroy_free(name2idx);
 
-    if ( i!=_n ) // not a ped file
+    if ( i!=nvals ) // not a ped file
     {
-        if ( i>0 ) error("Could not parse the samples, thought it was PED format, some rows have 5 columns?!\n");
+        if ( i>0 ) error("Could not parse samples, not a PED format.\n");
         return NULL;
     }
-    assert( n==_n );
-    for (i=0; i<call->nfams; i++)
-        assert( call->fams[i].sample[0]>=0 && call->fams[i].sample[1]>=0 && call->fams[i].sample[2]>=0 ); // multiple childs, not a trio
-
-    // for (i=0; i<call->nfams; i++)
-    //     fprintf(stderr,"mother=%s, father=%s, child=%s\n", sam[call->fams[i].sample[MOTHER]],sam[call->fams[i].sample[FATHER]],sam[call->fams[i].sample[CHILD]]);
-
-    return sam;
+    *nsmpl = nlines;
+    return lines;
 }
 
 
@@ -203,44 +250,80 @@ static char **parse_ped_samples(call_t *call, char **vals, int _n)
  *  Alternatively, if no such file exists, the file name is interpreted
  *  as a comma-separated list of samples. When ploidy is not present,
  *  the default ploidy 2 is assumed.
- *
- *  Returns an array of sample names, where the byte value just after \0
- *  indicates the ploidy.
  */
-static char **read_samples(call_t *call, const char *fn, int is_file, int *_n)
+static void set_samples(args_t *args, const char *fn, int is_file)
 {
-    int i, n;
-    char **vals = hts_readlist(fn, is_file, &n);
-    if ( !vals ) error("Could not read the file: %s\n", fn);
+    int i, nlines;
+    char **lines = hts_readlist(fn, is_file, &nlines);
+    if ( !lines ) error("Could not read the file: %s\n", fn);
+
+    int nsmpls;
+    char **smpls = parse_ped_samples(&args->aux, lines, nlines, &nsmpls);
+    if ( smpls )
+    {
+        for (i=0; i<nlines; i++) free(lines[i]);
+        free(lines);
+        lines = smpls;
+        nlines = nsmpls;
+    }
+
+    args->samples_map = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr)); // for subsetting
+    args->sample2sex  = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
+    int dflt_sex_id = ploidy_add_sex(args->ploidy, "F");
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) args->sample2sex[i] = dflt_sex_id;
+
+    int *old2new = (int*) malloc(sizeof(int)*bcf_hdr_nsamples(args->aux.hdr));
+    for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++) old2new[i] = -1;
 
-    char **smpls = parse_ped_samples(call, vals, n);
-    if ( !smpls )
+    int nsmpl = 0, map_needed = 0;
+    for (i=0; i<nlines; i++)
     {
-        smpls = (char**) malloc(sizeof(char*)*n);
-        for (i=0; i<n; i++)
+        char *ss = lines[i];
+        while ( *ss && isspace(*ss) ) ss++;
+        if ( !*ss ) error("Could not parse: %s\n", lines[i]);
+        if ( *ss=='#' ) continue;
+        char *se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        char x = *se, *xptr = se; *se = 0;
+
+        int ismpl = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, ss);
+        if ( ismpl < 0 ) { fprintf(stderr,"Warning: No such sample in the VCF: %s\n",ss); continue; }
+
+        ss = se+1;
+        while ( *ss && isspace(*ss) ) ss++;
+        if ( !*ss ) ss = "2";   // default ploidy
+        se = ss;
+        while ( *se && !isspace(*se) ) se++;
+        if ( se==ss ) { *xptr = x; error("Could not parse: \"%s\"\n", lines[i]); }
+
+        if ( ss[1]==0 && (ss[0]=='0' || ss[0]=='1' || ss[0]=='2') )
+            args->sample2sex[nsmpl] = -1*(ss[0]-'0');
+        else
+            args->sample2sex[nsmpl] = ploidy_add_sex(args->ploidy, ss);
+
+        if ( ismpl!=nsmpl ) map_needed = 1;
+        args->samples_map[nsmpl] = ismpl;
+        old2new[ismpl] = nsmpl;
+        nsmpl++;
+    }
+
+    for (i=0; i<args->aux.nfams; i++)
+    {
+        int j, nmiss = 0;
+        family_t *fam = &args->aux.fams[i];
+        for (j=0; j<3; j++)
         {
-            char *s = vals[i];
-            while ( *s && !isspace(*s) ) s++;
-            int len = s-vals[i];
-            smpls[i] = (char*) malloc(len+2);
-            strncpy(smpls[i],vals[i],len);
-            smpls[i][len] = 0;
-            while ( *s && isspace(*s) ) s++;
-            int x = 2;
-            if ( *s )
-            {
-                x = (int)s[0] - '0'; // Convert ASCII digit to decimal
-                if (x != 0 && x != 1 && x != 2) error("Ploidy can only be 0, 1 or 2: %s\n", vals[i]);
-            }
-            smpls[i][len+1] = x;
+            fam->sample[i] = old2new[fam->sample[i]];
+            if ( fam->sample[i]<0 ) nmiss++;
         }
+        assert( nmiss==0 || nmiss==3 );
     }
+    free(old2new);
 
-    for (i=0; i<n; i++) free(vals[i]);
-    free(vals);
+    if ( !map_needed ) { free(args->samples_map); args->samples_map = NULL; }
 
-    *_n = n;
-    return smpls;
+    args->nsamples = nsmpl;
+    args->samples = lines;
 }
 
 static void init_missed_line(args_t *args)
@@ -302,13 +385,29 @@ static void init_data(args_t *args)
             error("Failed to read the targets: %s\n", args->regions);
     }
 
-    int i;
     if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) ) error("Failed to open %s: %s\n", args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));
+    args->aux.hdr = bcf_sr_get_header(args->aux.srs,0);
 
-    if ( args->nsamples && args->nsamples != bcf_hdr_nsamples(args->aux.srs->readers[0].header) )
+    int i;
+    if ( args->samples_fname )
     {
-        args->samples_map = (int *) malloc(sizeof(int)*args->nsamples);
-        args->aux.hdr = bcf_hdr_subset(args->aux.srs->readers[0].header, args->nsamples, args->samples, args->samples_map);
+        set_samples(args, args->samples_fname, args->samples_is_file);
+        if ( args->aux.flag&CALL_CONSTR_TRIO )
+        {
+            if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname);
+            fprintf(stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams);
+        }
+        args->nsex = ploidy_nsex(args->ploidy);
+        args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int));
+        args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int));
+        args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
+        for (i=0; i<args->nsamples; i++) args->aux.ploidy[i] = 2;
+        for (i=0; i<args->nsex; i++) args->sex2ploidy_prev[i] = 2;
+    }
+
+    if ( args->samples_map )
+    {
+        args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map);
         if ( !args->aux.hdr ) error("Error occurred while subsetting samples\n");
         for (i=0; i<args->nsamples; i++)
             if ( args->samples_map[i]<0 ) error("No such sample: %s\n", args->samples[i]);
@@ -316,43 +415,12 @@ static void init_data(args_t *args)
     }
     else
     {
-        args->aux.hdr = bcf_hdr_dup(args->aux.srs->readers[0].header);
+        args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0));
         for (i=0; i<args->nsamples; i++)
             if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 )
                 error("No such sample: %s\n", args->samples[i]);
     }
 
-    // Reorder ploidy and family indexes to match mpileup's output and exclude samples which are not available
-    if ( args->aux.ploidy )
-    {
-        for (i=0; i<args->aux.nfams; i++)
-        {
-            int j;
-            for (j=0; j<3; j++)
-            {
-                int k = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, args->samples[ args->aux.fams[i].sample[j] ]);
-                if ( k<0 ) error("No such sample: %s\n", args->samples[ args->aux.fams[i].sample[j] ]);
-                args->aux.fams[i].sample[j] = k;
-            }
-        }
-        uint8_t *ploidy = (uint8_t*) calloc(bcf_hdr_nsamples(args->aux.hdr), 1);
-        for (i=0; i<args->nsamples; i++)    // i index in -s sample list
-        {
-            int j = bcf_hdr_id2int(args->aux.hdr, BCF_DT_SAMPLE, args->samples[i]);     // j index in the output VCF / subset VCF
-            if ( j<0 )
-            {
-                fprintf(stderr,"Warning: no such sample: \"%s\"\n", args->samples[i]);
-                continue;
-            }
-            ploidy[j] = args->aux.ploidy[i];
-        }
-        args->nsamples = bcf_hdr_nsamples(args->aux.hdr);
-        for (i=0; i<args->nsamples; i++)
-            assert( ploidy[i]==0 || ploidy[i]==1 || ploidy[i]==2 );
-        free(args->aux.ploidy);
-        args->aux.ploidy = ploidy;
-    }
-
     args->out_fh = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
 
@@ -400,11 +468,15 @@ static void destroy_data(args_t *args)
         free(args->aux.fams);
     }
     if ( args->missed_line ) bcf_destroy(args->missed_line);
+    ploidy_destroy(args->ploidy);
     if ( args->gvcf.line ) bcf_destroy(args->gvcf.line);
     free(args->gvcf.gt);
     free(args->gvcf.dp);
+    free(args->sex2ploidy);
+    free(args->sex2ploidy_prev);
     free(args->samples);
     free(args->samples_map);
+    free(args->sample2sex);
     free(args->aux.ploidy);
     bcf_hdr_destroy(args->aux.hdr);
     hts_close(args->out_fh);
@@ -455,6 +527,39 @@ static int parse_format_flag(const char *str)
 }
 
 
+ploidy_t *init_ploidy(char *alias)
+{
+    const ploidy_predef_t *pld = ploidy_predefs;
+
+    int detailed = 0, len = strlen(alias);
+    if ( alias[len-1]=='?' ) { detailed = 1; alias[len-1] = 0; }
+
+    while ( pld->alias && strcasecmp(alias,pld->alias) ) pld++;
+
+    if ( !pld->alias )
+    {
+        fprintf(stderr,"Predefined ploidies:\n");
+        pld = ploidy_predefs;
+        while ( pld->alias )
+        {
+            fprintf(stderr,"%s\n   .. %s\n\n", pld->alias,pld->about);
+            if ( detailed )
+                fprintf(stderr,"%s\n", pld->ploidy);
+            pld++;
+        }
+        fprintf(stderr,"Run as --ploidy <alias> (e.g. --ploidy GRCh37).\n");
+        fprintf(stderr,"To see the detailed ploidy definition, append a question mark (e.g. --ploidy GRCh37?).\n");
+        fprintf(stderr,"\n");
+        exit(-1);
+    }
+    else if ( detailed )
+    {
+        fprintf(stderr,"%s", pld->ploidy);
+        exit(-1);
+    }
+    return ploidy_init_string(pld->ploidy,2);
+}
+
 static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
@@ -468,6 +573,8 @@ static void usage(args_t *args)
     fprintf(stderr, "File format options:\n");
     fprintf(stderr, "   -o, --output <file>             write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>     output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
+    fprintf(stderr, "       --ploidy <assembly>[?]      predefined ploidy, 'list' to print available settings, append '?' for details\n");
+    fprintf(stderr, "       --ploidy-file <file>        space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n");
     fprintf(stderr, "   -r, --regions <region>          restrict to comma-separated list of regions\n");
     fprintf(stderr, "   -R, --regions-file <file>       restrict to regions listed in a file\n");
     fprintf(stderr, "   -s, --samples <list>            list of samples to include [all samples]\n");
@@ -506,7 +613,7 @@ static void usage(args_t *args)
 
 int main_vcfcall(int argc, char *argv[])
 {
-    char *samples_fname = NULL;
+    char *ploidy_fname = NULL, *ploidy = NULL;
     args_t args;
     memset(&args, 0, sizeof(args_t));
     args.argc = argc; args.argv = argv;
@@ -522,8 +629,7 @@ int main_vcfcall(int argc, char *argv[])
     args.aux.trio_Pm_SNPs = 1 - 1e-8;
     args.aux.trio_Pm_ins  = args.aux.trio_Pm_del  = 1 - 1e-9;
 
-    int i, c, samples_is_file = 0;
-
+    int c;
     static struct option loptions[] =
     {
         {"help",0,0,'h'},
@@ -551,6 +657,10 @@ int main_vcfcall(int argc, char *argv[])
         {"chromosome-X",0,0,'X'},
         {"chromosome-Y",0,0,'Y'},
         {"novel-rate",1,0,'n'},
+        {"ploidy",1,0,1},
+        {"ploidy-file",1,0,2},
+        {"chromosome-X",1,0,'X'},
+        {"chromosome-Y",1,0,'Y'},
         {0,0,0,0}
     };
 
@@ -564,6 +674,10 @@ int main_vcfcall(int argc, char *argv[])
                 args.gvcf.min_dp = strtol(optarg,&tmp,10);
                 if ( *tmp ) error("Could not parse, expected integer argument: -g %s\n", optarg);
                 break;
+            case  2 : ploidy_fname = optarg; break;
+            case  1 : ploidy = optarg; break;
+            case 'X': ploidy = "X"; fprintf(stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break;
+            case 'Y': ploidy = "Y"; fprintf(stderr,"Warning: -Y will be deprecated, please use --ploidy instead.\n"); break;
             case 'f': args.aux.output_tags |= parse_format_flag(optarg); break;
             case 'M': args.flag &= ~CF_ACGT_ONLY; break;     // keep sites where REF is N
             case 'N': args.flag |= CF_ACGT_ONLY; break;      // omit sites where first base in REF is N (the new default)
@@ -586,8 +700,6 @@ int main_vcfcall(int argc, char *argv[])
                       else if ( !strcasecmp(optarg,"trio") ) args.aux.flag |= CALL_CONSTR_TRIO;
                       else error("Unknown argument to -C: \"%s\"\n", optarg);
                       break;
-            case 'X': args.aux.flag |= CALL_CHR_X; break;
-            case 'Y': args.aux.flag |= CALL_CHR_Y; break;
             case 'V':
                       if ( !strcasecmp(optarg,"snps") ) args.flag |= CF_INDEL_ONLY;
                       else if ( !strcasecmp(optarg,"indels") ) args.flag |= CF_NO_INDEL;
@@ -606,11 +718,15 @@ int main_vcfcall(int argc, char *argv[])
             case 'R': args.regions = optarg; args.regions_is_file = 1; break;
             case 't': args.targets = optarg; break;
             case 'T': args.targets = optarg; args.targets_is_file = 1; break;
-            case 's': samples_fname = optarg; break;
-            case 'S': samples_fname = optarg; samples_is_file = 1; break;
+            case 's': args.samples_fname = optarg; break;
+            case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break;
             default: usage(&args);
         }
     }
+    // Sanity check options and initialize
+    if ( ploidy_fname ) args.ploidy = ploidy_init(ploidy_fname, 2);
+    else if ( ploidy ) args.ploidy = init_ploidy(ploidy);
+
     if ( optind>=argc )
     {
         if ( !isatty(fileno((FILE *)stdin)) ) args.bcf_fname = "-";  // reading from stdin
@@ -618,18 +734,13 @@ int main_vcfcall(int argc, char *argv[])
     }
     else args.bcf_fname = argv[optind++];
 
-    // Sanity check options and initialize
-    if ( samples_fname )
+    if ( !ploidy_fname && !ploidy )
     {
-        args.samples = read_samples(&args.aux, samples_fname, samples_is_file, &args.nsamples);
-        args.aux.ploidy = (uint8_t*) calloc(args.nsamples+1, 1);
-        args.aux.all_diploid = 1;
-        for (i=0; i<args.nsamples; i++)
-        {
-            args.aux.ploidy[i] = args.samples[i][strlen(args.samples[i]) + 1];
-            if ( args.aux.ploidy[i]!=2 ) args.aux.all_diploid = 0;
-        }
+        fprintf(stderr,"Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid\n");
+        args.ploidy = ploidy_init_string("",2);
     }
+
+    if ( !args.ploidy ) error("Could not initialize ploidy\n");
     if ( args.flag & CF_GVCF )
     {
         // Force some flags to avoid unnecessary branching
@@ -644,7 +755,6 @@ int main_vcfcall(int argc, char *argv[])
         if ( !args.targets ) error("Expected -t or -T with \"-C alleles\"\n");
         if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n");
     }
-    if ( args.aux.flag & CALL_CHR_X && args.aux.flag & CALL_CHR_Y ) error("Only one of -X or -Y should be given\n");
     if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n");
     init_data(&args);
 

From 942fbd20eb523c8898b93227a9cd8592a66979a3 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 5 Aug 2015 12:21:21 +0100
Subject: [PATCH 050/211] vcfnorm: merge records even if tags are missing from
 some records

* replaced some asserts with more informative error messages
* merging of Number=G INFO fields for haploid sites is still a todo
* tags that are not in the first record are going to be dropped, but
  this would require a more substantial rewrite

Fixes #282
---
 test/norm.merge.3.out | 34 ++++++++++++++++++++++++++++++++++
 test/norm.merge.3.vcf | 37 +++++++++++++++++++++++++++++++++++++
 test/test.pl          |  1 +
 vcfnorm.c             | 41 +++++++++++++++++++++++++++++++----------
 4 files changed, 103 insertions(+), 10 deletions(-)
 create mode 100644 test/norm.merge.3.out
 create mode 100644 test/norm.merge.3.vcf

diff --git a/test/norm.merge.3.out b/test/norm.merge.3.out
new file mode 100644
index 000000000..788a42751
--- /dev/null
+++ b/test/norm.merge.3.out
@@ -0,0 +1,34 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=11,length=2147483647>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=FL,Number=1,Type=Float,Description="Float">
+##FORMAT=<ID=FLG,Number=G,Type=Float,Description="FloatG">
+##FORMAT=<ID=FLA,Number=A,Type=Float,Description="FloatA">
+##FORMAT=<ID=FLR,Number=R,Type=Float,Description="FloatR">
+##FORMAT=<ID=INT,Number=1,Type=Float,Description="Int">
+##FORMAT=<ID=INTG,Number=G,Type=Float,Description="IntG">
+##FORMAT=<ID=INTA,Number=A,Type=Integer,Description="IntA">
+##FORMAT=<ID=INTR,Number=R,Type=Integer,Description="IntR">
+##FORMAT=<ID=ST,Number=1,Type=String,Description="String">
+##FORMAT=<ID=STA,Number=A,Type=String,Description="StringA">
+##FORMAT=<ID=STR,Number=R,Type=String,Description="StringR">
+##FORMAT=<ID=STG,Number=G,Type=String,Description="StringG">
+##INFO=<ID=FL,Number=1,Type=Float,Description="Float">
+##INFO=<ID=FLG,Number=G,Type=Float,Description="FloatG">
+##INFO=<ID=FLA,Number=A,Type=Float,Description="FloatA">
+##INFO=<ID=FLR,Number=R,Type=Float,Description="FloatR">
+##INFO=<ID=INT,Number=1,Type=Float,Description="Int">
+##INFO=<ID=INTG,Number=G,Type=Float,Description="IntG">
+##INFO=<ID=INTA,Number=A,Type=Integer,Description="IntA">
+##INFO=<ID=INTR,Number=R,Type=Integer,Description="IntR">
+##INFO=<ID=F1,Type=Flag,Description="Flag1">
+##INFO=<ID=ST,Number=1,Type=String,Description="String">
+##INFO=<ID=STA,Number=A,Type=String,Description="StringA">
+##INFO=<ID=STR,Number=R,Type=String,Description="StringR">
+##INFO=<ID=STG,Number=G,Type=String,Description="StringG">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_1	sample_2
+11	48245184	.	C	G	.	PASS	FL=0.34;FLG=0.1,0,0.9;FLA=88.4;FLR=99,88.4;INT=0;INTG=0,1,9;INTA=88;INTR=99,88;F1;ST=alpha;STA=alpha;STR=alpha,beta;STG=alpha,beta,gamma	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0|0:0.34:0.1,0,0.9:88.4:99,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:0.1,0,0.9:88.4:99,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma
+11	48245185	.	C	G,T	.	PASS	FL=0.34;FLG=0.1,0,0.9,.,.,.;FLA=88.4,.;FLR=99,88.4,.;INT=0;INTG=0,1,9,.,.,.;INTA=88,.;INTR=99,88,.;F1;ST=alpha;STA=alpha,.;STR=alpha,beta,.;STG=alpha,beta,gamma,.,.,.	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0|0:0.34:0.1,0,0.9,.,.,.:88.4,.:99,88.4,.:0:0,1,9,.,.,.:88,.:99,88,.:alpha:alpha,.:alpha,beta,.:alpha,beta,gamma,.,.,.	0|0:0.34:0.1,0,0.9,.,.,.:88.4,.:99,88.4,.:0:0,1,9,.,.,.:88,.:99,88,.:alpha:alpha,.:alpha,beta,.:alpha,beta,gamma,.,.,.
+11	48245186	.	C	G,T	.	PASS	FL=0.34;FLA=88.4,88.4;FLR=99,88.4,88.4;INT=0;INTA=88,11;INTR=99,88,11;F1;ST=alpha;STA=alpha,beta;STR=alpha,beta,gamma	GT:FL:FLA:FLR:INT:INTA:INTR:ST:STA:STR	0|0:0.34:88.4,11:99,88.4,11:0:88,11:99,88,11:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:88.4,11:99,88.4,11:0:88,11:99,88,11:alpha:alpha,beta:alpha,beta,gamma
+11	48245187	.	C	G,T	.	PASS	FL=0.34;FLA=88.4,.;FLR=99,88.4,.;INT=0;INTA=88,.;INTR=99,88,.;F1;ST=alpha;STA=alpha,.;STR=alpha,beta,.	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0:0.34:0.1,0,.:88.4,.:99,88.4,.:0:0,1,.:88,.:99,88,.:alpha:alpha,.:alpha,beta,.:alpha,beta,.	0:0.34:0.1,0,.:88.4,.:99,88.4,.:0:0,1,.:88,.:99,88,.:alpha:alpha,.:alpha,beta,.:alpha,beta,.
diff --git a/test/norm.merge.3.vcf b/test/norm.merge.3.vcf
new file mode 100644
index 000000000..f2b980a09
--- /dev/null
+++ b/test/norm.merge.3.vcf
@@ -0,0 +1,37 @@
+##fileformat=VCFv4.2
+##contig=<ID=11,length=2147483647>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=FL,Number=1,Type=Float,Description="Float">
+##FORMAT=<ID=FLG,Number=G,Type=Float,Description="FloatG">
+##FORMAT=<ID=FLA,Number=A,Type=Float,Description="FloatA">
+##FORMAT=<ID=FLR,Number=R,Type=Float,Description="FloatR">
+##FORMAT=<ID=INT,Number=1,Type=Float,Description="Int">
+##FORMAT=<ID=INTG,Number=G,Type=Float,Description="IntG">
+##FORMAT=<ID=INTA,Number=A,Type=Integer,Description="IntA">
+##FORMAT=<ID=INTR,Number=R,Type=Integer,Description="IntR">
+##FORMAT=<ID=ST,Number=1,Type=String,Description="String">
+##FORMAT=<ID=STA,Number=A,Type=String,Description="StringA">
+##FORMAT=<ID=STR,Number=R,Type=String,Description="StringR">
+##FORMAT=<ID=STG,Number=G,Type=String,Description="StringG">
+##INFO=<ID=FL,Number=1,Type=Float,Description="Float">
+##INFO=<ID=FLG,Number=G,Type=Float,Description="FloatG">
+##INFO=<ID=FLA,Number=A,Type=Float,Description="FloatA">
+##INFO=<ID=FLR,Number=R,Type=Float,Description="FloatR">
+##INFO=<ID=INT,Number=1,Type=Float,Description="Int">
+##INFO=<ID=INTG,Number=G,Type=Float,Description="IntG">
+##INFO=<ID=INTA,Number=A,Type=Integer,Description="IntA">
+##INFO=<ID=INTR,Number=R,Type=Integer,Description="IntR">
+##INFO=<ID=F1,Type=Flag,Description="Flag1">
+##INFO=<ID=ST,Number=1,Type=String,Description="String">
+##INFO=<ID=STA,Number=A,Type=String,Description="StringA">
+##INFO=<ID=STR,Number=R,Type=String,Description="StringR">
+##INFO=<ID=STG,Number=G,Type=String,Description="StringG">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample_1	sample_2
+11	48245184	.	C	G	.	PASS	FL=0.34;FLG=0.1,0,0.9;FLA=88.4;FLR=99.0,88.4;INT=0;INTG=0,1,9;INTA=88;INTR=99,88;F1;ST=alpha;STA=alpha;STR=alpha,beta;STG=alpha,beta,gamma	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0|0:0.34:0.1,0,0.9:88.4:99.0,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:0.1,0,0.9:88.4:99.0,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma
+11	48245184	.	C	G	.	PASS	.	GT	0/0	0/0
+11	48245185	.	C	G	.	PASS	FL=0.34;FLG=0.1,0,0.9;FLA=88.4;FLR=99.0,88.4;INT=0;INTG=0,1,9;INTA=88;INTR=99,88;F1;ST=alpha;STA=alpha;STR=alpha,beta;STG=alpha,beta,gamma	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0|0:0.34:0.1,0,0.9:88.4:99.0,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:0.1,0,0.9:88.4:99.0,88.4:0:0,1,9:88:99,88:alpha:alpha:alpha,beta:alpha,beta,gamma
+11	48245185	.	C	T	.	PASS	.	GT	0/0	0/0
+11	48245186	.	C	G,T	.	PASS	FL=0.34;FLA=88.4,88.4;FLR=99.0,88.4,88.4;INT=0;INTA=88,11;INTR=99,88,11;F1;ST=alpha;STA=alpha,beta;STR=alpha,beta,gamma	GT:FL:FLA:FLR:INT:INTA:INTR:ST:STA:STR	0|0:0.34:88.4,11:99.0,88.4,11:0:88,11:99,88,11:alpha:alpha,beta:alpha,beta,gamma	0|0:0.34:88.4,11:99.0,88.4,11:0:88,11:99,88,11:alpha:alpha,beta:alpha,beta,gamma
+11	48245186	.	C	T	.	PASS	.	GT	0/0	0/0
+11	48245187	.	C	G	.	PASS	FL=0.34;FLA=88.4;FLR=99.0,88.4;INT=0;INTA=88;INTR=99,88;F1;ST=alpha;STA=alpha;STR=alpha,beta	GT:FL:FLG:FLA:FLR:INT:INTG:INTA:INTR:ST:STA:STR:STG	0:0.34:0.1,0:88.4:99.0,88.4:0:0,1:88:99,88:alpha:alpha:alpha,beta:alpha,beta	0:0.34:0.1,0:88.4:99.0,88.4:0:0,1:88:99,88:alpha:alpha:alpha,beta:alpha,beta
+11	48245187	.	C	T	.	PASS	.	GT	0	0
diff --git a/test/test.pl b/test/test.pl
index cd9fbe462..0cbed476b 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -93,6 +93,7 @@
 test_vcf_norm($opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.out',args=>'-m+');
 test_vcf_norm($opts,in=>'norm.merge.2',out=>'norm.merge.2.out',args=>'-m+');
+test_vcf_norm($opts,in=>'norm.merge.3',out=>'norm.merge.3.out',args=>'-m+');
 test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.strict.out',args=>'-m+ -s');
 test_vcf_norm($opts,in=>'norm.setref',out=>'norm.setref.out',args=>'-Nc s',fai=>'norm');
 test_vcf_view($opts,in=>'view',out=>'view.1.out',args=>'-aUc1 -C1 -s NA00002 -v snps',reg=>'');
diff --git a/vcfnorm.c b/vcfnorm.c
index aa82e949d..9135430f5 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -803,7 +803,8 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
         int i,k,len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key);  \
         if ( len==BCF_VL_A ) \
         { \
-            assert( nvals_ori==lines[0]->n_allele - 1); \
+            if (nvals_ori!=lines[0]->n_allele - 1) \
+                error("vcfnorm: number of fields in first record at position %s:%d for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele-1); \
             int nvals = dst->n_allele - 1; \
             ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
             vals = (type_t*) args->tmp_arr1; \
@@ -811,8 +812,10 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
-                assert( nvals2==lines[i]->n_allele-1 ); \
+                if (nvals2!=lines[i]->n_allele-1) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (k=0; k<nvals2; k++) \
                 { \
@@ -824,7 +827,8 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
         } \
         else if ( len==BCF_VL_R ) \
         { \
-            assert( nvals_ori==lines[0]->n_allele ); \
+            if (nvals_ori!=lines[0]->n_allele) \
+                error("vcfnorm: number of fields in first record at position %s:%d for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele); \
             int nvals = dst->n_allele; \
             ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
             vals = (type_t*) args->tmp_arr1; \
@@ -832,8 +836,10 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
-                assert( nvals2==lines[i]->n_allele ); \
+                if (nvals2!=lines[i]->n_allele) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (k=0; k<nvals2; k++) \
                 { \
@@ -845,7 +851,11 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
         } \
         else if ( len==BCF_VL_G ) \
         { \
-            assert( nvals_ori==lines[0]->n_allele*(lines[0]->n_allele+1)/2 );   /* expecting diploid gt in INFO */ \
+            /* expecting diploid gt in INFO */ \
+            if (nvals_ori!=lines[0]->n_allele*(lines[0]->n_allele+1)/2) { \
+                fprintf(stderr, "todo: merge Number=G INFO fields for haploid sites\n"); \
+                error("vcfnorm: number of fields in first record at position %s:%d for INFO tag %s not as expected [found: %d vs expected:%d]\n", bcf_seqname(args->hdr,lines[0]),lines[0]->pos+1, tag, nvals_ori, lines[0]->n_allele*(lines[0]->n_allele+1)/2); \
+            } \
             int nvals = dst->n_allele*(dst->n_allele+1)/2; \
             ENLARGE_ARRAY(type_t,set_missing,args->tmp_arr1,args->ntmp_arr1,1,nvals_ori,nvals); \
             vals = (type_t*) args->tmp_arr1; \
@@ -853,8 +863,10 @@ static void merge_info_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_inf
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_info_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* info tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
-                assert( nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2 ); \
+                if (nvals2!=lines[i]->n_allele*(lines[i]->n_allele+1)/2) \
+                    error("vcfnorm: could not merge INFO tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals2 = (type_t*) args->tmp_arr2; \
                 int ia,ib; \
                 k = 0; \
@@ -906,6 +918,7 @@ static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info
         for (i=0; i<nlines; i++)
         {
             bcf_info_t *src = bcf_get_info(args->hdr,lines[i],tag);
+            if (!src) continue;
             for (j=jfrom; j<lines[i]->n_allele; j++)
                 copy_string_field((char*)src->vptr, j-jfrom, src->len, &str, args->maps[i].map[j]-jfrom);
         }
@@ -922,6 +935,7 @@ static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info
         for (i=0; i<nlines; i++)
         {
             bcf_info_t *src = bcf_get_info(args->hdr,lines[i],tag);
+            if (!src) continue;
             int iori, jori, kori = 0;
             for (iori=0; iori<lines[i]->n_allele; iori++)
             {
@@ -945,7 +959,6 @@ static void merge_info_string(args_t *args, bcf1_t **lines, int nlines, bcf_info
         bcf_get_info_string(args->hdr,lines[0],tag,&args->tmp_arr1,&args->ntmp_arr1);
         bcf_update_info_string(args->hdr,dst,tag,args->tmp_arr1);
     }
-
 }
 static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_fmt_t *fmt, bcf1_t *dst)
 {
@@ -1021,9 +1034,11 @@ static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_f
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
                 nvals2 /= nsmpl; \
-                assert( nvals2==lines[i]->n_allele-1 ); \
+                if (nvals2!=lines[i]->n_allele-1) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals  = (type_t*) args->tmp_arr1; \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (j=0; j<nsmpl; j++) \
@@ -1047,9 +1062,11 @@ static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_f
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
                 nvals2 /= nsmpl; \
-                assert( nvals2==lines[i]->n_allele ); \
+                if (nvals2!=lines[i]->n_allele) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals  = (type_t*) args->tmp_arr1; \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (j=0; j<nsmpl; j++) \
@@ -1090,11 +1107,13 @@ static void merge_format_numeric(args_t *args, bcf1_t **lines, int nlines, bcf_f
             { \
                 int ntmp2 = args->ntmp_arr2 / sizeof(type_t); \
                 int nvals2 = bcf_get_format_##type(args->hdr,lines[i],tag,&args->tmp_arr2,&ntmp2); \
+                if (nvals2<0) continue; /* format tag does not exist in this record, skip */ \
                 args->ntmp_arr2 = ntmp2 * sizeof(type_t); \
                 nvals2 /= nsmpl; \
                 int ndiploid = lines[i]->n_allele*(lines[i]->n_allele+1)/2; \
                 int line_diploid = nvals2==ndiploid ? 1 : 0; \
-                assert( nvals2==1 || nvals2==lines[i]->n_allele || nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2); \
+                if (!(nvals2==1 || nvals2==lines[i]->n_allele || nvals2==lines[i]->n_allele*(lines[i]->n_allele+1)/2)) \
+                    error("vcfnorm: could not merge FORMAT tag %s at position %s:%d\n", tag, bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1); \
                 vals  = (type_t*) args->tmp_arr1; \
                 vals2 = (type_t*) args->tmp_arr2; \
                 for (j=0; j<nsmpl; j++) \
@@ -1179,6 +1198,7 @@ static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fm
         for (i=0; i<nlines; i++)
         {
             int nret = bcf_get_format_char(args->hdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1);
+            if (nret<0) continue; /* format tag does not exist in this record, skip */ \
             nret /= nsmpl;
             for (k=0; k<nsmpl; k++)
             {
@@ -1225,6 +1245,7 @@ static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fm
             if ( i ) // we already have a copy
             {
                 nret = bcf_get_format_char(args->hdr,lines[i],tag,&args->tmp_arr1,&args->ntmp_arr1);
+                if (nret<0) continue; /* format tag does not exist in this record, skip */ \
                 nret /= nsmpl;
             }
             for (k=0; k<nsmpl; k++)

From 6deaf372e84fed4653f6fabb857e886324f88deb Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 5 Aug 2015 15:37:31 +0100
Subject: [PATCH 051/211] update man docs with new concat options

---
 doc/bcftools.1    | 21 ++++++++++++++++-----
 doc/bcftools.html | 16 ++++++++++++----
 doc/bcftools.txt  | 10 ++++++++--
 3 files changed, 36 insertions(+), 11 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index 1269ac051..4a428e327 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-07-28 16:00 BST
+.\"      Date: 2015-08-05 15:36 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-07\-28 16:00 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-08\-05 15:36 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-07\-28 16:00 BST\fR and refers to bcftools git version \fB1\&.2\-96\-g5d52a36+\fR\&.
+This manual page was last updated \fB2015\-08\-05 15:36 BST\fR and refers to bcftools git version \fB1\&.2\-104\-gf47097b+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -828,12 +828,23 @@ Concatenate or combine VCF/BCF files\&. All source files must have the same samp
 First coordinate of the next file can precede last record of the current file\&.
 .RE
 .PP
-\fB\-D, \-\-remove\-duplicates\fR
+\fB\-c, \-\-compact\-PS\fR
+.RS 4
+Do not output PS tag at each site, only at the start of a new phase set block\&.
+.RE
+.PP
+\fB\-d, \-\-rm\-dups\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fInone\fR
 .RS 4
-If a record is present in multiple files, output only the first instance\&. Requires
+Output duplicate records of specified type present in multiple files only once\&. Requires
 \fB\-a, \-\-allow\-overlaps\fR\&.
 .RE
 .PP
+\fB\-D, \-\-remove\-duplicates\fR
+.RS 4
+Alias for
+\fB\-d none\fR
+.RE
+.PP
 \fB\-f, \-\-file\-list\fR \fIFILE\fR
 .RS 4
 Read the list of files from a file\&.
diff --git a/doc/bcftools.html b/doc/bcftools.html
index 2202b9f30..1e85ce392 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp205456"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp146224"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
 work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-07-28 16:00 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-96-g5d52a36+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-08-05 15:36 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-104-gf47097b+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -440,11 +440,19 @@
 </span></dt><dd>
     First coordinate of the next file can precede last record of the current file.
 </dd><dt><span class="term">
-<span class="strong"><strong>-D, --remove-duplicates</strong></span>
+<span class="strong"><strong>-c, --compact-PS</strong></span>
+</span></dt><dd>
+    Do not output PS tag at each site, only at the start of a new phase set block.
+</dd><dt><span class="term">
+<span class="strong"><strong>-d, --rm-dups</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>all</em></span>|<span class="emphasis"><em>none</em></span>
 </span></dt><dd>
-    If a record is present in multiple files, output only the first instance.
+    Output duplicate records of specified type present in multiple files only once.
     Requires <span class="strong"><strong>-a, --allow-overlaps</strong></span>.
 </dd><dt><span class="term">
+<span class="strong"><strong>-D, --remove-duplicates</strong></span>
+</span></dt><dd>
+    Alias for <span class="strong"><strong>-d none</strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-f, --file-list</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     Read the list of files from a file.
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 7fa3361f3..657fefef8 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -476,10 +476,16 @@ the *-a, --allow-overlaps* option is specified.
 *-a, --allow-overlaps*::
     First coordinate of the next file can precede last record of the current file.
 
-*-D, --remove-duplicates*::
-    If a record is present in multiple files, output only the first instance.
+*-c, --compact-PS*::
+    Do not output PS tag at each site, only at the start of a new phase set block.
+
+*-d, --rm-dups* 'snps'|'indels'|'both'|'all'|'none'::
+    Output duplicate records of specified type present in multiple files only once.
     Requires *-a, --allow-overlaps*.
 
+*-D, --remove-duplicates*::
+    Alias for *-d none*
+
 *-f, --file-list* 'FILE'::
     Read the list of files from a file.
 

From 21aca6d0932792d0e4f479e1401a64c292f9d2c3 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 5 Aug 2015 15:59:46 +0100
Subject: [PATCH 052/211] cleanup GRCh38 alias description

---
 vcfcall.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcfcall.c b/vcfcall.c
index 181f73ef5..7eb56b33e 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -145,7 +145,7 @@ static ploidy_predef_t ploidy_predefs[] =
           "*  * *     F 2\n"
     },
     { .alias  = "GRCh38",
-      .about  = "Human Genome reference assembly GRCh38 / hg38, plain chromosome naming (1,2,3,..)",
+      .about  = "Human Genome reference assembly GRCh38 / hg38",
       .ploidy =
           "X 1 9999 M 1\n"
           "X 2781480 155701381 M 1\n"

From ef11927ac5fc6feca75279d93b56061cf3ae6e96 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 29 Jul 2015 21:35:22 +0100
Subject: [PATCH 053/211] Three ways to add values in annotate: -c +ID, =ID, or
 ID

- The same for FILTER, plus fix to make it behave as described
in the man page.
---
 doc/bcftools.txt   |  7 ++++--
 test/annotate4.out |  2 +-
 test/annotate5.out |  4 ++--
 test/annotate9.out | 29 ++++++++++++++++++++++
 test/annotate9.vcf | 28 ++++++++++++++++++++++
 test/annots9.tab   |  5 ++++
 test/annots9.vcf   | 28 ++++++++++++++++++++++
 test/test.pl       |  3 ++-
 vcfannotate.c      | 60 ++++++++++++++++++++++++++++++----------------
 9 files changed, 139 insertions(+), 27 deletions(-)
 create mode 100644 test/annotate9.out
 create mode 100644 test/annotate9.vcf
 create mode 100644 test/annots9.tab
 create mode 100644 test/annots9.vcf

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 657fefef8..0c64c4265 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -261,8 +261,11 @@ This command allows to add or remove annotations.
     can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG",
     and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
     To carry over all INFO annotations, use "INFO". To add all INFO annotations except
-    "TAG", use "&#94;INFO/TAG". By default, existing values are replaced. To add
-    values without overwriting existing annotations, use "+TAG" instead of "TAG".
+    "TAG", use "&#94;INFO/TAG". By default, existing values are replaced.
+    To add annotations without overwriting existing values (that is, to add missing tags or
+    add values to existing tags with missing values), use "+TAG" instead of "TAG".
+    To append to existing values (rather than replacing or leaving untouched), use "=TAG"
+    (instead of "TAG" or "+TAG").
     To replace only existing values without modifying missing annotations, use "-TAG".
     If the annotation file is not a VCF/BCF, all new annotations must be
     defined via *-h, --header-lines*.
diff --git a/test/annotate4.out b/test/annotate4.out
index 674024200..934cf8993 100644
--- a/test/annotate4.out
+++ b/test/annotate4.out
@@ -13,7 +13,7 @@
 ##FILTER=<ID=q11,Description="Quality below 10">
 ##FILTER=<ID=q99,Description="Quality below 10">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C
-1	3000001	xx	C	T	11	.	IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	.:11:1.1:xxx	.:11:1.1:x	0/0:11:1.1:x
+1	3000001	xx	C	T	11	PASS	IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	.:11:1.1:xxx	.:11:1.1:x	0/0:11:1.1:x
 1	3000002	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:77:7.7:77	1|1:88,99:8.8,9.9:888,999	.:.:.:.
 1	3000003	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:77:7.7:77	1|1:88,99:8.8,9.9:888,999	0/0:.:.:.
 1	3000004	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:77:7.7:77	1|1:88,99:8.8,9.9:888,999	0/0:11:1.1:xxx
diff --git a/test/annotate5.out b/test/annotate5.out
index d3ab76451..a57261ee6 100644
--- a/test/annotate5.out
+++ b/test/annotate5.out
@@ -15,5 +15,5 @@
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C
 1	3000001	xx	C	T	11	PASS	IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	.:11:1.1:xxx	0/0:11:1.1:x	0/0:11:1.1:x
 1	3000002	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT	0|1	.	.
-1	3000003	id	C	T	99	q11;q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:.:.:.	0/0:.:.:.	0/0:.:.:.
-1	3000004	id	C	T	99	q11;q99	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0|1:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
+1	3000003	id	C	T	99	q11	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	0|1:.:.:.	0/0:.:.:.	0/0:.:.:.
+1	3000004	id	C	T	99	q11	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0|1:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
diff --git a/test/annotate9.out b/test/annotate9.out
new file mode 100644
index 000000000..66c872da3
--- /dev/null
+++ b/test/annotate9.out
@@ -0,0 +1,29 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
+##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=test,Description="Testing filter">
+##contig=<ID=1,assembly=b37,length=249250621>
+##contig=<ID=2,assembly=b37,length=249250621>
+##contig=<ID=3,assembly=b37,length=198022430>
+##contig=<ID=4,assembly=b37,length=191154276>
+##test=<ID=4,IE=5>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##readme=AAAAAA
+##readme=BBBBBB
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	3000150	id150	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
+1	3000151	id3000151	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	id3106154	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
diff --git a/test/annotate9.vcf b/test/annotate9.vcf
new file mode 100644
index 000000000..659516744
--- /dev/null
+++ b/test/annotate9.vcf
@@ -0,0 +1,28 @@
+##fileformat=VCFv4.1
+##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
+##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=test,Description="Testing filter">
+##contig=<ID=1,assembly=b37,length=249250621>
+##contig=<ID=2,assembly=b37,length=249250621>
+##contig=<ID=3,assembly=b37,length=198022430>
+##contig=<ID=4,assembly=b37,length=191154276>
+##test=<ID=4,IE=5>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##readme=AAAAAA
+##readme=BBBBBB
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	3000150	id150	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
+1	3000151	.	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	idSNP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
diff --git a/test/annots9.tab b/test/annots9.tab
new file mode 100644
index 000000000..678e3c4ab
--- /dev/null
+++ b/test/annots9.tab
@@ -0,0 +1,5 @@
+1	3000150	C	T	id3000150
+1	3000151	C	T	id3000151
+1	3062915	GTTT	G	id3062915_3D
+1	3062915	G	T,C	id3062915_NP
+1	3106154	CAAA	C	id3106154
diff --git a/test/annots9.vcf b/test/annots9.vcf
new file mode 100644
index 000000000..6ff2cceb3
--- /dev/null
+++ b/test/annots9.vcf
@@ -0,0 +1,28 @@
+##fileformat=VCFv4.1
+##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
+##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=test,Description="Testing filter">
+##contig=<ID=1,assembly=b37,length=249250621>
+##contig=<ID=2,assembly=b37,length=249250621>
+##contig=<ID=3,assembly=b37,length=198022430>
+##contig=<ID=4,assembly=b37,length=191154276>
+##test=<ID=4,IE=5>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##readme=AAAAAA
+##readme=BBBBBB
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	3000150	id3000150	C	T	59.2	PASS	AN=4;AC=2	GT:GQ	0/1:245	0/1:245
+1	3000151	id3000151	C	T	59.2	PASS	AN=4;AC=2	GT:DP:GQ	0/1:32:245	0/1:32:245
+1	3062915	id3062915_3D	GTTT	G	12.9	q10	DP4=1,2,3,4;AN=4;AC=2;INDEL;STR=test	GT:GQ:DP:GL	0/1:409:35:-20,-5,-20	0/1:409:35:-20,-5,-20
+1	3062915	id3062915_NP	G	T,C	12.6	test	TEST=5;DP4=1,2,3,4;AN=3;AC=1,1	GT:TT:GQ:DP:GL	0/1:0,1:409:35:-20,-5,-20,-20,-5,-20	2:0,1:409:35:-20,-5,-20
+1	3106154	id3106154	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:245:32
diff --git a/test/test.pl b/test/test.pl
index 0cbed476b..08ab49bba 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -155,6 +155,7 @@
 test_vcf_annotate($opts,in=>'annotate4',vcf=>'annots4',out=>'annotate8.out',args=>'-c +INFO');
 test_vcf_annotate($opts,in=>'annotate4',tab=>'annots4',out=>'annotate8.out',args=>'-c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR');
 test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+missing2ref');
+test_vcf_annotate($opts,in=>'annotate9',tab=>'annots9',out=>'annotate9.out',args=>'-c CHROM,POS,REF,ALT,+ID');
 test_vcf_plugin($opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC');
 test_vcf_plugin($opts,in=>'plugin1',out=>'dosage.out',cmd=>'+dosage');
 test_vcf_plugin($opts,in=>'fixploidy',out=>'fixploidy.out',cmd=>'+fixploidy',args=>'-- -s {PATH}/fixploidy.samples -p {PATH}/fixploidy.ploidy');
@@ -682,7 +683,7 @@ sub test_vcf_annotate
         bgzip_tabix($opts,file=>$args{tab},suffix=>'tab',args=>'-s1 -b2 -e2');
         $annot_fname = "-a $$opts{tmp}/$args{tab}.tab.gz";
         $in_fname = "$$opts{path}/$args{in}.vcf";
-        $hdr = "-h $$opts{path}/$args{in}.hdr";
+        $hdr = -e "$$opts{path}/$args{in}.hdr" ? "-h $$opts{path}/$args{in}.hdr" : '';
     }
     elsif ( exists($args{vcf}) )
     {
diff --git a/vcfannotate.c b/vcfannotate.c
index 2723e7bc0..621da5739 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -66,6 +66,7 @@ annot_line_t;
 #define REPLACE_MISSING  0  // replace only missing values
 #define REPLACE_ALL      1  // replace both missing and existing values
 #define REPLACE_EXISTING 2  // replace only if tgt is not missing
+#define SET_OR_APPEND    3  // set new value if missing or non-existent, append otherwise
 typedef struct _annot_col_t
 {
     int icol, replace, number;  // number: one of BCF_VL_* types
@@ -362,41 +363,52 @@ static void init_header_lines(args_t *args)
 }
 static int setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
 {
+    // note: so far this works only with one filter, not a list of filters
     annot_line_t *tab = (annot_line_t*) data;
+    if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
     hts_expand(int,1,args->mtmpi,args->tmpi);
     args->tmpi[0] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, tab->cols[col->icol]);
     if ( args->tmpi[0]<0 ) error("The FILTER is not defined in the header: %s\n", tab->cols[col->icol]);
+    if ( col->replace==SET_OR_APPEND ) { bcf_add_filter(args->hdr_out,line,args->tmpi[0]); return 0; }
     if ( col->replace!=REPLACE_MISSING )
+    {
+        bcf_update_filter(args->hdr_out,line,NULL,0);
+        bcf_update_filter(args->hdr_out,line,args->tmpi,1); 
+        return 0; 
+    }
+    
+    // only update missing FILTER
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( !line->d.n_flt )
         bcf_update_filter(args->hdr_out,line,args->tmpi,1);
-    else
-        bcf_add_filter(args->hdr_out,line,args->tmpi[0]);
     return 0;
 }
 static int vcf_setter_filter(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
 {
+    int i;
     bcf1_t *rec = (bcf1_t*) data;
     if ( !(rec->unpacked & BCF_UN_FLT) ) bcf_unpack(rec, BCF_UN_FLT);
-    hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi);
-    int i;
-    if ( col->replace!=REPLACE_MISSING )
+    if ( !(line->unpacked & BCF_UN_FLT) ) bcf_unpack(line, BCF_UN_FLT);
+    if ( !rec->d.n_flt ) return 0;  // don't overwrite with a missing value
+    if ( col->replace==SET_OR_APPEND || col->replace==REPLACE_MISSING )
     {
+        if ( col->replace==REPLACE_MISSING && line->d.n_flt ) return 0; // only update missing FILTER
         for (i=0; i<rec->d.n_flt; i++)
         {
             const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
-            args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt);
+            bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt));
         }
-        bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt);
         return 0;
     }
-    else
+    hts_expand(int,rec->d.n_flt,args->mtmpi,args->tmpi);
+    for (i=0; i<rec->d.n_flt; i++)
     {
-        for (i=0; i<rec->d.n_flt; i++)
-        {
-            const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
-            bcf_add_filter(args->hdr_out,line,bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt));
-        }
-        return 0;
+        const char *flt = bcf_hdr_int2id(args->files->readers[1].header, BCF_DT_ID, rec->d.flt[i]);
+        args->tmpi[i] = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, flt);
     }
+    bcf_update_filter(args->hdr_out,line,NULL,0);
+    bcf_update_filter(args->hdr_out,line,args->tmpi,rec->d.n_flt);
+    return 0;
 }
 static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
 {
@@ -404,13 +416,14 @@ static int setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
     //      IN  ANNOT   OUT     ACHIEVED_BY
     //      x   y       x        -c +ID
     //      x   y       y        -c ID
-    //      x   y       x,y      /not supported/
+    //      x   y       x,y      -c =ID
     //      x   .       x        -c +ID, ID
     //      x   .       .        -x ID
     //      .   y       y        -c +ID, -c ID
     //
     annot_line_t *tab = (annot_line_t*) data;
     if ( tab->cols[col->icol] && tab->cols[col->icol][0]=='.' && !tab->cols[col->icol][1] ) return 0; // don't replace with "."
+    if ( col->replace==SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,tab->cols[col->icol]);
     if ( col->replace!=REPLACE_MISSING ) return bcf_update_id(args->hdr_out,line,tab->cols[col->icol]);
 
     // running with +ID, only update missing ids
@@ -422,6 +435,7 @@ static int vcf_setter_id(args_t *args, bcf1_t *line, annot_col_t *col, void *dat
 {
     bcf1_t *rec = (bcf1_t*) data;
     if ( rec->d.id && rec->d.id[0]=='.' && !rec->d.id[1] ) return 0;    // don't replace with "."
+    if ( col->replace==SET_OR_APPEND ) return bcf_add_id(args->hdr_out,line,rec->d.id);
     if ( col->replace!=REPLACE_MISSING ) return bcf_update_id(args->hdr_out,line,rec->d.id);
 
     // running with +ID, only update missing ids
@@ -1120,6 +1134,7 @@ static void init_columns(args_t *args)
         int replace = REPLACE_ALL;
         if ( *ss=='+' ) { replace = REPLACE_MISSING; ss++; }
         else if ( *ss=='-' ) { replace = REPLACE_EXISTING; ss++; }
+        else if ( *ss=='=' ) { replace = SET_OR_APPEND; ss++; }
         i++;
         str.l = 0;
         kputsn(ss, se-ss, &str);
@@ -1132,7 +1147,7 @@ static void init_columns(args_t *args)
         else if ( !strcasecmp("ALT",str.s) ) args->alt_idx = i;
         else if ( !strcasecmp("ID",str.s) )
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -ID\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -ID feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
             col->icol = i;
@@ -1142,7 +1157,7 @@ static void init_columns(args_t *args)
         }
         else if ( !strcasecmp("FILTER",str.s) )
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -FILTER\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -FILTER feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
             col->icol = i;
@@ -1168,7 +1183,8 @@ static void init_columns(args_t *args)
         }
         else if ( !strcasecmp("QUAL",str.s) )
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -QUAL\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -QUAL feature has not been implemented yet.\n");
+            if ( replace==SET_OR_APPEND ) error("Apologies, the =QUAL feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
             col->icol = i;
@@ -1178,7 +1194,8 @@ static void init_columns(args_t *args)
         }
         else if ( args->tgts_is_vcf && !strcasecmp("INFO",str.s) ) // All INFO fields
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -INFO/TAG\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n");
+            if ( replace==SET_OR_APPEND ) error("Apologies, the =INFO/TAG feature has not been implemented yet.\n");
             bcf_hdr_t *tgts_hdr = args->files->readers[1].header;
             int j;
             for (j=0; j<tgts_hdr->nhrec; j++)
@@ -1274,7 +1291,8 @@ static void init_columns(args_t *args)
         }
         else
         {
-            if ( replace==REPLACE_EXISTING ) error("todo: -INFO/TAG\n");
+            if ( replace==REPLACE_EXISTING ) error("Apologies, the -INFO/TAG feature has not been implemented yet.\n");
+            if ( replace==SET_OR_APPEND ) error("Apologies, the =INFO/TAG feature has not been implemented yet.\n");
             if ( !strncasecmp("INFO/",str.s,5) ) { memmove(str.s,str.s+5,str.l-4); }
             int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, str.s);
             if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_INFO,hdr_id) )
@@ -1396,7 +1414,7 @@ static void init_data(args_t *args)
     if ( args->mark_sites )
     {
         if ( !args->targets_fname ) error("The -a option not given\n");
-        if ( args->tgts_is_vcf ) error("todo: -a is a VCF\n");  // very easy to add..
+        if ( args->tgts_is_vcf ) error("Apologies, this has not been implemented yet: -a is a VCF\n");  // very easy to add..
         bcf_hdr_printf(args->hdr_out,"##INFO=<ID=%s,Number=0,Type=Flag,Description=\"Sites %slisted in %s\">",
             args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites);
     }

From b3257c19a208e66361f2edabdcc5b290b42bc1be Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 5 Aug 2015 16:04:28 +0100
Subject: [PATCH 054/211] update man docs after
 ef11927ac5fc6feca75279d93b56061cf3ae6e96

---
 doc/bcftools.1    |  8 ++++----
 doc/bcftools.html | 11 +++++++----
 2 files changed, 11 insertions(+), 8 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index 4a428e327..ac2f16c68 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-08-05 15:36 BST
+.\"      Date: 2015-08-05 16:03 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-08\-05 15:36 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-08\-05 16:03 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-08\-05 15:36 BST\fR and refers to bcftools git version \fB1\&.2\-104\-gf47097b+\fR\&.
+This manual page was last updated \fB2015\-08\-05 16:03 BST\fR and refers to bcftools git version \fB1\&.2\-106\-gef11927+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -493,7 +493,7 @@ and
 Comma\-separated list of columns or tags to carry over from the annotation file (see also
 \fB\-a, \-\-annotations\fR)\&. If the annotation file is not a VCF/BCF,
 \fIlist\fR
-describes the columns of the annotation file and must include CHROM, POS (or, alternatively, FROM and TO), and optionally REF and ALT\&. Unused columns which should be ignored can be indicated by "\-"\&. If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their order does not matter\&. The columns ID, QUAL, FILTER, INFO and FORMAT can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG", and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG"\&. To carry over all INFO annotations, use "INFO"\&. To add all INFO annotations except "TAG", use "^INFO/TAG"\&. By default, existing values are replaced\&. To add values without overwriting existing annotations, use "+TAG" instead of "TAG"\&. To replace only existing values without modifying missing annotations, use "\-TAG"\&. If the annotation file is not a VCF/BCF, all new annotations must be defined via
+describes the columns of the annotation file and must include CHROM, POS (or, alternatively, FROM and TO), and optionally REF and ALT\&. Unused columns which should be ignored can be indicated by "\-"\&. If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their order does not matter\&. The columns ID, QUAL, FILTER, INFO and FORMAT can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG", and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG"\&. To carry over all INFO annotations, use "INFO"\&. To add all INFO annotations except "TAG", use "^INFO/TAG"\&. By default, existing values are replaced\&. To add annotations without overwriting existing values (that is, to add missing tags or add values to existing tags with missing values), use "+TAG" instead of "TAG"\&. To append to existing values (rather than replacing or leaving untouched), use "=TAG" (instead of "TAG" or "+TAG")\&. To replace only existing values without modifying missing annotations, use "\-TAG"\&. If the annotation file is not a VCF/BCF, all new annotations must be defined via
 \fB\-h, \-\-header\-lines\fR\&.
 .RE
 .PP
diff --git a/doc/bcftools.html b/doc/bcftools.html
index 1e85ce392..630794e1b 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp146224"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp151728"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
 work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-08-05 15:36 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-104-gf47097b+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-08-05 16:03 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-106-gef11927+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -217,8 +217,11 @@
     can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG",
     and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
     To carry over all INFO annotations, use "INFO". To add all INFO annotations except
-    "TAG", use "^INFO/TAG". By default, existing values are replaced. To add
-    values without overwriting existing annotations, use "+TAG" instead of "TAG".
+    "TAG", use "^INFO/TAG". By default, existing values are replaced.
+    To add annotations without overwriting existing values (that is, to add missing tags or
+    add values to existing tags with missing values), use "+TAG" instead of "TAG".
+    To append to existing values (rather than replacing or leaving untouched), use "=TAG"
+    (instead of "TAG" or "+TAG").
     To replace only existing values without modifying missing annotations, use "-TAG".
     If the annotation file is not a VCF/BCF, all new annotations must be
     defined via <span class="strong"><strong>-h, --header-lines</strong></span>.

From 90d0a6a123bcf8df6417e8e3fff07982a27142fd Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 30 Jul 2015 08:44:02 +0100
Subject: [PATCH 055/211] Proper ploidy initialization when the sexes are added
 explicitly.

---
 ploidy.c | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ploidy.c b/ploidy.c
index 3d3027aa2..8449d66a4 100644
--- a/ploidy.c
+++ b/ploidy.c
@@ -228,6 +228,8 @@ int ploidy_add_sex(ploidy_t *ploidy, const char *sex)
     ploidy->nsex++;
     hts_expand0(char*,ploidy->nsex,ploidy->msex,ploidy->id2sex);
     ploidy->id2sex[ploidy->nsex-1] = strdup(sex);
+    ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
+    ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt;
     return khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
 }
 

From 3b0378f430ce1f14ff71edf593b943e5c9c0cb3c Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 31 Jul 2015 14:09:42 +0100
Subject: [PATCH 056/211] call -m fix: skip sites with too many alleles (>32)
 instead of silently overwriting internal data structures..

---
 call.h  |  4 ++--
 mcall.c | 22 +++++++++++++++++++---
 2 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/call.h b/call.h
index 72f6fd87c..cc5e6d7b0 100644
--- a/call.h
+++ b/call.h
@@ -100,8 +100,8 @@ typedef struct
 
     double pl2p[256];       // PL to 10^(-PL/10) table
     int32_t *PLs;           // VCF PL likelihoods (rw)
-    int nPLs, mPLs;
-    int32_t *gts, ac[4];    // GTs and AC (w)
+    int nPLs, mPLs, nac;
+    int32_t *gts, *ac;      // GTs and AC (w)
     double *pdg;            // PLs converted to P(D|G)
     float *anno16; int n16; // see anno[16] in bam2bcf.h
     double theta;           // prior
diff --git a/mcall.c b/mcall.c
index a6096d8ca..b37593c1b 100644
--- a/mcall.c
+++ b/mcall.c
@@ -311,6 +311,7 @@ void mcall_destroy(call_t *call)
     free(call->gts); free(call->cgts); free(call->ugts);
     free(call->pdg);
     free(call->als);
+    free(call->ac);
     return;
 }
 
@@ -726,7 +727,7 @@ static void mcall_call_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_a
     int nout_gts = nout_als*(nout_als+1)/2;
     hts_expand(float,nout_gts*nsmpl,call->nGPs,call->GPs);
 
-    for (i=0; i<4; i++) call->ac[i] = 0;
+    for (i=0; i<nout_als; i++) call->ac[i] = 0;
     call->nhets = 0;
     call->ndiploid = 0;
 
@@ -1346,6 +1347,7 @@ int mcall(call_t *call, bcf1_t *rec)
 
     int nsmpl = bcf_hdr_nsamples(call->hdr);
     int nals  = rec->n_allele;
+    hts_expand(int,nals,call->nac,call->ac);
     hts_expand(int,nals,call->nals_map,call->als_map);
     hts_expand(int,nals*(nals+1)/2,call->npl_map,call->pl_map);
 
@@ -1391,7 +1393,13 @@ int mcall(call_t *call, bcf1_t *rec)
     #endif
 
     // Find the best combination of alleles
-    int out_als, nout = mcall_find_best_alleles(call, nals, &out_als);
+    int out_als, nout;
+    if ( nals > 8*sizeof(out_als) )
+    { 
+        fprintf(stderr,"Too many alleles at %s:%d, skipping.\n", bcf_seqname(call->hdr,rec),rec->pos+1); 
+        return 0; 
+    }
+    nout = mcall_find_best_alleles(call, nals, &out_als);
 
     // Make sure the REF allele is always present
     if ( !(out_als&1) )
@@ -1431,12 +1439,20 @@ int mcall(call_t *call, bcf1_t *rec)
         if ( !is_variant )
             mcall_set_ref_genotypes(call,nals);     // running with -A, prevent mcall_call_genotypes from putting some ALT back
         else if ( call->flag & CALL_CONSTR_TRIO )
+        {
+            if ( nout>4 ) 
+            { 
+                fprintf(stderr,"Too many alleles at %s:%d, skipping.\n", bcf_seqname(call->hdr,rec),rec->pos+1); 
+                return 0; 
+            }
             mcall_call_trio_genotypes(call, rec, nals,nout,out_als);
+        }
         else
             mcall_call_genotypes(call,rec,nals,nout,out_als);
 
         // Skip the site if all samples are 0/0. This can happen occasionally.
-        nAC = call->ac[1] + call->ac[2] + call->ac[3];
+        nAC = 0;
+        for (i=1; i<nout; i++) nAC += call->ac[i];
         if ( !nAC && call->flag & CALL_VARONLY ) return 0;
         mcall_trim_PLs(call, rec, nals, nout, out_als);
     }

From d4d42ca7615dcf3014e5746c284b2f14b3ade8c0 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Fri, 7 Aug 2015 09:03:49 +0100
Subject: [PATCH 057/211] Check that opening chain and output files succeeded

Fixes #302.
---
 consensus.c | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/consensus.c b/consensus.c
index 08f3d7d63..732526a63 100644
--- a/consensus.c
+++ b/consensus.c
@@ -26,6 +26,8 @@
 
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
+#include <errno.h>
 #include <getopt.h>
 #include <unistd.h>
 #include <ctype.h>
@@ -205,11 +207,16 @@ static void init_data(args_t *args)
     if ( args->chain_fname )
     {
         args->fp_chain = fopen(args->chain_fname,"w");
+        if ( ! args->fp_chain ) error("Failed to create %s: %s\n", args->chain_fname, strerror(errno));
         args->chain_id = 0;
     }
     rbuf_init(&args->vcf_rbuf, 100);
     args->vcf_buf = (bcf1_t**) calloc(args->vcf_rbuf.m, sizeof(bcf1_t*));
-    args->fp_out = args->output_fname ? fopen(args->output_fname,"w") : stdout;
+    if ( args->output_fname ) {
+        args->fp_out = fopen(args->output_fname,"w");
+        if ( ! args->fp_out ) error("Failed to create %s: %s\n", args->output_fname, strerror(errno));
+    }
+    else args->fp_out = stdout;
 }
 
 static void destroy_data(args_t *args)

From 63dd6d11e751a26755f268939779c081c79a77c3 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 1 Sep 2015 13:58:17 +0100
Subject: [PATCH 058/211] include missing call to set ploidy and add test

mpileup.ploidy bed file has `*` lines commented out at
the moment as the bed reader does not like those lines
---
 test/mpileup.X.out   |   40 +
 test/mpileup.X.vcf   | 4127 ++++++++++++++++++++++++++++++++++++++++++
 test/mpileup.ped     |    3 +
 test/mpileup.ploidy  |    4 +
 test/mpileup.samples |    3 +
 test/test.pl         |    3 +
 vcfcall.c            |   21 +
 7 files changed, 4201 insertions(+)
 create mode 100644 test/mpileup.X.out
 create mode 100644 test/mpileup.X.vcf
 create mode 100644 test/mpileup.ped
 create mode 100644 test/mpileup.ploidy
 create mode 100644 test/mpileup.samples

diff --git a/test/mpileup.X.out b/test/mpileup.X.out
new file mode 100644
index 000000000..9a9d427a6
--- /dev/null
+++ b/test/mpileup.X.out
@@ -0,0 +1,40 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
+##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	302	.	T	TA	481	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=49	GT:PL:DP:DV	0/1:167,0,96:11:6	1:157,9:7:6	1/1:201,21,0:7:7
+X	828	.	T	C	321	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	1:116,91:9:5	1/1:120,12,0:4:4
+X	834	.	G	A	308	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,3,7,10;MQ=60	GT:PL:DP:DV	0/1:185,0,46:11:9	1:128,59:8:5	1/1:89,9,0:3:3
+X	1665	.	T	C	3.10665	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
+X	1869	.	A	T	138	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,9,5,4;MQ=58	GT:PL:DP:DV	0/1:115,0,224:18:7	0/1:16,0,104:5:1	1/1:42,3,0:1:1
+X	2041	.	G	A	447	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,5,12,7;MQ=58	GT:PL:DP:DV	0/1:229,0,212:21:11	0/1:32,0,24:2:1	1/1:223,21,0:7:7
+X	2220	.	G	A	303	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,2,1,11;MQ=58	GT:PL:DP:DV	0/1:139,0,130:12:6	0/1:69,0,46:4:2	1/1:131,12,0:4:4
+X	2564	.	A	G	233	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=1,4,4,5;MQ=60	GT:PL:DP:DV	0/1:88,0,78:6:3	0/1:57,0,56:4:2	1/1:124,12,0:4:4
+X	3104	.	C	T	24.1975	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=8,15,2,0;MQ=58	GT:PL:DP:DV	0/0:0,48,255:16:0	0:0,144:4:0	0/1:59,0,93:5:2
+X	3587	.	G	A	332	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=4,7,10,6;MQ=60	GT:PL:DP:DV	0/1:161,0,184:14:7	0:22,118:5:1	1/1:212,24,0:8:8
+X	3936	.	A	G	412	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=5,6,6,17;MQ=56	GT:PL:DP:DV	0/1:233,0,206:20:11	1:77,58:6:4	1/1:196,24,0:8:8
diff --git a/test/mpileup.X.vcf b/test/mpileup.X.vcf
new file mode 100644
index 000000000..ea2983a3b
--- /dev/null
+++ b/test/mpileup.X.vcf
@@ -0,0 +1,4127 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	1	.	A	<*>	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	2	.	A	<*>	0	.	DP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	3	.	G	<*>	0	.	DP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	4	.	C	<*>	0	.	DP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,71:3:0
+X	5	.	T	<*>	0	.	DP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	6	.	T	<*>	0	.	DP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	7	.	C	<*>	0	.	DP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	8	.	T	<*>	0	.	DP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	9	.	C	<*>	0	.	DP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	10	.	A	<*>	0	.	DP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,69:3:0
+X	11	.	C	<*>	0	.	DP=11;I16=11,0,0,0,413,15603,0,0,319,9251,0,0,241,5495,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	12	.	C	<*>	0	.	DP=11;I16=11,0,0,0,438,17506,0,0,319,9251,0,0,242,5562,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	13	.	C	<*>	0	.	DP=11;I16=11,0,0,0,437,17463,0,0,319,9251,0,0,243,5639,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	14	.	T	<*>	0	.	DP=11;I16=11,0,0,0,453,18715,0,0,319,9251,0,0,242,5628,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	15	.	G	<*>	0	.	DP=11;I16=11,0,0,0,439,17599,0,0,319,9251,0,0,240,5580,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	16	.	T	<*>	0	.	DP=11;I16=11,0,0,0,426,16546,0,0,319,9251,0,0,238,5544,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	17	.	T	<*>	0	.	DP=11;I16=11,0,0,0,407,15195,0,0,319,9251,0,0,235,5469,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	18	.	C	<*>	0	.	DP=12;I16=12,0,0,0,450,17136,0,0,379,12851,0,0,231,5353,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,113:6:0	0,9,72:3:0	0,9,72:3:0
+X	19	.	C	<*>	0	.	DP=13;I16=13,0,0,0,502,19652,0,0,439,16451,0,0,228,5246,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,112:6:0	0,12,89:4:0	0,9,72:3:0
+X	20	.	T	<*>	0	.	DP=13;I16=13,0,0,0,532,21878,0,0,439,16451,0,0,226,5150,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,116:6:0	0,12,98:4:0	0,9,72:3:0
+X	21	.	G	<*>	0	.	DP=13;I16=13,0,0,0,498,19254,0,0,439,16451,0,0,224,5066,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,117:6:0	0,12,94:4:0	0,9,72:3:0
+X	22	.	C	<*>	0	.	DP=13;I16=13,0,0,0,511,20289,0,0,470,19210,0,0,223,4993,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,115:6:0	0,12,91:4:0	0,9,76:3:0
+X	23	.	A	<*>	0	.	DP=14;I16=14,0,0,0,513,19399,0,0,530,22810,0,0,223,4931,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,133:7:0	0,12,82:4:0	0,9,82:3:0
+X	24	.	T	<*>	0	.	DP=14;I16=14,0,0,0,534,20540,0,0,530,22810,0,0,224,4882,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,131:7:0	0,12,96:4:0	0,9,80:3:0
+X	25	.	A	<*>	0	.	DP=15;I16=15,0,0,0,561,21133,0,0,590,26410,0,0,225,4847,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,140:8:0	0,12,96:4:0	0,9,81:3:0
+X	26	.	G	<*>	0	.	DP=15;I16=15,0,0,0,591,23429,0,0,590,26410,0,0,227,4827,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,96:4:0	0,9,81:3:0
+X	27	.	A	<*>	0	.	DP=15;I16=15,0,0,0,588,23120,0,0,590,26410,0,0,229,4823,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,12,98:4:0	0,9,83:3:0
+X	28	.	T	<*>	0	.	DP=16;I16=16,0,0,0,605,23001,0,0,650,30010,0,0,231,4835,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,147:8:0	0,12,97:4:0	0,12,101:4:0
+X	29	.	A	<*>	0	.	DP=17;I16=17,0,0,0,615,22533,0,0,710,33610,0,0,234,4864,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,15,102:5:0	0,12,104:4:0
+X	30	.	A	<*>	0	.	DP=17;I16=17,0,0,0,660,25914,0,0,710,33610,0,0,238,4912,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,149:8:0	0,15,115:5:0	0,12,108:4:0
+X	31	.	T	<*>	0	.	DP=17;I16=17,0,0,0,656,25392,0,0,710,33610,0,0,242,4980,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,150:8:0	0,15,113:5:0	0,12,105:4:0
+X	32	.	T	<*>	0	.	DP=17;I16=17,0,0,0,605,21789,0,0,741,36369,0,0,247,5067,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,143:8:0	0,15,104:5:0	0,12,104:4:0
+X	33	.	G	<*>	0	.	DP=17;I16=17,0,0,0,659,25757,0,0,741,36369,0,0,252,5124,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,158:8:0	0,15,118:5:0	0,12,105:4:0
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+X	1914	.	C	<*>	0	.	DP=27;I16=15,12,0,0,1010,38762,0,0,1577,93889,0,0,561,12703,0,0;QS=3,0;MQSB=0.958048;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,221:8:0	0,6,75:2:0
+X	1915	.	T	C,<*>	0	.	DP=27;I16=14,12,1,0,974,37184,16,256,1560,93600,17,289,543,12389,18,324;QS=2.97351,0.0264901,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.958048;BQB=1;MQ0F=0	PL:DP:DV	0,34,255,48,255,255:17:1	0,24,231,24,231,231:8:0	0,6,60,6,60,60:2:0
+X	1916	.	G	T,<*>	0	.	DP=27;I16=14,12,1,0,991,38291,15,225,1560,93600,17,289,544,12454,17,289;QS=2.97581,0.0241935,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.958048;BQB=1;MQ0F=0	PL:DP:DV	0,35,255,48,255,255:17:1	0,24,226,24,226,226:8:0	0,6,69,6,69,69:2:0
+X	1917	.	C	<*>	0	.	DP=27;I16=15,12,0,0,1030,39740,0,0,1577,93889,0,0,561,12793,0,0;QS=3,0;MQSB=0.958048;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,214:8:0	0,6,73:2:0
+X	1918	.	A	<*>	0	.	DP=27;I16=15,11,0,0,963,36201,0,0,1517,90289,0,0,542,12502,0,0;QS=3,0;MQSB=0.960078;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,24,217:8:0	0,6,72:2:0
+X	1919	.	C	<*>	0	.	DP=27;I16=15,12,0,0,987,36651,0,0,1577,93889,0,0,560,12902,0,0;QS=3,0;MQSB=0.958048;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,214:8:0	0,6,72:2:0
+X	1920	.	A	T,<*>	0	.	DP=29;I16=15,12,0,1,1007,38337,14,196,1546,91130,60,3600,538,12518,21,441;QS=2.97647,0.0235294,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.999735;BQB=1;MQ0F=0	PL:DP:DV	0,36,255,48,255,255:17:1	0,24,225,24,225,225:8:0	0,9,101,9,101,101:3:0
+X	1921	.	G	<*>	0	.	DP=30;I16=15,14,0,0,1059,39815,0,0,1666,98330,0,0,542,12474,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,182:7:0	0,12,132:4:0
+X	1922	.	T	<*>	0	.	DP=29;I16=14,14,0,0,1013,37513,0,0,1649,98041,0,0,532,12418,0,0;QS=3,0;MQSB=0.949591;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,197:7:0	0,12,134:4:0
+X	1923	.	G	<*>	0	.	DP=28;I16=14,14,0,0,1034,38974,0,0,1606,94730,0,0,545,12629,0,0;QS=3,0;MQSB=0.999736;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,188:7:0	0,12,126:4:0
+X	1924	.	C	<*>	0	.	DP=27;I16=13,13,0,0,965,36587,0,0,1486,87530,0,0,521,12017,0,0;QS=3,0;MQSB=0.999671;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,183:7:0	0,12,116:4:0
+X	1925	.	C	<*>	0	.	DP=27;I16=14,13,0,0,987,37021,0,0,1546,91130,0,0,546,12626,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,187:7:0	0,12,124:4:0
+X	1926	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1031,40057,0,0,1546,91130,0,0,545,12581,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,197:7:0	0,12,141:4:0
+X	1927	.	T	<*>	0	.	DP=27;I16=13,13,0,0,959,35773,0,0,1529,90841,0,0,538,12522,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,191:7:0	0,12,133:4:0
+X	1928	.	C	<*>	0	.	DP=27;I16=13,13,0,0,986,38264,0,0,1529,90841,0,0,538,12532,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,189:7:0	0,12,125:4:0
+X	1929	.	T	<*>	0	.	DP=27;I16=13,13,0,0,990,38630,0,0,1529,90841,0,0,538,12562,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,189:7:0	0,12,139:4:0
+X	1930	.	G	<*>	0	.	DP=26;I16=13,11,0,0,905,34865,0,0,1409,83641,0,0,521,12271,0,0;QS=3,0;MQSB=0.931547;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,179:6:0	0,9,99:3:0
+X	1931	.	C	<*>	0	.	DP=27;I16=15,12,0,0,967,36293,0,0,1546,91130,0,0,540,12578,0,0;QS=3,0;MQSB=0.99881;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,165:6:0	0,12,121:4:0
+X	1932	.	T	<*>	0	.	DP=27;I16=14,13,0,0,998,38154,0,0,1546,91130,0,0,541,12605,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,143:5:0	0,15,146:5:0
+X	1933	.	T	<*>	0	.	DP=27;I16=14,13,0,0,962,35344,0,0,1546,91130,0,0,542,12602,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,142:5:0	0,15,158:5:0
+X	1934	.	G	<*>	0	.	DP=27;I16=13,13,0,0,987,38219,0,0,1529,90841,0,0,543,12569,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,15,134:5:0	0,15,143:5:0
+X	1935	.	C	<*>	0	.	DP=27;I16=14,12,0,0,963,36627,0,0,1529,90841,0,0,520,11930,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,162:6:0	0,15,154:5:0
+X	1936	.	C	<*>	0	.	DP=27;I16=14,13,0,0,1018,39406,0,0,1589,94441,0,0,547,12561,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,177:6:0	0,15,159:5:0
+X	1937	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1036,40636,0,0,1589,94441,0,0,547,12489,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,182:6:0	0,15,170:5:0
+X	1938	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1001,38377,0,0,1589,94441,0,0,546,12392,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,166:6:0	0,15,155:5:0
+X	1939	.	T	<*>	0	.	DP=27;I16=14,12,0,0,964,36430,0,0,1560,93600,0,0,525,11909,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,167:6:0	0,12,144:4:0
+X	1940	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1003,37937,0,0,1589,94441,0,0,542,12172,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,159:6:0	0,15,155:5:0
+X	1941	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1004,38072,0,0,1589,94441,0,0,540,12098,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,176:6:0	0,15,156:5:0
+X	1942	.	C	<*>	0	.	DP=27;I16=14,12,0,0,996,38790,0,0,1560,93600,0,0,516,11564,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,174:6:0	0,12,140:4:0
+X	1943	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1044,40952,0,0,1589,94441,0,0,536,12022,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,184:6:0	0,15,167:5:0
+X	1944	.	T	<*>	0	.	DP=27;I16=14,13,0,0,987,37237,0,0,1589,94441,0,0,533,11971,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,15,170:5:0
+X	1945	.	T	<*>	0	.	DP=27;I16=14,13,0,0,993,37067,0,0,1589,94441,0,0,530,11946,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,174:6:0	0,15,171:5:0
+X	1946	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1013,38617,0,0,1589,94441,0,0,526,11896,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,162:6:0	0,15,162:5:0
+X	1947	.	A	<*>	0	.	DP=26;I16=13,13,0,0,950,35522,0,0,1529,90841,0,0,522,11818,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,167:6:0	0,15,160:5:0
+X	1948	.	G	C,<*>	0	.	DP=27;I16=14,12,0,1,966,36912,16,256,1560,93600,29,841,493,11135,25,625;QS=2.90361,0.0963855,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.94394;BQB=1;MQ0F=0	PL:DP:DV	0,45,255,45,255,255:15:0	0,21,190,21,190,190:7:0	1,0,123,13,126,132:5:1
+X	1949	.	A	<*>	0	.	DP=26;I16=14,11,0,0,871,31325,0,0,1469,87241,0,0,490,11048,0,0;QS=3,0;MQSB=0.929204;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,174:7:0	0,15,155:5:0
+X	1950	.	A	<*>	0	.	DP=27;I16=14,13,0,0,1007,38049,0,0,1589,94441,0,0,511,11559,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,205:7:0	0,18,176:6:0
+X	1951	.	G	<*>	0	.	DP=27;I16=14,13,0,0,960,35536,0,0,1589,94441,0,0,509,11469,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,180:7:0	0,18,181:6:0
+X	1952	.	A	<*>	0	.	DP=27;I16=14,12,0,0,924,33366,0,0,1529,90841,0,0,483,10779,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,184:7:0	0,18,182:6:0
+X	1953	.	A	<*>	0	.	DP=28;I16=15,12,0,0,925,32719,0,0,1589,94441,0,0,482,10740,0,0;QS=3,0;MQSB=0.935229;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,189:7:0	0,18,168:6:0
+X	1954	.	A	C,<*>	0	.	DP=29;I16=14,13,0,1,929,33219,18,324,1620,97200,29,841,475,10679,25,625;QS=2.90217,0.0978261,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.949591;BQB=1;MQ0F=0	PL:DP:DV	0,45,255,45,255,255:15:0	0,21,198,21,198,198:7:0	0,0,130,15,133,141:6:1
+X	1955	.	C	<*>	0	.	DP=29;I16=14,12,0,0,961,36067,0,0,1560,93600,0,0,451,10035,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,206:7:0	0,15,165:5:0
+X	1956	.	C	<*>	0	.	DP=29;I16=14,13,0,0,964,35402,0,0,1620,97200,0,0,475,10573,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,15,164:5:0
+X	1957	.	C	<*>	0	.	DP=29;I16=14,13,0,0,980,36212,0,0,1620,97200,0,0,472,10420,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,183:7:0	0,15,167:5:0
+X	1958	.	C	<*>	0	.	DP=29;I16=15,13,0,0,1003,37293,0,0,1649,98041,0,0,493,10825,0,0;QS=3,0;MQSB=0.942064;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,191:7:0	0,18,190:6:0
+X	1959	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1112,43258,0,0,1709,101641,0,0,491,10593,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,213:7:0	0,18,193:6:0
+X	1960	.	T	<*>	0	.	DP=30;I16=17,13,0,0,1053,37939,0,0,1769,105241,0,0,485,10339,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,196:7:0	0,18,186:6:0
+X	1961	.	C	<*>	0	.	DP=30;I16=17,13,0,0,1101,41737,0,0,1769,105241,0,0,480,10122,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,195:7:0	0,18,183:6:0
+X	1962	.	T	<*>	0	.	DP=29;I16=17,12,0,0,1134,44582,0,0,1709,101641,0,0,477,9941,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,208:7:0	0,18,198:6:0
+X	1963	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1066,41050,0,0,1649,98041,0,0,476,9794,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,192:7:0	0,18,188:6:0
+X	1964	.	G	<*>	0	.	DP=28;I16=16,12,0,0,970,34764,0,0,1649,98041,0,0,475,9681,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,178:7:0	0,18,169:6:0
+X	1965	.	T	<*>	0	.	DP=29;I16=16,12,0,0,964,34772,0,0,1649,98041,0,0,449,8977,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,18,171:6:0
+X	1966	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1029,37027,0,0,1709,101641,0,0,474,9558,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,191:7:0	0,18,181:6:0
+X	1967	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1030,37234,0,0,1709,101641,0,0,474,9550,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,187:7:0	0,18,182:6:0
+X	1968	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1075,40173,0,0,1709,101641,0,0,474,9578,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,195:7:0	0,18,190:6:0
+X	1969	.	A	<*>	0	.	DP=28;I16=16,12,0,0,992,35828,0,0,1649,98041,0,0,474,9592,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,18,186:6:0
+X	1970	.	C	<*>	0	.	DP=28;I16=16,12,0,0,1015,37503,0,0,1649,98041,0,0,474,9642,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,170:6:0	0,18,180:6:0
+X	1971	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1073,40273,0,0,1709,101641,0,0,474,9728,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,178:6:0	0,21,206:7:0
+X	1972	.	T	<*>	0	.	DP=30;I16=16,14,0,0,1068,38978,0,0,1769,105241,0,0,475,9851,0,0;QS=3,0;MQSB=0.946202;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,176:6:0	0,21,203:7:0
+X	1973	.	A	<*>	0	.	DP=30;I16=16,13,0,0,1046,38070,0,0,1740,104400,0,0,452,9388,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,172:6:0	0,18,196:6:0
+X	1974	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1086,41474,0,0,1709,101641,0,0,477,10065,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,157:5:0	0,21,214:7:0
+X	1975	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1067,41171,0,0,1649,98041,0,0,478,10156,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,133:4:0	0,21,195:7:0
+X	1976	.	A	<*>	0	.	DP=28;I16=16,12,0,0,981,34839,0,0,1649,98041,0,0,478,10234,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,125:4:0	0,21,199:7:0
+X	1977	.	C	<*>	0	.	DP=28;I16=16,12,0,0,1009,37471,0,0,1649,98041,0,0,477,10297,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,132:4:0	0,21,194:7:0
+X	1978	.	A	<*>	0	.	DP=28;I16=16,12,0,0,1082,42132,0,0,1649,98041,0,0,476,10394,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,144:4:0	0,21,220:7:0
+X	1979	.	G	<*>	0	.	DP=28;I16=16,11,0,0,1019,38927,0,0,1589,94441,0,0,454,10064,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,12,122:4:0	0,21,208:7:0
+X	1980	.	C	<*>	0	.	DP=27;I16=16,10,0,0,932,34456,0,0,1529,90841,0,0,452,10114,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,107:3:0	0,21,197:7:0
+X	1981	.	C	<*>	0	.	DP=28;I16=16,12,0,0,998,36510,0,0,1649,98041,0,0,469,10479,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,9,101:3:0	0,24,219:8:0
+X	1982	.	A	<*>	0	.	DP=29;I16=16,12,0,0,1035,38815,0,0,1649,98041,0,0,472,10548,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,110:3:0	0,27,254:9:0
+X	1983	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1048,40322,0,0,1649,98041,0,0,477,10599,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,96:3:0	0,27,249:9:0
+X	1984	.	A	<*>	0	.	DP=27;I16=16,11,0,0,1024,39232,0,0,1589,94441,0,0,482,10632,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,70:2:0	0,27,255:9:0
+X	1985	.	G	<*>	0	.	DP=27;I16=16,11,0,0,1009,38449,0,0,1589,94441,0,0,487,10695,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,66:2:0	0,27,231:9:0
+X	1986	.	A	<*>	0	.	DP=27;I16=16,10,0,0,926,33696,0,0,1560,93600,0,0,466,10112,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,76:2:0	0,24,223:8:0
+X	1987	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1034,39088,0,0,1649,98041,0,0,495,10807,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,78:2:0	0,27,247:9:0
+X	1988	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1050,39980,0,0,1649,98041,0,0,499,10855,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,63:2:0	0,27,239:9:0
+X	1989	.	G	<*>	0	.	DP=28;I16=17,10,0,0,994,37610,0,0,1589,94441,0,0,493,10801,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,73:2:0	0,27,237:9:0
+X	1990	.	G	T,<*>	0	.	DP=28;I16=17,9,0,1,965,36359,33,1089,1560,93600,29,841,472,10250,25,625;QS=2.90675,0.0932476,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.912952;BQB=1;MQ0F=0	PL:DP:DV	0,48,255,48,255,255:16:0	0,6,71,6,71,71:2:0	2,0,195,26,198,215:9:1
+X	1991	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1017,38203,0,0,1649,98041,0,0,507,10975,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,60:2:0	0,27,250:9:0
+X	1992	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1028,38852,0,0,1649,98041,0,0,509,11039,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,62:2:0	0,27,231:9:0
+X	1993	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1015,37325,0,0,1649,98041,0,0,511,11131,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,59:2:0	0,27,243:9:0
+X	1994	.	T	<*>	0	.	DP=27;I16=16,11,0,0,942,33698,0,0,1589,94441,0,0,514,11250,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,54:2:0	0,24,216:8:0
+X	1995	.	G	<*>	0	.	DP=28;I16=16,11,0,0,960,35432,0,0,1620,97200,0,0,492,10770,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,66:2:0	0,21,188:7:0
+X	1996	.	C	<*>	0	.	DP=29;I16=17,12,0,0,1022,37426,0,0,1709,101641,0,0,519,11469,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,64:2:0	0,24,192:8:0
+X	1997	.	C	<*>	0	.	DP=29;I16=17,11,0,0,934,32858,0,0,1649,98041,0,0,520,11524,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,70:2:0	0,24,193:8:0
+X	1998	.	C	<*>	0	.	DP=29;I16=17,12,0,0,1027,37843,0,0,1709,101641,0,0,522,11562,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,69:2:0	0,24,222:8:0
+X	1999	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1073,41493,0,0,1649,98041,0,0,525,11627,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,21,206:7:0
+X	2000	.	G	<*>	0	.	DP=28;I16=16,11,0,0,1036,40576,0,0,1589,94441,0,0,511,11395,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,18,168:6:0
+X	2001	.	G	<*>	0	.	DP=28;I16=15,11,0,0,955,35661,0,0,1529,90841,0,0,489,10853,0,0;QS=3,0;MQSB=0.927041;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,62:2:0	0,18,172:6:0
+X	2002	.	G	<*>	0	.	DP=28;I16=17,10,0,0,907,32227,0,0,1620,97200,0,0,519,11663,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,53:2:0	0,18,163:6:0
+X	2003	.	T	<*>	0	.	DP=28;I16=17,11,0,0,920,31866,0,0,1649,98041,0,0,541,12163,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,49:2:0	0,21,190:7:0
+X	2004	.	G	<*>	0	.	DP=27;I16=16,10,0,0,970,36928,0,0,1560,93600,0,0,530,12110,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,57:2:0	0,18,178:6:0
+X	2005	.	G	<*>	0	.	DP=27;I16=16,10,0,0,868,30936,0,0,1560,93600,0,0,536,12370,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,59:2:0	0,18,153:6:0
+X	2006	.	C	<*>	0	.	DP=27;I16=16,10,0,0,968,37046,0,0,1560,93600,0,0,541,12605,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,73:2:0	0,18,166:6:0
+X	2007	.	A	<*>	0	.	DP=27;I16=16,11,0,0,1000,37396,0,0,1589,94441,0,0,556,12882,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,76:2:0	0,21,193:7:0
+X	2008	.	C	<*>	0	.	DP=26;I16=16,10,0,0,964,36892,0,0,1529,90841,0,0,555,12833,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,21,183:7:0
+X	2009	.	A	<*>	0	.	DP=26;I16=16,10,0,0,997,38955,0,0,1529,90841,0,0,554,12802,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,21,210:7:0
+X	2010	.	G	<*>	0	.	DP=26;I16=16,9,0,0,936,36208,0,0,1500,90000,0,0,542,12640,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,18,169:6:0
+X	2011	.	C	<*>	0	.	DP=26;I16=16,9,0,0,966,37960,0,0,1500,90000,0,0,541,12617,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,18,175:6:0
+X	2012	.	A	<*>	0	.	DP=27;I16=16,11,0,0,956,35018,0,0,1589,94441,0,0,548,12676,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,74:2:0	0,21,189:7:0
+X	2013	.	C	<*>	0	.	DP=27;I16=15,10,0,0,876,31370,0,0,1500,90000,0,0,514,11950,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,69:2:0	0,18,160:6:0
+X	2014	.	G	<*>	0	.	DP=27;I16=17,10,0,0,903,31239,0,0,1589,94441,0,0,545,12591,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,80:3:0	0,18,160:6:0
+X	2015	.	T	<*>	0	.	DP=27;I16=17,10,0,0,999,37507,0,0,1589,94441,0,0,545,12577,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,95:3:0	0,18,178:6:0
+X	2016	.	T	<*>	0	.	DP=27;I16=17,10,0,0,971,35649,0,0,1589,94441,0,0,545,12583,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,93:3:0	0,18,178:6:0
+X	2017	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1013,37849,0,0,1649,98041,0,0,545,12609,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,91:3:0	0,18,172:6:0
+X	2018	.	C	<*>	0	.	DP=28;I16=17,11,0,0,1060,41414,0,0,1649,98041,0,0,546,12656,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,97:3:0	0,18,169:6:0
+X	2019	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1083,42253,0,0,1649,98041,0,0,547,12725,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,106:3:0	0,18,187:6:0
+X	2020	.	G	<*>	0	.	DP=29;I16=18,11,0,0,1095,42063,0,0,1678,98882,0,0,548,12816,0,0;QS=3,0;MQSB=0.987702;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,85:3:0	0,18,175:6:0
+X	2021	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1081,41535,0,0,1709,101641,0,0,551,12877,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,97:3:0	0,15,167:5:0
+X	2022	.	C	<*>	0	.	DP=30;I16=19,11,0,0,1115,42003,0,0,1769,105241,0,0,555,12907,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,18,177:6:0
+X	2023	.	A	<*>	0	.	DP=30;I16=19,10,0,0,1063,39991,0,0,1709,101641,0,0,549,12837,0,0;QS=3,0;MQSB=0.974027;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,18,186:6:0
+X	2024	.	G	<*>	0	.	DP=32;I16=20,12,0,0,1168,43872,0,0,1889,112441,0,0,564,12982,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,24,203:8:0
+X	2025	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1150,42122,0,0,1889,112441,0,0,569,12981,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,87:3:0	0,24,226:8:0
+X	2026	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1130,40724,0,0,1889,112441,0,0,572,12908,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,208:8:0
+X	2027	.	A	<*>	0	.	DP=32;I16=19,12,0,0,1121,40871,0,0,1829,108841,0,0,550,12240,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,84:3:0	0,21,207:7:0
+X	2028	.	C	<*>	0	.	DP=32;I16=20,12,0,0,1242,48548,0,0,1889,112441,0,0,577,12803,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,228:8:0
+X	2029	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1229,47605,0,0,1889,112441,0,0,578,12724,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,102:3:0	0,24,236:8:0
+X	2030	.	G	<*>	0	.	DP=32;I16=20,12,0,0,1222,47140,0,0,1889,112441,0,0,579,12679,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,93:3:0	0,24,216:8:0
+X	2031	.	C	<*>	0	.	DP=31;I16=19,12,0,0,1150,43656,0,0,1829,108841,0,0,581,12667,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,24,204:8:0
+X	2032	.	C	<*>	0	.	DP=31;I16=19,12,0,0,1157,44035,0,0,1829,108841,0,0,583,12687,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,90:3:0	0,24,210:8:0
+X	2033	.	A	<*>	0	.	DP=30;I16=19,11,0,0,1091,40223,0,0,1769,105241,0,0,585,12689,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,93:3:0	0,21,203:7:0
+X	2034	.	T	<*>	0	.	DP=30;I16=19,11,0,0,1104,41498,0,0,1769,105241,0,0,587,12723,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,91:3:0	0,21,208:7:0
+X	2035	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1084,41024,0,0,1709,101641,0,0,589,12739,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,211:7:0
+X	2036	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1080,40612,0,0,1709,101641,0,0,591,12787,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,67:2:0	0,21,216:7:0
+X	2037	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1082,40956,0,0,1709,101641,0,0,592,12818,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,217:7:0
+X	2038	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1117,43573,0,0,1709,101641,0,0,592,12832,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,211:7:0
+X	2039	.	A	<*>	0	.	DP=29;I16=18,11,0,0,1067,39581,0,0,1709,101641,0,0,592,12878,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,72:2:0	0,21,212:7:0
+X	2040	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1077,40469,0,0,1709,101641,0,0,590,12856,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,196:7:0
+X	2041	.	G	A,<*>	0	.	DP=31;I16=6,5,12,7,389,14023,721,28149,660,39600,1109,65641,235,5607,353,7259;QS=0.917304,2.0827,0;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0	PL:DP:DV	229,0,212,255,245,255:21:11	32,0,24,35,27,59:2:1	223,21,0,223,21,223:7:7
+X	2042	.	G	<*>	0	.	DP=32;I16=18,14,0,0,1189,45617,0,0,1889,112441,0,0,588,12910,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,86:3:0	0,21,206:7:0
+X	2043	.	G	<*>	0	.	DP=32;I16=17,14,0,0,1115,41585,0,0,1829,108841,0,0,581,12891,0,0;QS=3,0;MQSB=0.962133;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,90:3:0	0,21,197:7:0
+X	2044	.	C	<*>	0	.	DP=32;I16=18,14,0,0,1213,47029,0,0,1889,112441,0,0,588,13006,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,85:3:0	0,21,207:7:0
+X	2045	.	A	<*>	0	.	DP=32;I16=18,14,0,0,1181,44527,0,0,1889,112441,0,0,588,13108,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,83:3:0	0,21,213:7:0
+X	2046	.	T	<*>	0	.	DP=32;I16=18,14,0,0,1197,45135,0,0,1889,112441,0,0,587,13195,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,103:3:0	0,21,216:7:0
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+X	2729	.	T	<*>	0	.	DP=25;I16=12,13,0,0,871,31019,0,0,1407,81723,0,0,469,10233,0,0;QS=3,0;MQSB=0.619223;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,189:7:0	0,6,62:2:0
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+X	2735	.	T	<*>	0	.	DP=26;I16=13,12,0,0,955,36875,0,0,1438,84482,0,0,451,9877,0,0;QS=3,0;MQSB=0.778801;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,24,228:8:0	0,3,41:1:0
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+X	2737	.	T	<*>	0	.	DP=26;I16=13,13,0,0,967,36581,0,0,1467,85323,0,0,475,10403,0,0;QS=3,0;MQSB=0.606531;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,24,228:8:0	0,6,64:2:0
+X	2738	.	T	<*>	0	.	DP=26;I16=13,13,0,0,895,31873,0,0,1467,85323,0,0,474,10374,0,0;QS=3,0;MQSB=0.606531;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,24,201:8:0	0,6,47:2:0
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+X	2760	.	T	<*>	0	.	DP=25;I16=14,11,0,0,907,33965,0,0,1438,84482,0,0,457,10275,0,0;QS=3,0;MQSB=0.745495;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,204:7:0	0,15,150:5:0
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+X	2765	.	T	<*>	0	.	DP=24;I16=12,11,0,0,853,32173,0,0,1318,77282,0,0,457,10469,0,0;QS=3,0;MQSB=0.7613;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,154:5:0	0,18,189:6:0
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+X	2767	.	T	<*>	0	.	DP=24;I16=12,12,0,0,905,34757,0,0,1378,80882,0,0,458,10510,0,0;QS=3,0;MQSB=0.786628;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,153:5:0	0,21,217:7:0
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+X	2770	.	T	<*>	0	.	DP=23;I16=11,12,0,0,828,30854,0,0,1318,77282,0,0,459,10471,0,0;QS=3,0;MQSB=0.795196;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,152:5:0	0,21,199:7:0
+X	2771	.	T	<*>	0	.	DP=23;I16=11,11,0,0,817,30957,0,0,1258,73682,0,0,454,10456,0,0;QS=3,0;MQSB=0.770381;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,154:5:0	0,18,198:6:0
+X	2772	.	T	<*>	0	.	DP=23;I16=11,12,0,0,856,32206,0,0,1318,77282,0,0,459,10511,0,0;QS=3,0;MQSB=0.795196;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,160:5:0	0,21,210:7:0
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+X	3194	.	T	C,<*>	0	.	DP=21;I16=10,10,1,0,730,26992,18,324,1169,69241,29,841,332,7168,25,625;QS=2.95652,0.0434783,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.99938;BQB=1;MQ0F=0	PL:DP:DV	0,18,255,33,255,255:12:1	0,9,98,9,98,98:3:0	0,18,178,18,178,178:6:0
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+X	3212	.	T	<*>	0	.	DP=17;I16=10,6,0,0,575,21295,0,0,960,57600,0,0,316,6964,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,222:9:0	0,9,100:3:0	0,12,144:4:0
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+X	3230	.	T	<*>	0	.	DP=19;I16=12,6,0,0,669,25441,0,0,1049,62041,0,0,261,5187,0,0;QS=3,0;MQSB=0.961295;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,9,107:3:0	0,12,139:4:0
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+X	3237	.	T	<*>	0	.	DP=17;I16=11,6,0,0,589,21235,0,0,989,58441,0,0,273,5573,0,0;QS=3,0;MQSB=0.955563;MQ0F=0	PL:DP:DV	0,27,230:9:0	0,12,102:4:0	0,12,136:4:0
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+X	3239	.	T	<*>	0	.	DP=17;I16=11,6,0,0,574,20204,0,0,989,58441,0,0,273,5645,0,0;QS=3,0;MQSB=0.955563;MQ0F=0	PL:DP:DV	0,27,220:9:0	0,12,107:4:0	0,12,131:4:0
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+X	3242	.	T	<*>	0	.	DP=19;I16=12,7,0,0,655,23279,0,0,1140,68400,0,0,277,5911,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,30,252:10:0	0,12,104:4:0	0,15,152:5:0
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+X	3528	.	T	<*>	0	.	DP=31;I16=13,16,0,0,1076,41782,0,0,1678,98882,0,0,561,12369,0,0;QS=3,0;MQSB=0.997839;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,193:6:0	0,15,152:5:0
+X	3529	.	T	<*>	0	.	DP=31;I16=12,16,0,0,1016,38674,0,0,1649,98041,0,0,550,12290,0,0;QS=3,0;MQSB=0.96195;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,184:6:0	0,15,154:5:0
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+X	3533	.	T	<*>	0	.	DP=31;I16=13,17,0,0,1074,39206,0,0,1738,102482,0,0,595,13457,0,0;QS=3,0;MQSB=0.996503;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,180:6:0	0,18,176:6:0
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+X	3535	.	T	<*>	0	.	DP=31;I16=14,17,0,0,1042,36456,0,0,1767,103323,0,0,624,14314,0,0;QS=3,0;MQSB=0.924242;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,18,162:6:0	0,18,164:6:0
+X	3536	.	C	<*>	0	.	DP=31;I16=13,17,0,0,1102,41182,0,0,1738,102482,0,0,602,13842,0,0;QS=3,0;MQSB=0.996503;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,178:6:0	0,18,180:6:0
+X	3537	.	C	<*>	0	.	DP=32;I16=13,17,0,0,1142,43828,0,0,1769,105241,0,0,598,13854,0,0;QS=3,0;MQSB=0.963674;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,194:7:0	0,18,185:6:0
+X	3538	.	T	<*>	0	.	DP=32;I16=14,17,0,0,1151,43471,0,0,1798,106082,0,0,603,13923,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,211:7:0	0,18,185:6:0
+X	3539	.	C	<*>	0	.	DP=32;I16=12,17,0,0,1077,40959,0,0,1709,101641,0,0,600,13994,0,0;QS=3,0;MQSB=0.965321;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,170:6:0	0,18,173:6:0
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+X	3551	.	T	<*>	0	.	DP=30;I16=13,16,0,0,1026,36844,0,0,1709,101641,0,0,613,14295,0,0;QS=3,0;MQSB=0.960189;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,192:7:0	0,15,162:5:0
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+X	3553	.	T	A,<*>	0	.	DP=30;I16=13,16,1,0,1047,38333,20,400,1709,101641,29,841,616,14398,16,256;QS=2.96795,0.0320513,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.999136;BQB=1;MQ0F=0	PL:DP:DV	0,34,255,51,255,255:18:1	0,18,178,18,178,178:6:0	0,18,183,18,183,183:6:0
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+X	3559	.	T	<*>	0	.	DP=30;I16=14,16,0,0,1086,40202,0,0,1769,105241,0,0,619,14341,0,0;QS=3,0;MQSB=0.958545;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,171:6:0	0,18,192:6:0
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+X	3564	.	T	<*>	0	.	DP=31;I16=15,15,0,0,1132,43298,0,0,1769,105241,0,0,610,13932,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,192:6:0	0,21,214:7:0
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+X	3570	.	T	<*>	0	.	DP=30;I16=14,15,0,0,1029,37527,0,0,1709,101641,0,0,572,12730,0,0;QS=3,0;MQSB=0.954405;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,12,136:4:0	0,21,213:7:0
+X	3571	.	C	<*>	0	.	DP=28;I16=13,15,0,0,1066,41192,0,0,1649,98041,0,0,568,12564,0,0;QS=3,0;MQSB=0.956162;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,138:4:0	0,21,215:7:0
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+X	3574	.	T	<*>	0	.	DP=29;I16=13,16,0,0,1104,42220,0,0,1709,101641,0,0,552,11942,0,0;QS=3,0;MQSB=0.960189;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,175:5:0	0,21,218:7:0
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+X	3774	.	T	<*>	0	.	DP=25;I16=15,10,0,0,895,33455,0,0,1278,70004,0,0,485,10903,0,0;QS=3,0;MQSB=0.624282;MQ0F=0	PL:DP:DV	0,42,253:14:0	0,18,129:6:0	0,15,178:5:0
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+X	3786	.	T	<*>	0	.	DP=28;I16=16,11,0,0,935,35697,0,0,1375,74973,0,0,490,10774,0,0;QS=3,0;MQSB=0.467219;MQ0F=0	PL:DP:DV	0,48,250:16:0	0,18,145:6:0	0,15,186:5:0
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+X	3790	.	T	<*>	0	.	DP=26;I16=13,10,0,0,829,32293,0,0,1231,68535,0,0,435,9359,0,0;QS=3,0;MQSB=0.445672;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,18,150:6:0	0,12,159:4:0
+X	3791	.	T	<*>	0	.	DP=26;I16=15,10,0,0,887,34725,0,0,1301,72235,0,0,478,10336,0,0;QS=3,0;MQSB=0.382304;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,136:6:0	0,12,159:4:0
+X	3792	.	G	A,<*>	0	.	DP=26;I16=14,8,1,0,809,32805,38,1444,1175,66425,37,1369,417,8991,22,484;QS=2.92629,0.0737052,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.195278;BQB=1;MQ0F=0	PL:DP:DV	0,8,238,42,241,255:15:1	0,12,109,12,109,109:4:0	0,12,157,12,157,157:4:0
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+X	3794	.	C	<*>	0	.	DP=26;I16=15,9,0,0,845,33023,0,0,1241,68635,0,0,438,9324,0,0;QS=3,0;MQSB=0.439649;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,15,120:5:0	0,12,157:4:0
+X	3795	.	C	<*>	0	.	DP=26;I16=14,9,0,0,865,35649,0,0,1231,68535,0,0,408,8622,0,0;QS=3,0;MQSB=0.563599;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,132:5:0	0,12,161:4:0
+X	3796	.	T	<*>	0	.	DP=27;I16=15,11,0,0,964,38998,0,0,1361,75835,0,0,453,9821,0,0;QS=3,0;MQSB=0.334895;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,149:7:0	0,12,164:4:0
+X	3797	.	A	<*>	0	.	DP=27;I16=15,10,0,0,848,32392,0,0,1301,72235,0,0,424,9172,0,0;QS=3,0;MQSB=0.382304;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,124:6:0	0,12,159:4:0
+X	3798	.	T	<*>	0	.	DP=27;I16=14,11,0,0,921,37161,0,0,1301,72235,0,0,430,9554,0,0;QS=3,0;MQSB=0.283586;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,148:7:0	0,12,165:4:0
+X	3799	.	T	<*>	0	.	DP=27;I16=15,11,0,0,913,35929,0,0,1361,75835,0,0,439,9729,0,0;QS=3,0;MQSB=0.334895;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,150:7:0	0,12,161:4:0
+X	3800	.	C	<*>	0	.	DP=26;I16=13,10,0,0,866,36182,0,0,1181,65035,0,0,406,9092,0,0;QS=3,0;MQSB=0.272532;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,104:5:0	0,12,161:4:0
+X	3801	.	T	<*>	0	.	DP=23;I16=12,10,0,0,804,33600,0,0,1121,61435,0,0,430,9750,0,0;QS=3,0;MQSB=0.217267;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,99:5:0	0,9,133:3:0
+X	3802	.	G	<*>	0	.	DP=22;I16=10,9,0,0,730,30516,0,0,994,54486,0,0,380,8550,0,0;QS=3,0;MQSB=0.472367;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,106:4:0	0,9,130:3:0
+X	3803	.	G	<*>	0	.	DP=22;I16=11,9,0,0,703,27393,0,0,1051,57735,0,0,405,9241,0,0;QS=3,0;MQSB=0.372419;MQ0F=0	PL:DP:DV	0,39,249:13:0	0,12,92:4:0	0,9,129:3:0
+X	3804	.	A	<*>	0	.	DP=22;I16=11,9,0,0,740,30360,0,0,1051,57735,0,0,404,9274,0,0;QS=3,0;MQSB=0.372419;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,98:4:0	0,9,132:3:0
+X	3805	.	C	<*>	0	.	DP=22;I16=12,9,0,0,737,29243,0,0,1061,57835,0,0,428,9950,0,0;QS=3,0;MQSB=0.262932;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,12,81:4:0	0,9,130:3:0
+X	3806	.	A	<*>	0	.	DP=22;I16=12,9,0,0,798,32550,0,0,1061,57835,0,0,426,9968,0,0;QS=3,0;MQSB=0.262932;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,12,105:4:0	0,9,128:3:0
+X	3807	.	C	<*>	0	.	DP=22;I16=10,9,0,0,664,25304,0,0,994,54486,0,0,377,8885,0,0;QS=3,0;MQSB=0.472367;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,83:4:0	0,9,115:3:0
+X	3808	.	G	<*>	0	.	DP=21;I16=9,9,0,0,653,25297,0,0,957,53117,0,0,375,8873,0,0;QS=3,0;MQSB=0.597145;MQ0F=0	PL:DP:DV	0,33,233:11:0	0,12,109:4:0	0,9,132:3:0
+X	3809	.	T	<*>	0	.	DP=22;I16=11,10,0,0,779,32151,0,0,1084,60066,0,0,416,9810,0,0;QS=3,0;MQSB=0.285029;MQ0F=0	PL:DP:DV	0,39,249:13:0	0,12,115:4:0	0,12,161:4:0
+X	3810	.	C	<*>	0	.	DP=23;I16=9,11,0,0,811,34815,0,0,1077,60317,0,0,369,8739,0,0;QS=3,0;MQSB=0.499893;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,112:4:0	0,12,153:4:0
+X	3811	.	A	C,<*>	0	.	DP=23;I16=9,11,2,0,777,32631,39,785,1077,60317,67,3349,367,8669,42,914;QS=2.94104,0.0589569,0;VDB=0.18;SGB=0.346553;RPB=0.425;MQB=0.25;MQSB=0.246128;BQB=0.025;MQ0F=0	PL:DP:DV	0,15,248,36,254,255:14:2	0,12,116,12,116,116:4:0	0,12,158,12,158,158:4:0
+X	3812	.	T	<*>	0	.	DP=23;I16=10,11,0,0,802,32860,0,0,1084,60066,0,0,405,9447,0,0;QS=3,0;MQSB=0.187115;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,114:4:0	0,12,160:4:0
+X	3813	.	A	<*>	0	.	DP=22;I16=10,11,0,0,815,35077,0,0,1084,60066,0,0,402,9330,0,0;QS=3,0;MQSB=0.187115;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,119:4:0	0,12,170:4:0
+X	3814	.	G	<*>	0	.	DP=21;I16=8,11,0,0,775,33731,0,0,1037,58597,0,0,375,8605,0,0;QS=3,0;MQSB=0.41781;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,12,113:4:0	0,12,163:4:0
+X	3815	.	A	<*>	0	.	DP=20;I16=8,11,0,0,708,29130,0,0,1010,57328,0,0,397,9049,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,239:11:0	0,12,110:4:0	0,12,162:4:0
+X	3816	.	A	<*>	0	.	DP=20;I16=8,11,0,0,729,31027,0,0,1010,57328,0,0,395,8933,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,248:11:0	0,12,104:4:0	0,12,160:4:0
+X	3817	.	A	<*>	0	.	DP=20;I16=8,11,0,0,752,31580,0,0,1010,57328,0,0,393,8833,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,12,110:4:0	0,12,161:4:0
+X	3818	.	T	<*>	0	.	DP=20;I16=8,11,0,0,728,30466,0,0,1010,57328,0,0,391,8749,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,252:11:0	0,12,115:4:0	0,12,160:4:0
+X	3819	.	A	<*>	0	.	DP=21;I16=9,11,0,0,790,34094,0,0,1039,58169,0,0,389,8681,0,0;QS=3,0;MQSB=0.247381;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,121:4:0	0,12,167:4:0
+X	3820	.	G	<*>	0	.	DP=21;I16=9,11,0,0,788,33636,0,0,1039,58169,0,0,388,8630,0,0;QS=3,0;MQSB=0.247381;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,112:4:0	0,12,157:4:0
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+X	3823	.	T	<*>	0	.	DP=22;I16=9,11,0,0,753,30705,0,0,1042,58520,0,0,380,8460,0,0;QS=3,0;MQSB=0.434285;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,102:4:0	0,12,163:4:0
+X	3824	.	C	<*>	0	.	DP=22;I16=10,11,0,0,802,32368,0,0,1099,61769,0,0,384,8456,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,105:4:0	0,12,159:4:0
+X	3825	.	C	<*>	0	.	DP=23;I16=10,11,0,0,813,33955,0,0,1079,59889,0,0,379,8387,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,130:5:0	0,12,157:4:0
+X	3826	.	T	<*>	0	.	DP=23;I16=11,11,0,0,827,34611,0,0,1136,63138,0,0,381,8357,0,0;QS=3,0;MQSB=0.232836;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,15,133:5:0	0,12,155:4:0
+X	3827	.	G	<*>	0	.	DP=23;I16=11,10,0,0,820,34130,0,0,1076,59538,0,0,355,7715,0,0;QS=3,0;MQSB=0.269397;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,121:4:0	0,12,162:4:0
+X	3828	.	C	<*>	0	.	DP=23;I16=11,10,0,0,805,33147,0,0,1076,59538,0,0,354,7720,0,0;QS=3,0;MQSB=0.269397;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,114:4:0	0,12,157:4:0
+X	3829	.	A	<*>	0	.	DP=22;I16=9,11,0,0,763,31295,0,0,1069,59789,0,0,369,8241,0,0;QS=3,0;MQSB=0.477679;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,132:5:0	0,12,158:4:0
+X	3830	.	A	<*>	0	.	DP=23;I16=11,11,0,0,825,32693,0,0,1136,63138,0,0,377,8321,0,0;QS=3,0;MQSB=0.232836;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,15,143:5:0	0,12,150:4:0
+X	3831	.	C	A,<*>	0	.	DP=23;I16=10,11,1,0,802,32198,14,196,1126,63038,10,100,370,8294,7,49;QS=2.97758,0.0224215,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.232836;BQB=1;MQ0F=0	PL:DP:DV	0,27,255,36,255,255:13:1	0,15,134,15,134,134:5:0	0,12,149,12,149,149:4:0
+X	3832	.	A	<*>	0	.	DP=24;I16=12,11,0,0,836,32436,0,0,1196,66738,0,0,377,8389,0,0;QS=3,0;MQSB=0.291845;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,136:5:0	0,12,139:4:0
+X	3833	.	C	<*>	0	.	DP=23;I16=10,11,0,0,690,24938,0,0,1076,59538,0,0,377,8409,0,0;QS=3,0;MQSB=0.175325;MQ0F=0	PL:DP:DV	0,36,249:12:0	0,15,113:5:0	0,12,131:4:0
+X	3834	.	G	<*>	0	.	DP=22;I16=9,10,0,0,684,26250,0,0,1037,58597,0,0,357,8079,0,0;QS=3,0;MQSB=0.124514;MQ0F=0	PL:DP:DV	0,33,242:11:0	0,12,122:4:0	0,12,156:4:0
+X	3835	.	T	<*>	0	.	DP=22;I16=10,11,0,0,773,30373,0,0,1076,59538,0,0,381,8475,0,0;QS=3,0;MQSB=0.175325;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,140:5:0	0,12,153:4:0
+X	3836	.	G	C,<*>	0	.	DP=24;I16=10,12,1,0,833,33183,14,196,1132,61648,10,100,378,8412,2,4;QS=2.97647,0.0235294,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.251407;BQB=1;MQ0F=0	PL:DP:DV	0,27,255,36,255,255:13:1	0,15,149,15,149,149:5:0	0,15,188,15,188,188:5:0
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+X	3838	.	C	<*>	0	.	DP=24;I16=10,14,0,0,817,28975,0,0,1202,65348,0,0,409,8945,0,0;QS=3,0;MQSB=0.122456;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,18,143:6:0	0,15,148:5:0
+X	3839	.	C	<*>	0	.	DP=23;I16=9,13,0,0,688,22248,0,0,1132,61648,0,0,386,8238,0,0;QS=3,0;MQSB=0.248197;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,123:6:0	0,12,112:4:0
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+X	3841	.	T	<*>	0	.	DP=23;I16=9,14,0,0,867,33103,0,0,1192,65248,0,0,414,8734,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,167:6:0	0,15,162:5:0
+X	3842	.	C	<*>	0	.	DP=23;I16=9,14,0,0,890,34728,0,0,1192,65248,0,0,415,8689,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,167:6:0	0,15,159:5:0
+X	3843	.	T	<*>	0	.	DP=24;I16=9,14,0,0,896,35122,0,0,1192,65248,0,0,416,8674,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,164:6:0	0,15,159:5:0
+X	3844	.	G	<*>	0	.	DP=26;I16=10,16,0,0,959,35715,0,0,1372,76048,0,0,442,9314,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,177:7:0	0,18,172:6:0
+X	3845	.	T	<*>	0	.	DP=26;I16=10,16,0,0,970,36442,0,0,1372,76048,0,0,444,9310,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,186:7:0	0,18,166:6:0
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+X	3868	.	T	<*>	0	.	DP=33;I16=11,22,0,0,1255,48141,0,0,1792,101248,0,0,590,12494,0,0;QS=3,0;MQSB=0.161533;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,202:7:0	0,27,221:9:0
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+X	3870	.	T	<*>	0	.	DP=34;I16=11,23,0,0,1262,47808,0,0,1852,104848,0,0,608,12932,0,0;QS=3,0;MQSB=0.149071;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,24,215:8:0	0,27,211:9:0
+X	3871	.	T	<*>	0	.	DP=36;I16=11,25,0,0,1341,50655,0,0,1972,112048,0,0,617,13157,0,0;QS=3,0;MQSB=0.128391;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,24,221:8:0	0,27,223:9:0
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+X	3873	.	T	<*>	0	.	DP=35;I16=10,24,0,0,1242,46680,0,0,1852,104848,0,0,626,13428,0,0;QS=3,0;MQSB=0.0982034;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,21,194:7:0	0,24,212:8:0
+X	3874	.	T	<*>	0	.	DP=36;I16=12,24,0,0,1290,47660,0,0,1972,112048,0,0,646,13774,0,0;QS=3,0;MQSB=0.182088;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,24,228:8:0	0,24,204:8:0
+X	3875	.	T	<*>	0	.	DP=37;I16=13,24,0,0,1324,48418,0,0,2029,115297,0,0,657,14061,0,0;QS=3,0;MQSB=0.117872;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,231:8:0	0,24,197:8:0
+X	3876	.	C	<*>	0	.	DP=37;I16=13,22,0,0,1248,45354,0,0,1909,108097,0,0,623,13325,0,0;QS=3,0;MQSB=0.140806;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,21,196:7:0	0,24,180:8:0
+X	3877	.	C	<*>	0	.	DP=37;I16=13,24,0,0,1363,51201,0,0,2029,115297,0,0,681,14765,0,0;QS=3,0;MQSB=0.117872;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,217:8:0	0,24,196:8:0
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+X	3912	.	A	C,<*>	0	.	DP=41;I16=17,22,0,1,1358,49508,16,256,2081,116491,60,3600,830,19358,11,121;QS=2.95181,0.0481928,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.125266;BQB=1;MQ0F=0	PL:DP:DV	0,69,255,69,255,255:23:0	0,21,166,21,166,166:7:0	0,14,202,27,205,208:10:1
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+X	3914	.	T	<*>	0	.	DP=42;I16=16,24,0,0,1512,59342,0,0,2141,120091,0,0,823,19007,0,0;QS=3,0;MQSB=0.0846181;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,21,192:7:0	0,30,228:10:0
+X	3915	.	C	<*>	0	.	DP=42;I16=16,24,0,0,1537,60953,0,0,2141,120091,0,0,799,18321,0,0;QS=3,0;MQSB=0.0846181;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,176:6:0	0,30,229:10:0
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+X	3917	.	T	<*>	0	.	DP=43;I16=16,25,0,0,1601,65219,0,0,2201,123691,0,0,825,18875,0,0;QS=3,0;MQSB=0.0757469;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,191:7:0	0,30,254:10:0
+X	3918	.	T	<*>	0	.	DP=43;I16=16,25,0,0,1541,60711,0,0,2201,123691,0,0,801,18239,0,0;QS=3,0;MQSB=0.0757469;MQ0F=0	PL:DP:DV	0,75,255:25:0	0,18,179:6:0	0,30,254:10:0
+X	3919	.	C	<*>	0	.	DP=42;I16=15,26,0,0,1621,66337,0,0,2232,126450,0,0,826,18786,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,200:7:0	0,30,242:10:0
+X	3920	.	T	<*>	0	.	DP=42;I16=15,26,0,0,1605,64327,0,0,2232,126450,0,0,825,18691,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,207:7:0	0,30,251:10:0
+X	3921	.	T	<*>	0	.	DP=42;I16=15,26,0,0,1519,58507,0,0,2232,126450,0,0,824,18630,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,201:7:0	0,30,242:10:0
+X	3922	.	A	<*>	0	.	DP=42;I16=14,26,0,0,1539,61289,0,0,2195,125081,0,0,819,18545,0,0;QS=3,0;MQSB=0.168991;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,179:6:0	0,30,244:10:0
+X	3923	.	G	<*>	0	.	DP=41;I16=14,25,0,0,1515,60945,0,0,2135,121481,0,0,792,17834,0,0;QS=3,0;MQSB=0.182501;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,18,172:6:0	0,30,240:10:0
+X	3924	.	G	<*>	0	.	DP=41;I16=13,26,0,0,1524,61106,0,0,2135,121481,0,0,808,18356,0,0;QS=3,0;MQSB=0.128469;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,18,158:6:0	0,30,247:10:0
+X	3925	.	G	<*>	0	.	DP=41;I16=14,25,0,0,1425,55687,0,0,2135,121481,0,0,788,17758,0,0;QS=3,0;MQSB=0.182501;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,15,134:5:0	0,30,245:10:0
+X	3926	.	C	<*>	0	.	DP=41;I16=14,26,0,0,1512,59674,0,0,2195,125081,0,0,811,18393,0,0;QS=3,0;MQSB=0.168991;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,152:6:0	0,30,237:10:0
+X	3927	.	T	<*>	0	.	DP=41;I16=14,26,0,0,1512,59566,0,0,2195,125081,0,0,808,18384,0,0;QS=3,0;MQSB=0.168991;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,160:6:0	0,30,237:10:0
+X	3928	.	G	<*>	0	.	DP=41;I16=14,25,0,0,1479,58495,0,0,2135,121481,0,0,779,17731,0,0;QS=3,0;MQSB=0.182501;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,149:6:0	0,27,233:9:0
+X	3929	.	A	<*>	0	.	DP=41;I16=13,26,0,0,1452,56436,0,0,2135,121481,0,0,796,18256,0,0;QS=3,0;MQSB=0.128469;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,18,161:6:0	0,30,220:10:0
+X	3930	.	T	<*>	0	.	DP=40;I16=13,25,0,0,1387,52929,0,0,2078,118232,0,0,767,17521,0,0;QS=3,0;MQSB=0.25797;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,15,149:5:0	0,30,224:10:0
+X	3931	.	A	<*>	0	.	DP=40;I16=13,25,0,0,1387,52877,0,0,2078,118232,0,0,761,17439,0,0;QS=3,0;MQSB=0.25797;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,18,166:6:0	0,27,222:9:0
+X	3932	.	T	<*>	0	.	DP=39;I16=12,26,0,0,1394,53644,0,0,2078,118232,0,0,780,17964,0,0;QS=3,0;MQSB=0.190372;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,161:6:0	0,30,231:10:0
+X	3933	.	T	<*>	0	.	DP=38;I16=12,24,0,0,1389,54743,0,0,1958,111032,0,0,752,17366,0,0;QS=3,0;MQSB=0.218161;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,166:6:0	0,24,220:8:0
+X	3934	.	C	<*>	0	.	DP=38;I16=12,25,0,0,1395,54915,0,0,2018,114632,0,0,768,17758,0,0;QS=3,0;MQSB=0.203497;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,152:6:0	0,27,209:9:0
+X	3935	.	C	<*>	0	.	DP=38;I16=12,24,0,0,1239,44621,0,0,1958,111032,0,0,737,17075,0,0;QS=3,0;MQSB=0.218161;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,15,134:5:0	0,27,170:9:0
+X	3936	.	A	G,<*>	0	.	DP=37;I16=5,6,6,17,424,16384,801,30271,609,34563,1314,77018,225,5325,511,11851;QS=0.87994,2.12006,0;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0	PL:DP:DV	233,0,206,255,239,255:20:11	77,0,58,83,70,141:6:4	196,24,0,196,24,196:8:8
+X	3937	.	C	<*>	0	.	DP=36;I16=11,24,0,0,1155,39875,0,0,1952,112422,0,0,745,17291,0,0;QS=3,0;MQSB=0.219636;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,18,143:6:0	0,24,156:8:0
+X	3938	.	G	<*>	0	.	DP=35;I16=11,23,0,0,1155,41761,0,0,1892,108822,0,0,737,17079,0,0;QS=3,0;MQSB=0.231054;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,119:5:0	0,24,176:8:0
+X	3939	.	C	<*>	0	.	DP=35;I16=11,22,0,0,1273,50651,0,0,1832,105222,0,0,703,16221,0,0;QS=3,0;MQSB=0.243713;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,135:5:0	0,21,174:7:0
+X	3940	.	A	<*>	0	.	DP=35;I16=11,22,0,0,1148,42754,0,0,1832,105222,0,0,691,15867,0,0;QS=3,0;MQSB=0.243713;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,117:5:0	0,21,163:7:0
+X	3941	.	C	<*>	0	.	DP=35;I16=11,22,0,0,1216,47488,0,0,1832,105222,0,0,688,15892,0,0;QS=3,0;MQSB=0.243713;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,133:5:0	0,21,181:7:0
+X	3942	.	C	<*>	0	.	DP=35;I16=11,23,0,0,1336,54166,0,0,1892,108822,0,0,690,15772,0,0;QS=3,0;MQSB=0.231054;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,140:5:0	0,24,195:8:0
+X	3943	.	T	<*>	0	.	DP=35;I16=11,23,0,0,1296,51618,0,0,1892,108822,0,0,676,15406,0,0;QS=3,0;MQSB=0.231054;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,142:5:0	0,24,195:8:0
+X	3944	.	G	<*>	0	.	DP=34;I16=10,22,0,0,1199,46445,0,0,1803,104381,0,0,654,14954,0,0;QS=3,0;MQSB=0.1117;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,15,149:5:0	0,24,195:8:0
+X	3945	.	C	<*>	0	.	DP=33;I16=10,22,0,0,1256,51226,0,0,1772,101622,0,0,649,14657,0,0;QS=3,0;MQSB=0.187579;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,15,142:5:0	0,21,177:7:0
+X	3946	.	T	<*>	0	.	DP=33;I16=10,21,0,0,1170,45884,0,0,1712,98022,0,0,609,13599,0,0;QS=3,0;MQSB=0.199344;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,15,144:5:0	0,18,158:6:0
+X	3947	.	A	<*>	0	.	DP=32;I16=10,21,0,0,1094,41048,0,0,1712,98022,0,0,620,13820,0,0;QS=3,0;MQSB=0.199344;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,15,128:5:0	0,18,149:6:0
+X	3948	.	C	<*>	0	.	DP=32;I16=10,20,0,0,1134,45104,0,0,1652,94422,0,0,596,13344,0,0;QS=3,0;MQSB=0.212591;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,105:4:0	0,18,155:6:0
+X	3949	.	A	C,<*>	0	.	DP=32;I16=10,17,0,1,1027,39909,24,576,1472,83622,60,3600,541,12211,25,625;QS=2.85093,0.149068,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.244621;BQB=1;MQ0F=0	PL:DP:DV	0,60,255,60,255,255:20:0	0,9,89,9,89,89:3:0	9,0,107,21,110,124:5:1
+X	3950	.	C	<*>	0	.	DP=33;I16=11,21,0,0,1191,46247,0,0,1772,101622,0,0,576,12680,0,0;QS=3,0;MQSB=0.257801;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,118:5:0	0,18,168:6:0
+X	3951	.	T	<*>	0	.	DP=34;I16=12,19,0,0,1148,44272,0,0,1712,98022,0,0,530,11670,0,0;QS=3,0;MQSB=0.354733;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,15,146:5:0	0,15,152:5:0
+X	3952	.	C	<*>	0	.	DP=35;I16=13,20,0,0,1176,43762,0,0,1832,105222,0,0,545,12025,0,0;QS=3,0;MQSB=0.394875;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,158:6:0	0,15,143:5:0
+X	3953	.	C	<*>	0	.	DP=34;I16=13,20,0,0,1246,48436,0,0,1863,107981,0,0,538,11772,0,0;QS=3,0;MQSB=0.252983;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,18,163:6:0	0,18,168:6:0
+X	3954	.	T	<*>	0	.	DP=33;I16=13,19,0,0,1195,45815,0,0,1803,104381,0,0,526,11438,0,0;QS=3,0;MQSB=0.264585;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,18,171:6:0	0,18,167:6:0
+X	3955	.	T	<*>	0	.	DP=32;I16=13,18,0,0,1180,46092,0,0,1743,100781,0,0,515,11139,0,0;QS=3,0;MQSB=0.277468;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,18,173:6:0	0,18,174:6:0
+X	3956	.	C	<*>	0	.	DP=32;I16=13,18,0,0,1181,47021,0,0,1743,100781,0,0,504,10874,0,0;QS=3,0;MQSB=0.277468;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,18,167:6:0	0,18,167:6:0
+X	3957	.	T	<*>	0	.	DP=31;I16=13,17,0,0,1153,46051,0,0,1683,97181,0,0,494,10642,0,0;QS=3,0;MQSB=0.291833;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,18,161:6:0	0,15,162:5:0
+X	3958	.	T	<*>	0	.	DP=31;I16=13,16,0,0,1070,40600,0,0,1623,93581,0,0,483,10393,0,0;QS=3,0;MQSB=0.307929;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,15,139:5:0	0,15,157:5:0
+X	3959	.	A	<*>	0	.	DP=30;I16=14,15,0,0,1062,39758,0,0,1623,93581,0,0,474,10176,0,0;QS=3,0;MQSB=0.377103;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,118:4:0	0,15,154:5:0
+X	3960	.	T	<*>	0	.	DP=30;I16=14,15,0,0,995,36027,0,0,1623,93581,0,0,464,9892,0,0;QS=3,0;MQSB=0.377103;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,105:4:0	0,15,142:5:0
+X	3961	.	G	<*>	0	.	DP=29;I16=12,16,0,0,1067,40899,0,0,1586,92212,0,0,457,9739,0,0;QS=3,0;MQSB=0.455864;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,114:4:0	0,12,122:4:0
+X	3962	.	G	<*>	0	.	DP=29;I16=13,16,0,0,1025,37125,0,0,1623,93581,0,0,471,10053,0,0;QS=3,0;MQSB=0.307929;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,108:4:0	0,15,144:5:0
+X	3963	.	C	<*>	0	.	DP=28;I16=13,15,0,0,1040,39100,0,0,1563,89981,0,0,463,9871,0,0;QS=3,0;MQSB=0.326055;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,12,111:4:0	0,12,126:4:0
+X	3964	.	T	<*>	0	.	DP=27;I16=12,15,0,0,1036,39928,0,0,1503,86381,0,0,456,9720,0,0;QS=3,0;MQSB=0.273507;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,94:3:0	0,12,133:4:0
+X	3965	.	G	<*>	0	.	DP=26;I16=12,14,0,0,993,38165,0,0,1443,82781,0,0,450,9598,0,0;QS=3,0;MQSB=0.29215;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,92:3:0	0,12,134:4:0
+X	3966	.	A	<*>	0	.	DP=26;I16=12,13,0,0,930,34834,0,0,1406,81412,0,0,432,9310,0,0;QS=3,0;MQSB=0.520812;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,90:3:0	0,12,140:4:0
+X	3967	.	T	<*>	0	.	DP=26;I16=12,13,0,0,900,32830,0,0,1406,81412,0,0,421,9001,0,0;QS=3,0;MQSB=0.520812;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,90:3:0	0,9,100:3:0
+X	3968	.	A	<*>	0	.	DP=25;I16=12,13,0,0,885,31773,0,0,1406,81412,0,0,415,8853,0,0;QS=3,0;MQSB=0.520812;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,90:3:0	0,9,99:3:0
+X	3969	.	T	<*>	0	.	DP=24;I16=11,13,0,0,886,32972,0,0,1369,80043,0,0,410,8736,0,0;QS=3,0;MQSB=0.702671;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,85:3:0	0,9,108:3:0
+X	3970	.	T	<*>	0	.	DP=24;I16=11,13,0,0,861,31313,0,0,1369,80043,0,0,405,8649,0,0;QS=3,0;MQSB=0.702671;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,83:3:0	0,9,104:3:0
+X	3971	.	C	<*>	0	.	DP=22;I16=11,11,0,0,815,30625,0,0,1249,72843,0,0,402,8590,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,57:2:0	0,9,103:3:0
+X	3972	.	C	<*>	0	.	DP=22;I16=11,11,0,0,812,30486,0,0,1249,72843,0,0,399,8557,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,55:2:0	0,9,96:3:0
+X	3973	.	A	<*>	0	.	DP=22;I16=11,11,0,0,795,28873,0,0,1249,72843,0,0,395,8501,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,52:2:0	0,9,97:3:0
+X	3974	.	C	<*>	0	.	DP=22;I16=11,11,0,0,729,24447,0,0,1249,72843,0,0,392,8472,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,55:2:0	0,9,78:3:0
+X	3975	.	G	<*>	0	.	DP=22;I16=11,11,0,0,717,24525,0,0,1249,72843,0,0,390,8470,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,46:2:0	0,9,96:3:0
+X	3976	.	C	<*>	0	.	DP=22;I16=11,11,0,0,816,30652,0,0,1249,72843,0,0,387,8445,0,0;QS=3,0;MQSB=0.751921;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,55:2:0	0,9,97:3:0
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+X	4043	.	T	<*>	0	.	DP=10;I16=8,2,0,0,314,10428,0,0,554,31538,0,0,192,4190,0,0;QS=2,0;MQSB=0.75;MQ0F=0	PL:DP:DV	0,27,190:9:0	0,3,35:1:0	0,0,0:0:0
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+X	4045	.	C	<*>	0	.	DP=10;I16=7,2,0,0,291,10099,0,0,494,27938,0,0,176,3906,0,0;QS=1,0;MQSB=0.714286;MQ0F=0	PL:DP:DV	0,27,204:9:0	0,0,0:0:0	0,0,0:0:0
+X	4046	.	C	<*>	0	.	DP=10;I16=8,2,0,0,356,13032,0,0,554,31538,0,0,177,3833,0,0;QS=2,0;MQSB=0.75;MQ0F=0	PL:DP:DV	0,27,212:9:0	0,3,35:1:0	0,0,0:0:0
+X	4047	.	A	<*>	0	.	DP=10;I16=8,2,0,0,347,12557,0,0,554,31538,0,0,172,3734,0,0;QS=2,0;MQSB=0.75;MQ0F=0	PL:DP:DV	0,27,204:9:0	0,3,40:1:0	0,0,0:0:0
+X	4048	.	C	<*>	0	.	DP=10;I16=8,2,0,0,342,12124,0,0,554,31538,0,0,167,3645,0,0;QS=2,0;MQSB=0.75;MQ0F=0	PL:DP:DV	0,27,202:9:0	0,3,37:1:0	0,0,0:0:0
+X	4049	.	G	<*>	0	.	DP=10;I16=7,2,0,0,260,7786,0,0,494,27938,0,0,146,3310,0,0;QS=2,0;MQSB=0.714286;MQ0F=0	PL:DP:DV	0,24,173:8:0	0,3,24:1:0	0,0,0:0:0
+X	4050	.	C	<*>	0	.	DP=9;I16=6,2,0,0,291,10813,0,0,434,24338,0,0,157,3495,0,0;QS=1,0;MQSB=0.666667;MQ0F=0	PL:DP:DV	0,24,204:8:0	0,0,0:0:0	0,0,0:0:0
+X	4051	.	A	<*>	0	.	DP=8;I16=5,2,0,0,259,9679,0,0,374,20738,0,0,146,3370,0,0;QS=1,0;MQSB=0.6;MQ0F=0	PL:DP:DV	0,21,192:7:0	0,0,0:0:0	0,0,0:0:0
+X	4052	.	C	<*>	0	.	DP=8;I16=5,2,0,0,247,9025,0,0,374,20738,0,0,143,3281,0,0;QS=1,0;MQSB=0.6;MQ0F=0	PL:DP:DV	0,21,190:7:0	0,0,0:0:0	0,0,0:0:0
+X	4053	.	C	<*>	0	.	DP=8;I16=6,2,0,0,254,9000,0,0,434,24338,0,0,146,3234,0,0;QS=1,0;MQSB=0.666667;MQ0F=0	PL:DP:DV	0,24,184:8:0	0,0,0:0:0	0,0,0:0:0
+X	4054	.	C	<*>	0	.	DP=8;I16=3,2,0,0,160,5344,0,0,254,13538,0,0,122,2984,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,134:5:0	0,0,0:0:0	0,0,0:0:0
+X	4055	.	G	<*>	0	.	DP=8;I16=6,2,0,0,230,6982,0,0,434,24338,0,0,138,3066,0,0;QS=1,0;MQSB=0.666667;MQ0F=0	PL:DP:DV	0,24,169:8:0	0,0,0:0:0	0,0,0:0:0
+X	4056	.	C	<*>	0	.	DP=8;I16=6,2,0,0,275,10153,0,0,434,24338,0,0,134,2994,0,0;QS=1,0;MQSB=0.666667;MQ0F=0	PL:DP:DV	0,24,197:8:0	0,0,0:0:0	0,0,0:0:0
+X	4057	.	T	<*>	0	.	DP=8;I16=5,2,0,0,243,8603,0,0,374,20738,0,0,127,2877,0,0;QS=1,0;MQSB=0.6;MQ0F=0	PL:DP:DV	0,21,182:7:0	0,0,0:0:0	0,0,0:0:0
+X	4058	.	A	<*>	0	.	DP=7;I16=4,2,0,0,214,7742,0,0,314,17138,0,0,116,2728,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,171:6:0	0,0,0:0:0	0,0,0:0:0
+X	4059	.	C	<*>	0	.	DP=6;I16=4,2,0,0,204,7164,0,0,314,17138,0,0,119,2635,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,168:6:0	0,0,0:0:0	0,0,0:0:0
+X	4060	.	A	<*>	0	.	DP=6;I16=4,2,0,0,227,8683,0,0,314,17138,0,0,115,2501,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,177:6:0	0,0,0:0:0	0,0,0:0:0
+X	4061	.	C	<*>	0	.	DP=6;I16=4,2,0,0,193,6681,0,0,314,17138,0,0,111,2375,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,157:6:0	0,0,0:0:0	0,0,0:0:0
+X	4062	.	T	<*>	0	.	DP=6;I16=4,1,0,0,195,7621,0,0,254,13538,0,0,82,1632,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,15,151:5:0	0,0,0:0:0	0,0,0:0:0
+X	4063	.	C	<*>	0	.	DP=6;I16=4,2,0,0,216,7984,0,0,314,17138,0,0,102,2098,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,170:6:0	0,0,0:0:0	0,0,0:0:0
+X	4064	.	C	<*>	0	.	DP=6;I16=4,2,0,0,227,8747,0,0,314,17138,0,0,97,1949,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,177:6:0	0,0,0:0:0	0,0,0:0:0
+X	4065	.	T	<*>	0	.	DP=6;I16=4,2,0,0,202,6880,0,0,314,17138,0,0,92,1810,0,0;QS=1,0;MQSB=0.5;MQ0F=0	PL:DP:DV	0,18,161:6:0	0,0,0:0:0	0,0,0:0:0
+X	4066	.	T	<*>	0	.	DP=5;I16=3,2,0,0,180,6554,0,0,254,13538,0,0,88,1680,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,153:5:0	0,0,0:0:0	0,0,0:0:0
+X	4067	.	C	<*>	0	.	DP=5;I16=3,2,0,0,181,6637,0,0,254,13538,0,0,84,1558,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,153:5:0	0,0,0:0:0	0,0,0:0:0
+X	4068	.	T	<*>	0	.	DP=5;I16=3,2,0,0,198,7868,0,0,254,13538,0,0,80,1444,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,164:5:0	0,0,0:0:0	0,0,0:0:0
+X	4069	.	T	<*>	0	.	DP=5;I16=3,2,0,0,177,6325,0,0,254,13538,0,0,76,1338,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,154:5:0	0,0,0:0:0	0,0,0:0:0
+X	4070	.	A	<*>	0	.	DP=5;I16=3,2,0,0,161,5263,0,0,254,13538,0,0,72,1240,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,140:5:0	0,0,0:0:0	0,0,0:0:0
+X	4071	.	G	<*>	0	.	DP=5;I16=3,2,0,0,166,5658,0,0,254,13538,0,0,68,1150,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,142:5:0	0,0,0:0:0	0,0,0:0:0
+X	4072	.	G	<*>	0	.	DP=5;I16=2,2,0,0,138,4974,0,0,194,9938,0,0,55,987,0,0;QS=1,0;MQSB=0;MQ0F=0	PL:DP:DV	0,12,122:4:0	0,0,0:0:0	0,0,0:0:0
+X	4073	.	G	<*>	0	.	DP=5;I16=3,2,0,0,156,5082,0,0,254,13538,0,0,60,994,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,136:5:0	0,0,0:0:0	0,0,0:0:0
+X	4074	.	C	<*>	0	.	DP=5;I16=3,2,0,0,160,5602,0,0,254,13538,0,0,56,928,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,142:5:0	0,0,0:0:0	0,0,0:0:0
+X	4075	.	T	<*>	0	.	DP=5;I16=3,2,0,0,187,7069,0,0,254,13538,0,0,52,870,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,155:5:0	0,0,0:0:0	0,0,0:0:0
+X	4076	.	G	<*>	0	.	DP=5;I16=3,2,0,0,174,6298,0,0,254,13538,0,0,48,820,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,149:5:0	0,0,0:0:0	0,0,0:0:0
+X	4077	.	A	<*>	0	.	DP=4;I16=3,1,0,0,138,4810,0,0,194,9938,0,0,44,728,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,121:4:0	0,0,0:0:0	0,0,0:0:0
+X	4078	.	T	<*>	0	.	DP=4;I16=3,1,0,0,143,5173,0,0,194,9938,0,0,40,644,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,124:4:0	0,0,0:0:0	0,0,0:0:0
+X	4079	.	A	<*>	0	.	DP=4;I16=3,1,0,0,121,3847,0,0,194,9938,0,0,36,568,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,107:4:0	0,0,0:0:0	0,0,0:0:0
+X	4080	.	T	<*>	0	.	DP=4;I16=3,0,0,0,106,3778,0,0,134,6338,0,0,25,451,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,9,87:3:0	0,0,0:0:0	0,0,0:0:0
+X	4081	.	T	<*>	0	.	DP=4;I16=3,1,0,0,106,2934,0,0,194,9938,0,0,28,440,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,94:4:0	0,0,0:0:0	0,0,0:0:0
+X	4082	.	C	<*>	0	.	DP=3;I16=2,1,0,0,110,4042,0,0,134,6338,0,0,25,387,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,9,103:3:0	0,0,0:0:0	0,0,0:0:0
+X	4083	.	C	<*>	0	.	DP=3;I16=2,1,0,0,104,3648,0,0,134,6338,0,0,22,340,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,9,98:3:0	0,0,0:0:0	0,0,0:0:0
+X	4084	.	A	<*>	0	.	DP=2;I16=1,1,0,0,78,3050,0,0,97,4969,0,0,20,298,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,74:2:0	0,0,0:0:0	0,0,0:0:0
+X	4085	.	C	<*>	0	.	DP=2;I16=1,1,0,0,62,1940,0,0,97,4969,0,0,18,260,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,62:2:0	0,0,0:0:0	0,0,0:0:0
+X	4086	.	G	<*>	0	.	DP=2;I16=1,1,0,0,56,1640,0,0,97,4969,0,0,16,226,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,56:2:0	0,0,0:0:0	0,0,0:0:0
+X	4087	.	C	<*>	0	.	DP=2;I16=1,1,0,0,69,2405,0,0,97,4969,0,0,14,196,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,68:2:0	0,0,0:0:0	0,0,0:0:0
+X	4088	.	A	<*>	0	.	DP=1;I16=1,0,0,0,39,1521,0,0,37,1369,0,0,13,169,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4089	.	C	<*>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,12,144,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+X	4090	.	C	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,37,1369,0,0,11,121,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,33:1:0	0,0,0:0:0	0,0,0:0:0
+X	4091	.	T	<*>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,10,100,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+X	4092	.	G	<*>	0	.	DP=1;I16=1,0,0,0,37,1369,0,0,37,1369,0,0,9,81,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4093	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,8,64,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4094	.	T	<*>	0	.	DP=1;I16=1,0,0,0,40,1600,0,0,37,1369,0,0,7,49,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4095	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,6,36,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4096	.	C	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,5,25,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+X	4097	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,4,16,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4098	.	C	<*>	0	.	DP=1;I16=1,0,0,0,31,961,0,0,37,1369,0,0,3,9,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,31:1:0	0,0,0:0:0	0,0,0:0:0
+X	4099	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,2,4,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+X	4100	.	C	<*>	0	.	DP=1;I16=1,0,0,0,27,729,0,0,37,1369,0,0,1,1,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,27:1:0	0,0,0:0:0	0,0,0:0:0
+X	4101	.	C	<*>	0	.	DP=1;I16=1,0,0,0,26,676,0,0,37,1369,0,0,0,0,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,26:1:0	0,0,0:0:0	0,0,0:0:0
diff --git a/test/mpileup.ped b/test/mpileup.ped
new file mode 100644
index 000000000..c4226c6e5
--- /dev/null
+++ b/test/mpileup.ped
@@ -0,0 +1,3 @@
+HG00100 HG00100 0 0 2 0
+HG00101 HG00101 0 0 1 0
+HG00102 HG00102 0 0 2 0
diff --git a/test/mpileup.ploidy b/test/mpileup.ploidy
new file mode 100644
index 000000000..4a372abb8
--- /dev/null
+++ b/test/mpileup.ploidy
@@ -0,0 +1,4 @@
+X	1	1000	M	1
+X	3104	5000	M	1
+#*	*	*	M	2
+#*	*	*	F	2
diff --git a/test/mpileup.samples b/test/mpileup.samples
new file mode 100644
index 000000000..be818ea59
--- /dev/null
+++ b/test/mpileup.samples
@@ -0,0 +1,3 @@
+HG00100	F
+HG00101	M
+HG00102	F
diff --git a/test/test.pl b/test/test.pl
index cd9fbe462..8dca4e63d 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -127,6 +127,8 @@
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.1.out',args=>q[-H -q0.3:major],reg=>'');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.1.out',args=>'-mv');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mvg0');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_call_cAls($opts,in=>'mpileup',out=>'mpileup.cAls.out',tab=>'mpileup');
 test_vcf_filter($opts,in=>'filter.1',out=>'filter.1.out',args=>'-mx -g2 -G2');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.2.out',args=>q[-e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S.]);
@@ -524,6 +526,7 @@ sub test_vcf_view
 sub test_vcf_call
 {
     my ($opts,%args) = @_;
+    $args{args} =~ s/{PATH}/$$opts{path}/g;
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call $args{args} $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob $args{args} $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
diff --git a/vcfcall.c b/vcfcall.c
index 7eb56b33e..b6d201f52 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -526,6 +526,26 @@ static int parse_format_flag(const char *str)
     return flag;
 }
 
+static void set_ploidy(args_t *args, bcf1_t *rec)
+{
+    ploidy_query(args->ploidy,(char*)bcf_seqname(args->aux.hdr,rec),rec->pos,args->sex2ploidy,NULL,NULL);
+
+    int i;
+    for (i=0; i<args->nsex; i++)
+        if ( args->sex2ploidy[i]!=args->sex2ploidy_prev[i] ) break;
+
+    if ( i==args->nsex ) return;    // ploidy same as previously
+
+    for (i=0; i<args->nsamples; i++)
+    {
+        if ( args->sample2sex[i]<0 )
+            args->aux.ploidy[i] = -1*args->sample2sex[i];
+        else
+            args->aux.ploidy[i] = args->sex2ploidy[args->sample2sex[i]];
+    }
+
+    int *tmp = args->sex2ploidy; args->sex2ploidy = args->sex2ploidy_prev; args->sex2ploidy_prev = tmp;
+}
 
 ploidy_t *init_ploidy(char *alias)
 {
@@ -788,6 +808,7 @@ int main_vcfcall(int argc, char *argv[])
         if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue;   // REF[0] is 'N'
 
         bcf_unpack(bcf_rec, BCF_UN_ALL);
+        if ( args.nsex ) set_ploidy(&args, bcf_rec);
 
         // Various output modes: QCall output (todo)
         if ( args.flag & CF_QCALL )

From b1bf66a7287bfa67ca22cfb20633c53f3bf6a25e Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 1 Sep 2015 16:25:03 +0100
Subject: [PATCH 059/211] Fix parsing of the default ploidy lines, both tab or
 spaces will work now

---
 ploidy.c | 23 ++++++++++++++++-------
 1 file changed, 16 insertions(+), 7 deletions(-)

diff --git a/ploidy.c b/ploidy.c
index 8449d66a4..160bc3eae 100644
--- a/ploidy.c
+++ b/ploidy.c
@@ -54,16 +54,27 @@ regidx_t *ploidy_regions(ploidy_t *ploidy)
 
 int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
 {
+    int i, ret;
     ploidy_t *ploidy = (ploidy_t*) usr;
     void *sex2id = ploidy->sex2id;
 
-    // Fill CHR,FROM,TO
-    int i, ret = regidx_parse_tab(line,chr_beg,chr_end,reg,NULL,NULL);
-    if ( ret!=0 ) return ret;
+    // Check for special case of default ploidy "* * * <sex> <ploidy>"
+    int default_ploidy_def = 0;
 
-    // Skip the fields already parsed by regidx_parse_tab
     char *ss = (char*) line;
     while ( *ss && isspace(*ss) ) ss++;
+    if ( ss[0]=='*' && (!ss[1] || isspace(ss[1])) )
+        default_ploidy_def = 1; // definition of default ploidy, chr="*"
+    else
+    {
+        // Fill CHR,FROM,TO
+        ret = regidx_parse_tab(line,chr_beg,chr_end,reg,NULL,NULL);
+        if ( ret!=0 ) return ret;
+    }
+
+    // Skip the fields already parsed by regidx_parse_tab
+    ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
     for (i=0; i<3; i++)
     {
         while ( *ss && !isspace(*ss) ) ss++;
@@ -99,9 +110,7 @@ int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, v
     if ( sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy;
 
     // Special case, chr="*" stands for a default value
-    ss = (char*) line;
-    while ( *ss && isspace(*ss) ) ss++;
-    if ( ss[0]=='*' && (!ss[1] || isspace(ss[1])) ) 
+    if ( default_ploidy_def )
     {
         ploidy->sex2dflt[ploidy->nsex-1] = sp->ploidy;
         return -1;

From 9a06670bfe512824f9b1e026eab5927ea6b344b2 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 1 Sep 2015 16:29:18 +0100
Subject: [PATCH 060/211] default ploidy now ready from file after
 b1bf66a7287bfa67ca22cfb20633c53f3bf6a25e

---
 test/mpileup.ploidy | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/mpileup.ploidy b/test/mpileup.ploidy
index 4a372abb8..b9eba8a34 100644
--- a/test/mpileup.ploidy
+++ b/test/mpileup.ploidy
@@ -1,4 +1,4 @@
 X	1	1000	M	1
 X	3104	5000	M	1
-#*	*	*	M	2
-#*	*	*	F	2
+*	*	*	M	2
+*	*	*	F	2

From 354b980fe11568aeeab42ee77efd5ca05a1dc5cf Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 2 Sep 2015 11:11:23 +0100
Subject: [PATCH 061/211] docs: clarify `--include-type` and `--exclude-types`

addresses the documentation comment raised in #310, but not
the comment about bold vs italic for elements that are not
metasyntactic, which will require more extensive update to
the man page docs to be consistent across the board.
---
 doc/bcftools.txt | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 0c64c4265..9cfeb6ffe 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1599,14 +1599,14 @@ Convert between VCF and BCF. Former *bcftools subset*.
 *-P, --exclude-phased*::
     exclude sites where all samples are phased
 
-*-q, --min-af* 'FLOAT'[':nref'|':alt1'|':minor'|:'major'|:'nonmajor']::
+*-q, --min-af* 'FLOAT'[':nref'|':alt1'|':minor'|':major'|':nonmajor']::
     minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
     Specifying the type of allele is optional and can be set to 
     non-reference ('nref', the default), 1st alternate  ('alt1'), the least 
     frequent ('minor'), the most frequent ('major') or sum of all but the 
     most frequent ('nonmajor') alleles.
 
-*-Q, --max-af* 'FLOAT'[':nref'|':alt1'|':minor'|:'major'|:'nonmajor']::
+*-Q, --max-af* 'FLOAT'[':nref'|':alt1'|':minor'|':major'|':nonmajor']::
     maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
     Specifying the type of allele is optional and can be set to 
     non-reference ('nref', the default), 1st alternate  ('alt1'), the least 
@@ -1620,14 +1620,21 @@ Convert between VCF and BCF. Former *bcftools subset*.
     exclude sites without a called genotype
 
 *-v, --types* 'snps'|'indels'|'mnps'|'other'::
-    comma-separated list of variant types to select
+    comma-separated list of variant types to select. Site is selected if 
+    any of the ALT alleles is of the type requested. Types are determined 
+    by comparing the REF and ALT alleles in the VCF record not INFO tags 
+    like INFO/INDEL or INFO/VT. Use *--include* to select based on INFO 
+    tags.
 
 *-V, --exclude-types* 'snps'|'indels'|'mnps'|'other'::
-    comma-separated list of variant types to exclude
+    comma-separated list of variant types to exclude. Site is excluded if 
+    any of the ALT alleles is of the type requested. Types are determined 
+    by comparing the REF and ALT alleles in the VCF record not INFO tags 
+    like INFO/INDEL or INFO/VT. Use *--exclude* to exclude based on INFO tags.
 
 *-x, --private*::
     print sites where only the subset samples carry an non-reference allele.
-    Requires --samples or --samples-file.
+    Requires *--samples* or *--samples-file*.
 
 *-X, --exclude-private*::
     exclude sites where only the subset samples carry an non-reference allele

From 26778fa1f097a5463251ec17aca077ee0bc5df69 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 2 Sep 2015 11:49:53 +0100
Subject: [PATCH 062/211] fix FORMAT float filtering, resolves #312

hattip @mfoll for the test case
---
 filter.c           |  1 +
 test/filter.10.out | 11 +++++++++++
 test/filter.4.vcf  | 10 ++++++++++
 test/test.pl       |  2 ++
 4 files changed, 24 insertions(+)
 create mode 100644 test/filter.10.out
 create mode 100644 test/filter.4.vcf

diff --git a/filter.c b/filter.c
index ccc844568..9ae263b44 100644
--- a/filter.c
+++ b/filter.c
@@ -500,6 +500,7 @@ static void filters_set_format_float(filter_t *flt, bcf1_t *line, token_t *tok)
             tok->nsamples = tok->nvalues = nsmpl;
         }
     }
+    tok->nsamples = tok->nvalues;
 }
 static void filters_set_format_string(filter_t *flt, bcf1_t *line, token_t *tok)
 {
diff --git a/test/filter.10.out b/test/filter.10.out
new file mode 100644
index 000000000..05743909c
--- /dev/null
+++ b/test/filter.10.out
@@ -0,0 +1,11 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=chr1,length=135006516>
+##INFO=<ID=TEST1,Number=1,Type=Integer,Description="Test1">
+##INFO=<ID=TEST2,Number=1,Type=Float,Description="Test2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=TEST3,Number=1,Type=Integer,Description="Test3">
+##FORMAT=<ID=TEST4,Number=1,Type=Float,Description="Test4">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2
+chr1	1	.	A	T	100	PASS	TEST1=10;TEST2=10	GT:TEST3:TEST4	0/1:10:10	./.:30:30
+chr1	2	.	A	T	100	PASS	TEST1=50;TEST2=50	GT:TEST3:TEST4	0/1:20:20	./.:40:40
diff --git a/test/filter.4.vcf b/test/filter.4.vcf
new file mode 100644
index 000000000..78ce13a5c
--- /dev/null
+++ b/test/filter.4.vcf
@@ -0,0 +1,10 @@
+##fileformat=VCFv4.1
+##contig=<ID=chr1,length=135006516>
+##INFO=<ID=TEST1,Number=1,Type=Integer,Description="Test1">
+##INFO=<ID=TEST2,Number=1,Type=Float,Description="Test2">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=TEST3,Number=1,Type=Integer,Description="Test3">
+##FORMAT=<ID=TEST4,Number=1,Type=Float,Description="Test4">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2
+chr1	1	.	A	T	100	.	TEST1=10;TEST2=10	GT:TEST3:TEST4	0/1:10:10	0/1:30:30
+chr1	2	.	A	T	100	.	TEST1=50;TEST2=50	GT:TEST3:TEST4	0/1:20:20	0/1:40:40
diff --git a/test/test.pl b/test/test.pl
index 08ab49bba..e56347d95 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -144,6 +144,8 @@
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.8.out',args=>q[-i'FMT/GT="0/0" && AC[*]=2'],fmt=>'%POS\\t%AC[\\t%GT]\\n');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.8.out',args=>q[-i'AC[*]=2 && FMT/GT="0/0"'],fmt=>'%POS\\t%AC[\\t%GT]\\n');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.9.out',args=>q[-i'ALT="."'],fmt=>'%POS\\t%AC[\\t%GT]\\n');
+test_vcf_filter($opts,in=>'filter.4',out=>'filter.10.out',args=>q[-S . -i 'FORMAT/TEST3<25']);
+test_vcf_filter($opts,in=>'filter.4',out=>'filter.10.out',args=>q[-S . -i 'FORMAT/TEST4<25']);
 test_vcf_regions($opts,in=>'regions');
 test_vcf_annotate($opts,in=>'annotate',tab=>'annotate',out=>'annotate.out',args=>'-c CHROM,POS,REF,ALT,ID,QUAL,INFO/T_INT,INFO/T_FLOAT,INDEL');
 test_vcf_annotate($opts,in=>'annotate',tab=>'annotate2',out=>'annotate2.out',args=>'-c CHROM,FROM,TO,T_STR');

From 0dbe41e541b5a7796a84bc19bb52e742571266af Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Wed, 2 Sep 2015 14:37:58 +0100
Subject: [PATCH 063/211] Avoid using C99 NAN macro

CentOS 5.11's compiler doesn't believe in it, even though it accepts
isnan() and other C99 library functions.  Hat tip @mfoll.
---
 vcfstats.c | 12 +++---------
 1 file changed, 3 insertions(+), 9 deletions(-)

diff --git a/vcfstats.c b/vcfstats.c
index 578be7bce..1032bf87b 100644
--- a/vcfstats.c
+++ b/vcfstats.c
@@ -1341,7 +1341,7 @@ static void print_stats(args_t *args)
                 uint64_t mm = stats[i].mm[T2S(GT_HOM_RR)] + stats[i].mm[T2S(GT_HET_RA)] + stats[i].mm[T2S(GT_HOM_AA)];
                 // Calculate r by formula 19.2 - Biostatistical Analysis 4th edition - Jerrold H. Zar
                 smpl_r_t *smpl_r = smpl_r_array + i;
-                double r = NAN;
+                double r = 0.0;
                 if (smpl_r->n) {
                     double sum_crossprod = smpl_r->xy-(smpl_r->x*smpl_r->y)/smpl_r->n;//per 17.3 machine formula
                     double x2_xx = smpl_r->x2-(smpl_r->x*smpl_r->x)/smpl_r->n;
@@ -1351,14 +1351,8 @@ static void print_stats(args_t *args)
                 printf("GC%cS\t2\t%s\t%.3f",  x==0 ? 's' : 'i', args->files->samples[i], m+mm ? mm*100.0/(m+mm) : 0);
                 printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"", stats[i].m[T2S(GT_HOM_RR)],stats[i].m[T2S(GT_HET_RA)],stats[i].m[T2S(GT_HOM_AA)]);
                 printf("\t%"PRId64"\t%"PRId64"\t%"PRId64"", stats[i].mm[T2S(GT_HOM_RR)],stats[i].mm[T2S(GT_HET_RA)],stats[i].mm[T2S(GT_HOM_AA)]);
-                if (isnan(r))
-                {
-                    printf("\t"NA_STRING"\n");
-                }
-                else
-                {
-                    printf("\t%f\n", r*r);
-                }
+                if (smpl_r->n && !isnan(r)) printf("\t%f\n", r*r);
+                else printf("\t"NA_STRING"\n");
             }
         }
     }

From 8e82f7d537f784382f0a6261d6450d37acff2527 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 2 Sep 2015 15:21:45 +0100
Subject: [PATCH 064/211] update docs...

after fcd451b53be8c5121f2aed587ac6b6e406218a8d and 354b980fe11568aeeab42ee77efd5ca05a1dc5cf
---
 doc/bcftools.1    | 83 +++++++++++++++++++++++++++++++++++++++++------
 doc/bcftools.html | 68 +++++++++++++++++++++++++++++++-------
 doc/bcftools.txt  |  2 +-
 3 files changed, 131 insertions(+), 22 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index ac2f16c68..3194bad86 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-08-05 16:03 BST
+.\"      Date: 2015-09-02 15:10 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-08\-05 16:03 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-09\-02 15:10 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-08\-05 16:03 BST\fR and refers to bcftools git version \fB1\&.2\-106\-gef11927+\fR\&.
+This manual page was last updated \fB2015\-09\-02 15:10 BST\fR and refers to bcftools git version \fB1\&.2\-119\-g0dbe41e+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -411,10 +411,35 @@ Comma\-separated list of samples to include or exclude if prefixed with "^"\&.
 .RS 4
 File of sample names to include or exclude if prefixed with "^"\&. One sample per line\&. The command
 \fBbcftools call\fR
-accepts an optional second column indicating ploidy (0, 1 or 2) and can parse also PED files\&. With
+accepts an optional second column indicating ploidy (0, 1 or 2) or sex (as defined by
+\fB\-\-ploidy\fR, for example "F" or "M"), and can parse also PED files\&. If the second column is not present, the sex "F" is assumed\&. With
 \fBbcftools call\fR\fB \-C\fR
-\fItrio\fR, PED file is expected\&.
+\fItrio\fR, PED file is expected\&. File formats examples:
 .RE
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    sample1    1
+    sample2    2
+    sample3    2
+
+  or
+
+    sample1    M
+    sample2    F
+    sample3    F
+
+  or a \&.ped file (here is shown a minimum working example, the first column is
+  ignored and the last indicates sex: 1=male, 2=female)
+
+    ignored daughterA fatherA motherA 2
+    ignored sonB fatherB motherB 1
+.fi
+.if n \{\
+.RE
+.\}
 .PP
 \fB\-t, \-\-targets\fR [^]\fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
 .RS 4
@@ -655,6 +680,37 @@ see
 \fBCommon Options\fR
 .RE
 .PP
+\fB\-\-ploidy\fR \fIASSEMBLY\fR[\fI?\fR]
+.RS 4
+predefined ploidy, use
+\fIlist\fR
+(or any other unused word) to print a list of all predefined assemblies\&. Append a question mark to print the actual definition\&. See also
+\fB\-\-ploidy\-file\fR\&.
+.RE
+.PP
+\fB\-\-ploidy\-file\fR \fIFILE\fR
+.RS 4
+ploidy definition given as a space/tab\-delimited list of CHROM, FROM, TO, SEX, PLOIDY\&. The SEX codes are arbitrary and correspond to the ones used by
+\fB\-\-samples\-file\fR\&. The default ploidy can be given using the starred records (see below), unlisted regions have ploidy 2\&. The default ploidy definition is
+.RE
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    X 1 60000 M 1
+    X 2699521 154931043 M 1
+    Y 1 59373566 M 1
+    Y 1 59373566 F 0
+    MT 1 16569 M 1
+    MT 1 16569 F 1
+    *  * *     M 2
+    *  * *     F 2
+.fi
+.if n \{\
+.RE
+.\}
+.PP
 \fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
 .RS 4
 see
@@ -2806,12 +2862,12 @@ print sites where all samples are phased\&. Haploid genotypes are considered pha
 exclude sites where all samples are phased
 .RE
 .PP
-\fB\-q, \-\-min\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|:\*(Aqmajor\*(Aq|:\*(Aqnonmajor\*(Aq]
+\fB\-q, \-\-min\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|\fI:major\fR|\fI:nonmajor\fR]
 .RS 4
 minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed\&. Specifying the type of allele is optional and can be set to non\-reference (\fInref\fR, the default), 1st alternate (\fIalt1\fR), the least frequent (\fIminor\fR), the most frequent (\fImajor\fR) or sum of all but the most frequent (\fInonmajor\fR) alleles\&.
 .RE
 .PP
-\fB\-Q, \-\-max\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|:\*(Aqmajor\*(Aq|:\*(Aqnonmajor\*(Aq]
+\fB\-Q, \-\-max\-af\fR \fIFLOAT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|\fI:major\fR|\fI:nonmajor\fR]
 .RS 4
 maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed\&. Specifying the type of allele is optional and can be set to non\-reference (\fInref\fR, the default), 1st alternate (\fIalt1\fR), the least frequent (\fIminor\fR), the most frequent (\fImajor\fR) or sum of all but the most frequent (\fInonmajor\fR) alleles\&.
 .RE
@@ -2828,17 +2884,24 @@ exclude sites without a called genotype
 .PP
 \fB\-v, \-\-types\fR \fIsnps\fR|\fIindels\fR|\fImnps\fR|\fIother\fR
 .RS 4
-comma\-separated list of variant types to select
+comma\-separated list of variant types to select\&. Site is selected if any of the ALT alleles is of the type requested\&. Types are determined by comparing the REF and ALT alleles in the VCF record not INFO tags like INFO/INDEL or INFO/VT\&. Use
+\fB\-\-include\fR
+to select based on INFO tags\&.
 .RE
 .PP
 \fB\-V, \-\-exclude\-types\fR \fIsnps\fR|\fIindels\fR|\fImnps\fR|\fIother\fR
 .RS 4
-comma\-separated list of variant types to exclude
+comma\-separated list of variant types to exclude\&. Site is excluded if any of the ALT alleles is of the type requested\&. Types are determined by comparing the REF and ALT alleles in the VCF record not INFO tags like INFO/INDEL or INFO/VT\&. Use
+\fB\-\-exclude\fR
+to exclude based on INFO tags\&.
 .RE
 .PP
 \fB\-x, \-\-private\fR
 .RS 4
-print sites where only the subset samples carry an non\-reference allele\&. Requires \-\-samples or \-\-samples\-file\&.
+print sites where only the subset samples carry an non\-reference allele\&. Requires
+\fB\-\-samples\fR
+or
+\fB\-\-samples\-file\fR\&.
 .RE
 .PP
 \fB\-X, \-\-exclude\-private\fR
diff --git a/doc/bcftools.html b/doc/bcftools.html
index 630794e1b..a32fa9ddf 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp151728"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp150032"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
 work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-08-05 16:03 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-106-gef11927+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-09-02 15:10 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-119-g0dbe41e+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -151,14 +151,32 @@
     Comma-separated list of samples to include or exclude if prefixed
     with "^".
 </dd><dt><span class="term">
-<span class="strong"><strong>-S, --samples-file</strong></span> <span class="emphasis"><em><span class="^">FILE</span></em></span>
+<span class="strong"><strong>-S, --samples-file</strong></span> <span class="emphasis"><em><span class="^">FILE</span></em></span><a id="samples_file"></a>
 </span></dt><dd>
     File of sample names to include or exclude if prefixed with "^".
     One sample per line.
     The command <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">bcftools call</a></strong></span> accepts an optional second
-    column indicating ploidy (0, 1 or 2) and can parse also PED files.
-    With <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">bcftools call</a> -C</strong></span> <span class="emphasis"><em>trio</em></span>, PED file is expected.
-</dd><dt><span class="term">
+    column indicating ploidy (0, 1 or 2) or sex (as defined by
+    <span class="strong"><strong><a class="link" href="#ploidy">--ploidy</a></strong></span>, for example "F" or "M"), and can parse also PED
+    files. If the second column is not present,
+    the sex "F" is assumed.
+    With <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">bcftools call</a> -C</strong></span> <span class="emphasis"><em>trio</em></span>, PED file is expected. File
+    formats examples:
+</dd></dl></div><pre class="screen">    sample1    1
+    sample2    2
+    sample3    2
+
+  or
+
+    sample1    M
+    sample2    F
+    sample3    F
+
+  or a .ped file (here is shown a minimum working example, the first column is
+  ignored and the last indicates sex: 1=male, 2=female)
+
+    ignored daughterA fatherA motherA 2
+    ignored sonB fatherB motherB 1</pre><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-t, --targets</strong></span> [^]<span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
 </span></dt><dd>
     Similar as <span class="strong"><strong>-r, --regions</strong></span>, but the next position is accessed by streaming the
@@ -323,6 +341,27 @@
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
+<span class="strong"><strong>--ploidy</strong></span> <span class="emphasis"><em>ASSEMBLY</em></span>[<span class="emphasis"><em>?</em></span>]<a id="ploidy"></a>
+</span></dt><dd>
+    predefined ploidy, use <span class="emphasis"><em>list</em></span> (or any other unused word) to print a list
+    of all predefined assemblies. Append a question mark to print the actual
+    definition. See also <span class="strong"><strong>--ploidy-file</strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>--ploidy-file</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    ploidy definition given as a space/tab-delimited list of
+    CHROM, FROM, TO, SEX, PLOIDY. The SEX codes are arbitrary and
+    correspond to the ones used by <span class="strong"><strong><a class="link" href="#samples_file">--samples-file</a></strong></span>.
+    The default ploidy can be given using the starred records (see
+    below), unlisted regions have ploidy 2. The default ploidy definition is
+</dd></dl></div><pre class="screen">    X 1 60000 M 1
+    X 2699521 154931043 M 1
+    Y 1 59373566 M 1
+    Y 1 59373566 F 0
+    MT 1 16569 M 1
+    MT 1 16569 F 1
+    *  * *     M 2
+    *  * *     F 2</pre><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1560,7 +1599,7 @@
 </span></dt><dd>
     exclude sites where all samples are phased
 </dd><dt><span class="term">
-<span class="strong"><strong>-q, --min-af</strong></span> <span class="emphasis"><em>FLOAT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|:'major'|:'nonmajor']
+<span class="strong"><strong>-q, --min-af</strong></span> <span class="emphasis"><em>FLOAT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|<span class="emphasis"><em>:major</em></span>|<span class="emphasis"><em>:nonmajor</em></span>]
 </span></dt><dd>
     minimum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
     Specifying the type of allele is optional and can be set to
@@ -1568,7 +1607,7 @@
     frequent (<span class="emphasis"><em>minor</em></span>), the most frequent (<span class="emphasis"><em>major</em></span>) or sum of all but the
     most frequent (<span class="emphasis"><em>nonmajor</em></span>) alleles.
 </dd><dt><span class="term">
-<span class="strong"><strong>-Q, --max-af</strong></span> <span class="emphasis"><em>FLOAT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|:'major'|:'nonmajor']
+<span class="strong"><strong>-Q, --max-af</strong></span> <span class="emphasis"><em>FLOAT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|<span class="emphasis"><em>:major</em></span>|<span class="emphasis"><em>:nonmajor</em></span>]
 </span></dt><dd>
     maximum allele frequency (INFO/AC / INFO/AN) of sites to be printed.
     Specifying the type of allele is optional and can be set to
@@ -1586,16 +1625,23 @@
 </dd><dt><span class="term">
 <span class="strong"><strong>-v, --types</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>mnps</em></span>|<span class="emphasis"><em>other</em></span>
 </span></dt><dd>
-    comma-separated list of variant types to select
+    comma-separated list of variant types to select. Site is selected if
+    any of the ALT alleles is of the type requested. Types are determined
+    by comparing the REF and ALT alleles in the VCF record not INFO tags
+    like INFO/INDEL or INFO/VT. Use <span class="strong"><strong>--include</strong></span> to select based on INFO
+    tags.
 </dd><dt><span class="term">
 <span class="strong"><strong>-V, --exclude-types</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>mnps</em></span>|<span class="emphasis"><em>other</em></span>
 </span></dt><dd>
-    comma-separated list of variant types to exclude
+    comma-separated list of variant types to exclude. Site is excluded if
+    any of the ALT alleles is of the type requested. Types are determined
+    by comparing the REF and ALT alleles in the VCF record not INFO tags
+    like INFO/INDEL or INFO/VT. Use <span class="strong"><strong>--exclude</strong></span> to exclude based on INFO tags.
 </dd><dt><span class="term">
 <span class="strong"><strong>-x, --private</strong></span>
 </span></dt><dd>
     print sites where only the subset samples carry an non-reference allele.
-    Requires --samples or --samples-file.
+    Requires <span class="strong"><strong>--samples</strong></span> or <span class="strong"><strong>--samples-file</strong></span>.
 </dd><dt><span class="term">
 <span class="strong"><strong>-X, --exclude-private</strong></span>
 </span></dt><dd>
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 728e8f515..bd3270ba0 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -190,7 +190,7 @@ specific commands to see if they apply.
     Comma-separated list of samples to include or exclude if prefixed
     with "&#94;".
 
-*-S, --samples-file* [&#94;]'FILE'::
+*-S, --samples-file* [&#94;]'FILE'[[samples_file]]::
     File of sample names to include or exclude if prefixed with "&#94;".
     One sample per line.
     The command *<<call,bcftools call>>* accepts an optional second

From cabeeb269722a0c6882574dd13dd81b83957ccc2 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 2 Sep 2015 15:53:52 +0100
Subject: [PATCH 065/211] plot-vcfstats: fix bug in merging multiple stats
 files

d4c7d5c73db224084f94f11d0b0fd40b2ef77d38 introduced new columns
to the DP section of the stats files for the site depth distribiution.
However when run without the -s option this the genotype ditribution
will be now exist, but be filled with zeros causing the bug in #311.

Fixes #311 and adds a test for this. Todo check other merges are
working ok after any column additions.
---
 plot-vcfstats        | 22 ++++++++++++---
 test/check.chk       |  2 ++
 test/check.vcf       |  7 +++--
 test/check_merge.chk | 65 ++++++++++++++++++++++++++++++++++++++++++++
 test/test.pl         | 16 +++++++++--
 5 files changed, 102 insertions(+), 10 deletions(-)
 create mode 100644 test/check_merge.chk

diff --git a/plot-vcfstats b/plot-vcfstats
index 2ed9ec7f5..56cc4c77e 100755
--- a/plot-vcfstats
+++ b/plot-vcfstats
@@ -474,10 +474,24 @@ sub merge_dp
 {
     my ($a,$b) = @_;
     add_to_values($a,$b,\&cmp_num_op);
-    # recalculate fraction of GTs, cannot be simply summed
-    my $sum = 0;
-    for (my $i=0; $i<@$a; $i++) { $sum += $$a[$i][1]; }
-    for (my $i=0; $i<@$a; $i++) { $$a[$i][2] = $$a[$i][1]*100./$sum; }
+    # recalculate fraction of GTs and fraction of sites, cannot be simply summed
+    my $gsum = 0; # genotype sum
+    my $ssum = 0; # site sum
+    for (my $i=0; $i<@$a; $i++)
+    {
+        $gsum += $$a[$i][1];
+        if (@{$$a[$i]}>3) {
+            $ssum += $$a[$i][3];
+        }
+        else{
+            push @{$$a[$i]}, (0,0); # older stats files will not have last 2 columns for (number of sites, fraction of sites), so fill in as zero
+        }
+    }
+    for (my $i=0; $i<@$a; $i++)
+    {
+        $$a[$i][2] = $gsum ? $$a[$i][1]*100./$gsum : 0;
+        $$a[$i][4] = $ssum ? $$a[$i][3]*100./$ssum : 0;
+    }
 }
 
 sub merge_GCsS
diff --git a/test/check.chk b/test/check.chk
index 0f78e654e..7792e00a4 100644
--- a/test/check.chk
+++ b/test/check.chk
@@ -69,6 +69,8 @@ DP	0	30	2	5.555556	0	0.000000
 DP	0	31	16	44.444444	0	0.000000
 DP	0	32	4	11.111111	0	0.000000
 DP	0	35	4	11.111111	0	0.000000
+DP	0	60	0	0.000000	1	33.333333
+DP	0	62	0	0.000000	2	66.666667
 # PSC, Per-sample counts
 # PSC	[2]id	[3]sample	[4]nRefHom	[5]nNonRefHom	[6]nHets	[7]nTransitions	[8]nTransversions	[9]nIndels	[10]average depth	[11]nSingletons
 PSC	0	A	0	2	4	3	2	9	28.7	1
diff --git a/test/check.vcf b/test/check.vcf
index 8fe38e40c..055fd4342 100644
--- a/test/check.vcf
+++ b/test/check.vcf
@@ -1,6 +1,7 @@
 ##fileformat=VCFv4.1
 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="read depth">
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
@@ -27,9 +28,9 @@
 1	3184885	.	TAAAA	TA,T	61.5	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:12:10	1/2:12:10
 2	3199812	.	G	GTT,GT	82.7	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:322:26	1/2:322:26
 3	3212016	.	CTT	C,CT	79	PASS	AN=4;AC=2,2	GT:GQ:DP	1/2:91:26	1/2:91:26
-4	3258448	.	TACACACAC	T	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
-4	3258449	.	GCAAA	GA,G	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
-4	3258450	.	AAAAGAAAAAG	A,AAAAAAG	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
+4	3258448	.	TACACACAC	T	59.9	PASS	DP=62;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
+4	3258449	.	GCAAA	GA,G	59.9	PASS	DP=62;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
+4	3258450	.	AAAAGAAAAAG	A,AAAAAAG	59.9	PASS	DP=60;AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
 4	3258451	.	AAA	AGT	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
 4	3258452	.	AAA	AGA	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
 4	3258453	.	AACA	AGA	59.9	PASS	AN=4;AC=2	GT:GQ:DP	0/1:325:31	0/1:325:31
diff --git a/test/check_merge.chk b/test/check_merge.chk
new file mode 100644
index 000000000..846be5bf5
--- /dev/null
+++ b/test/check_merge.chk
@@ -0,0 +1,65 @@
+#
+# Definition of sets
+# ID	[2]id	[3]tab-separated file names
+# SN, Summary numbers
+# SN  [2]id   [3]key  [4]value
+SN	0	number of indels:	9
+SN	0	number of records:	18
+SN	0	number of multiallelic SNP sites:	1
+SN	0	number of SNPs:	5
+SN	0	number of others:	2
+SN	0	number of MNPs:	1
+SN	0	number of multiallelic sites:	6
+SN	0	number of samples:	2
+SN	0	number of no-ALTs:	1
+# # TSTV, transition/transversions:
+# TSTV	[2]id	[3]ts	[4]tv	[5]ts/tv	[6]ts (1st ALT)	[7]tv (1st ALT)	[8]ts/tv (1st ALT)
+TSTV	0	3	2	1.50	3	1	3.00
+# Sis, Singleton stats
+# SiS	[2]id	[3]allele count	[4]number of SNPs	[5]number of transitions	[6]number of transversions	[7]number of indels	[8]repeat-consistent	[9]repeat-inconsistent	[10]not applicable
+SiS	0	1	3	1	2	0	0	0	0
+# AF, Stats by non-reference allele frequency
+# AF	[2]id	[3]allele frequency	[4]number of SNPs	[5]number of transitions	[6]number of transversions	[7]number of indels	[8]repeat-consistent	[9]repeat-inconsistent	[10]not applicable
+AF	0	0.000000	3	1	2	2	0	0	2
+AF	0	49.000000	0	0	0	12	0	0	12
+AF	0	74.000000	1	1	0	0	0	0	0
+AF	0	99.000000	1	1	0	0	0	0	0
+# IDD, InDel distribution
+# IDD	[2]id	[3]length (deletions negative)	[4]count
+IDD	0	-10	1
+IDD	0	-8	1
+IDD	0	-4	3
+IDD	0	-3	4
+IDD	0	-2	1
+IDD	0	-1	2
+IDD	0	1	1
+IDD	0	2	1
+# ST, Substitution types
+# ST	[2]id	[3]type	[4]count
+ST	0	A>C	0
+ST	0	A>G	0
+ST	0	A>T	0
+ST	0	C>A	0
+ST	0	C>G	0
+ST	0	C>T	0
+ST	0	G>A	3
+ST	0	G>C	1
+ST	0	G>T	1
+ST	0	T>A	0
+ST	0	T>C	0
+ST	0	T>G	0
+# DP, Depth distribution
+# DP	[2]id	[3]bin	[4]number of genotypes	[5]fraction of genotypes (%)	[6]number of sites	[7]fraction of sites (%)
+DP	0	60	0	0.000000	1	33.333333
+DP	0	62	0	0.000000	2	66.666667
+# QUAL, Stats by quality
+# QUAL	[2]id	[3]Quality	[4]number of SNPs	[5]number of transitions (1st ALT)	[6]number of transversions (1st ALT)	[7]number of indels
+QUAL	0	12	1	0	1	1
+QUAL	0	45	0	0	0	1
+QUAL	0	59	2	1	0	3
+QUAL	0	60	1	1	0	0
+QUAL	0	61	0	0	0	1
+QUAL	0	79	0	0	0	1
+QUAL	0	82	0	0	0	1
+QUAL	0	90	1	1	0	0
+QUAL	0	342	0	0	0	1
diff --git a/test/test.pl b/test/test.pl
index 09087137d..595b8c0da 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -44,6 +44,7 @@
 test_vcf_idxstats($opts,in=>'empty',args=>'-s',out=>'empty.idx.out');
 test_vcf_idxstats($opts,in=>'empty',args=>'-n',out=>'empty.idx_count.out');
 test_vcf_check($opts,in=>'check',out=>'check.chk');
+test_vcf_check_merge($opts,in=>'check',out=>'check_merge.chk');
 test_vcf_stats($opts,in=>['stats.a','stats.b'],out=>'stats.chk',args=>'-s -');
 test_vcf_isec($opts,in=>['isec.a','isec.b'],out=>'isec.ab.out',args=>'-n =2');
 test_vcf_isec($opts,in=>['isec.a','isec.b'],out=>'isec.ab.flt.out',args=>'-n =2 -i"STRLEN(REF)==2"');
@@ -128,8 +129,6 @@
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.1.out',args=>q[-H -q0.3:major],reg=>'');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.1.out',args=>'-mv');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mvg0');
-test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
-test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_call_cAls($opts,in=>'mpileup',out=>'mpileup.cAls.out',tab=>'mpileup');
 test_vcf_filter($opts,in=>'filter.1',out=>'filter.1.out',args=>'-mx -g2 -G2');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.2.out',args=>q[-e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S.]);
@@ -423,6 +422,18 @@ sub test_vcf_check
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools stats -s - $$opts{tmp}/$args{in}.vcf.gz | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID\t'");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools stats -s - | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID\t'");
 }
+
+sub test_vcf_check_merge
+{
+    my ($opts,%args) = @_;
+    bgzip_tabix_vcf($opts,$args{in});
+    cmd("$$opts{bin}/bcftools stats -r 1 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.1.chk");
+    cmd("$$opts{bin}/bcftools stats -r 2 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.2.chk");
+    cmd("$$opts{bin}/bcftools stats -r 3 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.3.chk");
+    cmd("$$opts{bin}/bcftools stats -r 4 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.4.chk");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/plot-vcfstats -m $$opts{tmp}/$args{in}.1.chk $$opts{tmp}/$args{in}.2.chk $$opts{tmp}/$args{in}.3.chk $$opts{tmp}/$args{in}.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID\t'");
+}
+
 sub test_vcf_stats
 {
     my ($opts,%args) = @_;
@@ -530,7 +541,6 @@ sub test_vcf_view
 sub test_vcf_call
 {
     my ($opts,%args) = @_;
-    $args{args} =~ s/{PATH}/$$opts{path}/g;
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call $args{args} $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob $args{args} $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }

From 03cfc6a3058f0e02fe50b891b98248a16dbdd5ec Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 2 Sep 2015 16:28:03 +0100
Subject: [PATCH 066/211] add back in tests accidentally deleted in previous
 commit

---
 test/test.pl | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/test/test.pl b/test/test.pl
index 595b8c0da..d2497c4be 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -129,6 +129,8 @@
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.1.out',args=>q[-H -q0.3:major],reg=>'');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.1.out',args=>'-mv');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mvg0');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_call_cAls($opts,in=>'mpileup',out=>'mpileup.cAls.out',tab=>'mpileup');
 test_vcf_filter($opts,in=>'filter.1',out=>'filter.1.out',args=>'-mx -g2 -G2');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.2.out',args=>q[-e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S.]);
@@ -541,7 +543,8 @@ sub test_vcf_view
 sub test_vcf_call
 {
     my ($opts,%args) = @_;
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call $args{args} $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
+	$args{args} =~ s/{PATH}/$$opts{path}/g;
+	test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call $args{args} $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob $args{args} $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_call_cAls

From 590b69775fe04ef57527a3fcc071fb9ce4a9babb Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Wed, 2 Sep 2015 16:34:27 +0100
Subject: [PATCH 067/211] Fix whitespace [trivial]

---
 test/test.pl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/test/test.pl b/test/test.pl
index d2497c4be..2564c80d5 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -543,8 +543,8 @@ sub test_vcf_view
 sub test_vcf_call
 {
     my ($opts,%args) = @_;
-	$args{args} =~ s/{PATH}/$$opts{path}/g;
-	test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call $args{args} $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
+    $args{args} =~ s/{PATH}/$$opts{path}/g;
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call $args{args} $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob $args{args} $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_call_cAls

From 5cf52c44249ffdb4c823e0ae40eea48915a80523 Mon Sep 17 00:00:00 2001
From: Jason Piper <jpiper@HLI-MACPRO48.local>
Date: Thu, 3 Sep 2015 11:12:43 +0800
Subject: [PATCH 068/211] Add test for splitting and merging in one go

---
 test/norm.split.and.norm.out | 64 ++++++++++++++++++++++++++++++++++++
 test/test.pl                 |  1 +
 2 files changed, 65 insertions(+)
 create mode 100644 test/norm.split.and.norm.out

diff --git a/test/norm.split.and.norm.out b/test/norm.split.and.norm.out
new file mode 100644
index 000000000..86154affc
--- /dev/null
+++ b/test/norm.split.and.norm.out
@@ -0,0 +1,64 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=20,length=2147483647>
+##contig=<ID=21,length=2147483647>
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
+##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
+##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	XY00002
+1	105	.	TAAACCCTA	T	999	PASS	INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06;XRI=1111,2222;XRS=AAA,BBB;XAF=1e+06;XAI=1111;XAS=AAA;XGF=1e+06,2e+06,3e+06;XGI=1111,2222,3333;XGS=A,B,C	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC	1/0:1,2,3:1:1e+06,2e+06:1111,2222:AAAA,BBB:1e+06:1111:A:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC
+1	105	.	TA	T	999	PASS	INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF	0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
+2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACC	ACG	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
+2	101	.	A	ATT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+2	101	.	A	AT	999	PASS	INDEL;AN=4;AC=2	GT:DP	0/1:1	0/1:1
+2	114	.	T	TTC	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
+2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+20	3	.	G	CT	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
+20	5	.	TG	CT	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0
+20	5	.	TGG	T	.	PASS	INDEL;AN=4;AC=2	GT:PL:DP	0/1:1,4,6:1	0/1:1,4,6:1
+20	5	.	T	TG	.	PASS	INDEL;AN=4;AC=0	GT:PL:DP	0/0:1,7,10:1	0/0:1,7,10:1
+20	5	.	TGGG	AC	.	PASS	INDEL;AN=4;AC=0	GT:PL:DP	0/0:1,11,15:1	0/0:1,11,15:1
+20	6	.	GGG	AC	.	PASS	INDEL;AN=4;AC=2	GT:PL:DP	1/0:1,2,3:1	1/0:1,2,3:1
+20	59	.	AG	.	999	PASS	AN=4	GT:PL:DP	0/0:0:4	0/0:0:4
+20	81	.	A	C	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	84	.	G	T	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	95	.	T	A	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	95	.	TCACCG	AAAAAA	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	273	.	C	CAA	999	PASS	INDEL;AN=4;AC=2	GT:PL:DP	1/0:0,3,5:1	1/0:0,3,5:1
+20	273	.	C	CAAA	999	PASS	INDEL;AN=4;AC=2	GT:PL:DP	0/1:0,3,5:1	0/1:0,3,5:1
+20	273	.	C	CAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	273	.	C	CAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	275	.	A	C	999	PASS	INDEL;AN=2;AC=0	GT:PL:DP:FGF:FGI:FGS:FSTR	0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD	0:0,0:0:1e+06,2e+06:1111,2222:A,BB:WORD
+20	275	.	A	G	999	PASS	INDEL;AN=2;AC=2	GT:PL:DP:FGF:FGI:FGS:FSTR	1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD	1:0,0:0:1e+06,3e+06:1111,3333:A,CCC:WORD
+20	300	.	T	C	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	300	.	T	G	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+21	1	id	T	TTTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	T	TTTATTATTATTATTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	TTTA	T	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
+21	1	id	T	TTATTA	999	PASS	INDEL;AN=0;AC=0	GT:DP	./.:0	./.:0
diff --git a/test/test.pl b/test/test.pl
index 2564c80d5..6f5056519 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -92,6 +92,7 @@
 test_vcf_query($opts,in=>'annotate2',out=>'query.21.out',args=>q[-e'IFLT="."'  -f'%POS %IFLT\\n']);
 test_vcf_norm($opts,in=>'norm',out=>'norm.out',fai=>'norm');
 test_vcf_norm($opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
+test_vcf_norm($opts,in=>'norm.split',fai=>'norm',out=>'norm.split.and.norm.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.out',args=>'-m+');
 test_vcf_norm($opts,in=>'norm.merge.2',out=>'norm.merge.2.out',args=>'-m+');
 test_vcf_norm($opts,in=>'norm.merge.3',out=>'norm.merge.3.out',args=>'-m+');

From 77d9c1801e05bae982b1a8064f65d8a6f8c9830c Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 3 Sep 2015 14:11:07 +0100
Subject: [PATCH 069/211] Fix in consensus, last position in the buffer was not
 updated. Resolves #306

---
 consensus.c           |  2 +-
 test/consensus2.1.out | 10 ++++++++++
 test/consensus2.2.out | 12 ++++++++++++
 test/consensus2.fa    | 10 ++++++++++
 test/consensus2.vcf   |  9 +++++++++
 test/test.pl          |  2 ++
 6 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 test/consensus2.1.out
 create mode 100644 test/consensus2.2.out
 create mode 100644 test/consensus2.fa
 create mode 100644 test/consensus2.vcf

diff --git a/consensus.c b/consensus.c
index 732526a63..7a615fef0 100644
--- a/consensus.c
+++ b/consensus.c
@@ -567,7 +567,7 @@ static void consensus(args_t *args)
             }
 
             // is the cached fasta buffer full enough? if not, read more fasta, no flushing
-            if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos + rec->rlen )
+            if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off < rec->pos + rec->rlen )
             {
                 unread_vcf_line(args, rec_ptr);
                 break;
diff --git a/test/consensus2.1.out b/test/consensus2.1.out
new file mode 100644
index 000000000..65ec8528c
--- /dev/null
+++ b/test/consensus2.1.out
@@ -0,0 +1,10 @@
+>1
+CTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTA
+>2
+CCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTA
+>3
+CCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTT
+A
+>4
+CCCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGT
+TA
diff --git a/test/consensus2.2.out b/test/consensus2.2.out
new file mode 100644
index 000000000..2040354d9
--- /dev/null
+++ b/test/consensus2.2.out
@@ -0,0 +1,12 @@
+>1
+CTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTCA
+A
+>2
+CCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTC
+AA
+>3
+CCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTT
+CAA
+>4
+CCCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGT
+TCAA
diff --git a/test/consensus2.fa b/test/consensus2.fa
new file mode 100644
index 000000000..9f3522f0c
--- /dev/null
+++ b/test/consensus2.fa
@@ -0,0 +1,10 @@
+>1
+CTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTC
+>2
+CCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTC
+>3
+CCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTT
+C
+>4
+CCCCTACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGT
+TC
diff --git a/test/consensus2.vcf b/test/consensus2.vcf
new file mode 100644
index 000000000..ca4c0595d
--- /dev/null
+++ b/test/consensus2.vcf
@@ -0,0 +1,9 @@
+##fileformat=VCFv4.2
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##ALT=<ID=DEL,Description="Deletion">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA001
+1	59	.	C	a,Caa	.	PASS	.	GT	1|2
+2	60	.	C	a,Caa	.	PASS	.	GT	1|2
+3	61	.	C	a,Caa	.	PASS	.	GT	1|2
+4	62	.	C	a,Caa	.	PASS	.	GT	1|2
diff --git a/test/test.pl b/test/test.pl
index 2564c80d5..f1a589c38 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -206,6 +206,8 @@
 test_vcf_consensus_chain($opts,in=>'consensus',out=>'consensus.3.chain',chain=>'consensus.3.chain',fa=>'consensus.fa',mask=>'consensus.tab',args=>'-i');
 test_vcf_consensus($opts,in=>'consensus',out=>'consensus.4.out',fa=>'consensus.fa',args=>'-H 1');
 test_vcf_consensus_chain($opts,in=>'consensus',out=>'consensus.4.chain',chain=>'consensus.4.chain',fa=>'consensus.fa',args=>'-H 1');
+test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.1.out',fa=>'consensus2.fa',args=>'-H 1');
+test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.2.out',fa=>'consensus2.fa',args=>'-H 2');
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};

From 5940dc04d24120ddba8763b0f1bf7c1a1304778c Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 15 Sep 2015 10:05:30 +0100
Subject: [PATCH 070/211] plot-vcfstats: ensure merged SN fields are in a
 specific order

Fixes #318
---
 plot-vcfstats        | 20 +++++++++++++++-----
 test/check_merge.chk | 12 ++++++------
 2 files changed, 21 insertions(+), 11 deletions(-)

diff --git a/plot-vcfstats b/plot-vcfstats
index 56cc4c77e..e46b3eab8 100755
--- a/plot-vcfstats
+++ b/plot-vcfstats
@@ -124,7 +124,7 @@ sub parse_params
             {
                 id=>'SN',
                 header=>'SN, Summary numbers',
-                exp=>"# SN  [2]id   [3]key  [4]value"
+                exp=>"# SN\t[2]id\t[3]key\t[4]value"
             },
             {
                 id=>'TSTV',
@@ -222,6 +222,17 @@ sub parse_params
                 exp=>"# HWE\t[2]id\t[3]1st ALT allele frequency\t[4]Number of observations\t[5]25th percentile\t[6]median\t[7]75th percentile",
             },
         ],
+        SN_keys=>[
+            'number of samples:',
+            'number of records:',
+            'number of no-ALTs:',
+            'number of SNPs:',
+            'number of MNPs:',
+            'number of indels:',
+            'number of others:',
+            'number of multiallelic sites:',
+            'number of multiallelic SNP sites:',
+        ],
     };
     for my $sec (@{$$opts{sections}}) { $$opts{exp}{$$sec{id}} = $$sec{exp}; $$opts{id2sec}{$$sec{id}} = $sec; }
     while (defined(my $arg=shift(@ARGV)))
@@ -1613,10 +1624,8 @@ sub plot_overlap_by_AF_col
 
 
     ";
-
 }
 
-
 sub plot_indel_distribution
 {
     my ($opts,$id) = @_;
@@ -1769,6 +1778,7 @@ sub fmt_slide3v
             \\hslide{$title}{$slide}
         ];
 }
+
 sub fmt_slide3h
 {
     my ($opts, $image, $title) = @_;
@@ -2097,7 +2107,6 @@ sub create_pdf
     print STDERR "Finished: $pdf_file\n" unless !$$opts{verbose};
 }
 
-
 sub merge_vcfstats
 {
     my ($opts) = @_;
@@ -2131,8 +2140,9 @@ sub merge_vcfstats
             for my $id (keys %{$$opts{dat}})
             {
                 if ( exists($$opts{exp}{$id}) ) { next; }
-                for my $key (keys %{$$opts{dat}{$id}})
+                for my $key (@{$$opts{SN_keys}})
                 {
+                    next unless exists $$opts{dat}{$id}{$key};
                     print $fh "SN\t$id\t$key\t$$opts{dat}{$id}{$key}\n";
                 }
             }
diff --git a/test/check_merge.chk b/test/check_merge.chk
index 846be5bf5..3df3baefa 100644
--- a/test/check_merge.chk
+++ b/test/check_merge.chk
@@ -2,16 +2,16 @@
 # Definition of sets
 # ID	[2]id	[3]tab-separated file names
 # SN, Summary numbers
-# SN  [2]id   [3]key  [4]value
-SN	0	number of indels:	9
+# SN	[2]id	[3]key	[4]value
+SN	0	number of samples:	2
 SN	0	number of records:	18
-SN	0	number of multiallelic SNP sites:	1
+SN	0	number of no-ALTs:	1
 SN	0	number of SNPs:	5
-SN	0	number of others:	2
 SN	0	number of MNPs:	1
+SN	0	number of indels:	9
+SN	0	number of others:	2
 SN	0	number of multiallelic sites:	6
-SN	0	number of samples:	2
-SN	0	number of no-ALTs:	1
+SN	0	number of multiallelic SNP sites:	1
 # # TSTV, transition/transversions:
 # TSTV	[2]id	[3]ts	[4]tv	[5]ts/tv	[6]ts (1st ALT)	[7]tv (1st ALT)	[8]ts/tv (1st ALT)
 TSTV	0	3	2	1.50	3	1	3.00

From ae4c9b0fe44048137599cc6317ea6f3d6fc49bad Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 15 Sep 2015 11:42:40 +0100
Subject: [PATCH 071/211] docs: mention that --fasta-ref is required for
 left-alignment and normalization

as pointed out in #315
---
 doc/bcftools.1    | 12 +++++++-----
 doc/bcftools.html | 17 ++++++++++-------
 doc/bcftools.txt  | 13 ++++++++-----
 3 files changed, 25 insertions(+), 17 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index 3194bad86..d0e609ed1 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-09-02 15:10 BST
+.\"      Date: 2015-09-15 11:42 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-09\-02 15:10 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-09\-15 11:42 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-09\-02 15:10 BST\fR and refers to bcftools git version \fB1\&.2\-119\-g0dbe41e+\fR\&.
+This manual page was last updated \fB2015\-09\-15 11:42 BST\fR and refers to bcftools git version \fB1\&.2\-127\-g5940dc0+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -1857,7 +1857,7 @@ see
 .RE
 .SS "bcftools norm [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR"
 .sp
-Left\-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows\&.
+Left\-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows\&. Left\-alignment and normalization will only be applied if the \fB\-\-fasta\-ref\fR option is supplied\&.
 .PP
 \fB\-c, \-\-check\-ref\fR \fIe\fR|\fIw\fR|\fIx\fR|\fIs\fR
 .RS 4
@@ -1878,7 +1878,9 @@ remove duplicate lines of the same type
 .PP
 \fB\-f, \-\-fasta\-ref\fR \fIFILE\fR
 .RS 4
-reference sequence
+reference sequence\&. Supplying this option will turn on left\-alignment and normalization, however, see also the
+\fB\-\-do\-not\-normalize\fR
+option below\&.
 .RE
 .PP
 \fB\-m, \-\-multiallelics\fR ←|+>[\fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIany\fR]
diff --git a/doc/bcftools.html b/doc/bcftools.html
index a32fa9ddf..3ac3e8614 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,13 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp150032"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp213264"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
 work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-09-02 15:10 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-119-g0dbe41e+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-09-15 11:42 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-127-g5940dc0+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -1027,9 +1027,10 @@
 <span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
-</dd></dl></div></div><div class="refsect2" title="bcftools norm [OPTIONS] file.vcf.gz"><a id="norm"></a><h3>bcftools norm [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Left-align and normalize indels,  check if REF alleles match the reference,
+</dd></dl></div></div><div class="refsect2" title="bcftools norm [OPTIONS] file.vcf.gz"><a id="norm"></a><h3>bcftools norm [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Left-align and normalize indels, check if REF alleles match the reference,
 split multiallelic sites into multiple rows; recover multiallelics from
-multiple rows.</p><div class="variablelist"><dl><dt><span class="term">
+multiple rows. Left-alignment and normalization will only be applied if
+the <span class="strong"><strong><a class="link" href="#fasta_ref">--fasta-ref</a></strong></span> option is supplied.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-c, --check-ref</strong></span> <span class="emphasis"><em>e</em></span>|<span class="emphasis"><em>w</em></span>|<span class="emphasis"><em>x</em></span>|<span class="emphasis"><em>s</em></span>
 </span></dt><dd>
     what to do when incorrect or missing REF allele is encountered:
@@ -1042,9 +1043,11 @@
 </span></dt><dd>
     remove duplicate lines of the same type
 </dd><dt><span class="term">
-<span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>FILE</em></span>
+<span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>FILE</em></span><a id="fasta_ref"></a>
 </span></dt><dd>
-    reference sequence
+    reference sequence. Supplying this option will turn on left-alignment
+    and normalization, however, see also the <span class="strong"><strong><a class="link" href="#do_not_normalize">--do-not-normalize</a></strong></span>
+    option below.
 </dd><dt><span class="term">
 <span class="strong"><strong>-m, --multiallelics</strong></span> ←|+&gt;[<span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>any</em></span>]
 </span></dt><dd>
@@ -1056,7 +1059,7 @@
     <span class="emphasis"><em>both</em></span>; if SNPs and indels should be merged into a single record, specify
     <span class="emphasis"><em>any</em></span>.
 </dd><dt><span class="term">
-<span class="strong"><strong>-N, --do-not-normalize</strong></span>
+<span class="strong"><strong>-N, --do-not-normalize</strong></span><a id="do_not_normalize"></a>
 </span></dt><dd>
     the <span class="emphasis"><em>-c s</em></span> option can be used to fix or set the REF allele from the
     reference <span class="emphasis"><em>-f</em></span>. The <span class="emphasis"><em>-N</em></span> option will not turn on indel normalisation
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index bd3270ba0..94064e445 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1085,9 +1085,10 @@ For "vertical" merge take a look at *<<norm,bcftools norm>>* instead.
 
 [[norm]]
 === bcftools norm ['OPTIONS'] 'file.vcf.gz'
-Left-align and normalize indels,  check if REF alleles match the reference,
+Left-align and normalize indels, check if REF alleles match the reference,
 split multiallelic sites into multiple rows; recover multiallelics from
-multiple rows.
+multiple rows. Left-alignment and normalization will only be applied if
+the *<<fasta_ref,--fasta-ref>>* option is supplied.
 
 *-c, --check-ref* 'e'|'w'|'x'|'s':: 
     what to do when incorrect or missing REF allele is encountered: 
@@ -1099,8 +1100,10 @@ multiple rows.
 *-D, --remove-duplicates*::
     remove duplicate lines of the same type
 
-*-f, --fasta-ref* 'FILE'::
-    reference sequence
+*-f, --fasta-ref* 'FILE'[[fasta_ref]]::
+    reference sequence. Supplying this option will turn on left-alignment
+    and normalization, however, see also the *<<do_not_normalize,--do-not-normalize>>*
+    option below.
 
 *-m, --multiallelics* <-|+>['snps'|'indels'|'both'|'any']::
     split multiallelic sites into biallelic records ('-') or join
@@ -1111,7 +1114,7 @@ multiple rows.
     'both'; if SNPs and indels should be merged into a single record, specify
     'any'.
 
-*-N, --do-not-normalize*::
+*-N, --do-not-normalize*[[do_not_normalize]]::
     the '-c s' option can be used to fix or set the REF allele from the 
     reference '-f'. The '-N' option will not turn on indel normalisation
     as the '-f' option normally implies

From 274c64259d5ca4ac6ba6da1ed77ec89ce4c9081b Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 16 Sep 2015 10:21:10 +0100
Subject: [PATCH 072/211] PL to determine sex with +vcf2sex

---
 plugins/vcf2sex.c | 275 +++++++++++++++++++++++++++++++++++++---------
 1 file changed, 221 insertions(+), 54 deletions(-)

diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index bad4c3dba..17f561472 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -31,18 +31,41 @@
 #include <htslib/regidx.h>
 #include <htslib/synced_bcf_reader.h>
 #include <htslib/vcfutils.h>
+#include <inttypes.h>
 #include "bcftools.h"
 #include "ploidy.h"
 
+#define GUESS_GT 1
+#define GUESS_PL 2
+
+typedef struct
+{
+    uint64_t nhet, nhom, nmiss;
+}
+count_t;
+
+typedef struct
+{
+    char *chr;
+    uint32_t start, end;
+    int *sex2ploidy;    // sex ploidies
+    count_t *counts;    // per-sample counts: counts[isample]
+}
+reg_stats_t;
+
 typedef struct
 {
     int nsites, nsex, *sex2ploidy, dflt_ploidy, max_ploidy, guess;
-    int ncounts, *counts, nsample, verbose;
+    count_t bg_counts;          // background het/hom counts for regions with the same ploidy in all sexes
+    reg_stats_t *reg_stats;     // counts for all regions, used with -g
+    int nreg_stats, nsample, verbose;
+    int *counts, ncounts;       // number of observed GTs with given ploidy, used when -g is not given
     float *sex2prob, min_hets;
-    int32_t *gts, ngts;
+    int32_t *gts, ngts, *pls, npls;
     bcf_srs_t *sr;
     bcf_hdr_t *hdr;
     ploidy_t *ploidy;
+    char *background;
 }
 args_t;
 
@@ -55,15 +78,23 @@ const char *usage(void)
 {
     return 
         "\n"
-        "About: Determine sample sex by either checking the presence of haploid/diploid\n"
-        "       genotypes (requires correct ploidy in the VCF) or by counting homs/hets\n"
-        "       in haploid regions.\n"
+        "About: Determine sample sex by checking the presence of haploid/diploid genotypes\n"
+        "       (requires correct ploidy in the VCF). Alternatively, determine the sex by\n"
+        "       counting homs/hets (-g GT) or most likely hom/het genotypes (-g PL) in haploid\n"
+        "       regions. With -g, a region is deemed haploid when the fraction of hets in the\n"
+        "       region is significantly smaller than in the background region. For example,\n"
+        "       the default \"-m 0.3\" requires the het rate to be at least 30% of the background\n"
+        "       rate. If the background region is disabled (\"-b -\"), the threshold -m is interpreted\n"
+        "       directly as the minimum fraction of hets in the region.\n"
+        "\n"
         "Usage: bcftools +vcf2sex <file.vcf.gz> -- [Plugin Options]\n"
         "Plugin options:\n"
-        "   -g, --guess             do not trust genotypes ploidy, count hom/hets\n"
-        "   -m, --min-hets <float>  minimum fraction of hets in diploid regions [0.05]\n"
-        "   -n, --nsites <int>      number of sites to check per region (ignored with -g) [10]\n"
-        "   -p, --ploidy <file>     space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n"
+        "   -b, --background <region>   diploid region to determine normal hom/hets counts [X:60001-2699520]\n"
+        "   -g, --guess <tag>           determine ploidy by counting hom/hets (GT) or most likely genotypes (PL)\n"
+        "   -m, --min-hets <float>      minimum fraction of hets in diploid regions [0.3]\n"
+        "   -n, --nsites <int>          number of sites to check per region (ignored with -g) [10]\n"
+        "   -p, --ploidy <file>         space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n"
+        "   -v, --verbose               print debugging information\n"
         "\n"
         "Example:\n"
         "   # Default ploidy, if -p not given. Unlisted regions have ploidy 2\n"
@@ -74,9 +105,36 @@ const char *usage(void)
         "   \n"
         "   bcftools +vcf2sex in.vcf.gz\n"
         "   bcftools +vcf2sex in.vcf.gz -- -n 10\n"
+        "   bcftools +vcf2sex in.vcf.gz -- -g GT\n"
         "\n";
 }
 
+reg_stats_t *expand_regs(args_t *args, char *seq, uint32_t start, uint32_t end)
+{
+    args->nreg_stats++;
+    args->reg_stats = (reg_stats_t*) realloc(args->reg_stats,sizeof(reg_stats_t)*args->nreg_stats);
+    reg_stats_t *stats = args->reg_stats + args->nreg_stats-1;
+    stats->chr = strdup(seq);
+    stats->start = start;
+    stats->end = end;
+    stats->sex2ploidy = (int*) malloc(sizeof(int)*args->nsex);
+    memcpy(stats->sex2ploidy,args->sex2ploidy,sizeof(int)*args->nsex);
+    stats->counts = (count_t*) calloc(args->nsample,sizeof(count_t));
+    return stats;
+}
+void destroy_regs(args_t *args)
+{   
+    int i;
+    for (i=0; i<args->nreg_stats; i++)
+    {
+        free(args->reg_stats[i].chr);
+        free(args->reg_stats[i].counts);
+        free(args->reg_stats[i].sex2ploidy);
+    }
+    free(args->reg_stats);
+    args->nreg_stats = 0;
+}
+
 int process_region_precise(args_t *args, char *seq, regitr_t *itr)
 {
     int k = 1;
@@ -137,85 +195,188 @@ int process_region_precise(args_t *args, char *seq, regitr_t *itr)
 
 int process_region_guess(args_t *args, char *seq, regitr_t *itr)
 {
-    int ismpl, k = 1;
-    uint32_t start = itr->reg[itr->i].start, end = itr->reg[itr->i].end;
-    while ( itr->i+k<itr->n && start==itr->reg[itr->i+k].start && end==itr->reg[itr->i+k].end ) k++;
-    
-    int ret = ploidy_query(args->ploidy, seq, start, args->sex2ploidy, NULL, NULL);
-    assert(ret);
+    int kitr = 1;
+    uint32_t start = 0, end = INT_MAX;
+    reg_stats_t *stats = NULL;
 
-    memset(args->counts,0,args->ncounts*sizeof(int));
+    if ( itr )
+    {
+        start = itr->reg[itr->i].start;
+        end   = itr->reg[itr->i].end;
+        while ( itr->i+kitr<itr->n && start==itr->reg[itr->i+kitr].start && end==itr->reg[itr->i+kitr].end ) kitr++;
+
+        int min,max,ret = ploidy_query(args->ploidy, seq, start, args->sex2ploidy, &min, &max);
+        assert(ret);
+        stats = expand_regs(args, seq,start,end);
+    }
+    else
+    {
+        // background region
+        int spos, epos;
+        const char *ptr = hts_parse_reg(args->background, &spos, &epos);
+        if ( !ptr )
+            error("Could not parse the region: %s\n", args->background);
+        seq = (char*) malloc(ptr - args->background + 1);
+        memcpy(seq,args->background,ptr-args->background);
+        seq[ptr-args->background] = 0;
+    }
+
+    if ( bcf_sr_seek(args->sr,seq,start)!=0 ) 
+    {
+        // sequence not present
+        if ( !itr ) free(seq);
+        return kitr;
+    }
+    int ismpl, rid = bcf_hdr_name2id(args->hdr,seq);
+    if ( !itr ) free(seq);
 
-    if ( bcf_sr_seek(args->sr,seq,start)!=0 ) return k;   // sequence not present
-    int rid = bcf_hdr_name2id(args->hdr,seq);
     while ( bcf_sr_next_line(args->sr) )
     {
         bcf1_t *rec = bcf_sr_get_line(args->sr,0);
         if ( rec->rid!=rid || rec->pos > end ) break;
 
-        bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT");
-        for (ismpl=0; ismpl<args->nsample; ismpl++)
+        if ( args->guess & GUESS_GT )   // use GTs to guess the ploidy
+        {
+            bcf_fmt_t * fmt = bcf_get_fmt(args->hdr, rec, "GT");
+            for (ismpl=0; ismpl<args->nsample; ismpl++)
+            {
+                count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts;
+                int gt = bcf_gt_type(fmt, ismpl, NULL,NULL);
+                if ( gt==GT_UNKN ) counts->nmiss++;
+                else if ( gt==GT_HET_RA || gt==GT_HET_AA ) counts->nhet++;
+                else counts->nhom++;
+            }
+        }
+        else    // use PLs to guess the ploidy
         {
-            int gt = bcf_gt_type(fmt, ismpl, NULL,NULL);
-            if ( gt==GT_UNKN ) args->counts[ismpl*3+0]++;       // missing
-            else if ( gt==GT_HET_RA || gt==GT_HET_AA ) args->counts[ismpl*3+1]++;   // het
-            else args->counts[ismpl*3+2]++; // hom
+            int npl = bcf_get_format_int32(args->hdr,rec,"PL",&args->pls,&args->npls);
+            if ( npl<=0 ) continue;
+            npl /= args->nsample;
+            for (ismpl=0; ismpl<args->nsample; ismpl++)
+            {
+                int32_t *ptr = args->pls + ismpl*npl;
+                int phom = INT_MAX, phet = INT_MAX, ial, jal, k = 0;
+                for (ial=0; ial<rec->n_allele; ial++)
+                {
+                    if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
+                    if ( phom > ptr[k] ) phom = ptr[k];
+                    k++;
+                    for (jal=0; jal<ial; jal++)
+                    {
+                        if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
+                        if ( phet > ptr[k] ) phet = ptr[k];
+                        k++;
+                    }
+                }
+                count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts;
+                if ( k == rec->n_allele ) counts->nhom++;   // haploid
+                else if ( k != rec->n_allele*(rec->n_allele+1)/2 ) counts->nmiss++;
+                else if ( phet < phom ) counts->nhet++;
+                else counts->nhom++;
+            }
         }
     }
+    return kitr;
+}
 
-    for (ismpl=0; ismpl<args->nsample; ismpl++)
+void sex2prob_guess(args_t *args)
+{
+    int ismpl, ireg; 
+    uint64_t nhom,nhet,nmiss;
+    float bg_het = -1;
+
+    if ( args->background )
     {
-        float sum = 0, *probs = args->sex2prob + ismpl*args->nsex;
-        int i, *counts = args->counts + ismpl*(args->max_ploidy+1);
-        float fhet = (counts[1]+counts[2]) ? (float)counts[1]/(counts[1]+counts[2]) : 0;
-        for (i=0; i<args->max_ploidy+1; i++) sum += counts[i];
-        for (i=0; i<args->nsex; i++)
+        process_region_guess(args, NULL, NULL);
+        nhom  = args->bg_counts.nhom;
+        nhet  = args->bg_counts.nhet;
+        nmiss = args->bg_counts.nmiss;
+        bg_het = nhom+nhet ? (float)nhet/(nhom+nhet) : 0;
+
+        if ( args->verbose )
         {
-            // a very simple heuristics to determine sex by counting hets/homs/missing sites,
-            // in human nhet/nhom ~ 0.2
-            int ploidy = args->sex2ploidy[i];
-            float prob = 1;
-            if ( ploidy==0 )
-                prob = sum ? counts[0] / sum : 1;   // fraction of missing sites
-            else if ( ploidy==1 )
-            {
-                if ( counts[1]+counts[2] ) prob = fhet > args->min_hets ? 0.1 : 0.9;
-                prob *= sum ? 1 - counts[0] / sum : 1./args->nsex;
-            }
-            else 
+            printf("# [1]BGR\t[2]Region\t[3]Het fraction\t[4]nHet\t[5]nHom\t[6]nMissing\n");
+            printf("BGR\t%s\t%f\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", args->background,bg_het,nhet,nhom,nmiss);
+        }
+    }
+
+    // a very simple heuristics to determine sex by counting hets/homs/missing sites
+    for (ireg=0; ireg<args->nreg_stats; ireg++)
+    {
+        reg_stats_t *stats = &args->reg_stats[ireg];
+        for (ismpl=0; ismpl<args->nsample; ismpl++)
+        {
+            uint64_t nhom  = stats->counts[ismpl].nhom;
+            uint64_t nhet  = stats->counts[ismpl].nhet;
+            uint64_t nmiss = stats->counts[ismpl].nmiss;
+            float fhet = nhom+nhet ? (float)nhet/(nhom+nhet) : 0;
+
+            if ( args->verbose )
+                printf("DBG\t%s:%d-%d\t%s\t%f\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", stats->chr,stats->start+1,stats->end+1,args->hdr->samples[ismpl],fhet,nhet,nhom,nmiss);
+
+            int i, ntot = nhom + nhet + nmiss;
+            if ( !ntot ) continue;
+
+            float *probs = args->sex2prob + ismpl*args->nsex;
+            for (i=0; i<args->nsex; i++)
             {
-                if ( counts[1]+counts[2] ) prob = fhet > args->min_hets ? 0.9 : 0.1;
-                prob *= sum ? 1 - counts[0] / sum : 1./args->nsex;
+                int ploidy = stats->sex2ploidy[i];
+                float prob;
+                if ( ploidy==0 )
+                    prob = (float) nmiss / ntot;   // fraction of missing sites
+                else if ( ploidy==1 )
+                {
+                    // NB: these numbers (0.1,0.9) are made up, to be improved
+                    if ( bg_het<0 )
+                        prob = fhet > args->min_hets ? 0.1 : 0.9;
+                    else
+                        prob = fhet > args->min_hets*bg_het ? 0.1 : 0.9;
+                    prob *= 1 - (float)nmiss / ntot;
+                }
+                else 
+                {
+                    if ( bg_het<0 )
+                        prob = fhet > args->min_hets ? 0.9 : 0.1;
+                    else
+                        prob = fhet > args->min_hets*bg_het ? 0.9 : 0.1;
+                    prob *= 1 - (float)nmiss / ntot;
+                }
+                probs[i] *= prob;
             }
-            probs[i] *= prob;
         }
-        if ( args->verbose )
-            printf("DBG\t%s:%d-%d\t%s\t%f\t%d\t%d\t%d\n", seq,start+1,end+1,args->hdr->samples[ismpl], fhet,counts[0],counts[1],counts[2]);
     }
-
-    return k;
 }
 
 int run(int argc, char **argv)
 {
     args_t *args  = (args_t*) calloc(1,sizeof(args_t));
     args->nsites = 10;
-    args->min_hets = 0.05;
+    args->min_hets = 0.3;
+    args->background = "X:60001-2699520";
     static struct option loptions[] =
     {
         {"verbose",1,0,'v'},
         {"ploidy",1,0,'p'},
         {"nsites",1,0,'n'},
-        {"guess",0,0,'g'},
+        {"guess",1,0,'g'},
         {"min-hets",1,0,'m'},
+        {"background",1,0,'b'},
         {0,0,0,0}
     };
     char c, *tmp, *ploidy_fname = NULL;
-    while ((c = getopt_long(argc, argv, "p:n:gm:v",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "p:n:g:m:vb:",loptions,NULL)) >= 0)
     {
         switch (c) {
+            case 'b': 
+                if ( !strcmp("-",optarg) ) args->background = NULL;
+                else args->background = optarg; 
+                break; 
             case 'v': args->verbose = 1; break; 
-            case 'g': args->guess = 1; break;
+            case 'g':
+                if ( !strcasecmp(optarg,"GT") ) args->guess = GUESS_GT;
+                else if ( !strcasecmp(optarg,"PL") ) args->guess = GUESS_PL;
+                else error("The argument not recognised, expected --guess GT or --guess PL: %s\n", optarg);
+                break;
             case 'm': 
                 args->min_hets = strtod(optarg,&tmp); 
                 if ( *tmp ) error("Unexpected argument to --min-hets: %s\n", optarg);
@@ -232,7 +393,8 @@ int run(int argc, char **argv)
 
     args->sr = bcf_sr_init();
     args->sr->require_index = 1;
-    if ( !argv[0] || !bcf_sr_add_reader(args->sr,argv[0]) ) error("%s", usage());
+    if ( !argv[0] ) error("%s", usage());
+    if ( !bcf_sr_add_reader(args->sr,argv[0]) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum));
     args->hdr = args->sr->readers[0].header;
     args->nsample = bcf_hdr_nsamples(args->hdr);
  
@@ -271,11 +433,14 @@ int run(int argc, char **argv)
         regitr_t itr;
         regidx_overlap(idx, seqs[i], 0, UINT32_MAX, &itr);
         while ( itr.i < itr.n )
+        {
             if ( args->guess )
                 itr.i += process_region_guess(args, seqs[i], &itr);
             else
                 itr.i += process_region_precise(args, seqs[i], &itr);
+        }
     }
+    if ( args->guess ) sex2prob_guess(args);
 
     for (i=0; i<args->nsample; i++)
     {
@@ -298,9 +463,11 @@ int run(int argc, char **argv)
    
     bcf_sr_destroy(args->sr);
     ploidy_destroy(args->ploidy);
+    destroy_regs(args);
     free(args->sex2ploidy);
     free(args->counts);
     free(args->gts);
+    free(args->pls);
     free(args->sex2prob);
     free(args);
     return 0;

From 4dd02c378c874a0053a62e584e54c71597287fdf Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 16 Sep 2015 10:25:22 +0100
Subject: [PATCH 073/211] new setGT plugin

could deprecate or drop missing2ref plugin as functionality included
in setGT
---
 plugins/setGT.c | 223 ++++++++++++++++++++++++++++++++++++++++++++++++
 test/test.pl    |   1 +
 2 files changed, 224 insertions(+)
 create mode 100644 plugins/setGT.c

diff --git a/plugins/setGT.c b/plugins/setGT.c
new file mode 100644
index 000000000..55e0f27ea
--- /dev/null
+++ b/plugins/setGT.c
@@ -0,0 +1,223 @@
+/*  plugins/setGT.c -- set gentoypes to given values
+
+    Copyright (C) 2015 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <htslib/vcf.h>
+#include <htslib/vcfutils.h>
+#include <inttypes.h>
+#include <getopt.h>
+#include "bcftools.h"
+
+bcf_hdr_t *in_hdr, *out_hdr;
+int32_t *gts = NULL, mgts = 0;
+int *arr = NULL, marr = 0;
+uint64_t nchanged = 0;
+int tgt_mask = 0, new_mask = 0, new_gt = 0;
+
+#define GT_MISSING   1
+#define GT_PARTIAL  (1<<1)
+#define GT_REF      (1<<2)
+#define GT_MAJOR    (1<<3)
+#define GT_PHASED   (1<<4)
+#define GT_UNPHASED (1<<5)
+#define GT_ALL      (1<<6)
+
+const char *about(void)
+{
+    return "Set genotypes: partially missing to missing, missing to ref/major allele, etc.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "About: Sets genotypes. The target genotypes can be specified as:\n"
+        "           ./.  .. completely missing (\".\" or \"./.\", depending on ploidy)\n"
+        "           ./x  .. partially missing (e.g., \"./0\" or \".|1\" but not \"./.\")\n"
+        "           .    .. partially or completely missing\n"
+        "           a    .. all genotypes\n"
+        "       and the new genotype can be one of:\n"
+        "           .    .. missing (\".\" or \"./.\", keeps ploidy)\n"
+        "           0    .. reference allele\n"
+        "           M    .. major allele\n"
+        "           p    .. phased genotype\n"
+        "           u    .. unphase genotype and sort by allele (1|0 becomes 0/1)\n"
+        "Usage: bcftools +setGT [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -n, --new-gt <type>         Genotypes to set, see above\n"
+        "   -t, --target-gt <type>      Genotypes to change, see above\n"
+        "\n"
+        "Example:\n"
+        "   # set missing genotypes (\"./.\") to phased ref genotypes (\"0|0\")\n"
+        "   bcftools +setGT in.vcf -- -t . -n 0p\n"
+        "\n"
+        "   # set partially missing genotypes to completely missing\n"
+        "   bcftools +setGT in.vcf -- -t ./x -n .\n"
+        "\n";
+}
+
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    int c;
+    static struct option loptions[] =
+    {
+        {"new-gt",1,0,'n'},
+        {"target-gt",0,0,'t'},
+        {0,0,0,0}
+    };
+    while ((c = getopt_long(argc, argv, "?hn:t:",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 'n': new_mask = bcf_gt_phased(0); 
+                if ( strchr(optarg,'.') ) new_mask |= GT_MISSING;
+                if ( strchr(optarg,'0') ) new_mask |= GT_REF;
+                if ( strchr(optarg,'M') ) new_mask |= GT_MAJOR;
+                if ( strchr(optarg,'p') ) new_mask |= GT_PHASED;
+                if ( strchr(optarg,'u') ) new_mask |= GT_UNPHASED;
+                break;
+            case 't':
+                if ( !strcmp(optarg,".") ) tgt_mask |= GT_MISSING|GT_PARTIAL;
+                if ( !strcmp(optarg,"./x") ) tgt_mask |= GT_PARTIAL;
+                if ( !strcmp(optarg,"./.") ) tgt_mask |= GT_MISSING;
+                if ( !strcmp(optarg,"a") ) tgt_mask |= GT_ALL;
+                break;
+            case 'h':
+            case '?':
+            default: fprintf(stderr,"%s", usage()); exit(1); break;
+        }
+    }
+    in_hdr  = in;
+    out_hdr = out;
+
+    if ( !new_mask ) error("Expected -n option\n");
+    if ( !tgt_mask ) error("Expected -t option\n");
+
+    if ( new_mask & GT_MISSING ) new_gt = bcf_gt_missing;
+    if ( new_mask & GT_REF ) new_gt = new_mask&GT_PHASED ? bcf_gt_phased(0) : bcf_gt_unphased(0);
+
+    return 0;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    if ( !rec->n_sample ) return rec;
+
+    int ngts = bcf_get_genotypes(in_hdr, rec, &gts, &mgts);
+    ngts /= rec->n_sample;
+    int i, j, changed = 0;
+    
+    // Calculating allele frequency for each allele and determining major allele
+    // only do this if use_major is true
+    int an = 0, maxAC = -1, majorAllele = -1;
+    if ( new_mask & GT_MAJOR )
+    {
+        hts_expand(int,rec->n_allele,marr,arr);
+        int ret = bcf_calc_ac(in_hdr,rec,arr,BCF_UN_FMT);
+        if ( ret<= 0 )
+            error("Could not calculate allele count at %s:%d\n", bcf_seqname(in_hdr,rec),rec->pos+1);
+
+        for(i=0; i < rec->n_allele; ++i)
+        {
+            an += arr[i];
+            if (arr[i] > maxAC)
+            {
+                maxAC = arr[i];
+                majorAllele = i;
+            }
+        }
+
+        // replacing new_gt by major allele
+        new_gt = new_mask & GT_PHASED ?  bcf_gt_phased(majorAllele) : bcf_gt_unphased(majorAllele);
+    }
+
+    // replace gts
+    for (i=0; i<rec->n_sample; i++)
+    {
+        int ploidy = 0, nmiss = 0;
+        int32_t *ptr = gts + i*ngts;
+        for (j=0; j<ngts; j++)
+        {
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+            ploidy++;
+            if ( ptr[j]==bcf_gt_missing ) nmiss++;
+        }
+
+        int do_set = 0;
+        if ( tgt_mask&GT_ALL ) do_set = 1;
+        else if ( tgt_mask&GT_PARTIAL && nmiss ) do_set = 1;
+        else if ( tgt_mask&GT_MISSING && ploidy==nmiss ) do_set = 1;
+
+        if ( !do_set ) continue;
+
+        if ( new_mask&GT_UNPHASED )
+        {
+            for (j=0; j<ngts; j++)
+            {
+                if ( ptr[j]==bcf_int32_vector_end ) break;
+                if ( !bcf_gt_is_phased(ptr[j]) ) continue;
+                ptr[j] = bcf_gt_unphased(bcf_gt_allele(ptr[j]));    // remove phasing
+                changed++;
+            }
+
+            // insertion sort
+            int k, l;
+            for (k=1; k<j; k++)
+            {
+                int32_t x = ptr[k];
+                l = k;
+                while ( l>0 && ptr[l-1]>x )
+                {
+                    ptr[l] = ptr[l-1];
+                    l--;
+                }
+                ptr[l] = x;
+            }
+            continue;
+        }
+
+        for (j=0; j<ngts; j++)
+        {
+            if ( ptr[j]==bcf_int32_vector_end ) break;
+            ptr[j] = new_gt;
+            changed++;
+        }
+    }
+    nchanged += changed;
+    if ( changed ) bcf_update_genotypes(out_hdr, rec, gts, ngts*rec->n_sample);
+    return rec;
+}
+
+void destroy(void)
+{
+    free(arr);
+    fprintf(stderr,"Filled %"PRId64" alleles\n", nchanged);
+    free(gts);
+}
+
+
diff --git a/test/test.pl b/test/test.pl
index a1374881d..e89bee534 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -161,6 +161,7 @@
 test_vcf_annotate($opts,in=>'annotate4',vcf=>'annots4',out=>'annotate8.out',args=>'-c +INFO');
 test_vcf_annotate($opts,in=>'annotate4',tab=>'annots4',out=>'annotate8.out',args=>'-c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR');
 test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+missing2ref');
+test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+setGT',args=>'-- -t . -n 0');
 test_vcf_annotate($opts,in=>'annotate9',tab=>'annots9',out=>'annotate9.out',args=>'-c CHROM,POS,REF,ALT,+ID');
 test_vcf_plugin($opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC');
 test_vcf_plugin($opts,in=>'plugin1',out=>'dosage.out',cmd=>'+dosage');

From f46aa3eb40ee8ee1424f6000770aea5c41fd1411 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 8 Sep 2015 11:06:35 +0100
Subject: [PATCH 074/211] Plugins to use bcf_gt_is_missing instead of the old
 bcf_int32_missing

---
 plugins/dosage.c  | 2 +-
 plugins/vcf2sex.c | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/plugins/dosage.c b/plugins/dosage.c
index bbfe2e547..ddc6297e1 100644
--- a/plugins/dosage.c
+++ b/plugins/dosage.c
@@ -140,7 +140,7 @@ int calc_dosage_GT(bcf1_t *rec)
         float dsg = 0;
         for (j=0; j<nret; j++)
         {
-            if ( ptr[j]==bcf_int32_missing || ptr[j]==bcf_int32_vector_end || ptr[j]==bcf_gt_missing ) break;
+            if ( ptr[j]==bcf_int32_vector_end || bcf_gt_is_missing(ptr[j]) ) break;
             if ( bcf_gt_allele(ptr[j]) ) dsg += 1;
         }
         printf("\t%.1f", j>0 ? dsg : -1);
diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index 17f561472..6a9a626cf 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -169,8 +169,10 @@ int process_region_precise(args_t *args, char *seq, regitr_t *itr)
             int32_t *gts = args->gts + ngts*ismpl;
             int igt, ploidy = 0;
             for (igt=0; igt<ngts; igt++)
-                if ( gts[igt]==bcf_gt_missing || gts[igt]==bcf_int32_missing || gts[igt]==bcf_int32_vector_end ) break;
+            {
+                if ( gts[igt]==bcf_int32_vector_end || bcf_gt_is_missing(gts[igt]) ) break;
                 else ploidy++;
+            }
             args->counts[ismpl*(args->max_ploidy+1) + ploidy]++;
             if ( args->verbose )
                 fprintf(stderr,"%s:%d\t%s\tploidy=%d\n", seq,rec->pos+1,args->hdr->samples[ismpl],ploidy);

From 84aff628c299bcabe8814b5ef373cc0718dcc839 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 28 Apr 2015 14:00:33 +0100
Subject: [PATCH 075/211] fixploidy: Do not exit on lines without GT, leave
 unchanged

---
 plugins/fixploidy.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/plugins/fixploidy.c b/plugins/fixploidy.c
index ab4c8f597..717ffef3a 100644
--- a/plugins/fixploidy.c
+++ b/plugins/fixploidy.c
@@ -167,12 +167,15 @@ bcf1_t *process(bcf1_t *rec)
 {
     int i,j, max_ploidy;
 
-    ploidy_query(ploidy, (char*)bcf_seqname(in_hdr,rec), rec->pos, sex2ploidy,NULL,&max_ploidy);
-
     int ngts = bcf_get_genotypes(in_hdr, rec, &gt_arr, &ngt_arr);
+    if ( ngts<0 )
+        return rec;     // GT field not present
+
     if ( ngts % n_sample )
         error("Error at %s:%d: wrong number of GT fields\n",bcf_seqname(in_hdr,rec),rec->pos+1);
 
+    ploidy_query(ploidy, (char*)bcf_seqname(in_hdr,rec), rec->pos, sex2ploidy,NULL,&max_ploidy);
+
     ngts /= n_sample;
     if ( ngts < max_ploidy )
     {

From e63a37f5eba494ffc2878bc325145253f1f0388c Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 17 Feb 2015 10:39:39 +0000
Subject: [PATCH 076/211] convert: Report the number of written records

---
 vcfconvert.c | 17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/vcfconvert.c b/vcfconvert.c
index c3d793e86..b9cfc46b1 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -679,7 +679,7 @@ static void vcf_to_gensample(args_t *args)
     }
 
     int prev_rid = -1, prev_pos = -1;
-    int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0;
+    int no_alt = 0, non_biallelic = 0, filtered = 0, ndup = 0, nok = 0;
     BGZF *gout = bgzf_open(gen_fname, gen_compressed ? "wg" : "wu");
     while ( bcf_sr_next_line(args->files) )
     {
@@ -713,10 +713,11 @@ static void vcf_to_gensample(args_t *args)
         {
             int ret = bgzf_write(gout, str.s, str.l);
             if ( ret!= str.l ) error("Error writing %s: %s\n", gen_fname,strerror(errno));
+            nok++;
         }
     }
-    fprintf(stderr, "%d records skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n", 
-        no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup);
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d/%d no-ALT/non-biallelic/filtered/duplicated\n", 
+        nok, no_alt+non_biallelic+filtered+ndup, no_alt, non_biallelic, filtered, ndup);
 
     if ( str.m ) free(str.s);
     if ( bgzf_close(gout)!=0 ) error("Error closing %s: %s\n", gen_fname,strerror(errno));
@@ -804,7 +805,7 @@ static void vcf_to_haplegendsample(args_t *args)
         if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno));
     }
 
-    int no_alt = 0, non_biallelic = 0, filtered = 0;
+    int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
     while ( bcf_sr_next_line(args->files) )
     {
         bcf1_t *line = bcf_sr_get_line(args->files,0);
@@ -845,8 +846,9 @@ static void vcf_to_haplegendsample(args_t *args)
             ret = bgzf_write(lout, str.s, str.l);
             if ( ret != str.l ) error("Error writing %s: %s\n", legend_fname, strerror(errno));
         }
+        nok++;
     }
-    fprintf(stderr, "%d records skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok,no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
     if ( str.m ) free(str.s);
     if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno));
     if ( lout && bgzf_close(lout)!=0 ) error("Error closing %s: %s\n", legend_fname, strerror(errno));
@@ -937,7 +939,7 @@ static void vcf_to_hapsample(args_t *args)
     // open haps output
     BGZF *hout = hap_fname ? bgzf_open(hap_fname, hap_compressed ? "wg" : "wu") : NULL;
 
-    int no_alt = 0, non_biallelic = 0, filtered = 0;
+    int no_alt = 0, non_biallelic = 0, filtered = 0, nok = 0;
     while ( bcf_sr_next_line(args->files) )
     {
         bcf1_t *line = bcf_sr_get_line(args->files,0);
@@ -967,8 +969,9 @@ static void vcf_to_hapsample(args_t *args)
             ret = bgzf_write(hout, str.s, str.l); // write hap file
             if ( ret != str.l ) error("Error writing %s: %s\n", hap_fname, strerror(errno));
         }
+        nok++;
     }
-    fprintf(stderr, "%d records skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
+    fprintf(stderr, "%d records written, %d skipped: %d/%d/%d no-ALT/non-biallelic/filtered\n", nok, no_alt+non_biallelic+filtered, no_alt, non_biallelic, filtered);
     if ( str.m ) free(str.s);
     if ( hout && bgzf_close(hout)!=0 ) error("Error closing %s: %s\n", hap_fname, strerror(errno));
     if (hap_fname) free(hap_fname);

From f1129e66aa0940debff302fa788bdb5ba02713f5 Mon Sep 17 00:00:00 2001
From: Jason Piper <jpiper@HLI-MACPRO48.local>
Date: Thu, 17 Sep 2015 12:05:14 +0800
Subject: [PATCH 077/211] Update test VCF headers to v4.2

---
 test/norm.merge.out          | 2 +-
 test/norm.merge.strict.out   | 2 +-
 test/norm.merge.vcf          | 2 +-
 test/norm.out                | 2 +-
 test/norm.setref.out         | 2 +-
 test/norm.setref.vcf         | 2 +-
 test/norm.split.and.norm.out | 2 +-
 test/norm.split.out          | 2 +-
 test/norm.split.vcf          | 2 +-
 test/norm.vcf                | 2 +-
 10 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/test/norm.merge.out b/test/norm.merge.out
index 6dd3f3110..f5b1092ff 100644
--- a/test/norm.merge.out
+++ b/test/norm.merge.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.merge.strict.out b/test/norm.merge.strict.out
index c24dc9beb..1395d2224 100644
--- a/test/norm.merge.strict.out
+++ b/test/norm.merge.strict.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.merge.vcf b/test/norm.merge.vcf
index a24e36fba..e89178e78 100644
--- a/test/norm.merge.vcf
+++ b/test/norm.merge.vcf
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.out b/test/norm.out
index 6db87c14f..e6796d1e1 100644
--- a/test/norm.out
+++ b/test/norm.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.setref.out b/test/norm.setref.out
index 0f20abdad..2856b0ab7 100644
--- a/test/norm.setref.out
+++ b/test/norm.setref.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.setref.vcf b/test/norm.setref.vcf
index 8e0665793..da78f10ac 100644
--- a/test/norm.setref.vcf
+++ b/test/norm.setref.vcf
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.split.and.norm.out b/test/norm.split.and.norm.out
index 86154affc..64838edaa 100644
--- a/test/norm.split.and.norm.out
+++ b/test/norm.split.and.norm.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.split.out b/test/norm.split.out
index 38b1323df..b919211d7 100644
--- a/test/norm.split.out
+++ b/test/norm.split.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.split.vcf b/test/norm.split.vcf
index 2d8c0883b..7f039d16d 100644
--- a/test/norm.split.vcf
+++ b/test/norm.split.vcf
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/test/norm.vcf b/test/norm.vcf
index 52f5f8827..d000655cc 100644
--- a/test/norm.vcf
+++ b/test/norm.vcf
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

From ceb1524cffb03ec5e560d228f85c18309acd4bf2 Mon Sep 17 00:00:00 2001
From: kretzsch <wkretzsch@gmail.com>
Date: Tue, 22 Sep 2015 18:00:40 +0100
Subject: [PATCH 078/211] convert -H: Fixes issue #274; adds support for
 haploid and missing alleles

---
 test/convert.gt.noHead.vcf  | 35 +++++++++++++++++
 test/convert.gt.vcf         | 43 +++++++++++++++++++++
 test/convert.hls.gt.hap     | 34 ++++++++++++++++
 test/convert.hls.gt.legend  | 35 +++++++++++++++++
 test/convert.hls.gt.samples | 11 ++++++
 test/test.pl                |  8 ++++
 vcfconvert.c                | 77 ++++++++++++++++++++++++++++---------
 7 files changed, 224 insertions(+), 19 deletions(-)
 create mode 100644 test/convert.gt.noHead.vcf
 create mode 100644 test/convert.gt.vcf
 create mode 100644 test/convert.hls.gt.hap
 create mode 100644 test/convert.hls.gt.legend
 create mode 100644 test/convert.hls.gt.samples

diff --git a/test/convert.gt.noHead.vcf b/test/convert.gt.noHead.vcf
new file mode 100644
index 000000000..2d1d7cdcf
--- /dev/null
+++ b/test/convert.gt.noHead.vcf
@@ -0,0 +1,35 @@
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003	NA00004	NA00005	NA00006	NA00007	NA00008	NA00009	NA00010
+X	2698560	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698630	.	A	G	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698758	.	CAA	C	.	.	.	GT	0|0	0|1	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698769	.	AAG	A	.	.	.	GT	1|0	1|1	0|1	1|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698770	.	AG	A	.	.	.	GT	0|0	0|1	0|0	0|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698770	.	AG	AAGG	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698789	.	C	G	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698822	.	A	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698831	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698889	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698923	.	G	A	.	.	.	GT	1|0	0|1	0|1	1|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698953	.	A	AGG	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698954	.	G	A	.	.	.	GT	1|0	1|1	0|1	1|0	1|0	0|0	0|0	0|1	0|0	0|0
+X	2699002	.	C	A	.	.	.	GT	0|0	0|0	.|.	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699025	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699091	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699187	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0/1
+X	2699188	.	G	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699189	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699217	.	C	T	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699246	.	C	A	.	.	.	GT	1|0	1|1	0|1	1|1	1|0	0|1	0|0	0|1	0|0	1|0
+X	2699275	.	T	G	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|1	1|0	0|0	0|0	0|1
+X	2699350	.	A	T	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699360	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699450	.	A	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699507	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699555	.	C	A	.	.	.	GT	0	1	1	0	1	1|1	1|0	0|1	0|0	0|1
+X	2699645	.	G	T	.	.	.	GT	0	1	0	0	0	0|0	0|0	0|1	0|0	0|0
+X	2699676	.	G	A	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
+X	2699728	.	C	T	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699775	.	C	A	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699898	.	C	CT	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
+X	2699968	.	A	G	.	.	.	GT	.	0	0	1	0	0|1	0|0	0|0	0|1	1|0
+X	2699970	.	T	C	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
diff --git a/test/convert.gt.vcf b/test/convert.gt.vcf
new file mode 100644
index 000000000..7c719a2a3
--- /dev/null
+++ b/test/convert.gt.vcf
@@ -0,0 +1,43 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##contig=<ID=X,assembly=b37,length=155270560>
+##bcftools_normVersion=1.2+htslib-1.2.1
+##bcftools_normCommand=norm -m - convert.vcf
+##bcftools_annotateVersion=1.2+htslib-1.2.1
+##bcftools_annotateCommand=annotate -x FORMAT,QUAL
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003	NA00004	NA00005	NA00006	NA00007	NA00008	NA00009	NA00010
+X	2698560	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698630	.	A	G	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698758	.	CAA	C	.	.	.	GT	0|0	0|1	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698769	.	AAG	A	.	.	.	GT	1|0	1|1	0|1	1|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698770	.	AG	A	.	.	.	GT	0|0	0|1	0|0	0|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698770	.	AG	AAGG	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698789	.	C	G	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698822	.	A	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698831	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698889	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698923	.	G	A	.	.	.	GT	1|0	0|1	0|1	1|0	1|0	0|0	0|0	0|0	0|0	0|0
+X	2698953	.	A	AGG	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2698954	.	G	A	.	.	.	GT	1|0	1|1	0|1	1|0	1|0	0|0	0|0	0|1	0|0	0|0
+X	2699002	.	C	A	.	.	.	GT	0|0	0|0	.|.	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699025	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699091	.	G	A	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699187	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0/1
+X	2699188	.	G	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699189	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699217	.	C	T	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699246	.	C	A	.	.	.	GT	1|0	1|1	0|1	1|1	1|0	0|1	0|0	0|1	0|0	1|0
+X	2699275	.	T	G	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|1	1|0	0|0	0|0	0|1
+X	2699350	.	A	T	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699360	.	T	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699450	.	A	C	.	.	.	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
+X	2699507	.	T	C	.	.	.	GT	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0	0|0
+X	2699555	.	C	A	.	.	.	GT	0	1	1	0	1	1|1	1|0	0|1	0|0	0|1
+X	2699645	.	G	T	.	.	.	GT	0	1	0	0	0	0|0	0|0	0|1	0|0	0|0
+X	2699676	.	G	A	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
+X	2699728	.	C	T	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699775	.	C	A	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699898	.	C	CT	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
+X	2699968	.	A	G	.	.	.	GT	.	0	0	1	0	0|1	0|0	0|0	0|1	1|0
+X	2699970	.	T	C	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
diff --git a/test/convert.hls.gt.hap b/test/convert.hls.gt.hap
new file mode 100644
index 000000000..a5db463c0
--- /dev/null
+++ b/test/convert.hls.gt.hap
@@ -0,0 +1,34 @@
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+1 0 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0
+0 0 0 0 ? ? 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0* 1*
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+1 0 1 1 0 1 1 1 1 0 0 1 0 0 0 1 0 0 1 0
+0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 0 0 1
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+0 - 1 - 1 - 0 - 1 - 1 1 1 0 0 1 0 0 0 1
+0 - 1 - 0 - 0 - 0 - 0 0 0 0 0 1 0 0 0 0
+0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
+0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
+? - 0 - 0 - 1 - 0 - 0 1 0 0 0 0 0 1 1 0
+0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
diff --git a/test/convert.hls.gt.legend b/test/convert.hls.gt.legend
new file mode 100644
index 000000000..990d7725c
--- /dev/null
+++ b/test/convert.hls.gt.legend
@@ -0,0 +1,35 @@
+id position a0 a1
+X:2698560_G_A 2698560 G A
+X:2698630_A_G 2698630 A G
+X:2698758_CAA_C 2698758 CAA C
+X:2698769_AAG_A 2698769 AAG A
+X:2698770_AG_A 2698770 AG A
+X:2698770_AG_AAGG 2698770 AG AAGG
+X:2698789_C_G 2698789 C G
+X:2698822_A_C 2698822 A C
+X:2698831_G_A 2698831 G A
+X:2698889_T_C 2698889 T C
+X:2698923_G_A 2698923 G A
+X:2698953_A_AGG 2698953 A AGG
+X:2698954_G_A 2698954 G A
+X:2699002_C_A 2699002 C A
+X:2699025_T_C 2699025 T C
+X:2699091_G_A 2699091 G A
+X:2699187_T_C 2699187 T C
+X:2699188_G_C 2699188 G C
+X:2699189_T_C 2699189 T C
+X:2699217_C_T 2699217 C T
+X:2699246_C_A 2699246 C A
+X:2699275_T_G 2699275 T G
+X:2699350_A_T 2699350 A T
+X:2699360_T_C 2699360 T C
+X:2699450_A_C 2699450 A C
+X:2699507_T_C 2699507 T C
+X:2699555_C_A 2699555 C A
+X:2699645_G_T 2699645 G T
+X:2699676_G_A 2699676 G A
+X:2699728_C_T 2699728 C T
+X:2699775_C_A 2699775 C A
+X:2699898_C_CT 2699898 C CT
+X:2699968_A_G 2699968 A G
+X:2699970_T_C 2699970 T C
diff --git a/test/convert.hls.gt.samples b/test/convert.hls.gt.samples
new file mode 100644
index 000000000..c1eea1a98
--- /dev/null
+++ b/test/convert.hls.gt.samples
@@ -0,0 +1,11 @@
+sample population group sex
+NA00001 NA00001 NA00001 2
+NA00002 NA00002 NA00002 2
+NA00003 NA00003 NA00003 2
+NA00004 NA00004 NA00004 2
+NA00005 NA00005 NA00005 2
+NA00006 NA00006 NA00006 2
+NA00007 NA00007 NA00007 2
+NA00008 NA00008 NA00008 2
+NA00009 NA00009 NA00009 2
+NA00010 NA00010 NA00010 2
diff --git a/test/test.pl b/test/test.pl
index e89bee534..8b3ae3a21 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -196,6 +196,7 @@
 test_vcf_convert($opts,in=>'convert',out=>'convert.hls.haps',args=>'-h -,.,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hls.legend',args=>'-h .,-,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hls.samples',args=>'-h .,.,-');
+test_vcf_convert_hls2vcf($opts,h=>'convert.hls.gt.hap',l=>'convert.hls.gt.legend',s=>'convert.hls.gt.samples',out=>'convert.gt.noHead.vcf',args=>'-H');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hs.hap',args=>'--hapsample -,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hs.sample',args=>'--hapsample .,-');
 test_vcf_convert_gvcf($opts,in=>'convert.gvcf',out=>'convert.gvcf.out',fa=>'gvcf.fa',args=>'--gvcf2vcf');
@@ -506,6 +507,13 @@ sub test_vcf_convert
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $$opts{tmp}/$args{in}.vcf.gz");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args}");
 }
+sub test_vcf_convert_hls2vcf
+{
+    my ($opts,%args) = @_;
+    my $hls = join(',', map { "$$opts{path}/$_" }( $args{h}, $args{l}, $args{s} ) );
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls | grep -v ^##");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls -Ou | $$opts{bin}/bcftools view | grep -v ^##");
+}
 sub test_vcf_convert_gvcf
 {
     my ($opts,%args) = @_;
diff --git a/vcfconvert.c b/vcfconvert.c
index b9cfc46b1..f602648d5 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -241,27 +241,61 @@ static int tsv_setter_haps(tsv_t *tsv, bcf1_t *rec, void *usr)
     if ( args->rev_als ) { a0 = bcf_gt_phased(1); a1 = bcf_gt_phased(0); }
     else { a0 = bcf_gt_phased(0); a1 = bcf_gt_phased(1); }
 
+    // up is short for "unphased"
+    int nup = 0; 
     for (i=0; i<nsamples; i++)
     {
-        char *ss = tsv->ss + 4*i;
+        char *ss = tsv->ss + 4*i + nup;
+        int up = 0, all;
 
-        if ( !ss[0] || !ss[1] || !ss[2] )
+        for (all=0; all < 2; all++){
+            // checking for premature ending
+            if ( !ss[0] || !ss[1] || !ss[2] ||
+                 (up && (!ss[3] || !ss[4]) ) )
+            {
+                fprintf(stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]);
+                return -1;
+            }
+
+            switch(ss[all*2+up]){
+            case '0':
+                args->gts[2*i+all] = a0;
+                break;
+            case '1' :
+                args->gts[2*i+all] = a1;
+                break;
+            case '?' :
+                // there is no macro to express phased missing allele
+                args->gts[2*i+all] = bcf_gt_phased(-1);
+                break;
+            case '-' :
+                args->gts[2*i+all] = bcf_int32_vector_end;
+                break;
+            default :
+                fprintf(stderr,"Could not parse: [%c][%s]\n", ss[all*2+up],tsv->ss);
+                return -1; 
+            }
+            if( ss[all*2+up+1]=='*' ) up = up + 1;
+        }
+        
+        if(up && up != 2)
         {
-            fprintf(stderr,"Wrong number of fields at %d-th sample ([%c][%c][%c]). ",i+1,ss[0],ss[1],ss[2]);
+            fprintf(stderr,"Missing unphased marker '*': [%c][%s]", ss[2+up], tsv->ss);
             return -1;
         }
 
-        if ( ss[0]=='0' ) args->gts[2*i] = a0;
-        else if ( ss[0]=='1' ) args->gts[2*i] = a1;
-        else { fprintf(stderr,"Could not parse: [%c][%s]\n", ss[0],tsv->ss); return -1; }
-
-        if ( ss[2]=='0' ) args->gts[2*i+1] = a0;
-        else if ( ss[2]=='1' ) args->gts[2*i+1] = a1;
-        else { fprintf(stderr,"Could not parse: [%c][%s]\n", ss[2],tsv->ss); return -1; }
+        // change alleles to unphased if the alleles are unphased
+        if ( up )
+        {
+            args->gts[2*i] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i]));
+            args->gts[2*i+1] = bcf_gt_unphased(bcf_gt_allele(args->gts[2*i+1]));
+        }
+        nup = nup + up;
     }
-    if ( tsv->ss[(nsamples-1)*4+3] )
+    if ( tsv->ss[(nsamples-1)*4+3+nup] )
     {
-        fprintf(stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+1]);
+        fprintf(stderr,"nup: %d", nup);
+        fprintf(stderr,"Wrong number of fields (%d-th column = [%c]). ", nsamples*2,tsv->ss[(nsamples-1)*4+nup]);
         return -1;
     }
 
@@ -379,13 +413,14 @@ static void haplegendsample_to_vcf(args_t *args)
      *  Convert from IMPUTE2 hap/legend/sample output files to VCF
      *
      *      hap:
-     *          0 1 0 1 1 1
+     *          0 1 0 1
      *      legend:
      *          id position a0 a1
      *          1:186946386_G_T 186946386 G T
      *      sample:
-     *          QTL190044
-     *          QTL190053
+     *          sample population group sex
+     *          sample1 sample1 sample1 2
+     *          sample2 sample2 sample2 2
      *
      *  Output: VCF with filled GT
      */
@@ -444,16 +479,20 @@ static void haplegendsample_to_vcf(args_t *args)
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
     bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
 
-    int i, nsamples;
-    char **samples = hts_readlist(sample_fname, 1, &nsamples);
-    for (i=0; i<nsamples; i++)
+    int i, nrows, nsamples;
+    char **samples = hts_readlist(sample_fname, 1, &nrows);
+    nsamples = nrows - 1;
+
+    // sample_fname should contain a header line, so need to ignore first row
+    // returned from hts_readlist (i=1, and not i=0)
+    for (i=1; i<nrows; i++)
     {
         se = samples[i]; while ( *se && !isspace(*se) ) se++;
         *se = 0;
         bcf_hdr_add_sample(args->header,samples[i]);
     }
     bcf_hdr_add_sample(args->header,NULL);
-    for (i=0; i<nsamples; i++) free(samples[i]);
+    for (i=0; i<nrows; i++) free(samples[i]);
     free(samples);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));

From c29c8c31431642a0890e838b01028dc5b001682e Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 16 Mar 2015 21:10:48 +0000
Subject: [PATCH 079/211] Fixed bug in trio calling introduced by bcc7b26e

---
 mcall.c | 33 +++++++++++++++++----------------
 1 file changed, 17 insertions(+), 16 deletions(-)

diff --git a/mcall.c b/mcall.c
index b37593c1b..ddb5d625c 100644
--- a/mcall.c
+++ b/mcall.c
@@ -900,10 +900,11 @@ static void mcall_call_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_a
 static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int nout_als, int out_als)
 {
     int ia, ib, i;
-    int nsmpl   = bcf_hdr_nsamples(call->hdr);
-    int ngts    = nals*(nals+1)/2;
-    double *gls = call->GLs - ngts;
-    double *pdg = call->pdg - ngts;
+    int nsmpl    = bcf_hdr_nsamples(call->hdr);
+    int ngts     = nals*(nals+1)/2;
+    int nout_gts = nout_als*(nout_als+1)/2;
+    double *gls  = call->GLs - nout_gts;
+    double *pdg  = call->pdg - ngts;
 
     // Calculate individuals' genotype likelihoods P(X=i)
     int isample;
@@ -912,19 +913,19 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
         int ploidy = call->ploidy ? call->ploidy[isample] : 2;
         int32_t *gts = call->ugts + isample;
 
-        gls += ngts;
+        gls += nout_gts;
         pdg += ngts;
 
         // Skip samples with all pdg's equal to 1. These have zero depth.
         for (i=0; i<ngts; i++) if ( pdg[i]!=0.0 ) break;
         if ( i==ngts || !ploidy )
         {
-            gts[0] = bcf_gt_missing;
+            gts[0] = -1;
             gls[0] = 1;
             continue;
         }
 
-        for (i=0; i<ngts; i++) gls[i] = -HUGE_VAL;
+        for (i=0; i<nout_gts; i++) gls[i] = -HUGE_VAL;
 
         double sum_lk  = 0;
         double best_lk = 0;
@@ -963,7 +964,7 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
                 }
             }
         }
-        for (i=0; i<ngts; i++)
+        for (i=0; i<nout_gts; i++)
             if ( gls[i]!=-HUGE_VAL ) gls[i] = log(gls[i]/sum_lk);
     }
 
@@ -1002,11 +1003,11 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
         for (i=0; i<3; i++)     // for father, mother, child
         {
             int ismpl = fam->sample[i];
-            double *gl = call->GLs + ngts*ismpl;
+            double *gl = call->GLs + nout_gts*ismpl;
             if ( gl[0]==1 ) continue;
             int j, jmax = 0;
             double max  = gl[0];
-            for (j=1; j<ngts; j++)
+            for (j=1; j<nout_gts; j++)
                 if ( max < gl[j] ) { max = gl[j]; jmax = j; }
             uc_lk += max;
             uc_itr |= jmax << ((2-i)*4);
@@ -1022,7 +1023,7 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
             for (i=0; i<3; i++)     // for father, mother, child
             {
                 int ismpl = fam->sample[i];
-                double *gl = call->GLs + ngts*ismpl;
+                double *gl = call->GLs + nout_gts*ismpl;
                 if ( gl[0]==1 ) continue;
                 int igt = trio[itr]>>((2-i)*4) & 0xf;
                 assert( !call->ploidy || call->ploidy[ismpl]>0 );
@@ -1042,10 +1043,10 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
         if ( !uc_is_mendelian )
         {
             uc_lk += log(1 - trio_Pm);
-            //fprintf(stderr,"c_lk=%e uc_lk=%e c_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,uc_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
+            // fprintf(stderr,"c_lk=%e uc_lk=%e c_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,uc_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
             if ( c_lk < uc_lk ) { c_lk = uc_lk; c_itr = uc_itr; }
         }
-        //fprintf(stderr,"best_lk=%e best_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
+        // fprintf(stderr,"best_lk=%e best_itr=%d%d%d uc_itr=%d%d%d\n", c_lk,c_itr>>8&0xf,c_itr>>4&0xf,c_itr&0xf,uc_itr>>8&0xf,uc_itr>>4&0xf,uc_itr&0xf);
 
         // Set genotypes for father, mother, child and calculate genotype qualities
         for (i=0; i<3; i++)
@@ -1053,11 +1054,11 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
             // GT
             int ismpl    = fam->sample[i];
             int igt      = c_itr>>((2-i)*4) & 0xf;
-            double *gl   = call->GLs + ngts*ismpl;
+            double *gl   = call->GLs + nout_gts*ismpl;
             int32_t *gts = call->cgts + ismpl;
             if ( gl[0]==1 || igt==GT_SKIP )    // zero depth, set missing genotypes
             {
-                gts[0] = bcf_gt_missing;
+                gts[0] = -1;
                 // bcf_float_set_missing(call->GQs[ismpl]);
                 continue;
             }
@@ -1107,7 +1108,7 @@ static void mcall_call_trio_genotypes(call_t *call, bcf1_t *rec, int nals, int n
         cgts++;
         ugts++;
         gts += 2;
-        if ( bcf_gt_is_missing(ugts[0]) )
+        if ( ugts[0]==-1 )
         {
             gts[0] = bcf_gt_missing;
             gts[1] = ploidy==2 ? bcf_gt_missing : bcf_int32_vector_end;

From 537228096a897fc814cfb60d6599189835ba976e Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 30 Sep 2015 08:03:35 +0100
Subject: [PATCH 080/211] vcfindex: make index -s work even if length attribute
 is not present

---
 vcfindex.c | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/vcfindex.c b/vcfindex.c
index 24ac8a87a..e40fab52c 100644
--- a/vcfindex.c
+++ b/vcfindex.c
@@ -97,13 +97,7 @@ int vcf_index_stats(char *fname, int stats)
         if (stats&2 || !records) continue;
         bcf_hrec_t *hrec = bcf_hdr_get_hrec(hdr, BCF_HL_CTG, "ID", seq[i], NULL);
         int hkey = hrec ? bcf_hrec_find_key(hrec, "length") : -1;
-        if (hkey<0)
-        {
-            fprintf(stderr,"could not get contig length for %s\n", seq[i]);
-            return 1;
-        }
-        fprintf(out, "%s\t%s", seq[i], strcmp(hrec->vals[hkey], "2147483647")==0 ? "." : hrec->vals[hkey]);
-        fprintf(out, "\t%" PRIu64 "\n", records);
+        fprintf(out,"%s\t%s\t%" PRIu64 "\n", seq[i], hkey<0?".":hrec->vals[hkey], records);
     }
     if (!sum)
     {

From 6d2faf230ec8caf6d1dddbaeb6e3a152fc13c68d Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 24 Sep 2015 14:30:38 +0100
Subject: [PATCH 081/211] Bringing "call --gvcf" from experimental to main
 repo.

---
 call.h             |  18 +----
 gvcf.c             | 190 ++++++++++++++++++++++++++++++++++++++-------
 gvcf.h             |  41 ++++++++++
 mcall.c            |  31 +++-----
 test/mpileup.2.out |  27 +++----
 test/test.pl       |   2 +-
 vcfcall.c          | 110 ++++++++++----------------
 7 files changed, 277 insertions(+), 142 deletions(-)
 create mode 100644 gvcf.h

diff --git a/call.h b/call.h
index cc5e6d7b0..bbf0a52b4 100644
--- a/call.h
+++ b/call.h
@@ -33,8 +33,8 @@ THE SOFTWARE.  */
 #define CALL_VARONLY        (1<<1)
 #define CALL_CONSTR_TRIO    (1<<2)
 #define CALL_CONSTR_ALLELES (1<<3)
-#define CALL_CHR_X          (1<<4)
-#define CALL_CHR_Y          (1<<5)
+//
+//
 #define CALL_FMT_GQ         (1<<6)
 #define CALL_FMT_GP         (1<<7)
 
@@ -49,15 +49,6 @@ typedef struct
 }
 family_t;
 
-typedef struct
-{
-    int min_dp, mdp;    // minimum per-sample depth of a gVCF block
-    int32_t rid, start, end, *gt, *dp;
-    char ref[2];        // reference base at start position
-    bcf1_t *line;
-}
-gvcf_t;
-
 typedef struct _ccall_t ccall_t;
 typedef struct
 {
@@ -96,7 +87,7 @@ typedef struct
     bcf1_t *rec;
     bcf_hdr_t *hdr;
     uint32_t flag;          // One or more of the CALL_* flags defined above
-    uint8_t *ploidy, all_diploid;
+    uint8_t *ploidy, all_diploid, unseen;
 
     double pl2p[256];       // PL to 10^(-PL/10) table
     int32_t *PLs;           // VCF PL likelihoods (rw)
@@ -129,9 +120,6 @@ void qcall_destroy(call_t *call);
 void call_init_pl2p(call_t *call);
 uint32_t *call_trio_prep(int is_x, int is_son);
 
-/** gVCF */
-void gvcf_write(htsFile *fh, gvcf_t *gvcf, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref);
-
 void init_allele_trimming_maps(call_t *call, int als, int nals);
 void mcall_trim_numberR(call_t *call, bcf1_t *rec, int nals, int nout_als, int out_als);
 
diff --git a/gvcf.c b/gvcf.c
index bba5df767..b82d658d8 100644
--- a/gvcf.c
+++ b/gvcf.c
@@ -1,6 +1,6 @@
 /*  gvcf.c -- support for gVCF files.
 
-    Copyright (C) 2014 Genome Research Ltd.
+    Copyright (C) 2014-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -22,33 +22,117 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.  */
 
-#include "call.h"
+#include "gvcf.h"
+#include "bcftools.h"
 
-void gvcf_write(htsFile *fh, gvcf_t *gvcf, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref)
+struct _gvcf_t
+{
+    int *dp_range, ndp_range;   // per-sample DP ranges
+    int prev_range;             // 0 if not in a block
+    int32_t *dp, mdp, *pl, mpl, npl;
+    int32_t *tmp, mtmp, *gts, ngts,mgts, nqsum,mqsum;
+    float *qsum;
+    int32_t rid, start, end, min_dp;
+    kstring_t als;
+    bcf1_t *line;
+};
+
+void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr)
+{
+    bcf_hdr_append(hdr,"##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
+    bcf_hdr_append(hdr,"##INFO=<ID=MinDP,Number=1,Type=Integer,Description=\"Minimum per-sample depth in this gVCF block\">");
+}
+
+gvcf_t *gvcf_init(const char *dp_ranges)
+{
+    gvcf_t *gvcf = (gvcf_t*) calloc(1,sizeof(gvcf_t));
+    gvcf->line = bcf_init();
+
+    int n = 1;
+    const char *ss = dp_ranges;
+    while ( *ss )
+    {
+        if ( *ss==',' ) n++;
+        ss++;
+    }
+    gvcf->ndp_range = n;
+    gvcf->dp_range  = (int*) malloc(sizeof(int)*gvcf->ndp_range);
+
+    n  = 0;
+    ss = dp_ranges;
+    while ( *ss )
+    {
+        char *se = (char*) ss;
+        gvcf->dp_range[n++] = strtol(ss,&se,10);
+        if ( se==ss ) return NULL;
+        if ( *se==',' && se[1] ) { ss = se+1; continue; }
+        else if ( !*se ) break;
+        return NULL;
+    }
+    return gvcf;
+}
+
+void gvcf_destroy(gvcf_t *gvcf)
+{
+    free(gvcf->dp_range);
+    free(gvcf->dp);
+    free(gvcf->pl);
+    free(gvcf->tmp);
+    free(gvcf->qsum);
+    free(gvcf->gts);
+    free(gvcf->als.s);
+    if ( gvcf->line ) bcf_destroy(gvcf->line);
+    free(gvcf);
+}
+
+bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref)
 {
     int i, ret, nsmpl = bcf_hdr_nsamples(hdr);
+    int can_collapse = is_ref ? 1 : 0;
+    int32_t dp_range = 0, min_dp = 0;
+
+    // No record and nothing to flush?
+    if ( !rec && !gvcf->prev_range ) return NULL;
 
-    // Flush gVCF block if chr changed, non-ref call encountered, depth is too
-    // low, or no more records to come
-    if ( rec && is_ref )
+    // Flush gVCF block if there are no more records, chr changed, a gap
+    // encountered, or other conditions not met (block broken by a non-ref or DP too low).
+    int needs_flush = can_collapse ? 0 : 1;
+
+
+    // Can the record be included in a gVCF block? That is, is this a ref-only site?
+    if ( rec && can_collapse )
     {
         bcf_unpack(rec, BCF_UN_ALL);
 
         // per-sample depth
-        ret = bcf_get_format_int32(hdr, rec, "DP", &gvcf->dp, &gvcf->mdp);
+        ret = bcf_get_format_int32(hdr, rec, "DP", &gvcf->tmp, &gvcf->mtmp);
         if ( ret==nsmpl )
         {
-            for (i=0; i<nsmpl; i++)
-                if ( gvcf->dp[i] < gvcf->min_dp ) break;
-            if ( i<nsmpl )
+            min_dp = gvcf->tmp[0];
+            for (i=1; i<nsmpl; i++)
+                if ( min_dp > gvcf->tmp[i] ) min_dp = gvcf->tmp[i];
+
+            for (i=0; i<gvcf->ndp_range; i++)
+                if ( min_dp < gvcf->dp_range[i] ) break;
+
+            dp_range = i;
+            if ( !dp_range )
             {
-                is_ref = 0;  // the depth is too low
-                rec = NULL;
+                // leave the record unchanged, DP is too small. Alternatively, return NULL here
+                // to skip these sites
+                needs_flush  = 1;
+                can_collapse = 0;
             }
         }
+        else
+            needs_flush = 1;       // DP field not present
     }
 
-    if ( gvcf->rid!=-1 && (!rec || gvcf->rid!=rec->rid || !is_ref || rec->pos > gvcf->end+1) )
+    if ( gvcf->prev_range && gvcf->prev_range!=dp_range ) needs_flush = 1;
+    if ( !rec || gvcf->rid!=rec->rid || rec->pos > gvcf->end+1 ) needs_flush = 1;
+
+    // If prev_range is set, something can be flushed
+    if ( gvcf->prev_range && needs_flush )
     {
         // mpileup can output two records with the same position, SNP and
         // indel. Make sure the end position does not include the non-variant
@@ -61,29 +145,83 @@ void gvcf_write(htsFile *fh, gvcf_t *gvcf, bcf_hdr_t *hdr, bcf1_t *rec, int is_r
         gvcf->line->rid  = gvcf->rid;
         gvcf->line->pos  = gvcf->start;
         gvcf->line->rlen = gvcf->end - gvcf->start;
-        bcf_update_alleles_str(hdr, gvcf->line, gvcf->ref);
-        bcf_update_info_int32(hdr, gvcf->line, "END", &gvcf->end, 1);
-        bcf_update_genotypes(hdr, gvcf->line, gvcf->gt, nsmpl*2);
+        bcf_update_alleles_str(hdr, gvcf->line, gvcf->als.s);
+        if ( gvcf->start+1 < gvcf->end )    // create gVCF record only if it spans at least two sites
+            bcf_update_info_int32(hdr, gvcf->line, "END", &gvcf->end, 1);
+        bcf_update_info_int32(hdr, gvcf->line, "MinDP", &gvcf->min_dp, 1);
+        if ( gvcf->nqsum>0 )
+            bcf_update_info_float(hdr, gvcf->line, "QS", gvcf->qsum, gvcf->nqsum);
+        if ( gvcf->ngts )
+            bcf_update_genotypes(hdr,gvcf->line,gvcf->gts,gvcf->ngts);
+        if ( gvcf->npl>0 )
+            bcf_update_format_int32(hdr, gvcf->line, "PL", gvcf->pl, gvcf->npl);
+        bcf_update_format_int32(hdr, gvcf->line, "DP", gvcf->dp, nsmpl);
         bcf_write1(fh, hdr, gvcf->line);
+        gvcf->prev_range = 0;
+        gvcf->rid  = -1;
+        gvcf->npl  = 0;
+        gvcf->nqsum = 0;
+        gvcf->ngts  = 0;
 
-        gvcf->rid = -1;
+        if ( !rec ) return NULL;     // just flushing the buffer, this was last record
     }
 
-    if ( !rec ) return;
-
-    if ( is_ref )
+    if ( can_collapse )
     {
-        if ( gvcf->rid==-1 )
+        if ( !gvcf->prev_range )
         {
+            hts_expand(int32_t,nsmpl,gvcf->mdp,gvcf->dp);
+            memcpy(gvcf->dp,gvcf->tmp,nsmpl*sizeof(int32_t));   // tmp still contains DP from rec
+            gvcf->npl = bcf_get_format_int32(hdr, rec, "PL", &gvcf->pl, &gvcf->mpl);
+
+            gvcf->nqsum = bcf_get_info_float(hdr,rec,"QS",&gvcf->qsum,&gvcf->mqsum);
+            gvcf->ngts  = bcf_get_genotypes(hdr,rec,&gvcf->gts,&gvcf->mgts);
+
             gvcf->rid    = rec->rid;
             gvcf->start  = rec->pos;
-            gvcf->ref[0] = rec->d.allele[0][0];
-            gvcf->ref[1] = 0;
+            gvcf->als.l = 0;
+            kputs(rec->d.allele[0],&gvcf->als);
+            for (i=1; i<rec->n_allele; i++)
+            {
+                kputc(',',&gvcf->als);
+                kputs(rec->d.allele[i],&gvcf->als);
+            }
+            gvcf->min_dp = min_dp;
+        }
+        else
+        {
+            if ( gvcf->min_dp > min_dp ) gvcf->min_dp = min_dp;
+            for (i=0; i<nsmpl; i++)
+                if ( gvcf->dp[i] > gvcf->tmp[i] ) gvcf->dp[i] = gvcf->tmp[i];
+            ret = bcf_get_format_int32(hdr, rec, "PL", &gvcf->tmp, &gvcf->mtmp);
+            if ( ret>=0 )
+            {
+                if ( ret!=nsmpl*3 ) error("Unexpected number of PL fields\n");
+                for (i=0; i<nsmpl; i++)
+                {
+                    if ( gvcf->pl[3*i+1] > gvcf->tmp[3*i+1] )
+                    {
+                        gvcf->pl[3*i+1] = gvcf->tmp[3*i+1];
+                        gvcf->pl[3*i+2] = gvcf->tmp[3*i+2];
+                    }
+                    else if ( gvcf->pl[3*i+1]==gvcf->tmp[3*i+1] && gvcf->pl[3*i+2] > gvcf->tmp[3*i+2] )
+                        gvcf->pl[3*i+2] = gvcf->tmp[3*i+2];
+                }
+            }
+            else
+                gvcf->npl = 0;
         }
-        gvcf->end = rec->pos;
-        return;
+        gvcf->prev_range = dp_range;
+        if ( bcf_get_info_int32(hdr,rec,"END",&gvcf->tmp,&gvcf->mtmp)==1 )
+            gvcf->end = gvcf->tmp[0] - 1;   // from 1-based to 0-based
+        else
+            gvcf->end = rec->pos;
+        return NULL;
     }
 
-    bcf_write1(fh, hdr, rec);
+    if ( is_ref && min_dp )
+        bcf_update_info_int32(hdr, rec, "MinDP", &min_dp, 1);
+
+    return rec;
 }
 
diff --git a/gvcf.h b/gvcf.h
new file mode 100644
index 000000000..784e1f6d8
--- /dev/null
+++ b/gvcf.h
@@ -0,0 +1,41 @@
+/* gvcf.[ch] - Helper functions for gVCF support
+
+   The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#ifndef __GVCF_H__
+#define __GVCF_H__
+
+#include "bcftools.h"
+
+typedef struct _gvcf_t gvcf_t;
+
+gvcf_t *gvcf_init(const char *dp_ranges);
+void gvcf_update_header(gvcf_t *gvcf, bcf_hdr_t *hdr);
+bcf1_t *gvcf_write(gvcf_t *gvcf, htsFile *fh, bcf_hdr_t *hdr, bcf1_t *rec, int is_ref);
+void gvcf_destroy(gvcf_t *gvcf);
+
+#endif
diff --git a/mcall.c b/mcall.c
index ddb5d625c..e62fd4c47 100644
--- a/mcall.c
+++ b/mcall.c
@@ -691,7 +691,7 @@ static void mcall_set_ref_genotypes(call_t *call, int nals)
     int ngts  = nals*(nals+1)/2;
     int nsmpl = bcf_hdr_nsamples(call->hdr);
 
-    for (i=0; i<4; i++) call->ac[i] = 0;
+    for (i=0; i<nals; i++) call->ac[i] = 0;
     call->nhets = 0;
     call->ndiploid = 0;
 
@@ -1335,13 +1335,7 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
   */
 int mcall(call_t *call, bcf1_t *rec)
 {
-    int i, unseen = -1;
-    for (i=1; i<rec->n_allele; i++)
-    {
-        if ( rec->d.allele[i][0]=='X' ) { unseen = i; break; }  // old X
-        if ( rec->d.allele[i][0]=='<' && rec->d.allele[i][1]=='X' && rec->d.allele[i][1]=='>' ) { unseen = i; break; } // old <X>
-        if ( rec->d.allele[i][0]=='<' && rec->d.allele[i][1]=='*' && rec->d.allele[i][1]=='>' ) { unseen = i; break; } // new <*>
-    }
+    int i, unseen = call->unseen;
 
     // Force alleles when calling genotypes given alleles was requested
     if ( call->flag & CALL_CONSTR_ALLELES ) mcall_constrain_alleles(call, rec, unseen);
@@ -1417,9 +1411,7 @@ int mcall(call_t *call, bcf1_t *rec)
         nout = 0;
         for (i=0; i<nals; i++)
         {
-            if ( rec->d.allele[i][0]=='X' ) continue;   // old version of unseen allele "X"
-            if ( rec->d.allele[i][0]=='<' && rec->d.allele[i][1]=='X' && rec->d.allele[i][2]=='>' ) continue;   // old version of unseen allele, "<X>"
-            if ( rec->d.allele[i][0]=='<' && rec->d.allele[i][1]=='*' && rec->d.allele[i][2]=='>' ) continue;   // new version of unseen allele, "<*>"
+            if ( i>0 && i==unseen ) continue;
             out_als |= 1<<i;
             nout++;
         }
@@ -1469,12 +1461,12 @@ int mcall(call_t *call, bcf1_t *rec)
         if ( hob != HUGE_VAL ) bcf_update_info_float(call->hdr, rec, "HOB", &hob, 1);
 
         // Quality of a variant site. fabs() to avoid negative zeros in VCF output when CALL_KEEPALT is set
-        rec->qual = call->lk_sum==-HUGE_VAL ? 0 : fabs(-4.343*(call->ref_lk - call->lk_sum));
+        rec->qual = call->lk_sum==-HUGE_VAL || call->ref_lk==0 ? 0 : fabs(-4.343*(call->ref_lk - call->lk_sum));
     }
     else
     {
         // Set the quality of a REF site
-        rec->qual = call->lk_sum==-HUGE_VAL ? 0 : -4.343*log(1 - exp(call->ref_lk - call->lk_sum));
+        rec->qual = call->lk_sum==-HUGE_VAL || call->ref_lk==0 ? 0 : -4.343*log(1 - exp(call->ref_lk - call->lk_sum));
     }
     if ( rec->qual>999 ) rec->qual = 999;
     if ( rec->qual>50 ) rec->qual = rint(rec->qual);
@@ -1492,13 +1484,14 @@ int mcall(call_t *call, bcf1_t *rec)
     bcf_update_genotypes(call->hdr, rec, call->gts, nsmpl*2);
 
     // DP4 tag
-    if ( bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16)!=16 )
-        error("I16 hasn't 16 fields at %s:%d\n", call->hdr->id[BCF_DT_CTG][rec->rid].key,rec->pos+1);
-    int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3];
-    bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4);
+    if ( bcf_get_info_float(call->hdr, rec, "I16", &call->anno16, &call->n16)==16 )
+    {
+        int32_t dp[4]; dp[0] = call->anno16[0]; dp[1] = call->anno16[1]; dp[2] = call->anno16[2]; dp[3] = call->anno16[3];
+        bcf_update_info_int32(call->hdr, rec, "DP4", dp, 4);
 
-    int32_t mq = (call->anno16[8]+call->anno16[10])/(call->anno16[0]+call->anno16[1]+call->anno16[2]+call->anno16[3]);
-    bcf_update_info_int32(call->hdr, rec, "MQ", &mq, 1);
+        int32_t mq = (call->anno16[8]+call->anno16[10])/(call->anno16[0]+call->anno16[1]+call->anno16[2]+call->anno16[3]);
+        bcf_update_info_int32(call->hdr, rec, "MQ", &mq, 1);
+    }
 
     bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0);     // remove I16 tag
     bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0);      // remove QS tag
diff --git a/test/mpileup.2.out b/test/mpileup.2.out
index 4a415ea8e..1090fbd52 100644
--- a/test/mpileup.2.out
+++ b/test/mpileup.2.out
@@ -19,6 +19,8 @@
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=MinDP,Number=1,Type=Integer,Description="Minimum per-sample depth in this gVCF block">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
 ##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
@@ -26,28 +28,27 @@
 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
-##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
-17	1	.	A	.	.	.	END=301	GT	0/0	0/0	0/0
+17	1	.	A	.	.	.	END=301;MinDP=1	GT:DP	0/0:5	0/0:1	0/0:3
 17	302	.	T	TA	488	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=49	GT:PL:DP:DV	0/1:167,0,96:11:6	0/1:157,0,9:7:6	1/1:201,21,0:7:7
-17	303	.	G	.	.	.	END=827	GT	0/0	0/0	0/0
+17	303	.	G	.	.	.	END=827;MinDP=2	GT:DP	0/0:9	0/0:2	0/0:3
 17	828	.	T	C	409	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	0/1:116,0,91:9:5	1/1:120,12,0:4:4
-17	829	.	T	.	.	.	END=833	GT	0/0	0/0	0/0
+17	829	.	T	.	.	.	END=833;MinDP=4	GT:DP	0/0:11	0/0:8	0/0:4
 17	834	.	G	A	364	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,3,7,10;MQ=60	GT:PL:DP:DV	0/1:185,0,46:11:9	0/1:128,0,59:8:5	1/1:89,9,0:3:3
-17	835	.	T	.	.	.	END=1664	GT	0/0	0/0	0/0
+17	835	.	T	.	.	.	END=1664;MinDP=1	GT:DP	0/0:5	0/0:2	0/0:1
 17	1665	.	T	C	3.10665	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
-17	1666	.	G	.	.	.	END=1868	GT	0/0	0/0	0/0
+17	1666	.	G	.	.	.	END=1868;MinDP=0	GT:DP	0/0:6	0/0:0	0/0:1
 17	1869	.	A	T	138	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,9,5,4;MQ=58	GT:PL:DP:DV	0/1:115,0,224:18:7	0/1:16,0,104:5:1	1/1:42,3,0:1:1
-17	1870	.	C	.	.	.	END=2040	GT	0/0	0/0	0/0
+17	1870	.	C	.	.	.	END=2040;MinDP=1	GT:DP	0/0:13	0/0:2	0/0:1
 17	2041	.	G	A	447	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,5,12,7;MQ=58	GT:PL:DP:DV	0/1:229,0,212:21:11	0/1:32,0,24:2:1	1/1:223,21,0:7:7
-17	2042	.	G	.	.	.	END=2219	GT	0/0	0/0	0/0
+17	2042	.	G	.	.	.	END=2219;MinDP=1	GT:DP	0/0:8	0/0:1	0/0:3
 17	2220	.	G	A	303	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=6,2,1,11;MQ=58	GT:PL:DP:DV	0/1:139,0,130:12:6	0/1:69,0,46:4:2	1/1:131,12,0:4:4
-17	2221	.	G	.	.	.	END=2563	GT	0/0	0/0	0/0
+17	2221	.	G	.	.	.	END=2563;MinDP=0	GT:DP	0/0:5	0/0:0	0/0:2
 17	2564	.	A	G	233	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=1,4,4,5;MQ=60	GT:PL:DP:DV	0/1:88,0,78:6:3	0/1:57,0,56:4:2	1/1:124,12,0:4:4
-17	2565	.	A	.	.	.	END=3103	GT	0/0	0/0	0/0
+17	2565	.	A	.	.	.	END=3103;MinDP=0	GT:DP	0/0:6	0/0:0	0/0:1
 17	3104	.	C	T	24.2837	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=8,15,2,0;MQ=58	GT:PL:DP:DV	0/0:0,48,255:16:0	0/0:0,12,144:4:0	0/1:59,0,93:5:2
-17	3105	.	T	.	.	.	END=3586	GT	0/0	0/0	0/0
+17	3105	.	T	.	.	.	END=3586;MinDP=2	GT:DP	0/0:5	0/0:2	0/0:3
 17	3587	.	G	A	358	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=4,7,10,6;MQ=60	GT:PL:DP:DV	0/1:161,0,184:14:7	0/1:22,0,118:5:1	1/1:212,24,0:8:8
-17	3588	.	A	.	.	.	END=3935	GT	0/0	0/0	0/0
+17	3588	.	A	.	.	.	END=3935;MinDP=2	GT:DP	0/0:10	0/0:2	0/0:3
 17	3936	.	A	G	469	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=5,6,6,17;MQ=56	GT:PL:DP:DV	0/1:233,0,206:20:11	0/1:77,0,58:6:4	1/1:196,24,0:8:8
-17	3937	.	C	.	.	.	END=4101	GT	0/0	0/0	0/0
+17	3937	.	C	.	.	.	END=4101;MinDP=0	GT:DP	0/0:1	0/0:0	0/0:0
diff --git a/test/test.pl b/test/test.pl
index e89bee534..23a3fb499 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -129,7 +129,7 @@
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.2.out',args=>q[-H -c6:nonmajor],reg=>'');
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.1.out',args=>q[-H -q0.3:major],reg=>'');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.1.out',args=>'-mv');
-test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mvg0');
+test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mg0');
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_call_cAls($opts,in=>'mpileup',out=>'mpileup.cAls.out',tab=>'mpileup');
diff --git a/vcfcall.c b/vcfcall.c
index 7943b9a1b..5633256a1 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -40,6 +40,7 @@ THE SOFTWARE.  */
 #include "call.h"
 #include "prob1.h"
 #include "ploidy.h"
+#include "gvcf.h"
 
 void error(const char *format, ...);
 
@@ -51,7 +52,7 @@ void error(const char *format, ...);
 #define CF_NO_GENO      1
 #define CF_INS_MISSED   (1<<1)
 #define CF_CCALL        (1<<2)
-#define CF_GVCF         (1<<3)
+//                      (1<<3)
 //                      (1<<4)
 //                      (1<<5)
 #define CF_ACGT_ONLY    (1<<6)
@@ -71,7 +72,7 @@ typedef struct
     htsFile *bcf_in, *out_fh;
     char *bcf_fname, *output_fname;
     char **samples;             // for subsampling and ploidy
-    int nsamples, *samples_map;
+    int nsamples, *samples_map; // mapping from output sample names to original VCF
     char *regions, *targets;    // regions to process
     int regions_is_file, targets_is_file;
 
@@ -80,10 +81,10 @@ typedef struct
     int *sample2sex;    // mapping for ploidy. If negative, interpreted as -1*ploidy
     int *sex2ploidy, *sex2ploidy_prev, nsex;
     ploidy_t *ploidy;
+    gvcf_t *gvcf;
 
     bcf1_t *missed_line;
     call_t aux;     // parameters and temporary data
-    gvcf_t gvcf;
 
     int argc;
     char **argv;
@@ -145,7 +146,7 @@ static ploidy_predef_t ploidy_predefs[] =
           "*  * *     F 2\n"
     },
     { .alias  = "GRCh38",
-      .about  = "Human Genome reference assembly GRCh38 / hg38",
+      .about  = "Human Genome reference assembly GRCh38 / hg38, plain chromosome naming (1,2,3,..)",
       .ploidy =
           "X 1 9999 M 1\n"
           "X 2781480 155701381 M 1\n"
@@ -345,8 +346,6 @@ static void print_missed_line(bcf_sr_regions_t *regs, void *data)
     call_t *call = &args->aux;
     bcf1_t *missed = args->missed_line;
 
-    if ( args->flag & CF_GVCF ) error("todo: Combine --gvcf and --insert-missed\n");
-
     char *ss = regs->line.s;
     int i = 0;
     while ( i<args->aux.srs->targets_als-1 && *ss )
@@ -405,6 +404,9 @@ static void init_data(args_t *args)
         for (i=0; i<args->nsex; i++) args->sex2ploidy_prev[i] = 2;
     }
 
+    if ( args->gvcf ) 
+        gvcf_update_header(args->gvcf, args->aux.hdr);
+
     if ( args->samples_map )
     {
         args->aux.hdr = bcf_hdr_subset(bcf_sr_get_header(args->aux.srs,0), args->nsamples, args->samples, args->samples_map);
@@ -433,19 +435,6 @@ static void init_data(args_t *args)
     if ( args->flag & CF_CCALL )
         ccall_init(&args->aux);
 
-    if ( args->flag&CF_GVCF )
-    {
-        bcf_hdr_append(args->aux.hdr,"##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
-        args->gvcf.rid  = -1;
-        args->gvcf.line = bcf_init1();
-        args->gvcf.gt   = (int32_t*) malloc(2*sizeof(int32_t)*bcf_hdr_nsamples(args->aux.hdr));
-        for (i=0; i<bcf_hdr_nsamples(args->aux.hdr); i++)
-        {
-            args->gvcf.gt[2*i+0] = bcf_gt_unphased(0);
-            args->gvcf.gt[2*i+1] = bcf_gt_unphased(0);
-        }
-    }
-
     bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS");
     bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16");
 
@@ -469,15 +458,13 @@ static void destroy_data(args_t *args)
     }
     if ( args->missed_line ) bcf_destroy(args->missed_line);
     ploidy_destroy(args->ploidy);
-    if ( args->gvcf.line ) bcf_destroy(args->gvcf.line);
-    free(args->gvcf.gt);
-    free(args->gvcf.dp);
     free(args->sex2ploidy);
     free(args->sex2ploidy_prev);
     free(args->samples);
     free(args->samples_map);
     free(args->sample2sex);
     free(args->aux.ploidy);
+    if ( args->gvcf ) gvcf_destroy(args->gvcf);
     bcf_hdr_destroy(args->aux.hdr);
     hts_close(args->out_fh);
     bcf_sr_destroy(args->aux.srs);
@@ -598,14 +585,14 @@ static void usage(args_t *args)
     fprintf(stderr, "   -r, --regions <region>          restrict to comma-separated list of regions\n");
     fprintf(stderr, "   -R, --regions-file <file>       restrict to regions listed in a file\n");
     fprintf(stderr, "   -s, --samples <list>            list of samples to include [all samples]\n");
-    fprintf(stderr, "   -S, --samples-file <file>       PED file or a file with optional second column for ploidy (0, 1 or 2) [all samples]\n");
+    fprintf(stderr, "   -S, --samples-file <file>       PED file or a file with an optional column with sex (see man page for details) [all samples]\n");
     fprintf(stderr, "   -t, --targets <region>          similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "   -T, --targets-file <file>       similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Input/output options:\n");
     fprintf(stderr, "   -A, --keep-alts                 keep all possible alternate alleles at variant sites\n");
     fprintf(stderr, "   -f, --format-fields <list>      output format fields: GQ,GP (lowercase allowed) []\n");
-    fprintf(stderr, "   -g, --gvcf <minDP>              output gVCF blocks of homozygous REF calls\n");
+    fprintf(stderr, "   -g, --gvcf <int>,[...]          group non-variant sites into gVCF blocks by minimum per-sample DP\n");
     fprintf(stderr, "   -i, --insert-missed             output also sites missed by mpileup but present in -T\n");
     fprintf(stderr, "   -M, --keep-masked-ref           keep sites with masked reference allele (REF=N)\n");
     fprintf(stderr, "   -V, --skip-variants <type>      skip indels/snps\n");
@@ -618,8 +605,6 @@ static void usage(args_t *args)
     fprintf(stderr, "   -n, --novel-rate <float>,[...]  likelihood of novel mutation for constrained trio calling, see man page for details [1e-8,1e-9,1e-9]\n");
     fprintf(stderr, "   -p, --pval-threshold <float>    variant if P(ref|D)<FLOAT with -c [0.5]\n");
     fprintf(stderr, "   -P, --prior <float>             mutation rate (use bigger for greater sensitivity) [1.1e-3]\n");
-    fprintf(stderr, "   -X, --chromosome-X              haploid output for male samples (requires PED file with -s)\n");
-    fprintf(stderr, "   -Y, --chromosome-Y              haploid output for males and skips females (requires PED file with -s)\n");
 
     // todo (and more)
     // fprintf(stderr, "\nContrast calling and association test options:\n");
@@ -653,8 +638,8 @@ int main_vcfcall(int argc, char *argv[])
     static struct option loptions[] =
     {
         {"help",0,0,'h'},
-        {"gvcf",1,0,'g'},
         {"format-fields",1,0,'f'},
+        {"gvcf",1,0,'g'},
         {"output",1,0,'o'},
         {"output-type",1,0,'O'},
         {"regions",1,0,'r'},
@@ -674,24 +659,19 @@ int main_vcfcall(int argc, char *argv[])
         {"multiallelic-caller",0,0,'m'},
         {"pval-threshold",1,0,'p'},
         {"prior",1,0,'P'},
-        {"chromosome-X",0,0,'X'},
-        {"chromosome-Y",0,0,'Y'},
         {"novel-rate",1,0,'n'},
         {"ploidy",1,0,1},
         {"ploidy-file",1,0,2},
+        {"chromosome-X",1,0,'X'},
+        {"chromosome-Y",1,0,'Y'},
         {0,0,0,0}
     };
 
     char *tmp = NULL;
-    while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:XYn:P:f:ig:", loptions, NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:n:P:f:ig:XY", loptions, NULL)) >= 0)
     {
         switch (c)
         {
-            case 'g':
-                args.flag |= CF_GVCF;
-                args.gvcf.min_dp = strtol(optarg,&tmp,10);
-                if ( *tmp ) error("Could not parse, expected integer argument: -g %s\n", optarg);
-                break;
             case  2 : ploidy_fname = optarg; break;
             case  1 : ploidy = optarg; break;
             case 'X': ploidy = "X"; fprintf(stderr,"Warning: -X will be deprecated, please use --ploidy instead.\n"); break;
@@ -703,6 +683,10 @@ int main_vcfcall(int argc, char *argv[])
             case 'c': args.flag |= CF_CCALL; break;          // the original EM based calling method
             case 'i': args.flag |= CF_INS_MISSED; break;
             case 'v': args.aux.flag |= CALL_VARONLY; break;
+            case 'g': 
+                args.gvcf = gvcf_init(optarg);
+                if ( !args.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
+                break;
             case 'o': args.output_fname = optarg; break;
             case 'O':
                       switch (optarg[0]) {
@@ -759,12 +743,6 @@ int main_vcfcall(int argc, char *argv[])
     }
 
     if ( !args.ploidy ) error("Could not initialize ploidy\n");
-    if ( args.flag & CF_GVCF )
-    {
-        // Force some flags to avoid unnecessary branching
-        args.aux.flag &= ~CALL_KEEPALT;
-        args.aux.flag |= CALL_VARONLY;
-    }
     if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n");
     if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n");
     if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n");    // not sure about this, please fix
@@ -774,6 +752,7 @@ int main_vcfcall(int argc, char *argv[])
         if ( !(args.flag & CF_MCALL) ) error("The \"-C alleles\" mode requires -m\n");
     }
     if ( args.flag & CF_INS_MISSED && !(args.aux.flag&CALL_CONSTR_ALLELES) ) error("The -i option requires -C alleles\n");
+    if ( args.aux.flag&CALL_VARONLY && args.gvcf ) error("The two options cannot be combined: --variants-only and --gvcf\n");
     init_data(&args);
 
     while ( bcf_sr_next_line(args.aux.srs) )
@@ -783,27 +762,26 @@ int main_vcfcall(int argc, char *argv[])
         bcf_unpack(bcf_rec, BCF_UN_STR);
 
         // Skip unwanted sites
-        if ( args.aux.flag & CALL_VARONLY )
+        int i, is_indel = bcf_is_snp(bcf_rec) ? 0 : 1;
+        if ( (args.flag & CF_INDEL_ONLY) && !is_indel ) continue;
+        if ( (args.flag & CF_NO_INDEL) && is_indel ) continue;
+        if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue;   // REF[0] is 'N'
+
+        // Which allele is symbolic? All SNPs should have it, but not indels
+        args.aux.unseen = 0;
+        for (i=1; i<bcf_rec->n_allele; i++)
         {
-            int is_ref = 0;
-            if ( bcf_rec->n_allele==1 ) is_ref = 1;     // not a variant
-            else if ( bcf_rec->n_allele==2 )
-            {
-                // second allele is mpileup's X, not a variant
-                if ( bcf_rec->d.allele[1][0]=='X' ) is_ref = 1;
-                else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='X' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
-                else if ( bcf_rec->d.allele[1][0]=='<' && bcf_rec->d.allele[1][1]=='*' && bcf_rec->d.allele[1][2]=='>' ) is_ref = 1;
-            }
-            if ( is_ref )
+            if ( bcf_rec->d.allele[i][0]=='X' ) { args.aux.unseen = i; break; }  // old X
+            if ( bcf_rec->d.allele[i][0]=='<' )
             {
-                // gVCF output
-                if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, 1);
-                continue;
+                if ( bcf_rec->d.allele[i][1]=='X' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // old <X>
+                if ( bcf_rec->d.allele[i][1]=='*' && bcf_rec->d.allele[i][2]=='>' ) { args.aux.unseen = i; break; } // new <*>
             }
         }
-        if ( (args.flag & CF_INDEL_ONLY) && bcf_is_snp(bcf_rec) ) continue;    // not an indel
-        if ( (args.flag & CF_NO_INDEL) && !bcf_is_snp(bcf_rec) ) continue;     // not a SNP
-        if ( (args.flag & CF_ACGT_ONLY) && (bcf_rec->d.allele[0][0]=='N' || bcf_rec->d.allele[0][0]=='n') ) continue;   // REF[0] is 'N'
+        int is_ref = (bcf_rec->n_allele==1 || (bcf_rec->n_allele==2 && args.aux.unseen>0)) ? 1 : 0;
+
+        if ( is_ref && args.aux.flag&CALL_VARONLY )
+            continue;
 
         bcf_unpack(bcf_rec, BCF_UN_ALL);
         if ( args.nsex ) set_ploidy(&args, bcf_rec);
@@ -823,18 +801,14 @@ int main_vcfcall(int argc, char *argv[])
             ret = ccall(&args.aux, bcf_rec);
         if ( ret==-1 ) error("Something is wrong\n");
 
-        // gVCF output
-        if ( args.flag & CF_GVCF )
-        {
-            gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, bcf_rec, ret?0:1);
-            continue;
-        }
-
         // Normal output
-        if ( (args.aux.flag & CALL_VARONLY) && ret==0 ) continue;     // not a variant
-        bcf_write1(args.out_fh, args.aux.hdr, bcf_rec);
+        if ( (args.aux.flag & CALL_VARONLY) && ret==0 && !args.gvcf ) continue;     // not a variant
+        if ( args.gvcf )
+            bcf_rec = gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, bcf_rec, ret==1?1:0);
+        if ( bcf_rec )
+            bcf_write1(args.out_fh, args.aux.hdr, bcf_rec);
     }
-    if ( args.flag & CF_GVCF ) gvcf_write(args.out_fh, &args.gvcf, args.aux.hdr, NULL, 0);
+    if ( args.gvcf ) gvcf_write(args.gvcf, args.out_fh, args.aux.hdr, NULL, 0);
     if ( args.flag & CF_INS_MISSED ) bcf_sr_regions_flush(args.aux.srs->targets);
     destroy_data(&args);
     return 0;

From 2346a00c31f82638a6ec1a1c2a0ec6d9dbb13f7d Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 1 Oct 2015 09:29:57 +0100
Subject: [PATCH 082/211] vcfcall: gvcf calling not working with -c calling
 mode yet

---
 ccall.c              |  7 +++----
 test/mpileup.c.1.out | 43 +++++++++++++++++++++++++++++++++++++++++++
 test/mpileup.c.X.out | 43 +++++++++++++++++++++++++++++++++++++++++++
 test/test.pl         |  4 ++++
 vcfcall.c            |  1 +
 5 files changed, 94 insertions(+), 4 deletions(-)
 create mode 100644 test/mpileup.c.1.out
 create mode 100644 test/mpileup.c.X.out

diff --git a/ccall.c b/ccall.c
index 561b2e464..bb43d6138 100644
--- a/ccall.c
+++ b/ccall.c
@@ -232,11 +232,10 @@ static int update_bcf1(call_t *call, bcf1_t *rec, const bcf_p1rst_t *pr, double
 
     // Remove unused alleles
     int nals_ori = rec->n_allele, nals = !is_var && !(call->flag & CALL_KEEPALT) ? 1 : pr->rank0 < 2? 2 : pr->rank0+1;
-    if ( call->flag & CALL_KEEPALT && nals>1 )
+    if ( call->flag & CALL_KEEPALT && call->unseen>0 )
     {
-        if ( rec->d.allele[nals-1][0]=='X' ) nals--;   // old version of unseen allele "X"
-        else if ( rec->d.allele[nals-1][0]=='<' && rec->d.allele[nals-1][1]=='X' && rec->d.allele[nals-1][2]=='>' ) nals--;   // old version of unseen allele, "<X>"
-        else if ( rec->d.allele[nals-1][0]=='<' && rec->d.allele[nals-1][1]=='*' && rec->d.allele[nals-1][2]=='>' ) nals--;   // new version of unseen allele, "<*>"
+        assert( call->unseen==nals-1 );
+        nals--;
     }
     
     if ( nals<rec->n_allele )
diff --git a/test/mpileup.c.1.out b/test/mpileup.c.1.out
new file mode 100644
index 000000000..1c4a0c82e
--- /dev/null
+++ b/test/mpileup.c.1.out
@@ -0,0 +1,43 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=17,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	302	.	T	TA	999	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;AF1=0.685575;AC1=4;DP4=2,4,8,11;MQ=51;FQ=61.4911;PV4=1,1,1,1	GT:PL:DP:DV	0/1:167,0,96:11:6	0/1:157,0,9:7:6	1/1:201,21,0:7:7
+17	828	.	T	C	999	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;AF1=0.656389;AC1=4;DP4=2,4,8,11;MQ=60;FQ=89.3748;PV4=1,1,1,0.32233	GT:PL:DP:DV	0/1:211,0,35:12:10	0/1:116,0,91:9:5	1/1:120,12,0:4:4
+17	834	.	G	A	999	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;AF1=0.646503;AC1=4;DP4=2,3,7,10;MQ=60;FQ=68.6952;PV4=1,1,1,0.228905	GT:PL:DP:DV	0/1:185,0,46:11:9	0/1:128,0,59:8:5	1/1:89,9,0:3:3
+17	1665	.	T	C	3.14059	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;AF1=0.167199;AC1=1;DP4=7,11,1,1;MQ=56;FQ=3.56819;PV4=1,0.239991,0.0798553,0.27333	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
+17	1869	.	A	T	134.348	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;AF1=0.598209;AC1=4;DP4=6,9,5,4;MQ=59;FQ=138.299;PV4=0.675175,0.0234896,1,0.324361	GT:PL:DP:DV	0/1:115,0,224:18:7	0/1:16,0,104:5:1	1/1:42,3,0:1:1
+17	2041	.	G	A	999	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;AF1=0.665982;AC1=4;DP4=6,5,12,7;MQ=59;FQ=999;PV4=0.71163,1,0.228209,0.143795	GT:PL:DP:DV	0/1:229,0,212:21:11	0/1:32,0,24:2:1	1/1:223,21,0:7:7
+17	2220	.	G	A	999	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AF1=0.656341;AC1=4;DP4=6,2,1,11;MQ=59;FQ=139.373;PV4=0.00443756,1,1,1	GT:PL:DP:DV	0/1:139,0,130:12:6	0/1:69,0,46:4:2	1/1:131,12,0:4:4
+17	2564	.	A	G	227.769	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;AF1=0.656337;AC1=4;DP4=1,4,4,5;MQ=60;FQ=97.3723;PV4=0.58042,1,1,1	GT:PL:DP:DV	0/1:88,0,78:6:3	0/1:57,0,56:4:2	1/1:124,12,0:4:4
+17	3104	.	C	T	24.364	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;AF1=0.170892;AC1=1;DP4=8,15,2,0;MQ=59;FQ=25.179;PV4=0.15,1,1,1	GT:PL:DP:DV	0/0:0,48,255:16:0	0/0:0,12,144:4:0	0/1:59,0,93:5:2
+17	3587	.	G	A	353.302	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;AF1=0.665739;AC1=4;DP4=4,7,10,6;MQ=60;FQ=358.057;PV4=0.25186,0.0986321,1,1	GT:PL:DP:DV	0/1:161,0,184:14:7	0/1:22,0,118:5:1	1/1:212,24,0:8:8
+17	3936	.	A	G	999	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;AF1=0.666004;AC1=4;DP4=5,6,6,17;MQ=57;FQ=999;PV4=0.434446,0.125787,1,1	GT:PL:DP:DV	0/1:233,0,206:20:11	0/1:77,0,58:6:4	1/1:196,24,0:8:8
diff --git a/test/mpileup.c.X.out b/test/mpileup.c.X.out
new file mode 100644
index 000000000..e35b12bce
--- /dev/null
+++ b/test/mpileup.c.X.out
@@ -0,0 +1,43 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	302	.	T	TA	999	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;AF1=0.685575;AC1=4;DP4=2,4,8,11;MQ=51;FQ=61.4911;PV4=1,1,1,1	GT:PL:DP:DV	0/1:167,0,96:11:6	0:157,0,9:7:6	1/1:201,21,0:7:7
+X	828	.	T	C	999	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;AF1=0.656389;AC1=4;DP4=2,4,8,11;MQ=60;FQ=89.3748;PV4=1,1,1,0.32233	GT:PL:DP:DV	0/1:211,0,35:12:10	0:116,91:9:5	1/1:120,12,0:4:4
+X	834	.	G	A	999	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;AF1=0.646503;AC1=4;DP4=2,3,7,10;MQ=60;FQ=68.6952;PV4=1,1,1,0.228905	GT:PL:DP:DV	0/1:185,0,46:11:9	0:128,59:8:5	1/1:89,9,0:3:3
+X	1665	.	T	C	3.14059	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;AF1=0.167199;AC1=1;DP4=7,11,1,1;MQ=56;FQ=3.56819;PV4=1,0.239991,0.0798553,0.27333	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
+X	1869	.	A	T	134.348	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;AF1=0.598209;AC1=4;DP4=6,9,5,4;MQ=59;FQ=138.299;PV4=0.675175,0.0234896,1,0.324361	GT:PL:DP:DV	0/1:115,0,224:18:7	0/1:16,0,104:5:1	1/1:42,3,0:1:1
+X	2041	.	G	A	999	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;AF1=0.665982;AC1=4;DP4=6,5,12,7;MQ=59;FQ=999;PV4=0.71163,1,0.228209,0.143795	GT:PL:DP:DV	0/1:229,0,212:21:11	0/1:32,0,24:2:1	1/1:223,21,0:7:7
+X	2220	.	G	A	999	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AF1=0.656341;AC1=4;DP4=6,2,1,11;MQ=59;FQ=139.373;PV4=0.00443756,1,1,1	GT:PL:DP:DV	0/1:139,0,130:12:6	0/1:69,0,46:4:2	1/1:131,12,0:4:4
+X	2564	.	A	G	227.769	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;AF1=0.656337;AC1=4;DP4=1,4,4,5;MQ=60;FQ=97.3723;PV4=0.58042,1,1,1	GT:PL:DP:DV	0/1:88,0,78:6:3	0/1:57,0,56:4:2	1/1:124,12,0:4:4
+X	3104	.	C	T	24.364	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;AF1=0.170892;AC1=1;DP4=8,15,2,0;MQ=59;FQ=25.179;PV4=0.15,1,1,1	GT:PL:DP:DV	0/0:0,48,255:16:0	0:0,144:4:0	0/1:59,0,93:5:2
+X	3587	.	G	A	353.302	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;AF1=0.665739;AC1=4;DP4=4,7,10,6;MQ=60;FQ=358.057;PV4=0.25186,0.0986321,1,1	GT:PL:DP:DV	0/1:161,0,184:14:7	0:22,118:5:1	1/1:212,24,0:8:8
+X	3936	.	A	G	999	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;AF1=0.666004;AC1=4;DP4=5,6,6,17;MQ=57;FQ=999;PV4=0.434446,0.125787,1,1	GT:PL:DP:DV	0/1:233,0,206:20:11	0:77,58:6:4	1/1:196,24,0:8:8
diff --git a/test/test.pl b/test/test.pl
index 23a3fb499..1c5259269 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -133,6 +133,10 @@
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_call_cAls($opts,in=>'mpileup',out=>'mpileup.cAls.out',tab=>'mpileup');
+test_vcf_call($opts,in=>'mpileup',out=>'mpileup.c.1.out',args=>'-cv');
+# test_vcf_call($opts,in=>'mpileup',out=>'mpileup.c.2.out',args=>'-cg0');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_filter($opts,in=>'filter.1',out=>'filter.1.out',args=>'-mx -g2 -G2');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.2.out',args=>q[-e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S.]);
 test_vcf_filter($opts,in=>'filter.3',out=>'filter.3.out',args=>q[-e'DP=19'],fmt=>'%POS\\t%FILTER\\t%DP[\\t%GT]\\n');
diff --git a/vcfcall.c b/vcfcall.c
index 5633256a1..2287936bc 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -745,6 +745,7 @@ int main_vcfcall(int argc, char *argv[])
     if ( !args.ploidy ) error("Could not initialize ploidy\n");
     if ( (args.flag & CF_CCALL ? 1 : 0) + (args.flag & CF_MCALL ? 1 : 0) + (args.flag & CF_QCALL ? 1 : 0) > 1 ) error("Only one of -c or -m options can be given\n");
     if ( !(args.flag & CF_CCALL) && !(args.flag & CF_MCALL) && !(args.flag & CF_QCALL) ) error("Expected -c or -m option\n");
+    if ( (args.flag & CF_CCALL ? 1: 0) && args.gvcf ) error("gvcf -g option not functional with -c calling mode yet\n");
     if ( args.aux.n_perm && args.aux.ngrp1_samples<=0 ) error("Expected -1 with -U\n");    // not sure about this, please fix
     if ( args.aux.flag & CALL_CONSTR_ALLELES )
     {

From 1d3d6fd6f6bc181ea1d80d5ce88f38609ffd8d8a Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 1 Oct 2015 11:24:24 +0100
Subject: [PATCH 083/211] vcfconvert: support for END tag when converting from
 oxford formats to VCF

* add support for optional END tag defined in the parsed ID field as CHROM:POS_REF_ALT(_END)?
* the oxford phase3 release legend file ID is of the format (RSID|CHROM):POS:REF:ALT(:END)? so would need to be preprocessed to use with the current convert command. The ALT fields in the phase3 release do contain ":" characters which makes parsing this a little trickier.
* there is still a possibility that one could come across an underscore _ in the ALT fields. we are not dealing with that yet
* add tests for hapsample2vcf
* still todo: write out optional END when converting from VCF
---
 test/convert.gt.noHead.vcf |  1 +
 test/convert.hls.gt.hap    |  1 +
 test/convert.hls.gt.legend |  1 +
 test/convert.hs.gt.hap     | 35 +++++++++++++++++++++++++++++++++++
 test/convert.hs.gt.samples | 12 ++++++++++++
 test/test.pl               |  8 ++++++++
 vcfconvert.c               | 15 +++++++++++++--
 7 files changed, 71 insertions(+), 2 deletions(-)
 create mode 100644 test/convert.hs.gt.hap
 create mode 100644 test/convert.hs.gt.samples

diff --git a/test/convert.gt.noHead.vcf b/test/convert.gt.noHead.vcf
index 2d1d7cdcf..53cdd859a 100644
--- a/test/convert.gt.noHead.vcf
+++ b/test/convert.gt.noHead.vcf
@@ -33,3 +33,4 @@ X	2699775	.	C	A	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
 X	2699898	.	C	CT	.	.	.	GT	0	0	1	0	1	1|0	1|0	0|0	0|0	0|1
 X	2699968	.	A	G	.	.	.	GT	.	0	0	1	0	0|1	0|0	0|0	0|1	1|0
 X	2699970	.	T	C	.	.	.	GT	0	0	0	0	0	0|0	0|0	0|0	0|0	0|0
+X	2699990	.	C	<INS:ME:LINE1>	.	.	END=2700054	GT	0|0	0|0	1|0	0|0	0|1	1|0	1|0	0|0	0|0	0|1
diff --git a/test/convert.hls.gt.hap b/test/convert.hls.gt.hap
index a5db463c0..fe34c3074 100644
--- a/test/convert.hls.gt.hap
+++ b/test/convert.hls.gt.hap
@@ -32,3 +32,4 @@
 0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
 ? - 0 - 0 - 1 - 0 - 0 1 0 0 0 0 0 1 1 0
 0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
diff --git a/test/convert.hls.gt.legend b/test/convert.hls.gt.legend
index 990d7725c..1c88f60be 100644
--- a/test/convert.hls.gt.legend
+++ b/test/convert.hls.gt.legend
@@ -33,3 +33,4 @@ X:2699775_C_A 2699775 C A
 X:2699898_C_CT 2699898 C CT
 X:2699968_A_G 2699968 A G
 X:2699970_T_C 2699970 T C
+X:2699990_C_<INS:ME:LINE1>_2700054 2699990 C <INS:ME:LINE1>
diff --git a/test/convert.hs.gt.hap b/test/convert.hs.gt.hap
new file mode 100644
index 000000000..2e41c5c5b
--- /dev/null
+++ b/test/convert.hs.gt.hap
@@ -0,0 +1,35 @@
+X:2698560_G_A X:2698560_G_A 2698560 G A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698630_A_G X:2698630_A_G 2698630 A G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698758_CAA_C X:2698758_CAA_C 2698758 CAA C 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698769_AAG_A X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0
+X:2698770_AG_A X:2698770_AG_A 2698770 AG A 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
+X:2698770_AG_AAGG X:2698770_AG_AAGG 2698770 AG AAGG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698789_C_G X:2698789_C_G 2698789 C G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698822_A_C X:2698822_A_C 2698822 A C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698831_G_A X:2698831_G_A 2698831 G A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698889_T_C X:2698889_T_C 2698889 T C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698923_G_A X:2698923_G_A 2698923 G A 1 0 0 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0
+X:2698953_A_AGG X:2698953_A_AGG 2698953 A AGG 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2698954_G_A X:2698954_G_A 2698954 G A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 1 0 0 0 0
+X:2699002_C_A X:2699002_C_A 2699002 C A 0 0 0 0 ? ? 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699025_T_C X:2699025_T_C 2699025 T C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699091_G_A X:2699091_G_A 2699091 G A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699187_T_C X:2699187_T_C 2699187 T C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0* 1*
+X:2699188_G_C X:2699188_G_C 2699188 G C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699189_T_C X:2699189_T_C 2699189 T C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699217_C_T X:2699217_C_T 2699217 C T 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699246_C_A X:2699246_C_A 2699246 C A 1 0 1 1 0 1 1 1 1 0 0 1 0 0 0 1 0 0 1 0
+X:2699275_T_G X:2699275_T_G 2699275 T G 0 0 0 0 1 0 0 0 0 1 1 1 1 0 0 0 0 0 0 1
+X:2699350_A_T X:2699350_A_T 2699350 A T 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699360_T_C X:2699360_T_C 2699360 T C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699450_A_C X:2699450_A_C 2699450 A C 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
+X:2699507_T_C X:2699507_T_C 2699507 T C 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+X:2699555_C_A X:2699555_C_A 2699555 C A 0 - 1 - 1 - 0 - 1 - 1 1 1 0 0 1 0 0 0 1
+X:2699645_G_T X:2699645_G_T 2699645 G T 0 - 1 - 0 - 0 - 0 - 0 0 0 0 0 1 0 0 0 0
+X:2699676_G_A X:2699676_G_A 2699676 G A 0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
+X:2699728_C_T X:2699728_C_T 2699728 C T 0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+X:2699775_C_A X:2699775_C_A 2699775 C A 0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+X:2699898_C_CT X:2699898_C_CT 2699898 C CT 0 - 0 - 1 - 0 - 1 - 1 0 1 0 0 0 0 0 0 1
+X:2699968_A_G X:2699968_A_G 2699968 A G ? - 0 - 0 - 1 - 0 - 0 1 0 0 0 0 0 1 1 0
+X:2699970_T_C X:2699970_T_C 2699970 T C 0 - 0 - 0 - 0 - 0 - 0 0 0 0 0 0 0 0 0 0
+X:2699990_C_<INS:ME:LINE1>_2700054 X:2699990_C_<INS:ME:LINE1>_2700054 2699990 C <INS:ME:LINE1> 0 0 0 0 1 0 0 0 0 1 1 0 1 0 0 0 0 0 0 1
diff --git a/test/convert.hs.gt.samples b/test/convert.hs.gt.samples
new file mode 100644
index 000000000..080f72a0a
--- /dev/null
+++ b/test/convert.hs.gt.samples
@@ -0,0 +1,12 @@
+ID_1 ID_2 missing
+0 0 0
+NA00001 NA00001 0
+NA00002 NA00002 0
+NA00003 NA00003 0
+NA00004 NA00004 0
+NA00005 NA00005 0
+NA00006 NA00006 0
+NA00007 NA00007 0
+NA00008 NA00008 0
+NA00009 NA00009 0
+NA00010 NA00010 0
diff --git a/test/test.pl b/test/test.pl
index 60e98df23..176243e3f 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -201,6 +201,7 @@
 test_vcf_convert($opts,in=>'convert',out=>'convert.hls.legend',args=>'-h .,-,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hls.samples',args=>'-h .,.,-');
 test_vcf_convert_hls2vcf($opts,h=>'convert.hls.gt.hap',l=>'convert.hls.gt.legend',s=>'convert.hls.gt.samples',out=>'convert.gt.noHead.vcf',args=>'-H');
+test_vcf_convert_hs2vcf($opts,h=>'convert.hs.gt.hap',s=>'convert.hs.gt.samples',out=>'convert.gt.noHead.vcf',args=>'--hapsample2vcf');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hs.hap',args=>'--hapsample -,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.hs.sample',args=>'--hapsample .,-');
 test_vcf_convert_gvcf($opts,in=>'convert.gvcf',out=>'convert.gvcf.out',fa=>'gvcf.fa',args=>'--gvcf2vcf');
@@ -518,6 +519,13 @@ sub test_vcf_convert_hls2vcf
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls | grep -v ^##");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls -Ou | $$opts{bin}/bcftools view | grep -v ^##");
 }
+sub test_vcf_convert_hs2vcf
+{
+    my ($opts,%args) = @_;
+    my $hs = join(',', map { "$$opts{path}/$_" }( $args{h}, $args{s} ) );
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hs | grep -v ^##");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hs -Ou | $$opts{bin}/bcftools view | grep -v ^##");
+}
 sub test_vcf_convert_gvcf
 {
     my ($opts,%args) = @_;
diff --git a/vcfconvert.c b/vcfconvert.c
index f602648d5..54d066602 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -158,11 +158,19 @@ static int tsv_setter_chrom_pos_ref_alt(tsv_t *tsv, bcf1_t *rec, void *usr)
     if ( *se!='_' ) error("Could not parse REF in CHROM:POS_REF_ALT id: %s\n", tsv->ss);
     kputsn(ss,se-ss,&args->str);
     ss = ++se;
-    while ( se < tsv->se && *se!=':' ) se++;
-    if ( se < tsv->se && *se!=':' ) error("Could not parse ALT in CHROM:POS_REF_ALT id: %s\n", tsv->ss);
+    while ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) se++;
+    if ( se < tsv->se && *se!='_' && isspace(*tsv->se) ) error("Could not parse ALT in CHROM:POS_REF_ALT id: %s\n", tsv->ss);
     kputc(',',&args->str);
     kputsn(ss,se-ss,&args->str);
     bcf_update_alleles_str(args->header, rec, args->str.s);
+
+    // END - optional
+    if (*se && *se=='_') {
+        long end = strtol(se+1,&ss,10);
+        if ( ss==se+1 ) error("Could not parse END in CHROM:POS_REF_ALT_END: %s\n", tsv->ss);
+        bcf_update_info_int32(args->header, rec, "END", &end, 1);
+    }
+
     return 0;
 }
 static int tsv_setter_verify_pos(tsv_t *tsv, bcf1_t *rec, void *usr)
@@ -357,6 +365,7 @@ static void gensample_to_vcf(args_t *args)
     tsv_register(tsv, "GT_GP", tsv_setter_gt_gp, args);
 
     args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
@@ -475,6 +484,7 @@ static void haplegendsample_to_vcf(args_t *args)
     tsv_register(hap_tsv, "HAPS", tsv_setter_haps, args);
 
     args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
     bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
@@ -589,6 +599,7 @@ static void hapsample_to_vcf(args_t *args)
     tsv_register(tsv, "HAPS", tsv_setter_haps, args);
 
     args->header = bcf_hdr_init("w");
+    bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
     bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");

From 1c126ece65bd04730a7114d942cb06abc3156654 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 1 Oct 2015 13:48:10 +0100
Subject: [PATCH 084/211] docs: clarify merge behaviour for INFO and QUAL
 fields

Resolves #305
---
 doc/bcftools.txt | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 94064e445..f485507f6 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1053,7 +1053,11 @@ For "vertical" merge take a look at *<<norm,bcftools norm>>* instead.
 
 *-i, --info-rules* '-'|'TAG:METHOD'[,...]::
     Rules for merging INFO fields (scalars or vectors) or '-' to disable the
-    default rules.  'METHOD' is one of 'sum', 'avg', 'min', 'max', 'join'.
+    default rules. 'METHOD' is one of 'sum', 'avg', 'min', 'max', 'join'.
+    Default is 'DP:sum,DP4:sum' if these fields exist in the input files.
+    Fields with no specified rule will take the value from the first input file.
+    The merged QUAL value is currently set to the maximum. This behaviour is 
+    not user controllable at the moment.
 
 *-l, --file-list* 'FILE'::
     read file names from 'FILE'

From 489657cc185ff530787dc383d26e3928a7b4ecfd Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 2 Oct 2015 12:07:13 +0100
Subject: [PATCH 085/211] add info plugin to add information metrics from GP
 tags

---
 plugins/info.c | 163 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 163 insertions(+)
 create mode 100644 plugins/info.c

diff --git a/plugins/info.c b/plugins/info.c
new file mode 100644
index 000000000..2252b3a8f
--- /dev/null
+++ b/plugins/info.c
@@ -0,0 +1,163 @@
+/*  plugins/info.c -- adds info metrics to a VCF file.
+
+    Copyright (C) 2015 Genome Research Ltd.
+
+    Author: Shane McCarthy <sm15@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+
+/*
+
+Marchini & Howie, Nature Genetics, 11 (July 2010)
+
+Let G_ij in {0,1,2} be the genotype of the ith individual at the
+jth SNP in a study cohort of N samples. Let
+
+    p_ijk = P(G_ij = k | H,G)
+
+be the probability that the genotype at the jth SNP of the ith
+individual is k.
+
+Let the expected allele dosage for the genotype at the jth SNP
+of the ith individual be
+    
+    e_ij = p_ij1 + 2 * p_ij2
+
+and define
+
+    f_ij = p_ij1 + 4 * p_ij2
+
+Let theta_j denote the (unknown) population allele frequency of the jth SNP
+with:
+
+    theta_j = SUM[i=1..N] e_ij / 2 * N
+
+The IMPUTE2 information measure is then:
+
+    if theta_j in (0,1):
+        I(theta_j) = 1 - SUM[i=1..N](f_ij - e_ij^2) / 2 * N * theta_j * (1 - theta_j)
+    else:
+        I(theta_j) = 1
+
+*/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <htslib/vcf.h>
+#include <math.h>
+#include <getopt.h>
+
+const char *about(void)
+{
+    return "Add information metrics to the INFO field based on selected FORMAT tags.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Add information metrics to the INFO field based on selected\n"
+        "       FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP\n"
+        "       tags is currently available.\n"
+        "Usage: bcftools +info [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        // "Plugin options:\n"
+        // "   -i, --info <list>   information metrics to add [INFO]\n" // [BEAGLE_R2,MACH_R2]
+        // "   -t, --tags <tag>    VCF tags to determine the information from [GP]\n"
+        // "\n"
+        "Example:\n"
+        "   bcftools +info in.vcf\n"
+        "\n";
+}
+
+bcf_hdr_t *in_hdr = NULL, *out_hdr = NULL;
+int gp_type = BCF_HT_REAL;
+uint8_t *buf = NULL;
+int nbuf = 0;   // NB: number of elements, not bytes
+int nrec = 0, nskip_gp = 0, nskip_dip = 0;
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    in_hdr  = in;
+    out_hdr = out;
+    bcf_hdr_append(out_hdr,"##INFO=<ID=INFO,Number=1,Type=Float,Description=\"IMPUTE2 info score\">");
+    return 0;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    int nval = 0, i, j, nret = bcf_get_format_values(in_hdr,rec,"GP",(void**)&buf,&nbuf,gp_type);
+    if ( nret<0 )
+    {
+        if (!nskip_gp) fprintf(stderr, "[info.c] Warning: info tag not added to sites without GP tag\n");
+        nskip_gp++;
+        return rec; // require FORMAT/GP tag, return site unchanged
+    }
+
+    nret /= rec->n_sample;
+    if ( nret != 3 )
+    {
+        if (!nskip_dip) fprintf(stderr, "[info.c] Warning: info tag not added to sites that are not biallelic diploid\n");
+        nskip_dip++;
+        return rec; // require biallelic diploid, return site unchanged
+    }
+
+    float esum = 0, e2sum = 0, fsum = 0;
+    #define BRANCH(type_t,is_missing,is_vector_end) \
+    { \
+        type_t *ptr = (type_t*) buf; \
+        for (i=0; i<rec->n_sample; i++) \
+        { \
+            float vals[3] = {0,0,0}; \
+            for (j=0; j<nret; j++) \
+            { \
+                if ( is_missing || is_vector_end ) break; \
+                vals[j] = ptr[j]; \
+            } \
+            esum  += vals[1] + 2*vals[2]; \
+            e2sum += (vals[1] + 2*vals[2]) * (vals[1] + 2*vals[2]); \
+            fsum  += vals[1] + 4*vals[2]; \
+            ptr   += nret; \
+            nval++; \
+        } \
+    }
+    switch (gp_type)
+    {
+        case BCF_HT_INT:  BRANCH(int32_t,ptr[j]==bcf_int32_missing,ptr[j]==bcf_int32_vector_end); break;
+        case BCF_HT_REAL: BRANCH(float,bcf_float_is_missing(ptr[j]),bcf_float_is_vector_end(ptr[j])); break;
+    }
+    #undef BRANCH
+
+    float theta = esum / (2 * (float)nval);
+    float info  = (theta>0 && theta<1) ? 1 - (fsum - e2sum) / (2 * (float)nval * theta * (1.0 - theta)) : 1;
+
+    bcf_update_info_float(out_hdr, rec, "INFO", &info, 1);
+    nrec++;
+    return rec;
+}
+
+
+void destroy(void)
+{
+    fprintf(stderr,"Lines total/info-added/unchanged-no-tag/unchanged-not-biallelic-diploid:\t%d/%d/%d/%d\n", nrec+nskip_gp+nskip_dip, nrec, nskip_gp, nskip_dip);
+    free(buf);
+}

From c6458221addebc13e1749d716933ef84416bf11a Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 2 Oct 2015 12:15:21 +0100
Subject: [PATCH 086/211] mendelian plugin to check for mendelian
 inconsistencies

---
 plugins/mendelian.c | 248 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 248 insertions(+)
 create mode 100644 plugins/mendelian.c

diff --git a/plugins/mendelian.c b/plugins/mendelian.c
new file mode 100644
index 000000000..186e3e512
--- /dev/null
+++ b/plugins/mendelian.c
@@ -0,0 +1,248 @@
+/* The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <errno.h>
+#include "bcftools.h"
+
+#define MODE_COUNT     1
+#define MODE_LIST_GOOD 2
+#define MODE_LIST_BAD  4
+#define MODE_DELETE    8
+
+typedef struct
+{
+    int nok, nbad;
+    int imother,ifather,ichild;
+}
+trio_t;
+
+typedef struct _args_t
+{
+    bcf_hdr_t *hdr;
+    int32_t *gt_arr;
+    int mode;
+    int ngt_arr, nrec;
+    trio_t *trios;
+    int ntrios;
+}
+args_t;
+
+static args_t args;
+
+const char *about(void)
+{
+    return "Count Mendelian consistent / inconsistent genotypes.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Count Mendelian consistent / inconsistent genotypes.\n"
+        "Usage: bcftools +mendelian [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -c, --count             count the number of consistent sites\n"
+        "   -d, --delete            delete inconsistent genotypes (set to \"./.\")\n"
+        "   -l, --list [+x]         list consistent (+) or inconsistent (x) sites\n"
+        "   -t, --trio <m,f,c>      names of mother, father and the child\n"
+        "   -T, --trio-file <file>  list of trios, one per line\n"
+        "\n"
+        "Example:\n"
+        "   bcftools +mendelian in.vcf -- -t Mother,Father,Child -c\n"
+        "\n";
+}
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    char *trio_samples = NULL, *trio_file = NULL;
+    memset(&args,0,sizeof(args_t));
+    args.hdr  = in;
+    args.mode = 0;
+
+    static struct option loptions[] =
+    {
+        {"trio",1,0,'t'},
+        {"trio-file",1,0,'T'},
+        {"delete",0,0,'d'},
+        {"list",1,0,'l'},
+        {"count",0,0,'c'},
+        {0,0,0,0}
+    };
+    char c;
+    while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 'd': args.mode |= MODE_DELETE; break;
+            case 'c': args.mode |= MODE_COUNT; break;
+            case 'l': 
+                if ( !strcmp("+",optarg) ) args.mode |= MODE_LIST_GOOD; 
+                else if ( !strcmp("x",optarg) ) args.mode |= MODE_LIST_BAD; 
+                else error("The argument not recognised: --list %s\n", optarg);
+                break;
+            case 't': trio_samples = optarg; break;
+            case 'T': trio_file = optarg; break;
+            case 'h':
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( optind != argc ) error(usage());
+    if ( !trio_samples && !trio_file ) error("Expected the -t/T option\n");
+    if ( !args.mode ) error("Expected one of the -c, -d or -l options\n");
+    if ( args.mode&MODE_DELETE && !(args.mode&(MODE_LIST_GOOD|MODE_LIST_BAD)) ) args.mode |= MODE_LIST_GOOD|MODE_LIST_BAD;
+
+    int i, n = 0;
+    char **list;
+    if ( trio_samples )
+    {
+        args.ntrios = 1;
+        args.trios = (trio_t*) calloc(1,sizeof(trio_t));
+        list = hts_readlist(trio_samples, 0, &n);
+        if ( n!=3 ) error("Expected three sample names with -t\n");
+        args.trios[0].imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[0]);
+        args.trios[0].ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[1]);
+        args.trios[0].ichild  = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[2]);
+        for (i=0; i<n; i++) free(list[i]);
+        free(list);
+    }
+    if ( trio_file )
+    {
+        list = hts_readlist(trio_file, 1, &n);
+        args.ntrios = n;
+        args.trios = (trio_t*) calloc(n,sizeof(trio_t));
+        for (i=0; i<n; i++)
+        {
+            char *ss = list[i], *se = list[i];
+            while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s: %s\n",trio_file, ss);
+            *se = 0;
+            args.trios[i].imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
+            if ( args.trios[i].imother<0 ) error("No such sample: \"%s\"\n", ss);
+            ss = ++se; 
+            while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s\n",trio_file);
+            *se = 0;
+            args.trios[i].ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
+            if ( args.trios[i].ifather<0 ) error("No such sample: \"%s\"\n", ss);
+            ss = ++se; 
+            while ( *se ) se++; if ( ss==se ) error("Could not parse %s\n",trio_file);
+            args.trios[i].ichild = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
+            if ( args.trios[i].ichild<0 ) error("No such sample: \"%s\"\n", ss);
+            free(list[i]);
+        }
+        free(list);
+    }
+    return args.mode&(MODE_LIST_GOOD|MODE_LIST_BAD) ? 0 : 1;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    bcf1_t *dflt = args.mode&MODE_LIST_GOOD ? rec : NULL;
+    args.nrec++;
+
+    int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.ngt_arr);
+    if ( ngt<0 ) return dflt;
+    if ( ngt!=2*bcf_hdr_nsamples(args.hdr) ) return dflt;
+
+    int i, has_bad = 0, needs_update = 0;
+    for (i=0; i<args.ntrios; i++)
+    {
+        int mother,father,child;
+        int32_t a,b,c,d,e,f;
+        trio_t *trio = &args.trios[i];
+
+        a = args.gt_arr[2*trio->imother];
+        b = args.gt_arr[2*trio->imother+1];
+        c = args.gt_arr[2*trio->ifather];
+        d = args.gt_arr[2*trio->ifather+1];
+        e = args.gt_arr[2*trio->ichild];
+        f = args.gt_arr[2*trio->ichild+1];
+        if ( bcf_gt_is_missing(a) || bcf_gt_is_missing(b) ) continue; 
+        if ( bcf_gt_is_missing(c) || bcf_gt_is_missing(d) ) continue; 
+        if ( bcf_gt_is_missing(e) || bcf_gt_is_missing(f) ) continue; 
+
+        mother = (1<<bcf_gt_allele(a)) | (1<<bcf_gt_allele(b));
+        father = (1<<bcf_gt_allele(c)) | (1<<bcf_gt_allele(d));
+        child  = (1<<bcf_gt_allele(e)) | (1<<bcf_gt_allele(f));
+
+        if ( (mother&child) && (father&child) ) 
+        {
+            trio->nok++;
+        }
+        else
+        {
+            trio->nbad++;
+            has_bad = 1;
+            if ( args.mode&MODE_DELETE )
+            {
+                args.gt_arr[2*trio->imother]   = bcf_gt_missing;
+                args.gt_arr[2*trio->imother+1] = bcf_gt_missing;
+                args.gt_arr[2*trio->ifather]   = bcf_gt_missing;
+                args.gt_arr[2*trio->ifather+1] = bcf_gt_missing;
+                args.gt_arr[2*trio->ichild]    = bcf_gt_missing;
+                args.gt_arr[2*trio->ichild+1]  = bcf_gt_missing;
+                needs_update = 1;
+            }
+        }
+    }
+
+    if ( needs_update && bcf_update_genotypes(args.hdr,rec,args.gt_arr,ngt) )
+        error("Could not update GT field at %s:%d\n", bcf_seqname(args.hdr,rec),rec->pos+1);
+
+    if ( args.mode&MODE_LIST_GOOD ) return has_bad ? NULL : rec;
+    if ( args.mode&MODE_LIST_BAD ) return has_bad ? rec : NULL;
+
+    return NULL;
+}
+
+void destroy(void)
+{
+    int i;
+    fprintf(stderr,"# [1]nOK\t[2]nBad\t[3]nSkipped\t[4]Trio\n");
+    for (i=0; i<args.ntrios; i++)
+    {
+        trio_t *trio = &args.trios[i];
+        fprintf(stderr,"%d\t%d\t%d\t%s,%s,%s\n", 
+            trio->nok,trio->nbad,args.nrec-(trio->nok+trio->nbad),
+            bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->imother),
+            bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->ifather),
+            bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, trio->ichild)
+            );
+    }
+    free(args.gt_arr);
+    free(args.trios);
+}
+
+
+

From fe79a91112d7ac041e63eda423e56e61c12855c1 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 2 Oct 2015 12:26:46 +0100
Subject: [PATCH 087/211] add plugin to color shared chromosomal segments

---
 Makefile              |   4 +-
 plugins/color-chrs.c  | 559 ++++++++++++++++++++++++++++++++++++++++++
 plugins/color-chrs.mk |   2 +
 plugins/color-chrs.pl | 509 ++++++++++++++++++++++++++++++++++++++
 4 files changed, 1073 insertions(+), 1 deletion(-)
 create mode 100644 plugins/color-chrs.c
 create mode 100644 plugins/color-chrs.mk
 create mode 100755 plugins/color-chrs.pl

diff --git a/Makefile b/Makefile
index 851e4ec89..ccc6563e2 100644
--- a/Makefile
+++ b/Makefile
@@ -77,6 +77,8 @@ INSTALL_PROGRAM = $(INSTALL)
 INSTALL_DATA    = $(INSTALL) -m 644
 INSTALL_DIR     = $(MKDIR_P) -m 755
 
+MISC_PROGRAMS = \
+	plot-vcfstats vcfutils.pl plugins/color-chrs.pl \
 
 all:$(PROG) plugins
 
@@ -190,7 +192,7 @@ docs: doc/bcftools.1 doc/bcftools.html
 # make docs can be run to update if asciidoc is available
 install: $(PROG)
 	$(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir) $(DESTDIR)$(plugindir)
-	$(INSTALL_PROGRAM) $(PROG) plot-vcfstats vcfutils.pl $(DESTDIR)$(bindir)
+	$(INSTALL_PROGRAM) $(PROG) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
 	$(INSTALL_DATA) doc/bcftools.1 $(DESTDIR)$(man1dir)
 	$(INSTALL_PROGRAM) plugins/*.so $(DESTDIR)$(plugindir)
 
diff --git a/plugins/color-chrs.c b/plugins/color-chrs.c
new file mode 100644
index 000000000..6a9175e70
--- /dev/null
+++ b/plugins/color-chrs.c
@@ -0,0 +1,559 @@
+/* The MIT License
+
+   Copyright (c) 2015 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+/*
+    Trio haplotypes: mother (A,B), father (C,D), child (E,F)
+    Modeling the following states:
+        01|23|02 
+        01|23|03
+        01|23|12
+        01|23|13
+        01|23|20
+        01|23|30
+        01|23|21
+        01|23|31
+    with the likelihoods of two haplotypes A,B segments sharing an allele:
+        P(01|A==B)  .. e (P of error)
+        P(00|A==B)  .. 1-e
+    and
+        P(ab,cd,ef|E=A,F=C) = P(ea|E=A)*P(fc|F=C)
+
+
+    Unrelated samples: (A,B) and (C,D)
+    Modeling the states:
+        xxxx .. A!=C,A!=D,B!=C,B!=D
+        0x0x .. A=C,B!=D
+        0xx0 .. A=D,B!=C
+        x00x .. B=C,A!=D
+        x0x0 .. B=D,A!=C
+        0101 .. A=C,B=D
+        0110 .. A=D,B=C
+    with the likelihoods
+        P(01|A!=B)  .. f*(1-f)
+        P(00|A!=B)  .. (1-f)*(1-f)
+        P(11|A!=B)  .. f*f
+
+    Assuming 2x30 crossovers, P=2e-8.
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <errno.h>
+#include "bcftools.h"
+#include "HMM.h"
+
+#define C_TRIO 1
+#define C_UNRL 2
+
+// states for unrelated samples
+#define UNRL_xxxx  0
+#define UNRL_0x0x  1
+#define UNRL_0xx0  2
+#define UNRL_x00x  3
+#define UNRL_x0x0  4
+#define UNRL_0101  5
+#define UNRL_0110  6
+
+// trio states
+#define TRIO_AC 0
+#define TRIO_AD 1
+#define TRIO_BC 2
+#define TRIO_BD 3
+#define TRIO_CA 4
+#define TRIO_DA 5
+#define TRIO_CB 6
+#define TRIO_DB 7
+
+typedef struct _args_t
+{
+    bcf_hdr_t *hdr;
+    hmm_t *hmm;
+    double *eprob, *tprob, pij, pgt_err;
+    uint32_t *sites;
+    int32_t *gt_arr;
+    int nsites, msites, ngt_arr, prev_rid;
+    int mode, nstates, nhet_father, nhet_mother;
+    int imother,ifather,ichild, isample,jsample;
+    void (*set_observed_prob) (bcf1_t *rec);
+    char *prefix;
+    FILE *fp;
+}
+args_t;
+
+static args_t args;
+
+#define SW_MOTHER 1
+#define SW_FATHER 2
+static int hap_switch[8][8];
+
+static void set_observed_prob_trio(bcf1_t *rec);
+static void set_observed_prob_unrelated(bcf1_t *rec);
+static void init_hmm_trio(args_t *args);
+static void init_hmm_unrelated(args_t *args);
+
+
+const char *about(void)
+{
+    return "Color shared chromosomal segments, requires phased GTs.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Color shared chromosomal segments, requires phased GTs.\n"
+        "Usage: bcftools +color-chrs [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -p, --prefix <path>     output files prefix\n"
+        "   -t, --trio <m,f,c>      names of mother, father and the child\n"
+        "   -u, --unrelated <a,b>   names of two unrelated samples\n"
+        "\n"
+        "Example:\n"
+        "   bcftools +color-chrs in.vcf --\n"
+        "\n";
+}
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    char *trio_samples = NULL, *unrelated_samples = NULL;
+    memset(&args,0,sizeof(args_t));
+    args.prev_rid = -1;
+    args.hdr = in;
+    args.pij = 2e-8;
+    args.pgt_err = 1e-9;
+
+    static struct option loptions[] =
+    {
+        {"prefix",1,0,'p'},
+        {"trio",1,0,'t'},
+        {"unrelated",1,0,'u'},
+        {0,0,0,0}
+    };
+    char c;
+    while ((c = getopt_long(argc, argv, "?ht:u:p:",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 'p': args.prefix = optarg; break;
+            case 't': trio_samples = optarg; break;
+            case 'u': unrelated_samples = optarg; break;
+            case 'h':
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( optind != argc ) error(usage());
+    if ( trio_samples && unrelated_samples ) error("Expected only one of the -t/-u options\n");
+    if ( !trio_samples && !unrelated_samples ) error("Expected one of the -t/-u options\n");
+    if ( !args.prefix ) error("Expected the -p option\n");
+
+    int ret = bcf_hdr_set_samples(args.hdr, trio_samples ? trio_samples : unrelated_samples, 0);
+    if ( ret<0 ) error("Could not parse samples: %s\n", trio_samples ? trio_samples : unrelated_samples);
+    else if ( ret>0 ) error("%d-th sample not found: %s\n", ret,trio_samples ? trio_samples : unrelated_samples);
+
+    if ( trio_samples )
+    {
+        int i,n = 0;
+        char **list = hts_readlist(trio_samples, 0, &n);
+        if ( n!=3 ) error("Expected three sample names with -t\n");
+        args.imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[0]);
+        args.ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[1]);
+        args.ichild  = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[2]);
+        for (i=0; i<n; i++) free(list[i]);
+        free(list);
+        args.set_observed_prob = set_observed_prob_trio;
+        args.mode = C_TRIO;
+        init_hmm_trio(&args);
+    }
+    else
+    {
+        int i,n = 0;
+        char **list = hts_readlist(unrelated_samples, 0, &n);
+        if ( n!=2 ) error("Expected two sample names with -u\n");
+        args.isample = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[0]);
+        args.jsample = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, list[1]);
+        for (i=0; i<n; i++) free(list[i]);
+        free(list);
+        args.set_observed_prob = set_observed_prob_unrelated;
+        args.mode = C_UNRL;
+        init_hmm_unrelated(&args);
+    }
+    return 1;
+}
+
+static void init_hmm_trio(args_t *args)
+{
+    int i,j;
+    args->nstates = 8;
+    args->tprob   = (double*) malloc(sizeof(double)*args->nstates*args->nstates);
+
+    for (i=0; i<args->nstates; i++)
+        for (j=0; j<args->nstates; j++) hap_switch[i][j] = 0;
+
+    hap_switch[TRIO_AD][TRIO_AC] = SW_FATHER;
+    hap_switch[TRIO_BC][TRIO_AC] = SW_MOTHER;
+    hap_switch[TRIO_BD][TRIO_AC] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_AC][TRIO_AD] = SW_FATHER;
+    hap_switch[TRIO_BC][TRIO_AD] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_BD][TRIO_AD] = SW_MOTHER;
+    hap_switch[TRIO_AC][TRIO_BC] = SW_MOTHER;
+    hap_switch[TRIO_AD][TRIO_BC] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_BD][TRIO_BC] = SW_FATHER;
+    hap_switch[TRIO_AC][TRIO_BD] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_AD][TRIO_BD] = SW_MOTHER;
+    hap_switch[TRIO_BC][TRIO_BD] = SW_FATHER;
+
+    hap_switch[TRIO_DA][TRIO_CA] = SW_FATHER;
+    hap_switch[TRIO_CB][TRIO_CA] = SW_MOTHER;
+    hap_switch[TRIO_DB][TRIO_CA] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_CA][TRIO_DA] = SW_FATHER;
+    hap_switch[TRIO_CB][TRIO_DA] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_DB][TRIO_DA] = SW_MOTHER;
+    hap_switch[TRIO_CA][TRIO_CB] = SW_MOTHER;
+    hap_switch[TRIO_DA][TRIO_CB] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_DB][TRIO_CB] = SW_FATHER;
+    hap_switch[TRIO_CA][TRIO_DB] = SW_MOTHER | SW_FATHER;
+    hap_switch[TRIO_DA][TRIO_DB] = SW_MOTHER;
+    hap_switch[TRIO_CB][TRIO_DB] = SW_FATHER;
+
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+        {
+            if ( !hap_switch[i][j] ) MAT(args->tprob,args->nstates,i,j) = 0;
+            else
+            {
+                MAT(args->tprob,args->nstates,i,j) = 1;
+                if ( hap_switch[i][j] & SW_MOTHER ) MAT(args->tprob,args->nstates,i,j) *= args->pij;
+                if ( hap_switch[i][j] & SW_FATHER ) MAT(args->tprob,args->nstates,i,j) *= args->pij;
+            }
+        }
+    }
+    for (i=0; i<args->nstates; i++)
+    {
+        double sum = 0;
+        for (j=0; j<args->nstates; j++)
+        {
+            if ( i!=j ) sum += MAT(args->tprob,args->nstates,i,j);
+        }
+        MAT(args->tprob,args->nstates,i,i) = 1 - sum;
+    }
+
+    #if 0
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+            fprintf(stderr,"\t%d",hap_switch[j][i]);
+        fprintf(stderr,"\n");
+    }
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+            fprintf(stderr,"\t%e",MAT(args->tprob,args->nstates,j,i));
+        fprintf(stderr,"\n");
+    }
+    #endif
+
+    args->hmm = hmm_init(args->nstates, args->tprob, 10000);
+}
+static void init_hmm_unrelated(args_t *args)
+{
+    int i,j;
+    args->nstates = 7;
+    args->tprob   = (double*) malloc(sizeof(double)*args->nstates*args->nstates);
+
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+            MAT(args->tprob,args->nstates,i,j) = args->pij;
+    }
+    MAT(args->tprob,args->nstates,UNRL_0101,UNRL_xxxx) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0110,UNRL_xxxx) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_x0x0,UNRL_0x0x) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0110,UNRL_0x0x) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_x00x,UNRL_0xx0) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0101,UNRL_0xx0) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0101,UNRL_x00x) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0110,UNRL_x0x0) = args->pij*args->pij;
+    MAT(args->tprob,args->nstates,UNRL_0110,UNRL_0101) = args->pij*args->pij;
+
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=i+1; j<args->nstates; j++)
+            MAT(args->tprob,args->nstates,i,j) = MAT(args->tprob,args->nstates,j,i);
+    }
+    for (i=0; i<args->nstates; i++)
+    {
+        double sum = 0;
+        for (j=0; j<args->nstates; j++)
+            if ( i!=j ) sum += MAT(args->tprob,args->nstates,i,j);
+        MAT(args->tprob,args->nstates,i,i) = 1 - sum;
+    }
+
+    #if 0
+    for (i=0; i<args->nstates; i++)
+    {
+        for (j=0; j<args->nstates; j++)
+            fprintf(stderr,"\t%e",MAT(args->tprob,args->nstates,j,i));
+        fprintf(stderr,"\n");
+    }
+    #endif
+
+    args->hmm = hmm_init(args->nstates, args->tprob, 10000);
+}
+static inline double prob_shared(float af, int a, int b)
+{
+    return a==b ? 1-args.pgt_err : args.pgt_err;
+}
+static inline double prob_not_shared(float af, int a, int b)
+{
+    if ( a!=b ) return af*(1-af);
+    else if ( a==0 ) return (1-af)*(1-af);
+    else return af*af;
+}
+static void set_observed_prob_unrelated(bcf1_t *rec)
+{
+    float af = 0.5;  // alternate allele frequency
+
+    int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.ngt_arr);
+    if ( ngt<0 ) return;
+    if ( ngt!=4 ) return;   // chrX
+
+    int32_t a,b,c,d;
+    a = args.gt_arr[2*args.isample];
+    b = args.gt_arr[2*args.isample+1];
+    c = args.gt_arr[2*args.jsample];
+    d = args.gt_arr[2*args.jsample+1];
+    if ( bcf_gt_is_missing(a) || bcf_gt_is_missing(b) ) return;
+    if ( bcf_gt_is_missing(c) || bcf_gt_is_missing(d) ) return;
+    if ( !bcf_gt_is_phased(a) && !bcf_gt_is_phased(b) ) return; // only the second allele should be set when phased
+    if ( !bcf_gt_is_phased(c) && !bcf_gt_is_phased(d) ) return;
+    a = bcf_gt_allele(a);
+    b = bcf_gt_allele(b);
+    c = bcf_gt_allele(c);
+    d = bcf_gt_allele(d);
+
+    int m = args.msites;
+    args.nsites++;
+    hts_expand(uint32_t,args.nsites,args.msites,args.sites);
+    if ( m!=args.msites ) args.eprob = (double*) realloc(args.eprob, sizeof(double)*args.msites*args.nstates);
+
+    args.sites[args.nsites-1] = rec->pos;
+    double *prob = args.eprob + args.nstates*(args.nsites-1);
+    prob[UNRL_xxxx] = prob_not_shared(af,a,c) * prob_not_shared(af,a,d) * prob_not_shared(af,b,c) * prob_not_shared(af,b,d);
+    prob[UNRL_0x0x] = prob_shared(af,a,c) * prob_not_shared(af,b,d);
+    prob[UNRL_0xx0] = prob_shared(af,a,d) * prob_not_shared(af,b,c);
+    prob[UNRL_x00x] = prob_shared(af,b,c) * prob_not_shared(af,a,d);
+    prob[UNRL_x0x0] = prob_shared(af,b,d) * prob_not_shared(af,a,c);
+    prob[UNRL_0101] = prob_shared(af,a,c) * prob_shared(af,b,d);
+    prob[UNRL_0110] = prob_shared(af,a,d) * prob_shared(af,b,c);
+
+#if 0
+    static int x = 0;
+    if ( !x++)
+    {
+        printf("p(0==0) .. %f\n", prob_shared(af,0,0));
+        printf("p(0!=0) .. %f\n", prob_not_shared(af,0,0));
+        printf("p(0==1) .. %f\n", prob_shared(af,0,1));
+        printf("p(0!=1) .. %f\n", prob_not_shared(af,0,1));
+    }
+    printf("%d|%d %d|%d  x:%f 11:%f 12:%f 21:%f 22:%f 11,22:%f 12,21:%f  %d\n", a,b,c,d,
+            prob[UNRL_xxxx], prob[UNRL_0x0x], prob[UNRL_0xx0], prob[UNRL_x00x], prob[UNRL_x0x0], prob[UNRL_0101], prob[UNRL_0110], rec->pos+1);
+#endif
+}
+static void set_observed_prob_trio(bcf1_t *rec)
+{
+    int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.ngt_arr);
+    if ( ngt<0 ) return;
+    if ( ngt!=6 ) return;   // chrX
+
+    int32_t a,b,c,d,e,f;
+    a = args.gt_arr[2*args.imother];
+    b = args.gt_arr[2*args.imother+1];
+    c = args.gt_arr[2*args.ifather];
+    d = args.gt_arr[2*args.ifather+1];
+    e = args.gt_arr[2*args.ichild];
+    f = args.gt_arr[2*args.ichild+1];
+    if ( bcf_gt_is_missing(a) || bcf_gt_is_missing(b) ) return;
+    if ( bcf_gt_is_missing(c) || bcf_gt_is_missing(d) ) return;
+    if ( bcf_gt_is_missing(e) || bcf_gt_is_missing(f) ) return;
+    if ( !bcf_gt_is_phased(a) && !bcf_gt_is_phased(b) ) return; // only the second allele should be set when phased
+    if ( !bcf_gt_is_phased(c) && !bcf_gt_is_phased(d) ) return;
+    if ( !bcf_gt_is_phased(e) && !bcf_gt_is_phased(f) ) return;
+    a = bcf_gt_allele(a);
+    b = bcf_gt_allele(b);
+    c = bcf_gt_allele(c);
+    d = bcf_gt_allele(d);
+    e = bcf_gt_allele(e);
+    f = bcf_gt_allele(f);
+
+    int mother = (1<<a) | (1<<b);
+    int father = (1<<c) | (1<<d);
+    int child  = (1<<e) | (1<<f);
+    if ( !(mother&child) || !(father&child) )  return;      // Mendelian-inconsistent site, skip
+
+    if ( a!=b ) args.nhet_mother++;
+    if ( c!=d ) args.nhet_father++;
+
+    int m = args.msites;
+    args.nsites++;
+    hts_expand(uint32_t,args.nsites,args.msites,args.sites);
+    if ( m!=args.msites ) args.eprob = (double*) realloc(args.eprob, sizeof(double)*args.msites*args.nstates);
+
+    args.sites[args.nsites-1] = rec->pos;
+    double *prob = args.eprob + args.nstates*(args.nsites-1);
+    prob[TRIO_AC] = prob_shared(0,e,a) * prob_shared(0,f,c);
+    prob[TRIO_AD] = prob_shared(0,e,a) * prob_shared(0,f,d);
+    prob[TRIO_BC] = prob_shared(0,e,b) * prob_shared(0,f,c);
+    prob[TRIO_BD] = prob_shared(0,e,b) * prob_shared(0,f,d);
+    prob[TRIO_CA] = prob_shared(0,e,c) * prob_shared(0,f,a);
+    prob[TRIO_DA] = prob_shared(0,e,d) * prob_shared(0,f,a);
+    prob[TRIO_CB] = prob_shared(0,e,c) * prob_shared(0,f,b);
+    prob[TRIO_DB] = prob_shared(0,e,d) * prob_shared(0,f,b);
+}
+
+void flush_viterbi(args_t *args)
+{
+    const char *s1, *s2, *s3 = NULL;
+    if ( args->mode==C_UNRL )
+    {
+        s1 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->isample);
+        s2 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->jsample);
+    }
+    else if ( args->mode==C_TRIO )
+    {
+        s1 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->imother);
+        s3 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->ifather);
+        s2 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->ichild);
+    }
+
+    if ( !args->fp )
+    {
+        kstring_t str = {0,0,0};
+        kputs(args->prefix, &str);
+        kputs(".dat", &str);
+        args->fp = fopen(str.s,"w");
+        if ( !args->fp ) error("%s: %s\n", str.s,strerror(errno));
+        free(str.s);
+        fprintf(args->fp,"# SG, shared segment\t[2]Chromosome\t[3]Start\t[4]End\t[5]%s:1\t[6]%s:2\n",s2,s2);
+        fprintf(args->fp,"# SW, number of switches\t[3]Sample\t[4]Chromosome\t[5]nHets\t[5]nSwitches\t[6]switch rate\n");
+    }
+
+    hmm_run_viterbi(args->hmm,args->nsites,args->eprob,args->sites);
+    uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
+    int i, iprev = -1, prev_state = -1, nstates = hmm_get_nstates(args->hmm);
+    int nswitch_mother = 0, nswitch_father = 0;
+    for (i=0; i<args->nsites; i++)
+    {
+        int state = vpath[i*nstates];
+        if ( state!=prev_state || i+1==args->nsites )
+        {
+            uint32_t start = iprev>=0 ? args->sites[iprev]+1 : 1, end = i>0 ? args->sites[i-1] : 1;
+            const char *chr = bcf_hdr_id2name(args->hdr,args->prev_rid);
+            if ( args->mode==C_UNRL )
+            {
+                switch (prev_state)
+                {
+                    case UNRL_0x0x:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t-\n", chr,start,end,s1); break;
+                    case UNRL_0xx0:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t-\t%s:1\n", chr,start,end,s1); break;
+                    case UNRL_x00x:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t-\n", chr,start,end,s1); break;
+                    case UNRL_x0x0:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t-\t%s:2\n", chr,start,end,s1); break;
+                    case UNRL_0101:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s1,s1); break;
+                    case UNRL_0110:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s1,s1); break;
+                }
+            }
+            else if ( args->mode==C_TRIO )
+            {
+                switch (prev_state)
+                {
+                    case TRIO_AC:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:1\n", chr,start,end,s1,s3); break;
+                    case TRIO_AD:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s1,s3); break;
+                    case TRIO_BC:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s1,s3); break;
+                    case TRIO_BD:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:2\n", chr,start,end,s1,s3); break;
+                    case TRIO_CA:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:1\n", chr,start,end,s3,s1); break;
+                    case TRIO_DA:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:1\n", chr,start,end,s3,s1); break;
+                    case TRIO_CB:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:1\t%s:2\n", chr,start,end,s3,s1); break;
+                    case TRIO_DB:
+                        fprintf(args->fp,"SG\t%s\t%d\t%d\t%s:2\t%s:2\n", chr,start,end,s3,s1); break;
+                }
+                if ( hap_switch[state][prev_state] & SW_MOTHER ) nswitch_mother++;
+                if ( hap_switch[state][prev_state] & SW_FATHER ) nswitch_father++;
+            }
+            iprev = i-1;
+        }
+        prev_state = state;
+    }
+    float mrate = args->nhet_mother>1 ? (float)nswitch_mother/(args->nhet_mother-1) : 0;
+    float frate = args->nhet_father>1 ? (float)nswitch_father/(args->nhet_father-1) : 0;
+    fprintf(args->fp,"SW\t%s\t%s\t%d\t%d\t%f\n", s1,bcf_hdr_id2name(args->hdr,args->prev_rid),args->nhet_mother,nswitch_mother,mrate);
+    fprintf(args->fp,"SW\t%s\t%s\t%d\t%d\t%f\n", s3,bcf_hdr_id2name(args->hdr,args->prev_rid),args->nhet_father,nswitch_father,frate);
+    args->nsites = 0;
+    args->nhet_father = args->nhet_mother = 0;
+}
+    
+bcf1_t *process(bcf1_t *rec)
+{
+    if ( args.prev_rid==-1 ) args.prev_rid = rec->rid;
+    if ( args.prev_rid!=rec->rid ) flush_viterbi(&args);
+    args.prev_rid = rec->rid;
+    args.set_observed_prob(rec);
+    return NULL;
+}
+
+void destroy(void)
+{
+    flush_viterbi(&args);
+    fclose(args.fp);
+
+    free(args.gt_arr);
+    free(args.tprob);
+    free(args.sites);
+    free(args.eprob);
+    hmm_destroy(args.hmm);
+}
+
+
+
diff --git a/plugins/color-chrs.mk b/plugins/color-chrs.mk
new file mode 100644
index 000000000..ca7a8a408
--- /dev/null
+++ b/plugins/color-chrs.mk
@@ -0,0 +1,2 @@
+plugins/color-chrs.so: plugins/color-chrs.c version.h version.c HMM.h HMM.c $(HTSDIR)/libhts.so
+	$(CC) -fPIC -shared $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -L$(HTSDIR) $(LDFLAGS) -o $@ HMM.c version.c $< -lhts $(LIBS)
diff --git a/plugins/color-chrs.pl b/plugins/color-chrs.pl
new file mode 100755
index 000000000..39c4b74c4
--- /dev/null
+++ b/plugins/color-chrs.pl
@@ -0,0 +1,509 @@
+#!/usr/bin/env perl
+#
+# Author: petr.danecek@sanger
+#
+
+use strict;
+use warnings;
+use Carp;
+
+my $opts = parse_params();
+chr_dims($opts);
+for my $file (@{$$opts{files}})
+{
+    read_dat($opts,$file);
+}
+merge_regs($opts);
+plot($opts);
+
+exit;
+
+#--------------------------------
+
+sub error
+{
+    my (@msg) = @_;
+    if ( scalar @msg ) { confess @msg; }
+    print 
+        "About: Plot output of \"bcftools +color-chrs\"\n",
+        "Usage: color-chrs.pl [OPTIONS] output.dat\n",
+        "Options:\n",
+        "   -c, --colors <file>         File with list of \"chr hap color\".\n",
+        "   -p, --prefix <name>         Prefix of output files.\n",
+        "   -h, -?, --help              This help message.\n",
+        "\n";
+    exit -1;
+}
+
+sub parse_params
+{
+    my $opts =
+    {
+        #colors => ['red','green','blue','yellow'],
+        colors => ['#ff0000','#008000','#0000ff','#ffff00'],
+        height => 350,
+        pad    => 10,
+        dimL   => 300,     # arm length
+        dimD   => 10,      # arm width
+        dimE   => 7,       # arm pad
+        dimB   => 5,       # arm end curve
+    };
+    $$opts{chr_width} = 2*$$opts{pad} + 2*$$opts{dimD} + $$opts{dimE};
+    $$opts{width} = $$opts{chr_width}*23;
+    while (defined(my $arg=shift(@ARGV)))
+    {
+        if ( -e $arg ) { push @{$$opts{files}},$arg; next }
+        if ( $arg eq '-p' || $arg eq '--prefix' ) { $$opts{prefix}=shift(@ARGV); next }
+        if ( $arg eq '-c' || $arg eq '--colors' ) { read_colors($opts,shift(@ARGV)); next; }
+        if ( $arg eq '-?' || $arg eq '-h' || $arg eq '--help' ) { error(); }
+        error("Unknown parameter \"$arg\". Run -h for help.\n");
+    }
+    if ( !exists($$opts{files}) ) { error("No files given?\n") }
+    if ( !exists($$opts{prefix}) ) { error("Expected -p option\n") }
+    return $opts;
+}
+
+sub read_colors
+{
+    my ($opts,$fname) = @_;
+    open(my $fh,'<',$fname) or error("$fname: $!");
+    while (my $line=<$fh>)
+    {
+        if ( $line=~/^\s*$/ ) { next; }
+        $line =~ s/^\s*//;
+        $line =~ s/\s*$//;
+        my ($chr,$hap,$col) = split(/\s+/,$line);
+        $$opts{hap_cols}{$chr}{$hap} = $col;
+    }
+    close($fh);
+}
+
+sub plot
+{
+    my ($opts) = @_;
+
+    my $width  = $$opts{width};
+    my $height = $$opts{height};
+    my $pad    = $$opts{pad};
+
+    my $svg = $$opts{svg} = [];
+    push @$svg, q[<?xml version="1.0" encoding="UTF-8" standalone="yes"?>];
+    push @$svg, q[<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.0//EN" "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">];
+    push @$svg, qq[<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" height="100%" viewBox="0 0 $width $height" width="100%">];
+
+    my $xpos = $pad;
+    for my $chr (qw(1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X))
+    {
+        draw_chr($opts,$chr,$xpos,$pad);
+        $xpos += $$opts{chr_width};
+    }
+    $xpos = $pad + 10*$$opts{chr_width};
+    for my $sample (keys %{$$opts{samples}})
+    {
+        $$opts{chrs}{$sample} = { len=>59e6, acen=>[24e6,26e6,28e6] };
+        my $chr  = $$opts{chrs}{$sample};
+        my $len1 = $$opts{dimL}*$$chr{acen}[0]/$$opts{max_chr_len};
+        my $len2 = $$opts{dimL}*$$chr{acen}[2]/$$opts{max_chr_len};
+        my $len3 = $$opts{dimL}*$$chr{len}/$$opts{max_chr_len};
+        if ( exists($$opts{samples}{$sample}{1}) )
+        {
+            my $col = $$opts{samples}{$sample}{1};
+            $$chr{px1} = [[0,$len1,{$col=>1.0}],[$len2,$len3,{$col=>1.0}]]; 
+        }
+        if ( exists($$opts{samples}{$sample}{2}) )
+        {
+            my $col = $$opts{samples}{$sample}{2};
+            $$chr{px2} = [[0,$len1,{$col=>1.0}],[$len2,$len3,{$col=>1.0}]]; 
+        }
+        my $ypos = $$opts{dimL} - $len3 + $pad;
+        draw_chr($opts,$sample,$xpos,$ypos);
+        $xpos += 2*$$opts{chr_width};
+    }
+
+    push @$svg, q[</svg>];
+    open(my $fh,'>',"$$opts{prefix}.svg");
+    print $fh join("\n",@$svg);
+    close($fh);
+}
+
+sub draw_chr
+{
+    my ($opts,$chr_name,$xpos,$ypos) = @_;
+
+    my $svg = $$opts{svg};
+    my $chr = $$opts{chrs}{$chr_name};
+    my $dimL  = $$opts{dimL};
+    my $dimC  = $dimL*($$chr{acen}[2]-$$chr{acen}[0])/$$opts{max_chr_len};
+    my $dimL1 = $dimL*$$chr{acen}[0]/$$opts{max_chr_len};
+    my $dimL2 = $dimL*($$chr{len} - $$chr{acen}[2])/$$opts{max_chr_len};
+    my $dimD  = $$opts{dimD};   # arm width
+    my $dimB  = $$opts{dimB};
+    my $dimE  = $$opts{dimE};   # the gap width between arms
+    my $dimE05 = $dimE*0.5;
+    my $dimD05 = $dimD*0.5;
+    my $dimB05 = $dimB*0.5;
+    my $dimC05 = 0.5*$dimC;
+
+    my $xtext = $xpos + $dimD + $dimE*0.5;
+    my $ytext = $ypos;
+    push @$svg, qq[<text text-anchor="middle" x="$xtext" y="$ytext">$chr_name</text>\n];
+
+    $ypos += $$opts{pad};
+
+    push @$svg, qq[
+        <path d="M$xpos $ypos
+                 l0 $dimL1
+                 q$dimB $dimC05 0 $dimC
+                 l0 $dimL2
+                 q$dimD05 $dimB $dimD 0
+                 l0 -$dimL2
+                 q$dimE05 -$dimB $dimE 0 ];
+
+    # bottom part of the right arm 
+    push @$svg, qq[
+                 l0 $dimL2
+                 q$dimD05 $dimB $dimD 0
+                 l0 -$dimL2
+                 q-$dimB -$dimC05 0 -$dimC
+                 l0 -$dimL1
+                 q-$dimD05 -$dimB -$dimD 0
+                 l0 $dimL1
+                 q-$dimE05 $dimB -$dimE 0
+                 l0 -$dimL1
+                 q-$dimD05 -$dimB -$dimD 0
+                 "
+              style="stroke:#333; fill:#aaa;"/> ];
+
+    if ( $$chr{px1} ) { draw_regs($opts,$chr_name,$$chr{px1},$xpos,$ypos); }
+    if ( $$chr{px2} ) { draw_regs($opts,$chr_name,$$chr{px2},$xpos+$dimD+$dimE,$ypos); }
+}
+
+sub parse_hex_color
+{
+    my ($color) = @_;
+    if ( !($color=~/^#/) ) { error("Could not parse: $color"); }
+    $color =~ s/^#//;
+    my @vals = split(//, $color);
+    my ($r,$g,$b);
+    if ( @vals==6 )
+    {
+        $r = hex($vals[0].$vals[1]);
+        $g = hex($vals[2].$vals[3]);
+        $b = hex($vals[4].$vals[5]);
+    }
+    elsif ( @vals==3 )
+    {
+        $r = hex($vals[0].$vals[0]);
+        $g = hex($vals[1].$vals[1]);
+        $b = hex($vals[2].$vals[2]);
+    }
+    else { error("Could not parse: $color\n"); }
+    return ($r,$g,$b);
+}
+
+sub scale_color
+{
+    my ($color,$scale) = @_;
+    my ($r1,$g1,$b1) = parse_hex_color($color);
+    my ($r0,$g0,$b0) = parse_hex_color('#aaa');
+    my $r = $scale*($r1-$r0) + $r0;
+    my $g = $scale*($g1-$g0) + $g0;
+    my $b = $scale*($b1-$b0) + $b0;
+    return sprintf("#%0.2x%0.2x%0.2x",$r,$g,$b);
+}
+
+sub draw_regs
+{
+    my ($opts,$chr_name,$regs,$xpos,$ypos) = @_;
+
+    my $svg = $$opts{svg};
+    my $chr = $$opts{chrs}{$chr_name};
+    my $dimL  = $$opts{dimL};
+    my $dimC  = $dimL*($$chr{acen}[2]-$$chr{acen}[0])/$$opts{max_chr_len};
+    my $dimL1 = $dimL*$$chr{acen}[0]/$$opts{max_chr_len};
+    my $dimL2 = $$opts{dimL} - $dimL*$$chr{acen}[2]/$$opts{max_chr_len};
+    my $dimD  = $$opts{dimD};   # arm width
+    my $dimB  = $$opts{dimB};
+    my $dimE  = $$opts{dimE};
+    my $dimE05 = $dimE*0.5;
+    my $dimD05 = $dimD*0.5;
+    my $dimB05 = $dimB*0.5;
+    my $dimC05 = 0.5*$dimC;
+
+    for my $reg (@$regs)
+    {
+        my $sum = 0;
+        my $cmax = undef;
+        for my $c (keys %{$$reg[2]})
+        {
+            $sum += $$reg[2]{$c};
+            if ( !defined $cmax or $$reg[2]{$cmax} < $$reg[2]{$c} ) { $cmax = $c; }
+        }
+        my $color = scale_color($cmax,$$reg[2]{$cmax}/$sum);
+        my $y  = $ypos + $$reg[0];
+        my $dy = $$reg[1] - $$reg[0] + 1;
+        push @$svg, qq[
+            <path d="M$xpos $y
+                     l0 $dy
+                     l$dimD 0
+                     l0 -$dy
+                     l-$dimD 0
+                    "
+                  style="stroke:$color;fill:$color;stroke-width:0;"/> ];
+    }
+
+}
+
+sub hap2color
+{
+    my ($opts,$chr,$hap) = @_;
+    if ( exists($$opts{hap_cols}{$chr}{$hap}) )
+    {
+        if ( !exists($$opts{hap_cols}{'*'}{$hap}) ) 
+        {
+            $$opts{hap_cols}{'*'}{$hap} = $$opts{hap_cols}{$chr}{$hap};
+        }
+        return $$opts{hap_cols}{$chr}{$hap};
+    }
+    elsif ( exists($$opts{hap_cols}{'*'}{$hap}) )
+    {
+        return $$opts{hap_cols}{'*'}{$hap};
+    }
+    if ( !exists($$opts{haps}) ) { $$opts{haps} = {}; }
+    if ( !exists($$opts{haps}{$hap}) )
+    {
+        my $nhaps = scalar keys %{$$opts{haps}};
+        my $color = $$opts{colors}[$nhaps];
+        $$opts{haps}{$hap} = $color;
+    }
+    return $$opts{haps}{$hap};
+}
+
+sub read_dat
+{
+    my ($opts,$file) = @_;
+    open(my $fh,'<',$file) or error("$file: $!");
+    while (my $line=<$fh>)
+    {
+        if ( !($line=~/^SG/) ) { next; }
+        my @items = split(/\s+/,$line);
+        my $chr   = $items[1];
+        my $start = $items[2];
+        my $end   = $items[3];
+        my $hap1  = $items[4];
+        my $hap2  = $items[5];
+        my $col1  = hap2color($opts,$chr,$hap1); 
+        my $col2  = hap2color($opts,$chr,$hap2); 
+        push @{$$opts{chrs}{$chr}{regs1}},[$start,$end,$col1];
+        push @{$$opts{chrs}{$chr}{regs2}},[$start,$end,$col2];
+        my ($smpl,$hap);
+        ($smpl,$hap) = split(/:/,$hap1); $$opts{samples}{$smpl}{$hap} = $col1;
+        ($smpl,$hap) = split(/:/,$hap2); $$opts{samples}{$smpl}{$hap} = $col2;
+    }
+    close($fh);
+}
+
+sub merge_regs
+{
+    my ($opts) = @_;
+    for my $chr (keys %{$$opts{chrs}})
+    {
+        my $dat = $$opts{chrs}{$chr};
+        if ( exists($$dat{regs1}) ) { $$dat{px1} = merge($opts,$dat,$$dat{regs1}); }
+        if ( exists($$dat{regs2}) ) { $$dat{px2} = merge($opts,$dat,$$dat{regs2}); }
+    }
+}
+
+sub merge
+{
+    my ($opts,$chr_dat,$regs) = @_;
+
+    # merge adjacent regions of the same color
+    for (my $i=1; $i<@$regs; $i++)
+    {
+        if ( $$regs[$i-1][2] eq $$regs[$i][2] ) 
+        { 
+            $$regs[$i-1][1] = $$regs[$i][1];
+            splice(@$regs,$i,1);
+            $i--;
+            next; 
+        }
+    }
+    for (my $i=0; $i<@$regs; $i++)
+    {
+        if ( $$regs[$i][1] < $$chr_dat{acen}[0] ) { next; }
+        if ( $$regs[$i][0] > $$chr_dat{acen}[2] ) { next; }
+        if ( $$regs[$i][0] >= $$chr_dat{acen}[0] && $$regs[$i][1] <= $$chr_dat{acen}[2] )
+        {
+            splice(@$regs,$i,1);
+            $i--;
+            next;
+        }
+        if ( $$regs[$i][1] < $$chr_dat{acen}[2] )
+        {
+            $$regs[$i][1] = $$chr_dat{acen}[0];
+            next;
+        }
+        if ( $$regs[$i][0] > $$chr_dat{acen}[0] )
+        {
+            $$regs[$i][0] = $$chr_dat{acen}[2];
+            next;
+        }
+        my $start = $$chr_dat{acen}[2];
+        my $end   = $$regs[$i][1];
+        my $color = $$regs[$i][2];
+        $$regs[$i][1] = $$chr_dat{acen}[0];
+        splice(@$regs,$i+1,0,[$start,$end,$color]);
+    }
+
+    # pixelize
+    my @px = ([0,0,{}]);  # start,end,hash of contributions from colors
+    my $dy = $$opts{max_chr_len}/$$opts{dimL};  # 1px covers $dy base pairs
+    for my $reg (@$regs)
+    {
+        my $px_start = int($$reg[0] / $dy);
+        my $px_end   = int($$reg[1] / $dy);
+        my $color    = $$reg[2];
+        my $contrib  = ($$reg[1] - $$reg[0])/$dy;
+
+        if ( $px_start==$px_end )
+        {
+            if ( $px_end<=$px[-1][1] ) { $px[-1][2]{$color} += $contrib; }
+            else { push @px, [$px_start,$px_end,{$color=>$contrib}]; }
+            next;
+        }
+
+        my $rem_start = 1 - ($$reg[0]/$dy - $px_start);     # fractional remainders
+        my $rem_end   = $$reg[1]/$dy - $px_end;
+
+        if ( $px_start==$px[-1][1] )
+        {
+            $px[-1][2]{$color} += $rem_start;
+        }
+
+        if ( $px_end==$px[-1][1] )
+        {
+            $px[-1][2]{$color} += $rem_end;
+            if ( $px_start+1<$px_end ) { error("really?!\n"); }
+        }
+        elsif ( $px_end>$px[-1][1] )
+        {
+            if ( $rem_start ) { $px_start++; $contrib -= $rem_start; }
+            push @px, [ $px_start, $px_end, { $color=>$contrib } ];
+        }
+        else { error("really?!\n"); }
+    }
+    return \@px;
+}
+
+sub chr_dims
+{
+    my ($opts) = @_;
+
+    # http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/cytoBand.txt.gz
+    my $ktype = q[
+        chr1	121500000	125000000	p11.1	acen
+        chr1	125000000	128900000	q11	acen
+        chr1	243700000	249250621	q44	gneg
+        chr10	38000000	40200000	p11.1	acen
+        chr10	40200000	42300000	q11.1	acen
+        chr10	130600000	135534747	q26.3	gneg
+        chr11	51600000	53700000	p11.11	acen
+        chr11	53700000	55700000	q11	acen
+        chr11	130800000	135006516	q25	gneg
+        chr12	33300000	35800000	p11.1	acen
+        chr12	35800000	38200000	q11	acen
+        chr12	129300000	133851895	q24.33	gneg
+        chr13	16300000	17900000	p11.1	acen
+        chr13	17900000	19500000	q11	acen
+        chr13	110300000	115169878	q34	gneg
+        chr14	16100000	17600000	p11.1	acen
+        chr14	17600000	19100000	q11.1	acen
+        chr14	104000000	107349540	q32.33	gneg
+        chr15	15800000	19000000	p11.1	acen
+        chr15	19000000	20700000	q11.1	acen
+        chr15	98500000	102531392	q26.3	gneg
+        chr16	34600000	36600000	p11.1	acen
+        chr16	36600000	38600000	q11.1	acen
+        chr16	88700000	90354753	q24.3	gneg
+        chr17	22200000	24000000	p11.1	acen
+        chr17	24000000	25800000	q11.1	acen
+        chr17	75300000	81195210	q25.3	gneg
+        chr18	15400000	17200000	p11.1	acen
+        chr18	17200000	19000000	q11.1	acen
+        chr18	73100000	78077248	q23	gneg
+        chr19	24400000	26500000	p11	acen
+        chr19	26500000	28600000	q11	acen
+        chr19	56300000	59128983	q13.43	gpos25
+        chr2	90500000	93300000	p11.1	acen
+        chr2	93300000	96800000	q11.1	acen
+        chr2	237300000	243199373	q37.3	gneg
+        chr20	25600000	27500000	p11.1	acen
+        chr20	27500000	29400000	q11.1	acen
+        chr20	58400000	63025520	q13.33	gneg
+        chr21	10900000	13200000	p11.1	acen
+        chr21	13200000	14300000	q11.1	acen
+        chr21	42600000	48129895	q22.3	gneg
+        chr22	12200000	14700000	p11.1	acen
+        chr22	14700000	17900000	q11.1	acen
+        chr22	49400000	51304566	q13.33	gneg
+        chr3	87900000	91000000	p11.1	acen
+        chr3	91000000	93900000	q11.1	acen
+        chr3	192300000	198022430	q29	gneg
+        chr4	48200000	50400000	p11	acen
+        chr4	50400000	52700000	q11	acen
+        chr4	187100000	191154276	q35.2	gpos25
+        chr5	46100000	48400000	p11	acen
+        chr5	48400000	50700000	q11.1	acen
+        chr5	176600000	180915260	q35.3	gneg
+        chr6	58700000	61000000	p11.1	acen
+        chr6	61000000	63300000	q11.1	acen
+        chr6	164500000	171115067	q27	gneg
+        chr7	58000000	59900000	p11.1	acen
+        chr7	59900000	61700000	q11.1	acen
+        chr7	155100000	159138663	q36.3	gneg
+        chr8	43100000	45600000	p11.1	acen
+        chr8	45600000	48100000	q11.1	acen
+        chr8	139900000	146364022	q24.3	gneg
+        chr9	47300000	49000000	p11.1	acen
+        chr9	49000000	50700000	q11	acen
+        chr9	137400000	141213431	q34.3	gneg
+        chrX	58100000	60600000	p11.1	acen
+        chrX	60600000	63000000	q11.1	acen
+        chrX	147100000	155270560	q28	gneg
+    ];
+    my @lines = split(/\n/,$ktype);
+    my %chrs  = ();
+    my $max_len = 0;
+    for my $line (@lines)
+    {
+        if ( $line =~ /^\s*$/ ) { next; }
+        $line =~ s/^\s*//;
+        $line =~ s/\s*$//;
+        my @items = split(/\s+/,$line);
+        my $chr   = $items[0];
+        my $start = $items[1];
+        my $end   = $items[2];
+        $chr =~ s/^chr//;
+        if ( $items[-1] eq 'acen' )
+        {
+            push @{$chrs{$chr}{acen}},$start;
+            push @{$chrs{$chr}{acen}},$end;
+        }
+        if ( !defined $chrs{$chr}{len} or $chrs{$chr}{len} < $end )
+        { 
+            $chrs{$chr}{len} = $end; 
+        }
+        if ( $max_len < $end ) { $max_len = $end; }
+    }
+    for my $chr (keys %chrs)
+    {
+        splice(@{$chrs{$chr}{acen}},1,1);
+    }
+    $$opts{chrs} = \%chrs;
+    $$opts{max_chr_len} = $max_len;
+}
+
+
+
+

From 2f3bc55ccaee35f8a51c875eb067c1a271586888 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 2 Oct 2015 12:27:35 +0100
Subject: [PATCH 088/211] tag2tag.c: minor fix to boilerplate header

---
 plugins/tag2tag.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/tag2tag.c b/plugins/tag2tag.c
index 03a841613..ec8956582 100644
--- a/plugins/tag2tag.c
+++ b/plugins/tag2tag.c
@@ -1,4 +1,4 @@
-/*  plugins/fill-AN-AC.c -- fills AN and AC INFO fields.
+/*  plugins/tag2tag.c -- Convert between similar tags, such as GL and GP.
 
     Copyright (C) 2014 Genome Research Ltd.
 

From 2f3ab49e4784839680468d804e65d8a7fc0b71b3 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 2 Oct 2015 14:00:06 +0100
Subject: [PATCH 089/211] color-chrs.pl: add copyright boilerplate

---
 plugins/color-chrs.pl | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/plugins/color-chrs.pl b/plugins/color-chrs.pl
index 39c4b74c4..4afb9c709 100755
--- a/plugins/color-chrs.pl
+++ b/plugins/color-chrs.pl
@@ -1,7 +1,26 @@
 #!/usr/bin/env perl
 #
-# Author: petr.danecek@sanger
+#   Copyright (C) 2015 Genome Research Ltd.
 #
+#   Author: Petr Danecek <pd3@sanger.ac.uk>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in
+# all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+# DEALINGS IN THE SOFTWARE.
 
 use strict;
 use warnings;

From 4923227eb2761ef8dd60512ff3e7f12f4c24d619 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 2 Oct 2015 14:00:52 +0100
Subject: [PATCH 090/211] Makefile: remove unnecessary "\"

---
 Makefile | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index ccc6563e2..d6f620f86 100644
--- a/Makefile
+++ b/Makefile
@@ -77,8 +77,7 @@ INSTALL_PROGRAM = $(INSTALL)
 INSTALL_DATA    = $(INSTALL) -m 644
 INSTALL_DIR     = $(MKDIR_P) -m 755
 
-MISC_PROGRAMS = \
-	plot-vcfstats vcfutils.pl plugins/color-chrs.pl \
+MISC_PROGRAMS = plot-vcfstats vcfutils.pl plugins/color-chrs.pl
 
 all:$(PROG) plugins
 

From 735702053f2f88bf3ec1a7435603be640ee56fa9 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 2 Oct 2015 16:06:04 +0100
Subject: [PATCH 091/211] rename plugin/info.c -> plugin/impute-info.c

---
 plugins/{info.c => impute-info.c} | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)
 rename plugins/{info.c => impute-info.c} (86%)

diff --git a/plugins/info.c b/plugins/impute-info.c
similarity index 86%
rename from plugins/info.c
rename to plugins/impute-info.c
index 2252b3a8f..c3c74ecea 100644
--- a/plugins/info.c
+++ b/plugins/impute-info.c
@@ -1,4 +1,4 @@
-/*  plugins/info.c -- adds info metrics to a VCF file.
+/*  plugins/impute-info.c -- adds info metrics to a VCF file.
 
     Copyright (C) 2015 Genome Research Ltd.
 
@@ -66,17 +66,17 @@ The IMPUTE2 information measure is then:
 
 const char *about(void)
 {
-    return "Add information metrics to the INFO field based on selected FORMAT tags.\n";
+    return "Add imputation information metrics to the INFO field based on selected FORMAT tags.\n";
 }
 
 const char *usage(void)
 {
     return 
         "\n"
-        "About: Add information metrics to the INFO field based on selected\n"
-        "       FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP\n"
-        "       tags is currently available.\n"
-        "Usage: bcftools +info [General Options] -- [Plugin Options]\n"
+        "About: Add imputation information metrics to the INFO field based\n"
+        "       on selected FORMAT tags. Only the IMPUTE2 INFO metric from\n"
+        "       FORMAT/GP tags is currently available.\n"
+        "Usage: bcftools +impute-info [General Options] -- [Plugin Options]\n"
         "Options:\n"
         "   run \"bcftools plugin\" for a list of common options\n"
         "\n"
@@ -85,7 +85,7 @@ const char *usage(void)
         // "   -t, --tags <tag>    VCF tags to determine the information from [GP]\n"
         // "\n"
         "Example:\n"
-        "   bcftools +info in.vcf\n"
+        "   bcftools +impute-info in.vcf\n"
         "\n";
 }
 
@@ -108,7 +108,7 @@ bcf1_t *process(bcf1_t *rec)
     int nval = 0, i, j, nret = bcf_get_format_values(in_hdr,rec,"GP",(void**)&buf,&nbuf,gp_type);
     if ( nret<0 )
     {
-        if (!nskip_gp) fprintf(stderr, "[info.c] Warning: info tag not added to sites without GP tag\n");
+        if (!nskip_gp) fprintf(stderr, "[impute-info.c] Warning: info tag not added to sites without GP tag\n");
         nskip_gp++;
         return rec; // require FORMAT/GP tag, return site unchanged
     }
@@ -116,7 +116,7 @@ bcf1_t *process(bcf1_t *rec)
     nret /= rec->n_sample;
     if ( nret != 3 )
     {
-        if (!nskip_dip) fprintf(stderr, "[info.c] Warning: info tag not added to sites that are not biallelic diploid\n");
+        if (!nskip_dip) fprintf(stderr, "[impute-info.c] Warning: info tag not added to sites that are not biallelic diploid\n");
         nskip_dip++;
         return rec; // require biallelic diploid, return site unchanged
     }

From 818cfbe8f6b2a75a9abb425a6035d83dea797427 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 12 Oct 2015 16:55:08 +0100
Subject: [PATCH 092/211] add tests for trimming many alleles and dropping
 header+format

add test cases for recently closed issues:

* issue #319 closed via samtools/htslib@636d70436bc67ae234510caaaafc22a1339ce3fa
* issue #332 closed via samtools/htslib@4c35976a90223302350cb6a8ebe2d2a400f74aff
---
 test/many.alleles.trim.out           | 10 ++++++++++
 test/many.alleles.vcf                |  7 +++++++
 test/test.pl                         |  2 ++
 test/view.dropgenotypes.noheader.out |  5 +++++
 4 files changed, 24 insertions(+)
 create mode 100644 test/many.alleles.trim.out
 create mode 100644 test/many.alleles.vcf
 create mode 100644 test/view.dropgenotypes.noheader.out

diff --git a/test/many.alleles.trim.out b/test/many.alleles.trim.out
new file mode 100644
index 000000000..7b622e150
--- /dev/null
+++ b/test/many.alleles.trim.out
@@ -0,0 +1,10 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=chr7>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR1528791
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCG	.	.	AC=2;AN=2	GT	1/1
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCG	.	.	AC=2;AN=2	GT	1/1
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCG	.	.	AC=2;AN=2	GT	1/1
diff --git a/test/many.alleles.vcf b/test/many.alleles.vcf
new file mode 100644
index 000000000..491bc89a4
--- /dev/null
+++ b/test/many.alleles.vcf
@@ -0,0 +1,7 @@
+##fileformat=VCFv4.1
+##contig=<ID=chr7>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SRR1528791
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCC,CCATCTCTCTCCCCG,CCTTCTCTCTGCCCC,CCCTCTCTCTCCCCC,CCACCTCTCTGCCCC,CCACCCCTCTGCCCA,CCACCTCCCTCCCCC,CCACCTCCCTGCCCA,CCACCTCTCGGCCCC,CCACCTCTCGGCCCA,CCACCTCTCTCCCCC,CCACCTCTCTCCCCA,CCATCCCCCTCCCCC,CCATCCCCCTGCCCC,CCATCCCCCTGCCCA,CCATCCCTCGGCCCC,CCATCCCTCGGCCCA,CCATCCCTCTCCCCC,CCATCCCTCTCCCCA,CCATCCCTCTGCCCC,CCATCTCCCGGCCCC,CCATCTCCCGGCCCA,CCATCTCCCGCCCCC,CCATCTCCCTCCCCC,CCATCTCCCTCCCCA,CCATCTCCCTGCCCC,CCATCTCTCGGCCCC,CCATCTCTCCCCCCC,CCATCTCTCGCCCCC,CCATCTCTGGGCCCA,CCATCTCTCCCCCCA,CCATCTCTCGCCCCA,CCATCTCTCTCCCCA	.	.	.	GT	2/2
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCC,CCATCTCTCTCCCCG,CCTTCTCTCTGCCCC,CCCTCTCTCTCCCCC,CCACCTCTCTGCCCC,CCACCCCTCTGCCCA,CCACCTCCCTCCCCC,CCACCTCCCTGCCCA,CCACCTCTCGGCCCC,CCACCTCTCGGCCCA,CCACCTCTCTCCCCC,CCACCTCTCTCCCCA,CCATCCCCCTCCCCC,CCATCCCCCTGCCCC,CCATCCCCCTGCCCA,CCATCCCTCGGCCCC,CCATCCCTCGGCCCA,CCATCCCTCTCCCCC,CCATCCCTCTCCCCA,CCATCCCTCTGCCCC,CCATCTCCCGGCCCC,CCATCTCCCGGCCCA,CCATCTCCCGCCCCC,CCATCTCCCTCCCCC,CCATCTCCCTCCCCA,CCATCTCCCTGCCCC,CCATCTCTCGGCCCC,CCATCTCTCCCCCCC,CCATCTCTCGCCCCC,CCATCTCTGGGCCCA,CCATCTCTCCCCCCA,CCATCTCTCGCCCCA,CCATCTCTCTCCCCA,CCTTCTCTCTGCCCC	.	.	.	GT	2/2
+chr7	142459798	.	CCATCTCTCTGCCCA	CCATCTCTCTCCCCC,CCATCTCTCTCCCCG,CCTTCTCTCTGCCCC,CCCTCTCTCTCCCCC,CCACCTCTCTGCCCC,CCACCCCTCTGCCCA,CCACCTCCCTCCCCC,CCACCTCTCGGCCCC,CCACCTCTCGGCCCA,CCACCTCTCTCCCCC,CCACCTCTCTCCCCA,CCATCCCCCTCCCCC,CCATCCCCCTGCCCC,CCATCCCCCTGCCCA,CCATCCCTCGGCCCC,CCATCCCTCGGCCCA,CCATCCCTCTCCCCC,CCATCCCTCTCCCCA,CCATCCCTCTGCCCC,CCATCTCCCGGCCCC,CCATCTCCCGGCCCA,CCATCTCCCGCCCCC,CCATCTCCCTCCCCC,CCATCTCCCTCCCCA,CCATCTCCCTGCCCC,CCATCTCTCGGCCCC,CCATCTCTCCCCCCC,CCATCTCTCGCCCCC,CCATCTCTGGGCCCA,CCATCTCTCCCCCCA,CCATCTCTCGCCCCA,CCATCTCTCTCCCCA,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC,CCTTCTCTCTGCCCC	.	.	.	GT	2/2
diff --git a/test/test.pl b/test/test.pl
index 176243e3f..4120a3c4e 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -111,6 +111,8 @@
 test_vcf_view($opts,in=>'view',out=>'view.exclude.out',args=>'-s ^NA00003',reg=>'');
 test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.omitgenotypes.out',args=>'',reg=>'');
 test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.dropgenotypes.out',args=>'-G',reg=>'');
+test_vcf_view($opts,in=>'view.omitgenotypes',out=>'view.dropgenotypes.noheader.out',args=>'-HG',reg=>'');
+test_vcf_view($opts,in=>'many.alleles',out=>'many.alleles.trim.out',args=>'-a',reg=>'');
 test_vcf_view($opts,in=>'view.vectors',out=>'view.vectors.A.out',args=>'-asA',reg=>'');
 test_vcf_view($opts,in=>'view.vectors',out=>'view.vectors.B.out',args=>'-asB',reg=>'');
 test_vcf_view($opts,in=>'view.filter',out=>'view.filter.1.out',args=>q[-H -i'FMT/FGS[0]="AAAAAA"'],reg=>'');    # test expressions
diff --git a/test/view.dropgenotypes.noheader.out b/test/view.dropgenotypes.noheader.out
new file mode 100644
index 000000000..7b5a3c809
--- /dev/null
+++ b/test/view.dropgenotypes.noheader.out
@@ -0,0 +1,5 @@
+20	14370	rs6054257	G	A	29	PASS	NS=3;DP=14
+20	17330	.	T	A	3	PASS	NS=3;DP=11
+20	1110696	rs6040355	A	G,T	67	PASS	NS=2;DP=10
+20	1230237	.	T	.	47	PASS	NS=3;DP=13
+20	1234567	microsat1	GTC	G,GTCT	50	PASS	NS=3;DP=9

From dacc705b8817a20dc2e909a9758d8b6e7fb80a0c Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 15 Oct 2015 09:27:21 +0100
Subject: [PATCH 093/211] genaralise mcall_trim_numberR beyond DPR to any
 Number=R/Type=Integer tag

Fixes #338
---
 mcall.c | 82 +++++++++++++++++++++++++++++++++++----------------------
 1 file changed, 51 insertions(+), 31 deletions(-)

diff --git a/mcall.c b/mcall.c
index e62fd4c47..67ae04482 100644
--- a/mcall.c
+++ b/mcall.c
@@ -1186,51 +1186,71 @@ void mcall_trim_numberR(call_t *call, bcf1_t *rec, int nals, int nout_als, int o
 {
     int i, ret;
 
-    // only DPR so far, we may generalize to arbitrary Number=R if necessary
-    ret = bcf_get_info_int32(call->hdr, rec, "DPR", &call->itmp, &call->n_itmp);
-    if ( ret>0 )
+    // at the moment we have DPR,AD,ADF,ADR all Number=R,Type=Integer,
+    // so only dealing with these cases at the moment
+    for (i=0; i<rec->n_info; i++)
     {
-        assert( ret==nals );
-        if ( out_als==1 )
-            bcf_update_info_int32(call->hdr, rec, "DPR", call->itmp, 1);
-        else
+        bcf_info_t *info = &rec->d.info[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_INFO,info->key);
+        if ( vlen!=BCF_VL_R ) continue;
+        int type = bcf_hdr_id2type(call->hdr,BCF_HL_INFO,info->key);
+        if ( type!=BCF_HT_INT ) continue;
+
+        ret = bcf_get_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), &call->itmp, &call->n_itmp);
+        if ( ret>0 )
         {
-            for (i=0; i<nals; i++)
+            assert( ret==nals );
+            if ( out_als==1 )
+                bcf_update_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), call->itmp, 1);
+            else
             {
-                if ( call->als_map[i]==-1 ) continue;   // to be dropped
-                call->PLs[ call->als_map[i] ] = call->itmp[i]; // reusing PLs storage which is not used at this point
+                int j;
+                for (j=0; j<nals; j++)
+                {
+                    if ( call->als_map[j]==-1 ) continue;   // to be dropped
+                    call->PLs[ call->als_map[j] ] = call->itmp[j]; // reusing PLs storage which is not used at this point
+                }
+                bcf_update_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), call->PLs, nout_als);
             }
-            bcf_update_info_int32(call->hdr, rec, "DPR", call->PLs, nout_als);
         }
     }
 
-    ret = bcf_get_format_int32(call->hdr, rec, "DPR", &call->itmp, &call->n_itmp);
-    if ( ret>0 )
+    for (i=0; i<rec->n_fmt; i++)
     {
-        int nsmpl = bcf_hdr_nsamples(call->hdr);
-        int ndp = ret / nsmpl;
-        assert( ndp==nals );
-        if ( out_als==1 )
+        bcf_fmt_t *fmt = &rec->d.fmt[i];
+        int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id);
+        if ( vlen!=BCF_VL_R ) continue;
+        int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id);
+        if ( type!=BCF_HT_INT ) continue;
+
+        ret = bcf_get_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), &call->itmp, &call->n_itmp);
+        if ( ret>0 )
         {
-            for (i=0; i<nsmpl; i++)
-                call->PLs[i] = call->itmp[i*ndp];
+            int j, nsmpl = bcf_hdr_nsamples(call->hdr);
+            int ndp = ret / nsmpl;
+            assert( ndp==nals );
+            if ( out_als==1 )
+            {
+                for (j=0; j<nsmpl; j++)
+                    call->PLs[j] = call->itmp[j*ndp];
 
-            bcf_update_format_int32(call->hdr, rec, "DPR", call->PLs, nsmpl);
-        }
-        else
-        {
-            int j;
-            for (i=0; i<nsmpl; i++)
+                bcf_update_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), call->PLs, nsmpl);
+            }
+            else
             {
-                int32_t *dp_dst = call->PLs + i*nout_als;
-                int32_t *dp_src = call->itmp + i*ndp;
-                for (j=0; j<nals; j++)
+                int k;
+                for (j=0; j<nsmpl; j++)
                 {
-                    if ( call->als_map[j]==-1 ) continue;   // to be dropped
-                    dp_dst[ call->als_map[j] ] = dp_src[j]; // reusing PLs storage which is not used at this point
+                    int32_t *dp_dst = call->PLs + j*nout_als;
+                    int32_t *dp_src = call->itmp + j*ndp;
+                    for (k=0; k<nals; k++)
+                    {
+                        if ( call->als_map[k]==-1 ) continue;   // to be dropped
+                        dp_dst[ call->als_map[k] ] = dp_src[k]; // reusing PLs storage which is not used at this point
+                    }
                 }
+                bcf_update_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), call->PLs, nsmpl*nout_als);
             }
-            bcf_update_format_int32(call->hdr, rec, "DPR", call->PLs, nsmpl*nout_als);
         }
     }
 }

From 9fc3364f44c5bee267442e5423995f15767a26ef Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 23 Sep 2015 08:33:52 +0100
Subject: [PATCH 094/211] Small polysomy improvements

- fix in printout of peak centers with the -v option, constrained parameters
  were not updated
- detect failed fits with peaks to narrow or too broad to contribute meaningfully
- print the best function for all three states with the -v option
- reversed the --cn-penalty to the expected meaning: larger is stricter
---
 peakfit.c  | 30 +++++++++++++++------------
 polysomy.c | 59 +++++++++++++++++++++++++++++++++++++++---------------
 2 files changed, 60 insertions(+), 29 deletions(-)

diff --git a/peakfit.c b/peakfit.c
index 89bdcb0c4..2bc849226 100644
--- a/peakfit.c
+++ b/peakfit.c
@@ -134,12 +134,12 @@ double bounded_gaussian_convert_set(peak_t *pk, int iparam, double value)
 }
 void bounded_gaussian_convert_get(peak_t *pk, double *params)
 {
-    params[0] = fabs(params[0]);
-    params[2] = fabs(params[2]);
-    double b = params[1];
-    double d = params[3];
-    double e = params[4];
-    params[1] = 0.5*(cos(b)+1)*(e-d) + d;
+    params[0] = fabs(pk->params[0]);
+    params[2] = fabs(pk->params[2]);
+    double center = pk->params[1];
+    double d = pk->params[3];
+    double e = pk->params[4];
+    params[1] = 0.5*(cos(center)+1)*(e-d) + d;
 }
 
 void peakfit_add_bounded_gaussian(peakfit_t *pkf, double a, double b, double c, double d, double e, int fit_mask)
@@ -226,8 +226,9 @@ void gaussian_sprint_func(struct _peak_t *pk, kstring_t *str)
 }
 void gaussian_convert_get(peak_t *pk, double *params)
 {
-    params[0] = fabs(params[0]);
-    params[2] = fabs(params[2]);
+    params[0] = fabs(pk->params[0]);
+    params[1] = fabs(pk->params[1]);
+    params[2] = fabs(pk->params[2]);
 }
 
 
@@ -306,9 +307,9 @@ void exp_sprint_func(struct _peak_t *pk, kstring_t *str)
 }
 void exp_convert_get(peak_t *pk, double *params)
 {
-    params[0] = fabs(params[0]);
-    params[1] = fabs(params[1]);
-    params[2] = fabs(params[2]);
+    params[0] = fabs(pk->params[0]);
+    params[1] = fabs(pk->params[1]);
+    params[2] = fabs(pk->params[2]);
 }
 
 void peakfit_add_exp(peakfit_t *pkf, double a, double b, double c, int fit_mask)
@@ -352,9 +353,12 @@ void peakfit_set_params(peakfit_t *pkf, int ipk, double *params, int nparams)
 void peakfit_get_params(peakfit_t *pkf, int ipk, double *params, int nparams)
 {
     peak_t *pk = &pkf->peaks[ipk];
-    int i;
-    for (i=0; i<nparams; i++) params[i] = pk->params[i];
     if ( pk->convert_get ) pk->convert_get(pk, params);
+    else
+    {
+        int i;
+        for (i=0; i<nparams; i++) params[i] = pk->params[i];
+    }
 }
 
 peakfit_t *peakfit_init(void)
diff --git a/polysomy.c b/polysomy.c
index 3962cf8a1..3d83a6d87 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -54,7 +54,7 @@ typedef struct
     double *xvals;
     dist_t *dist;
     char **argv, *output_dir;
-    double fit_th, peak_symmetry, cn_penalty, bump_size, min_fraction;
+    double fit_th, peak_symmetry, cn_penalty, min_peak_size, min_fraction;
     int argc, plot, verbose, regions_is_file, targets_is_file, include_aa, force_cn;
     char *dat_fname, *fname, *regions_list, *targets_list, *sample;
     FILE *dat_fp;
@@ -425,6 +425,7 @@ static void fit_curves(args_t *args)
         peakfit_get_params(pkf,0,cn3rra_params,5);
         peakfit_get_params(pkf,1,cn3raa_params,5);
         double cn3_dx = (0.5-cn3rra_params[1] + cn3raa_params[1]-0.5)*0.5;
+        if ( cn3_dx > 0.5/3 ) cn3_dx = 0.5/3;   // CN3 peaks should not be separated by more than 1/3
         peakfit_reset(pkf);
         peakfit_add_gaussian(pkf, cn3rra_params[0],0.5-cn3_dx,cn3rra_params[2], 5);
         peakfit_add_gaussian(pkf, cn3raa_params[0],0.5+cn3_dx,cn3raa_params[2], 5);
@@ -438,10 +439,13 @@ static void fit_curves(args_t *args)
         double cn3_dy      = cn3rra_size > cn3raa_size ? cn3raa_size/cn3rra_size : cn3rra_size/cn3raa_size;
         double cn3_frac    = (1 - 2*cn3rra_params[1]) / cn3rra_params[1];
         double cn3_fit     = cn3ra_fit + cn3aa_fit;
+        // A very reasonable heuristics: check if the peak's width converged, exclude far too broad or far too narrow peaks
+        if ( cn3rra_params[2]>0.3  || cn3raa_params[2]>0.3 ) cn3_fit = HUGE_VAL;
+        if ( cn3rra_params[2]<1e-2 || cn3raa_params[2]<1e-2 ) cn3_fit = HUGE_VAL;
 
 
         // CN4 (contaminations)
-        // - similarly to CN3, fit three peaks, then enforce the symmetry and fit again
+        // - first fit only the [0,0.5] part of the data, then enforce the symmetry and fit again
         // - min_frac=1 (resp. 0.5) is interpreted as 50:50% (rep. 75:25%) contamination
         double cn4AAaa_params[3] = {1,1,1} ,cn4AAra_params[3] = {1,1,1}, cn4RAra_params[3], cn4RArr_params[5], cn4RAaa_params[5];
         double cn4aa_fit = 0, cn4ra_fit;
@@ -460,18 +464,20 @@ static void fit_curves(args_t *args)
             peakfit_get_params(pkf,1,cn4AAra_params,5);
         }
         peakfit_reset(pkf);
+        // first fit only the [0,0.5] part of the data
         peakfit_add_gaussian(pkf, 1.0,0.5,0.03, 5);
         peakfit_add_bounded_gaussian(pkf, 0.6,0.3,0.03, xrr,xra-min_dx4, 7);
         peakfit_set_mc(pkf, xrr,xra-min_dx4,2,nmc);
         peakfit_run(pkf, nrr_ra , xrr_vals, yrr_vals);
-        // suggest symmetry around x=0.5
+        // now forcet symmetry around x=0.5
         peakfit_get_params(pkf,0,cn4RAra_params,3);
         peakfit_get_params(pkf,1,cn4RArr_params,5);
         double cn4_dx = 0.5-cn4RArr_params[1];
+        if ( cn4_dx > 0.25 ) cn4_dx = 0.25;   // CN4 peaks should not be separated by more than 0.5
         peakfit_reset(pkf);
         peakfit_add_gaussian(pkf, cn4RAra_params[0],0.5,cn4RAra_params[2], 5);
-        peakfit_add_gaussian(pkf, cn4RArr_params[0],0.5-cn4_dx,cn4RArr_params[2], 7);
-        peakfit_add_gaussian(pkf, cn4RArr_params[0],0.5+cn4_dx,cn4RArr_params[2], 7);
+        peakfit_add_gaussian(pkf, cn4RArr_params[0],0.5-cn4_dx,cn4RArr_params[2], 5);
+        peakfit_add_gaussian(pkf, cn4RArr_params[0],0.5+cn4_dx,cn4RArr_params[2], 5);
         peakfit_set_mc(pkf, 0.1,cn4RAra_params[0],0,nmc);
         peakfit_set_mc(pkf, 0.01,0.1,2,nmc);
         cn4ra_fit  = peakfit_run(pkf, nrr_aa , xrr_vals, yrr_vals);
@@ -489,6 +495,9 @@ static void fit_curves(args_t *args)
         cn4_dx              = (cn4RAaa_params[1]-0.5) - (0.5-cn4RArr_params[1]);
         double cn4_frac     = cn4RAaa_params[1] - cn4RArr_params[1];
         double cn4_fit      = cn4ra_fit + cn4aa_fit;
+        // A very reasonable heuristics: check if the peak's width converged, exclude far too broad or far too narrow peaks
+        if ( cn4RAra_params[2]>0.3 || cn4RArr_params[2]>0.3 || cn4RAaa_params[2]>0.3 ) cn4_fit = HUGE_VAL;
+        if ( cn4RAra_params[2]<1e-2 || cn4RArr_params[2]<1e-2 || cn4RAaa_params[2]<1e-2 ) cn4_fit = HUGE_VAL;
 
 
         // Choose the best match
@@ -499,7 +508,7 @@ static void fit_curves(args_t *args)
         else if ( cn3_dy < args->peak_symmetry ) cn3_fail = 'y';    // size difference is too big
 
         if ( cn4_fit > args->fit_th ) cn4_fail = 'f';
-        else if ( cn4_ymin < args->bump_size ) cn4_fail = 'y';      // side peak is too small
+        else if ( cn4_ymin < args->min_peak_size ) cn4_fail = 'y';      // side peak is too small
         else if ( cn4_dy < args->peak_symmetry ) cn4_fail = 'Y';    // size difference is too big
         else if ( cn4_dx > 0.1 ) cn4_fail = 'x';                    // side peaks placed assymetrically
 
@@ -507,8 +516,8 @@ static void fit_curves(args_t *args)
         if ( cn2_fail == '*' ) { cn = 2; fit = cn2_fit; }
         if ( cn3_fail == '*' )
         {
-            // use cn_penalty as a tiebreaker
-            if ( cn<0 || cn3_fit < args->cn_penalty * fit )
+            // Use cn_penalty as a tiebreaker. If set to 0.3, cn3_fit must be 30% smaller than cn2_fit.
+            if ( cn<0 || cn3_fit < (1-args->cn_penalty) * fit )
             {
                 cn = 2 + cn3_frac; 
                 fit = cn3_fit; 
@@ -518,7 +527,7 @@ static void fit_curves(args_t *args)
         }
         if ( cn4_fail == '*' )
         {
-            if ( cn<0 || cn4_fit < args->cn_penalty * fit )
+            if ( cn<0 || cn4_fit < (1-args->cn_penalty) * fit )
             {
                 cn = 3 + cn4_frac;
                 fit = cn4_fit;
@@ -535,12 +544,20 @@ static void fit_curves(args_t *args)
             fprintf(stderr,"\t            RA:   %f %f %f\n", cn2ra_params[0],cn2ra_params[1],cn2ra_params[2]);
             fprintf(stderr,"\t       .. %e\n", cn2aa_fit);
             fprintf(stderr,"\t            AA:   %f %f %f\n", cn2aa_params[0],cn2aa_params[1],cn2aa_params[2]);
+            fprintf(stderr,"\t      func:\n");
+            fprintf(stderr,"\t            %s\n", cn2ra_func);
+            fprintf(stderr,"\t            %s\n", cn2aa_func);
+            fprintf(stderr,"\n");
             fprintf(stderr,"\tcn3 %c fit=%e  frac=%f  symmetry=%f\n", cn3_fail, cn3_fit, cn3_frac, cn3_dy);
             fprintf(stderr,"\t       .. %e\n", cn3ra_fit);
             fprintf(stderr,"\t            RRA:  %f %f %f\n", cn3rra_params[0],cn3rra_params[1],cn3rra_params[2]);
             fprintf(stderr,"\t            RAA:  %f %f %f\n", cn3raa_params[0],cn3raa_params[1],cn3raa_params[2]);
             fprintf(stderr,"\t       .. %e\n", cn3aa_fit);
             fprintf(stderr,"\t            AAA:  %f %f %f\n", cn3aa_params[0],cn3aa_params[1],cn3aa_params[2]);
+            fprintf(stderr,"\t      func:\n");
+            fprintf(stderr,"\t            %s\n", cn3ra_func);
+            fprintf(stderr,"\t            %s\n", cn3aa_func);
+            fprintf(stderr,"\n");
             fprintf(stderr,"\tcn4 %c fit=%e  frac=%f  symmetry=%f ymin=%f\n", cn4_fail, cn4_fit, cn4_frac, cn4_dy, cn4_ymin);
             fprintf(stderr,"\t       .. %e\n", cn4ra_fit);
             fprintf(stderr,"\t            RArr:  %f %f %f\n", cn4RArr_params[0],cn4RArr_params[1],cn4RArr_params[2]);
@@ -548,6 +565,10 @@ static void fit_curves(args_t *args)
             fprintf(stderr,"\t            RAaa:  %f %f %f\n", cn4RAaa_params[0],cn4RAaa_params[1],cn4RAaa_params[2]);
             fprintf(stderr,"\t       .. %e\n", cn4aa_fit);
             fprintf(stderr,"\t            AAaa:  %f %f %f\n", cn4AAaa_params[0],cn4AAaa_params[1],cn4AAaa_params[2]);
+            fprintf(stderr,"\t      func:\n");
+            fprintf(stderr,"\t            %s\n", cn4ra_func);
+            fprintf(stderr,"\t            %s\n", cn4aa_func);
+            fprintf(stderr,"\n");
         }
 
         if ( args->force_cn==2 || cn2_fail == '*' )
@@ -593,12 +614,12 @@ static void usage(args_t *args)
     fprintf(stderr, "    -v, --verbose                  \n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Algorithm options:\n");
-    fprintf(stderr, "    -b, --bump-size <float>        minimum bump size (larger is stricter) [0.1]\n");
-    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (smaller is stricter) [0.3]\n");
-    fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (smaller is stricter) [3.3]\n");
+    fprintf(stderr, "    -b, --peak-size <float>        minimum peak size (0-1, larger is stricter) [0.1]\n");
+    fprintf(stderr, "    -c, --cn-penalty <float>       penalty for increasing CN (0-1, larger is stricter) [0.7]\n");
+    fprintf(stderr, "    -f, --fit-th <float>           goodness of fit threshold (>0, smaller is stricter) [3.3]\n");
     fprintf(stderr, "    -i, --include-aa               include the AA peak in CN2 and CN3 evaluation\n");
     fprintf(stderr, "    -m, --min-fraction <float>     minimum distinguishable fraction of aberrant cells [0.1]\n");
-    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (larger is stricter) [0.5]\n");
+    fprintf(stderr, "    -p, --peak-symmetry <float>    peak symmetry threshold (0-1, larger is stricter) [0.5]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -609,9 +630,9 @@ int main_polysomy(int argc, char *argv[])
     args->argc   = argc; args->argv = argv;
     args->nbins  = 150;
     args->fit_th = 3.3;
-    args->cn_penalty = 0.3;
+    args->cn_penalty = 0.7;
     args->peak_symmetry = 0.5;
-    args->bump_size = 0.1;
+    args->min_peak_size = 0.1;
     args->ra_rr_scaling = 1;
     args->min_fraction = 0.1;
 
@@ -620,6 +641,7 @@ int main_polysomy(int argc, char *argv[])
         {"ra-rr-scaling",0,0,1},    // hidden option
         {"force-cn",1,0,2},         // hidden option
         {"include-aa",0,0,'i'},
+        {"peak-size",1,0,'b'},
         {"min-fraction",1,0,'m'},
         {"verbose",0,0,'v'},
         {"fit-th",1,0,'f'},
@@ -634,13 +656,18 @@ int main_polysomy(int argc, char *argv[])
         {0,0,0,0}
     };
     char c, *tmp;
-    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:b:",loptions,NULL)) >= 0)
     {
         switch (c)
         {
             case  1 : args->ra_rr_scaling = 0; break;
             case  2 : args->force_cn = atoi(optarg); break;
             case 'i': args->include_aa = 1; break;
+            case 'b':
+                args->min_peak_size = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -b %s\n", optarg);
+                if ( args->min_peak_size<0 || args->min_peak_size>1 ) error("Range error: -b %s\n", optarg);
+                break;
             case 'm':
                 args->min_fraction = strtod(optarg,&tmp);
                 if ( *tmp ) error("Could not parse: -n %s\n", optarg);

From f0889c4802aa5a87632cf792d5e9d8f2efe41585 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 23 Sep 2015 13:47:36 +0100
Subject: [PATCH 095/211] New hidden -n and -S options to polysomy

---
 polysomy.c | 40 +++++++++++++++++++++++++++++++---------
 1 file changed, 31 insertions(+), 9 deletions(-)

diff --git a/polysomy.c b/polysomy.c
index 3d83a6d87..c5a5394e1 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -50,7 +50,7 @@ dist_t;
 
 typedef struct
 {
-    int ndist, nbins, ra_rr_scaling;
+    int ndist, nbins, ra_rr_scaling, smooth;
     double *xvals;
     dist_t *dist;
     char **argv, *output_dir;
@@ -70,15 +70,31 @@ static void init_dist(args_t *args, dist_t *dist, int verbose)
 
     // smooth the distribution, this is just to find the peaks
     double *tmp = (double*) malloc(sizeof(double)*n);
-    int win = 0.04*n < 1 ? 1 : 0.04*n;
-    double avg = 0;
-    for (i=0; i<win; i++) avg += dist->yvals[i];
-    for (i=0; i<n-win; i++)
+    int win  = args->smooth ? fabs(args->smooth)*2 + 1 : 7;   // must be an odd number
+    int hwin = win/2;
+    double avg = tmp[0] = dist->yvals[0];
+    for (i=1; i<hwin; i++)
     {
-        tmp[i] = avg / win;
-        avg += -dist->yvals[i] + dist->yvals[i+win];
+        avg += dist->yvals[2*i-1]; 
+        tmp[i] = avg/(2*i+1);
+    }
+    avg = 0;
+    for (i=0; i<n; i++)
+    {
+        avg += dist->yvals[i];
+        if ( i>=win-1 )
+        {
+            tmp[i-hwin] = avg/win;
+            avg -= dist->yvals[i-win+1];
+        }
+    }
+    for (i=n-hwin; i<n; i++)
+    {
+        avg -= dist->yvals[i-hwin];
+        hwin--;
+        tmp[i] = avg/(2*hwin+1);
+        avg -= dist->yvals[i-hwin];
     }
-    for (; i<n; i++) tmp[i] = avg;
 
     // find the extremes; first a simple approach: find a gap
     for (irr=0,i=0; i<n/2; i++) if ( tmp[i] < tmp[irr] ) irr = i;
@@ -87,6 +103,7 @@ static void init_dist(args_t *args, dist_t *dist, int verbose)
     iaa += win*0.5;
     if ( iaa>=n ) iaa = n-1;
     if ( irr>=iaa ) error("FIXME: oops, dist normalization failed for %s: %d vs %d\n", dist->chr,irr,iaa); // we may need to be smarter
+    if ( args->smooth>0 ) for (i=0; i<n; i++) dist->yvals[i] = tmp[i];
     free(tmp);
 
     // clean the data: the AA peak is occasionally not centered at 1.0 but is closer to the center, chop off
@@ -635,11 +652,14 @@ int main_polysomy(int argc, char *argv[])
     args->min_peak_size = 0.1;
     args->ra_rr_scaling = 1;
     args->min_fraction = 0.1;
+    args->smooth = -3;
 
     static struct option loptions[] =
     {
         {"ra-rr-scaling",0,0,1},    // hidden option
         {"force-cn",1,0,2},         // hidden option
+        {"smooth",1,0,'S'},         // hidden option
+        {"nbins",1,0,'n'},          // hidden option
         {"include-aa",0,0,'i'},
         {"peak-size",1,0,'b'},
         {"min-fraction",1,0,'m'},
@@ -656,12 +676,14 @@ int main_polysomy(int argc, char *argv[])
         {0,0,0,0}
     };
     char c, *tmp;
-    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:b:",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:b:n:S:",loptions,NULL)) >= 0)
     {
         switch (c)
         {
             case  1 : args->ra_rr_scaling = 0; break;
             case  2 : args->force_cn = atoi(optarg); break;
+            case 'n': args->nbins = atoi(optarg); break;
+            case 'S': args->smooth = atoi(optarg); break;
             case 'i': args->include_aa = 1; break;
             case 'b':
                 args->min_peak_size = strtod(optarg,&tmp);

From 83c9593f7a6c45d35f5bf16ca0df298500629ec8 Mon Sep 17 00:00:00 2001
From: Adam Spargo <aws@sanger.ac.uk>
Date: Wed, 14 Oct 2015 16:32:32 +0100
Subject: [PATCH 096/211] change to filter.c:filters_init()

Search all elements of INFO tag arrays UNLESS an array index
has been detected.

Fix indentation.

Add 3 tests to test/test.pl. This closes #320.
---
 filter.c                       | 28 +++++++++---------
 test/test.pl                   |  3 ++
 test/view.filter.annovar.1.out |  2 ++
 test/view.filter.annovar.2.out |  1 +
 test/view.filter.annovar.3.out |  1 +
 test/view.filter.annovar.vcf   | 52 ++++++++++++++++++++++++++++++++++
 6 files changed, 73 insertions(+), 14 deletions(-)
 create mode 100644 test/view.filter.annovar.1.out
 create mode 100644 test/view.filter.annovar.2.out
 create mode 100644 test/view.filter.annovar.3.out
 create mode 100644 test/view.filter.annovar.vcf

diff --git a/filter.c b/filter.c
index 9ae263b44..82d19f2a2 100644
--- a/filter.c
+++ b/filter.c
@@ -1282,25 +1282,25 @@ static int filters_init1(filter_t *filter, char *str, int len, token_t *tok)
             {
                 if ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) == BCF_HT_STR ) tok->is_str = 1;
                 if ( bcf_hdr_id2number(filter->hdr,BCF_HL_INFO,tok->hdr_id)==1 )
-                tok->setter = filters_set_info;
-            else
-            {
-                switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) )
+                    tok->setter = filters_set_info;
+                else
                 {
-                    case BCF_HT_INT:  tok->setter = &filters_set_info_int; break;
-                    case BCF_HT_REAL: tok->setter = &filters_set_info_float; break;
-                    case BCF_HT_STR:  tok->setter = &filters_set_info_string; tok->is_str = 1; break;
-                    default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__);
+                    switch ( bcf_hdr_id2type(filter->hdr,BCF_HL_INFO,tok->hdr_id) )
+                    {
+                        case BCF_HT_INT:  tok->setter = &filters_set_info_int; break;
+                        case BCF_HT_REAL: tok->setter = &filters_set_info_float; break;
+                        case BCF_HT_STR:  tok->setter = &filters_set_info_string; tok->is_str = 1; break;
+                        default: error("[%s:%d %s] FIXME\n", __FILE__,__LINE__,__FUNCTION__);
+                    }
+                    if(!is_array) tok->idx = -2;
                 }
-                    //tok->idx = -2;
-            }
             }
             filter->max_unpack |= BCF_UN_INFO;
-            }
-            tok->tag = strdup(tmp.s);
-            if ( tmp.s ) free(tmp.s);
-            return 0;
         }
+        tok->tag = strdup(tmp.s);
+        if ( tmp.s ) free(tmp.s);
+        return 0;
+    }
     else if ( !strcasecmp(tmp.s,"ALT") )
     {
         tok->setter = &filters_set_alt_string;
diff --git a/test/test.pl b/test/test.pl
index 4120a3c4e..c3819fd58 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -130,6 +130,9 @@
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.1.out',args=>q[-H -C5:nonmajor],reg=>'');
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.2.out',args=>q[-H -c6:nonmajor],reg=>'');
 test_vcf_view($opts,in=>'view.minmaxac',out=>'view.minmaxac.1.out',args=>q[-H -q0.3:major],reg=>'');
+test_vcf_view($opts,in=>'view.filter.annovar',out=>'view.filter.annovar.1.out',args=>q[-H -i 'Gene.refGene=="RAD21L1"'],reg=>'');
+test_vcf_view($opts,in=>'view.filter.annovar',out=>'view.filter.annovar.2.out',args=>q[-H -i 'Gene.refGene~"NOD"'],reg=>'');
+test_vcf_view($opts,in=>'view.filter.annovar',out=>'view.filter.annovar.3.out',args=>q[-H -i 'LJB2_MutationTaster=="0.291000"'],reg=>'');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.1.out',args=>'-mv');
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mg0');
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
diff --git a/test/view.filter.annovar.1.out b/test/view.filter.annovar.1.out
new file mode 100644
index 000000000..e71068c15
--- /dev/null
+++ b/test/view.filter.annovar.1.out
@@ -0,0 +1,2 @@
+20	1230237	.	T	G	47	PASS	NS=3;DP=13;AA=T;ANNOVAR_DATE=2015-06-17;Func.refGene=intronic;Gene.refGene=RAD21L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.ensGene=intronic;Gene.ensGene=ENSG00000244588;GeneDetail.ensGene=.;ExonicFunc.ensGene=.;AAChange.ensGene=.;esp6500si_ea=.;esp6500si_all=.;1000g2012apr_eur=.;1000g2012apr_all=.;snp138=.;LJB2_SIFT=.;LJB2_PolyPhen2_HDIV=.;LJB2_PP2_HDIV_Pred=.;LJB2_PolyPhen2_HVAR=.;LJB2_PolyPhen2_HVAR_Pred=.;LJB2_LRT=.;LJB2_LRT_Pred=.;LJB2_MutationTaster=.;LJB2_MutationTaster_Pred=.;LJB_MutationAssessor=.;LJB_MutationAssessor_Pred=.;LJB2_FATHMM=.;LJB2_GERP++=.;LJB2_PhyloP=.;LJB2_SiPhy=.;ALLELE_END	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:.
+20	1230288	.	T	.	50	PASS	NS=3;DP=13;AA=T;ANNOVAR_DATE=2015-06-17;Func.refGene=intronic;Gene.refGene=RAD21L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.ensGene=intronic;Gene.ensGene=ENSG00000244588;GeneDetail.ensGene=.;ExonicFunc.ensGene=.;AAChange.ensGene=.;esp6500si_ea=.;esp6500si_all=.;1000g2012apr_eur=.;1000g2012apr_all=.;snp138=.;LJB2_SIFT=.;LJB2_PolyPhen2_HDIV=.;LJB2_PP2_HDIV_Pred=.;LJB2_PolyPhen2_HVAR=.;LJB2_PolyPhen2_HVAR_Pred=.;LJB2_LRT=.;LJB2_LRT_Pred=.;LJB2_MutationTaster=.;LJB2_MutationTaster_Pred=.;LJB_MutationAssessor=.;LJB_MutationAssessor_Pred=.;LJB2_FATHMM=.;LJB2_GERP++=.;LJB2_PhyloP=.;LJB2_SiPhy=.;ALLELE_END	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2:.
diff --git a/test/view.filter.annovar.2.out b/test/view.filter.annovar.2.out
new file mode 100644
index 000000000..6ac94a101
--- /dev/null
+++ b/test/view.filter.annovar.2.out
@@ -0,0 +1 @@
+16	50745926	rs2066844	C	T	80	PASS	NS=3;DP=14;AF=0.5;DB;H2;ANNOVAR_DATE=2015-06-17;Func.refGene=exonic;Gene.refGene=NOD2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=NOD2:NM_001293557:exon3:c.C2023T:p.R675W,NOD2:NM_022162:exon4:c.C2104T:p.R702W;Func.ensGene=exonic;Gene.ensGene=ENSG00000167207;GeneDetail.ensGene=.;ExonicFunc.ensGene=nonsynonymous_SNV;AAChange.ensGene=ENSG00000167207:ENST00000300589:exon4:c.C2104T:p.R702W;esp6500si_ea=0.043488;esp6500si_all=0.031558;1000g2012apr_eur=0.05;1000g2012apr_all=0.02;snp138=rs2066844;LJB2_SIFT=0.010000;LJB2_PolyPhen2_HDIV=0.999;LJB2_PP2_HDIV_Pred=D;LJB2_PolyPhen2_HVAR=0.901;LJB2_PolyPhen2_HVAR_Pred=P;LJB2_LRT=0.993490;LJB2_LRT_Pred=N;LJB2_MutationTaster=0.291000;LJB2_MutationTaster_Pred=N;LJB_MutationAssessor=2.32;LJB_MutationAssessor_Pred=medium;LJB2_FATHMM=-0.5;LJB2_GERP++=3.66;LJB2_PhyloP=1.421000;LJB2_SiPhy=6.9139;ALLELE_END	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
diff --git a/test/view.filter.annovar.3.out b/test/view.filter.annovar.3.out
new file mode 100644
index 000000000..6ac94a101
--- /dev/null
+++ b/test/view.filter.annovar.3.out
@@ -0,0 +1 @@
+16	50745926	rs2066844	C	T	80	PASS	NS=3;DP=14;AF=0.5;DB;H2;ANNOVAR_DATE=2015-06-17;Func.refGene=exonic;Gene.refGene=NOD2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=NOD2:NM_001293557:exon3:c.C2023T:p.R675W,NOD2:NM_022162:exon4:c.C2104T:p.R702W;Func.ensGene=exonic;Gene.ensGene=ENSG00000167207;GeneDetail.ensGene=.;ExonicFunc.ensGene=nonsynonymous_SNV;AAChange.ensGene=ENSG00000167207:ENST00000300589:exon4:c.C2104T:p.R702W;esp6500si_ea=0.043488;esp6500si_all=0.031558;1000g2012apr_eur=0.05;1000g2012apr_all=0.02;snp138=rs2066844;LJB2_SIFT=0.010000;LJB2_PolyPhen2_HDIV=0.999;LJB2_PP2_HDIV_Pred=D;LJB2_PolyPhen2_HVAR=0.901;LJB2_PolyPhen2_HVAR_Pred=P;LJB2_LRT=0.993490;LJB2_LRT_Pred=N;LJB2_MutationTaster=0.291000;LJB2_MutationTaster_Pred=N;LJB_MutationAssessor=2.32;LJB_MutationAssessor_Pred=medium;LJB2_FATHMM=-0.5;LJB2_GERP++=3.66;LJB2_PhyloP=1.421000;LJB2_SiPhy=6.9139;ALLELE_END	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
diff --git a/test/view.filter.annovar.vcf b/test/view.filter.annovar.vcf
new file mode 100644
index 000000000..7613667ad
--- /dev/null
+++ b/test/view.filter.annovar.vcf
@@ -0,0 +1,52 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=myImputationProgramV3.1
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele">
+##INFO=<ID=Gene.refGene,Number=.,Type=String,Description="Gene.refGene annotation provided by ANNOVAR">
+##INFO=<ID=GeneDetail.refGene,Number=.,Type=String,Description="GeneDetail.refGene annotation provided by ANNOVAR">
+##INFO=<ID=ExonicFunc.refGene,Number=.,Type=String,Description="ExonicFunc.refGene annotation provided by ANNOVAR">
+##INFO=<ID=AAChange.refGene,Number=.,Type=String,Description="AAChange.refGene annotation provided by ANNOVAR">
+##INFO=<ID=Func.ensGene,Number=.,Type=String,Description="Func.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=Gene.ensGene,Number=.,Type=String,Description="Gene.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=GeneDetail.ensGene,Number=.,Type=String,Description="GeneDetail.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=ExonicFunc.ensGene,Number=.,Type=String,Description="ExonicFunc.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=AAChange.ensGene,Number=.,Type=String,Description="AAChange.ensGene annotation provided by ANNOVAR">
+##INFO=<ID=esp6500si_ea,Number=1,Type=Float,Description="esp6500si_ea annotation provided by ANNOVAR">
+##INFO=<ID=esp6500si_all,Number=1,Type=Float,Description="esp6500si_all annotation provided by ANNOVAR">
+##INFO=<ID=1000g2012apr_eur,Number=1,Type=Float,Description="1000g2012apr_eur annotation provided by ANNOVAR">
+##INFO=<ID=1000g2012apr_all,Number=1,Type=Float,Description="1000g2012apr_all annotation provided by ANNOVAR">
+##INFO=<ID=snp138,Number=.,Type=String,Description="snp138 annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_SIFT,Number=.,Type=String,Description="LJB2_SIFT annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PolyPhen2_HDIV,Number=.,Type=String,Description="LJB2_PolyPhen2_HDIV annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PP2_HDIV_Pred,Number=.,Type=String,Description="LJB2_PP2_HDIV_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PolyPhen2_HVAR,Number=.,Type=String,Description="LJB2_PolyPhen2_HVAR annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PolyPhen2_HVAR_Pred,Number=.,Type=String,Description="LJB2_PolyPhen2_HVAR_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_LRT,Number=.,Type=String,Description="LJB2_LRT annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_LRT_Pred,Number=.,Type=String,Description="LJB2_LRT_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_MutationTaster,Number=1,Type=String,Description="LJB2_MutationTaster annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_MutationTaster_Pred,Number=.,Type=String,Description="LJB2_MutationTaster_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB_MutationAssessor,Number=.,Type=String,Description="LJB_MutationAssessor annotation provided by ANNOVAR">
+##INFO=<ID=LJB_MutationAssessor_Pred,Number=1,Type=String,Description="LJB_MutationAssessor_Pred annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_FATHMM,Number=.,Type=String,Description="LJB2_FATHMM annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_GERP++,Number=.,Type=String,Description="LJB2_GERP++ annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_PhyloP,Number=.,Type=String,Description="LJB2_PhyloP annotation provided by ANNOVAR">
+##INFO=<ID=LJB2_SiPhy,Number=.,Type=String,Description="LJB2_SiPhy annotation provided by ANNOVAR">
+##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+16	50745926	rs2066844	C	T	80	PASS	NS=3;DP=14;AF=0.5;DB;H2;ANNOVAR_DATE=2015-06-17;Func.refGene=exonic;Gene.refGene=NOD2;GeneDetail.refGene=.;ExonicFunc.refGene=nonsynonymous_SNV;AAChange.refGene=NOD2:NM_001293557:exon3:c.C2023T:p.R675W,NOD2:NM_022162:exon4:c.C2104T:p.R702W;Func.ensGene=exonic;Gene.ensGene=ENSG00000167207;GeneDetail.ensGene=.;ExonicFunc.ensGene=nonsynonymous_SNV;AAChange.ensGene=ENSG00000167207:ENST00000300589:exon4:c.C2104T:p.R702W;esp6500si_ea=0.043488;esp6500si_all=0.031558;1000g2012apr_eur=0.05;1000g2012apr_all=0.02;snp138=rs2066844;LJB2_SIFT=0.010000;LJB2_PolyPhen2_HDIV=0.999;LJB2_PP2_HDIV_Pred=D;LJB2_PolyPhen2_HVAR=0.901;LJB2_PolyPhen2_HVAR_Pred=P;LJB2_LRT=0.993490;LJB2_LRT_Pred=N;LJB2_MutationTaster=0.291000;LJB2_MutationTaster_Pred=N;LJB_MutationAssessor=2.32;LJB_MutationAssessor_Pred=medium;LJB2_FATHMM=-0.5;LJB2_GERP++=3.66;LJB2_PhyloP=1.421000;LJB2_SiPhy=6.9139;ALLELE_END	GT:GQ:DP:HQ	0|0:48:1:51,51	1|0:48:8:51,51	1/1:43:5:.,.
+20	1230237	.	T	G	47	PASS	NS=3;DP=13;AA=T;ANNOVAR_DATE=2015-06-17;Func.refGene=intronic;Gene.refGene=RAD21L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.ensGene=intronic;Gene.ensGene=ENSG00000244588;GeneDetail.ensGene=.;ExonicFunc.ensGene=.;AAChange.ensGene=.;esp6500si_ea=.;esp6500si_all=.;1000g2012apr_eur=.;1000g2012apr_all=.;snp138=.;LJB2_SIFT=.;LJB2_PolyPhen2_HDIV=.;LJB2_PP2_HDIV_Pred=.;LJB2_PolyPhen2_HVAR=.;LJB2_PolyPhen2_HVAR_Pred=.;LJB2_LRT=.;LJB2_LRT_Pred=.;LJB2_MutationTaster=.;LJB2_MutationTaster_Pred=.;LJB_MutationAssessor=.;LJB_MutationAssessor_Pred=.;LJB2_FATHMM=.;LJB2_GERP++=.;LJB2_PhyloP=.;LJB2_SiPhy=.;ALLELE_END	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2
+20	1230288	.	T	.	50	PASS	NS=3;DP=13;AA=T;ANNOVAR_DATE=2015-06-17;Func.refGene=intronic;Gene.refGene=RAD21L1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;Func.ensGene=intronic;Gene.ensGene=ENSG00000244588;GeneDetail.ensGene=.;ExonicFunc.ensGene=.;AAChange.ensGene=.;esp6500si_ea=.;esp6500si_all=.;1000g2012apr_eur=.;1000g2012apr_all=.;snp138=.;LJB2_SIFT=.;LJB2_PolyPhen2_HDIV=.;LJB2_PP2_HDIV_Pred=.;LJB2_PolyPhen2_HVAR=.;LJB2_PolyPhen2_HVAR_Pred=.;LJB2_LRT=.;LJB2_LRT_Pred=.;LJB2_MutationTaster=.;LJB2_MutationTaster_Pred=.;LJB_MutationAssessor=.;LJB_MutationAssessor_Pred=.;LJB2_FATHMM=.;LJB2_GERP++=.;LJB2_PhyloP=.;LJB2_SiPhy=.;ALLELE_END	GT:GQ:DP:HQ	0|0:54:7:56,60	0|0:48:4:51,51	0/0:61:2

From aa6bc176a7abfbabb1d16b9b7aae06dd9445124c Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 22 Oct 2015 09:55:45 +0100
Subject: [PATCH 097/211] add test for consensus on empty vcf file

this is a test for #339 that was resolved in samtools/htslib@df3fcad84004434a9092c599aa0b1fe44c9e731a
---
 test/consensus.5.out | 20 ++++++++++++++++++++
 test/test.pl         |  1 +
 2 files changed, 21 insertions(+)
 create mode 100644 test/consensus.5.out

diff --git a/test/consensus.5.out b/test/consensus.5.out
new file mode 100644
index 000000000..4631ebee2
--- /dev/null
+++ b/test/consensus.5.out
@@ -0,0 +1,20 @@
+>1:2-501
+TACCATATGTGACATATAAAAAAGAACATAACCTACGTATCAACTAAAGTGGTTGTTTGC
+AGAAAAGGAAGACTTAAAAAGAGTCAGTACTAACCTACATAATATATACAATGTTCATTA
+AATAATAAAATGAGCTCATCATACTTAGGTCATCATAAATATATCTGAAATTCACAAATA
+TTGATCAAATGGTAAAATAGACAAGTAGATTTTAATAGGTTAAACAATTACTGATTCTCT
+TGAAAGAATAAATTTAATATGAGACCTATTTCATTATAATGAACTCACAAATTAGAAACT
+TCACACTGGGGGCTGGAGAGATGGCTCAGTAGTTAAGAACACTGACTGCTCTTCTGAAGG
+TCCTGAGTTCAAATCCCAGCAACCACATGGTGACTTACAACCATCTGTAATGACATCTGA
+TGCCCTCTGGTGTGTCTGAAGACAGCTACAGTGTACTTACATAAAATAATAAATAAATCT
+TTAAAAACAAAAAAAAAGAA
+>2
+GAAGATCTTTTCCTTATTAAGGATCTGAAGCTCTGTAGATTTGTATTCTATTAAACATGG
+AGAGATTAGTGATTTTCCATATTCTTTAAGTCATTTTAGAGTAATGTGTTCTTAAGATAA
+ATCAGAAAAACAAAAACTTGTGCTTTCCTGTTTGAAAAACAAACAGCTGTGGGGAATGGT
+GTCGGGACAGCCTTTTTATAAAATTTTTCTAAATAATGTTGAGGCTTTGATACGTCAAAG
+TTATATTTCAAATGGAATCACTTAGACCTCGTTTCTGAGTGTCAATGGCCATATTGGGGA
+TTTGCTGCTGCCAATGACAGCACACCCTGGGAATGCCCCAACTACTTACTACAAAGCAGT
+GTTACATGGAGAAGATCTTCAAGAGTCTTTTTGCTAGATCTTTCCTTGGCTTTTGATGTG
+ACTCCTCTCAATAAAATCCACAGTAATATAGTGAGTGGTCTCCTGCTCCAAACCAGTATT
+TCAGACACAGTTAATCCAGAC
diff --git a/test/test.pl b/test/test.pl
index c3819fd58..a845bf47b 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -221,6 +221,7 @@
 test_vcf_consensus_chain($opts,in=>'consensus',out=>'consensus.4.chain',chain=>'consensus.4.chain',fa=>'consensus.fa',args=>'-H 1');
 test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.1.out',fa=>'consensus2.fa',args=>'-H 1');
 test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.2.out',fa=>'consensus2.fa',args=>'-H 2');
+test_vcf_consensus($opts,in=>'empty',out=>'consensus.5.out',fa=>'consensus.fa',args=>'');
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};

From f6831b591a1abdfa09e28341041efd4e1862bad3 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 21 Oct 2015 14:05:49 +0100
Subject: [PATCH 098/211] norm: Expand round buffer if needed. Fixes #336

add test thanks to @wangyugui and @wkretzsch
---
 test/norm.split.2.out | 107 ++++++++++++++++++++++++++++++++++++++++++
 test/norm.split.2.vcf |  85 +++++++++++++++++++++++++++++++++
 test/test.pl          |   1 +
 vcfnorm.c             |   6 ++-
 4 files changed, 197 insertions(+), 2 deletions(-)
 create mode 100644 test/norm.split.2.out
 create mode 100644 test/norm.split.2.vcf

diff --git a/test/norm.split.2.out b/test/norm.split.2.out
new file mode 100644
index 000000000..52fcecde0
--- /dev/null
+++ b/test/norm.split.2.out
@@ -0,0 +1,107 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.2-216-gdffc67f-dirty+htslib-1.2.1-216-gd2ed7e6-dirty
+##reference=file:///usr/bio-ref/GRCh38.81/GRCh38.fa
+##contig=<ID=1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+1	789241	.	C	G	41.4503	.	.
+1	789262	.	G	A	36.0809	.	.
+1	789280	.	T	C	40.0265	.	.
+1	789334	.	A	T	67	.	.
+1	789348	.	T	A	44.5622	.	.
+1	789368	.	A	T	18.5381	.	.
+1	789369	.	C	T	30.0396	.	.
+1	789396	.	A	C	35.7056	.	.
+1	789402	.	G	T	35.0554	.	.
+1	789403	.	T	A	35.0681	.	.
+1	789417	.	T	G	35.0681	.	.
+1	789420	.	T	A	35.0681	.	.
+1	789429	.	A	C	39.1119	.	.
+1	789435	.	C	T	35.1179	.	.
+1	789481	.	G	A	94	.	.
+1	789489	.	C	A	89	.	.
+1	789491	.	C	G	100	.	.
+1	789568	.	TATGGAATGGAATGGAATGGAATG	TATGGAATGGAATGGAATG	295	.	.
+1	789631	.	G	A	3.18972	.	.
+1	789642	.	T	G	3.66362	.	.
+1	789660	.	C	T	35.0294	.	.
+1	789666	.	T	G	16.1313	.	.
+1	789673	.	A	T	52	.	.
+1	789675	.	T	G	20.7408	.	.
+1	789676	.	C	T	26.6621	.	.
+1	789680	.	A	T	21.5713	.	.
+1	789680	.	AGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATG	AGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATG	23.495	.	.
+1	789685	.	T	G	6.53871	.	.
+1	789690	.	T	G	16.2287	.	.
+1	789690	.	T	C	16.2287	.	.
+1	789691	.	G	T	21.8633	.	.
+1	789691	.	G	C	21.8633	.	.
+1	789692	.	G	A	31.8203	.	.
+1	789695	.	T	A	7.03922	.	.
+1	789696	.	G	A	64	.	.
+1	789696	.	G	T	64	.	.
+1	789696	.	G	C	64	.	.
+1	789697	.	G	A	116	.	.
+1	789700	.	T	A	27.3447	.	.
+1	789700	.	T	G	27.3447	.	.
+1	789704	.	A	C	12.9378	.	.
+1	789704	.	A	T	12.9378	.	.
+1	789704	.	A	G	12.9378	.	.
+1	789706	.	G	C	4.49441	.	.
+1	789706	.	G	A	4.49441	.	.
+1	789707	.	G	C	6.28796	.	.
+1	789707	.	G	A	6.28796	.	.
+1	789710	.	T	G	59	.	.
+1	789710	.	T	A	59	.	.
+1	789711	.	G	T	15.1544	.	.
+1	789713	.	A	C	6.69714	.	.
+1	789717	.	G	A	82	.	.
+1	789720	.	T	G	26.241	.	.
+1	789721	.	G	A	99	.	.
+1	789721	.	G	T	99	.	.
+1	789727	.	G	A	5.18898	.	.
+1	789727	.	G	C	5.18898	.	.
+1	789730	.	T	A	73	.	.
+1	789730	.	T	C	73	.	.
+1	789731	.	G	T	111	.	.
+1	789732	.	G	T	24.8095	.	.
+1	789735	.	T	G	61	.	.
+1	789737	.	G	T	69	.	.
+1	789737	.	G	A	69	.	.
+1	789739	.	A	T	48.5355	.	.
+1	789740	.	T	A	29.8166	.	.
+1	789747	.	A	G	187	.	.
+1	789747	.	A	C	187	.	.
+1	789747	.	A	T	187	.	.
+1	789749	.	C	G	19.1565	.	.
+1	789750	.	T	A	12.5086	.	.
+1	789750	.	T	C	12.5086	.	.
+1	789752	.	C	G	284	.	.
+1	789757	.	G	A	7.13117	.	.
+1	789765	.	T	A	191	.	.
+1	789767	.	G	A	16.2222	.	.
+1	789769	.	C	T	17.4827	.	.
+1	789770	.	T	G	64	.	.
+1	789770	.	T	A	64	.	.
+1	789772	.	G	A	31.6793	.	.
+1	789772	.	G	C	31.6793	.	.
+1	789775	.	T	A	125	.	.
+1	789775	.	T	G	125	.	.
+1	789776	.	A	G	151	.	.
+1	789777	.	G	C	22.9639	.	.
+1	789781	.	G	A	89	.	.
+1	789795	.	A	T	11.555	.	.
+1	789816	.	G	A	29.3537	.	.
+1	789957	.	C	G	19.4796	.	.
+1	790009	.	C	T	55	.	.
+1	790136	.	A	G	85	.	.
+1	790156	.	G	A	19.4198	.	.
+1	790176	.	A	G	86	.	.
+1	790179	.	C	T	4.20807	.	.
+1	790181	.	C	T	12.5149	.	.
+1	790186	.	G	A	86	.	.
+1	790189	.	T	A	76	.	.
+1	790202	.	G	A	86	.	.
+1	790202	.	G	C	86	.	.
+1	790206	.	C	A	18.4041	.	.
+1	790206	.	C	T	18.4041	.	.
diff --git a/test/norm.split.2.vcf b/test/norm.split.2.vcf
new file mode 100644
index 000000000..b8147fc8e
--- /dev/null
+++ b/test/norm.split.2.vcf
@@ -0,0 +1,85 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.2-216-gdffc67f-dirty+htslib-1.2.1-216-gd2ed7e6-dirty
+##reference=file:///usr/bio-ref/GRCh38.81/GRCh38.fa
+##contig=<ID=1,length=248956422>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER
+1	789241	.	C	G	41.4503	.
+1	789262	.	G	A	36.0809	.
+1	789280	.	T	C	40.0265	.
+1	789334	.	A	T	67	.
+1	789348	.	T	A	44.5622	.
+1	789368	.	A	T	18.5381	.
+1	789369	.	C	T	30.0396	.
+1	789396	.	A	C	35.7056	.
+1	789402	.	G	T	35.0554	.
+1	789403	.	T	A	35.0681	.
+1	789417	.	T	G	35.0681	.
+1	789420	.	T	A	35.0681	.
+1	789429	.	A	C	39.1119	.
+1	789435	.	C	T	35.1179	.
+1	789481	.	G	A	94	.
+1	789489	.	C	A	89	.
+1	789491	.	C	G	100	.
+1	789568	.	TATGGAATGGAATGGAATGGAATG	TATGGAATGGAATGGAATG	295	.
+1	789631	.	G	A	3.18972	.
+1	789642	.	T	G	3.66362	.
+1	789660	.	C	T	35.0294	.
+1	789666	.	T	G	16.1313	.
+1	789673	.	A	T	52	.
+1	789675	.	T	G	20.7408	.
+1	789676	.	C	T	26.6621	.
+1	789680	.	A	T	21.5713	.
+1	789680	.	AGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATG	AGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAATG	23.495	.
+1	789685	.	T	G	6.53871	.
+1	789690	.	T	G,C	16.2287	.
+1	789691	.	G	T,C	21.8633	.
+1	789692	.	G	A	31.8203	.
+1	789695	.	T	A	7.03922	.
+1	789696	.	G	A,T,C	64	.
+1	789697	.	G	A	116	.
+1	789700	.	T	A,G	27.3447	.
+1	789704	.	A	C,T,G	12.9378	.
+1	789706	.	G	C,A	4.49441	.
+1	789707	.	G	C,A	6.28796	.
+1	789710	.	T	G,A	59	.
+1	789711	.	G	T	15.1544	.
+1	789713	.	A	C	6.69714	.
+1	789717	.	G	A	82	.
+1	789720	.	T	G	26.241	.
+1	789721	.	G	A,T	99	.
+1	789727	.	G	A,C	5.18898	.
+1	789730	.	T	A,C	73	.
+1	789731	.	G	T	111	.
+1	789732	.	G	T	24.8095	.
+1	789735	.	T	G	61	.
+1	789737	.	G	T,A	69	.
+1	789739	.	A	T	48.5355	.
+1	789740	.	T	A	29.8166	.
+1	789747	.	A	G,C,T	187	.
+1	789749	.	C	G	19.1565	.
+1	789750	.	T	A,C	12.5086	.
+1	789752	.	C	G	284	.
+1	789757	.	G	A	7.13117	.
+1	789765	.	T	A	191	.
+1	789767	.	G	A	16.2222	.
+1	789769	.	C	T	17.4827	.
+1	789770	.	T	G,A	64	.
+1	789772	.	G	A,C	31.6793	.
+1	789775	.	T	A,G	125	.
+1	789776	.	A	G	151	.
+1	789777	.	G	C	22.9639	.
+1	789781	.	G	A	89	.
+1	789795	.	A	T	11.555	.
+1	789816	.	G	A	29.3537	.
+1	789957	.	C	G	19.4796	.
+1	790009	.	C	T	55	.
+1	790136	.	A	G	85	.
+1	790156	.	G	A	19.4198	.
+1	790176	.	A	G	86	.
+1	790179	.	C	T	4.20807	.
+1	790181	.	C	T	12.5149	.
+1	790186	.	G	A	86	.
+1	790189	.	T	A	76	.
+1	790202	.	G	A,C	86	.
+1	790206	.	C	A,T	18.4041	.
\ No newline at end of file
diff --git a/test/test.pl b/test/test.pl
index a845bf47b..2c56e0aea 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -92,6 +92,7 @@
 test_vcf_query($opts,in=>'annotate2',out=>'query.21.out',args=>q[-e'IFLT="."'  -f'%POS %IFLT\\n']);
 test_vcf_norm($opts,in=>'norm',out=>'norm.out',fai=>'norm');
 test_vcf_norm($opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
+test_vcf_norm($opts,in=>'norm.split.2',out=>'norm.split.2.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.split',fai=>'norm',out=>'norm.split.and.norm.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.out',args=>'-m+');
 test_vcf_norm($opts,in=>'norm.merge.2',out=>'norm.merge.2.out',args=>'-m+');
diff --git a/vcfnorm.c b/vcfnorm.c
index 9135430f5..9bffddbb3 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -75,7 +75,7 @@ typedef struct
     struct { int tot, set, swap; } nref;
     char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets;
     int argc, rmdup, output_type, check_ref, strict_filter, do_indels;
-    int nchanged, nskipped, ntotal, mrows_op, mrows_collapse, parsimonious;
+    int nchanged, nskipped, nsplit, ntotal, mrows_op, mrows_collapse, parsimonious;
 }
 args_t;
 
@@ -1564,6 +1564,7 @@ static void normalize_line(args_t *args, bcf1_t **line_ptr)
     }
 
     // insert into sorted buffer
+    rbuf_expand0(&args->rbuf,bcf1_t*,args->rbuf.n+1,args->lines);
     int i,j;
     i = j = rbuf_append(&args->rbuf);
     if ( !args->lines[i] ) args->lines[i] = bcf_init1();
@@ -1620,6 +1621,7 @@ static void normalize_vcf(args_t *args)
             }
             if ( split && line->n_allele>2 )
             {
+                args->nsplit++;
                 split_multiallelic_to_biallelics(args, line);
                 for (j=0; j<args->ntmp_lines; j++)
                     normalize_line(args, &args->tmp_lines[j]);
@@ -1644,7 +1646,7 @@ static void normalize_vcf(args_t *args)
     flush_buffer(args, out, args->rbuf.n);
     hts_close(out);
 
-    fprintf(stderr,"Lines   total/modified/skipped:\t%d/%d/%d\n", args->ntotal,args->nchanged,args->nskipped);
+    fprintf(stderr,"Lines   total/split/realigned/skipped:\t%d/%d/%d/%d\n", args->ntotal,args->nsplit,args->nchanged,args->nskipped);
     if ( args->check_ref & CHECK_REF_FIX )
         fprintf(stderr,"REF/ALT total/modified/added:  \t%d/%d/%d\n", args->nref.tot,args->nref.swap,args->nref.set);
 }

From 983067a2646d82baeb4f869e8014f6ca63fd477e Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 6 Oct 2015 09:42:34 +0100
Subject: [PATCH 099/211] cnv: New -k option, fixed non-functional parsing of
 -dfloat,float

---
 main.c   |  2 +-
 vcfcnv.c | 56 +++++++++++++++++++++++++++++++++++++++-----------------
 2 files changed, 40 insertions(+), 18 deletions(-)

diff --git a/main.c b/main.c
index 599503323..f08b5c7e1 100644
--- a/main.c
+++ b/main.c
@@ -138,7 +138,7 @@ static cmd_t cmds[] =
     },
     { .func  = main_vcfcnv,
       .alias = "cnv",
-      .help  = "-HMM CNV calling"    // do not advertise yet
+      .help  = "HMM CNV calling"
     },
     { .func  = main_vcffilter,
       .alias = "filter",
diff --git a/vcfcnv.c b/vcfcnv.c
index a9dfb7fb0..c286d4744 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -61,7 +61,7 @@ typedef struct
 {
     char *name;
     int idx;    // VCF sample index
-    float *lrr,*baf, baf_dev2, baf_dev2_dflt;
+    float *lrr,*baf, baf_dev2, baf_dev2_dflt, lrr_dev2;
     float cell_frac, cell_frac_dflt;
     gauss_param_t gauss_param[18];
     double pobs[N_STATES];
@@ -78,7 +78,6 @@ typedef struct _args_t
     sample_t query_sample, control_sample;
 
     int nstates;    // number of states: N_STATES for one sample, N_STATES^2 for two samples
-    double lrr_dev2;                        // squared std dev of LRR distribution
     double lrr_bias, baf_bias;              // LRR/BAF weights
     double same_prob, ij_prob;              // prior of both samples being the same and the transition probability P(i|j)
     double err_prob;                        // constant probability of erroneous measurement
@@ -608,7 +607,7 @@ static inline double norm_prob(double baf, gauss_param_t *param)
 static int set_observed_prob(args_t *args, sample_t *smpl, int isite)
 {
     float baf = smpl->baf[isite];
-    float lrr = smpl->lrr[isite];
+    float lrr = args->lrr_bias>0 ? smpl->lrr[isite] : 0;
 
     float fRR = args->fRR;
     float fRA = args->fRA;
@@ -645,9 +644,9 @@ static int set_observed_prob(args_t *args, sample_t *smpl, int isite)
     if ( args->verbose ) fprintf(stderr,"%f\t%f %f %f\n", baf,cn1_baf,cn2_baf,cn3_baf);
     #endif
 
-    double cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/args->lrr_dev2);
-    double cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/args->lrr_dev2);
-    double cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/args->lrr_dev2);
+    double cn1_lrr = exp(-(lrr + 0.45)*(lrr + 0.45)/smpl->lrr_dev2);
+    double cn2_lrr = exp(-(lrr - 0.00)*(lrr - 0.00)/smpl->lrr_dev2);
+    double cn3_lrr = exp(-(lrr - 0.30)*(lrr - 0.30)/smpl->lrr_dev2);
 
     smpl->pobs[CN0] = 0;
     smpl->pobs[CN1] = args->err_prob + (1 - args->baf_bias + args->baf_bias*cn1_baf)*(1 - args->lrr_bias + args->lrr_bias*cn1_lrr);
@@ -915,8 +914,11 @@ static void cnv_flush_viterbi(args_t *args)
     hmm_set_tprob(args->hmm, args->tprob, 10000);
 
     // Smooth LRR values to reduce noise
-    smooth_data(args->query_sample.lrr,args->nsites, args->lrr_smooth_win);
-    if ( args->control_sample.name ) smooth_data(args->control_sample.lrr,args->nsites, args->lrr_smooth_win);
+    if ( args->lrr_bias > 0 )
+    {
+        smooth_data(args->query_sample.lrr,args->nsites, args->lrr_smooth_win);
+        if ( args->control_sample.name ) smooth_data(args->control_sample.lrr,args->nsites, args->lrr_smooth_win);
+    }
 
     // Set the BAF peak likelihoods, such as P(RRR|CN3), taking account the
     // estimated fraction of aberrant cells in the mixture. With the new chromosome,
@@ -1063,8 +1065,13 @@ static int parse_lrr_baf(sample_t *smpl, bcf_fmt_t *baf_fmt, bcf_fmt_t *lrr_fmt,
     *baf = ((float*)(baf_fmt->p + baf_fmt->size*smpl->idx))[0];
     if ( bcf_float_is_missing(*baf) || isnan(*baf) ) *baf = -0.1;    // arbitrary negative value == missing value
 
-    *lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0];
-    if ( bcf_float_is_missing(*lrr) || isnan(*lrr) ) { *lrr = 0; *baf = -0.1; }
+    if ( lrr_fmt )
+    {
+        *lrr = ((float*)(lrr_fmt->p + lrr_fmt->size*smpl->idx))[0];
+        if ( bcf_float_is_missing(*lrr) || isnan(*lrr) ) { *lrr = 0; *baf = -0.1; }
+    }
+    else
+        *lrr = 0;
 
     return *baf<0 ? 0 : 1;
 }
@@ -1092,9 +1099,9 @@ static void cnv_next_line(args_t *args, bcf1_t *line)
     // Process line
     args->ntot++;
 
-    bcf_fmt_t *baf_fmt, *lrr_fmt;
+    bcf_fmt_t *baf_fmt, *lrr_fmt = NULL;
     if ( !(baf_fmt = bcf_get_fmt(args->hdr, line, "BAF")) ) return; 
-    if ( !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return;
+    if ( args->lrr_bias>0 && !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return;
 
     float baf1,lrr1,baf2,lrr2;
     int ret = 0;
@@ -1168,6 +1175,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -b, --BAF-weight <float>           relative contribution from BAF [1]\n");
     fprintf(stderr, "    -d, --BAF-dev <float[,float]>      expected BAF deviation in query and control [0.04,0.04]\n"); // experimental
     fprintf(stderr, "    -e, --err-prob <float>             uniform error probability [1e-4]\n");
+    fprintf(stderr, "    -k, --LRR-dev <float[,float]>      expected LRR deviation [0.2,0.2]\n"); // experimental
     fprintf(stderr, "    -l, --LRR-weight <float>           relative contribution from LRR [0.2]\n");
     fprintf(stderr, "    -L, --LRR-smooth-win <int>         window of LRR moving average smoothing [10]\n");
     fprintf(stderr, "    -O, --optimize <float>             estimate fraction of aberrant cells down to <float> [1.0]\n");
@@ -1201,12 +1209,13 @@ int main_vcfcnv(int argc, char *argv[])
 
     // Squared std dev of BAF and LRR values (gaussian noise), estimated from real data (hets, one sample, one chr)
     args->query_sample.baf_dev2_dflt = args->control_sample.baf_dev2_dflt = 0.04*0.04; // illumina: 0.03
-    args->lrr_dev2 = 0.1*0.1; //0.20*0.20;   // illumina: 0.18
+    args->query_sample.lrr_dev2 = args->control_sample.lrr_dev2 = 0.2*0.2; //0.20*0.20;   // illumina: 0.18
 
     int regions_is_file = 0, targets_is_file = 0;
     static struct option loptions[] = 
     {
         {"BAF-dev",1,0,'d'},
+        {"LRR-dev",1,0,'k'},
         {"LRR-smooth-win",1,0,'L'},
         {"AF-file",1,0,'f'},
         {"baum-welch",1,0,'W'}, // hidden
@@ -1228,7 +1237,7 @@ int main_vcfcnv(int argc, char *argv[])
         {0,0,0,0}
     };
     char *tmp = NULL;
-    while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W:f:a:L:d:",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "h?r:R:t:T:s:o:p:l:T:c:b:P:x:e:O:W:f:a:L:d:k:",loptions,NULL)) >= 0) {
         switch (c) {
             case 'L': 
                 args->lrr_smooth_win = strtol(optarg,&tmp,10);
@@ -1244,20 +1253,33 @@ int main_vcfcnv(int argc, char *argv[])
                 if ( *tmp )
                 {
                     if ( *tmp!=',') error("Could not parse: -d %s\n", optarg);
-                    args->control_sample.baf_dev2_dflt = strtod(optarg,&tmp);
-                    if ( *tmp ) error("Could not parse: -a %s\n", optarg);
+                    args->control_sample.baf_dev2_dflt = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -d %s\n", optarg);
                 }
                 else
                     args->control_sample.baf_dev2_dflt = args->query_sample.baf_dev2_dflt;
                 args->query_sample.baf_dev2_dflt   *= args->query_sample.baf_dev2_dflt;
                 args->control_sample.baf_dev2_dflt *= args->control_sample.baf_dev2_dflt;
                 break;
+            case 'k':
+                args->query_sample.lrr_dev2 = strtod(optarg,&tmp);
+                if ( *tmp )
+                {
+                    if ( *tmp!=',') error("Could not parse: -k %s\n", optarg);
+                    args->control_sample.lrr_dev2 = strtod(tmp+1,&tmp);
+                    if ( *tmp ) error("Could not parse: -d %s\n", optarg);
+                }
+                else
+                    args->control_sample.lrr_dev2 = args->query_sample.lrr_dev2;
+                args->query_sample.lrr_dev2   *= args->query_sample.lrr_dev2;
+                args->control_sample.lrr_dev2 *= args->control_sample.lrr_dev2;
+                break;
             case 'a':
                 args->query_sample.cell_frac_dflt = strtod(optarg,&tmp);
                 if ( *tmp )
                 {
                     if ( *tmp!=',') error("Could not parse: -a %s\n", optarg);
-                    args->control_sample.cell_frac_dflt = strtod(optarg,&tmp);
+                    args->control_sample.cell_frac_dflt = strtod(tmp+1,&tmp);
                     if ( *tmp ) error("Could not parse: -a %s\n", optarg);
                 }
                 break;

From 2fc54de889a241372f26ff41ee7b58989484ab6f Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 9 Oct 2015 08:29:01 +0100
Subject: [PATCH 100/211] CNV output include number of sites/hets in regions

---
 vcfcnv.c | 40 +++++++++++++++++++++++++++++++---------
 1 file changed, 31 insertions(+), 9 deletions(-)

diff --git a/vcfcnv.c b/vcfcnv.c
index c286d4744..5fbdf2a6b 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -216,7 +216,7 @@ static void init_sample_files(sample_t *smpl, char *dir)
     smpl->summary_fh = open_file(&smpl->summary_fname,"w","%s/summary.%s.tab",dir,smpl->name);
     fprintf(smpl->dat_fh,"# [1]Chromosome\t[2]Position\t[3]BAF\t[4]LRR\n");
     fprintf(smpl->cn_fh,"# [1]Chromosome\t[2]Position\t[3]CN\t[4]P(CN0)\t[5]P(CN1)\t[6]P(CN2)\t[7]P(CN3)\n");
-    fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\n");
+    fprintf(smpl->summary_fh,"# RG, Regions [2]Chromosome\t[3]Start\t[4]End\t[5]Copy Number state\t[6]Quality\t[7]nSites\t[8]nHETs\n");
 }
 static void close_sample_files(sample_t *smpl)
 {
@@ -286,12 +286,13 @@ static void init_data(args_t *args)
     for (i=1; i<args->argc; i++) fprintf(fh, " %s",args->argv[i]);
     if ( args->control_sample.name )
         fprintf(fh, "\n#\n"
-                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Copy number:%s\t[7]Quality\n",
+                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Copy number:%s\t[7]Quality"
+                "\t[8]nSites in (5)\t[9]nHETs in (5)\t[10]nSites in (6)\t[11]nHETs in(6)\n",
                 args->query_sample.name,args->control_sample.name
                );
     else
         fprintf(fh, "\n#\n"
-                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\n",
+                "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\t[7]nSites\t[8]nHETs\n",
                 args->query_sample.name
                );
 }
@@ -903,6 +904,9 @@ static int update_args(args_t *args)
     return converged ? 0 : 1;
 }
 
+// for an approximate estimate of the number of het genotypes in a region
+#define BAF_LIKELY_HET(val)   (val)>0.25 && (val)<0.75
+
 static void cnv_flush_viterbi(args_t *args)
 {
     if ( !args->nsites ) return;
@@ -995,6 +999,7 @@ static void cnv_flush_viterbi(args_t *args)
     uint8_t *vpath = hmm_get_viterbi_path(hmm);
     double qual = 0, *fwd = hmm_get_fwd_bwd_prob(hmm);
     int i,j, isite, start_cn = vpath[0], start_pos = args->sites[0], istart_pos = 0;
+    int ctrl_ntot = 0, smpl_ntot = 0, ctrl_nhet = 0, smpl_nhet = 0;
     for (isite=0; isite<args->nsites; isite++)
     {
         int state = vpath[args->nstates*isite];
@@ -1016,6 +1021,11 @@ static void cnv_flush_viterbi(args_t *args)
                     fprintf(args->query_sample.cn_fh, "\t%f", sum);
                 }
             fprintf(args->query_sample.cn_fh, "\n");
+            if ( args->query_sample.baf[isite]>=0 )     // if non-missing
+            {
+                if ( BAF_LIKELY_HET(args->query_sample.baf[isite]) ) smpl_nhet++;
+                smpl_ntot++;
+            }
         }
         if ( args->control_sample.cn_fh )
         {
@@ -1027,36 +1037,48 @@ static void cnv_flush_viterbi(args_t *args)
                 fprintf(args->control_sample.cn_fh, "\t%f", sum);
             }
             fprintf(args->control_sample.cn_fh, "\n");
+            if ( args->control_sample.baf[isite]>=0 )     // if non-missing
+            {
+                if ( BAF_LIKELY_HET(args->control_sample.baf[isite]) ) ctrl_nhet++;
+                ctrl_ntot++;
+            }
         }
 
         if ( start_cn != state )
         {
             char start_cn_query = copy_number_state(args,start_cn,0);
             qual = phred_score(1 - qual/(isite - istart_pos));
-            fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,qual);
+            fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+                bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,qual,smpl_ntot,smpl_nhet);
 
             if ( args->control_sample.name )
             {
                 // regions 0-based, half-open
                 char start_cn_ctrl = copy_number_state(args,start_cn,1);
-                fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_ctrl,qual);
-                fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,start_cn_ctrl,qual);
+                fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet);
+                fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite],start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet);
             }
 
             istart_pos = isite;
             start_pos = args->sites[isite];
             start_cn = state;
             qual = 0;
+            smpl_ntot = smpl_nhet = ctrl_ntot = ctrl_nhet = 0;
         }
     }
     qual = phred_score(1 - qual/(isite - istart_pos));
     char start_cn_query = copy_number_state(args,start_cn,0);
-    fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,qual);
+    fprintf(args->query_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+        bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,qual,smpl_ntot,smpl_nhet);
     if ( args->control_sample.name )
     {
         char start_cn_ctrl = copy_number_state(args,start_cn,1);
-        fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_ctrl,qual);
-        fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\n",bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,start_cn_ctrl,qual);
+        fprintf(args->control_sample.summary_fh,"RG\t%s\t%d\t%d\t%c\t%.1f\t%d\t%d\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_ctrl,qual,ctrl_ntot,ctrl_nhet);
+        fprintf(args->summary_fh,"RG\t%s\t%d\t%d\t%c\t%c\t%.1f\t%d\t%d\t%d\t%d\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid), start_pos+1, args->sites[isite-1]+1,start_cn_query,start_cn_ctrl,qual,smpl_ntot,smpl_nhet,ctrl_ntot,ctrl_nhet);
     }
 }
 

From e325cd0e46d3219bf556e0392c83bde8e7ffa1ef Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 21 Oct 2015 09:51:39 +0100
Subject: [PATCH 101/211] Reduce memory consumption in cnv plotting script

---
 vcfcnv.c | 47 ++++++++++++++++++++++-------------------------
 1 file changed, 22 insertions(+), 25 deletions(-)

diff --git a/vcfcnv.c b/vcfcnv.c
index 5fbdf2a6b..e4b9372c9 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -433,24 +433,21 @@ static void create_plots(args_t *args)
             "else:\n"
             "   plot_chroms = chroms_to_plot(args.plot_threshold)\n"
             "\n"
-            "def read_dat(file,dat):\n"
+            "def read_dat(file,dat,plot_chr):\n"
             "   with open(file, 'rb') as f:\n"
             "       reader = csv.reader(f, 'tab')\n"
             "       for row in reader:\n"
             "           chr = row[0]\n"
-            "           if chr[0]=='#': continue\n"
-            "           if chr not in plot_chroms: continue\n"
-            "           if chr not in dat: dat[chr] = []\n"
-            "           dat[chr].append([row[1], float(row[2]), float(row[3])])\n"
-            "def read_cnv(file,cnv):\n"
+            "           if chr != plot_chr: continue\n"
+            "           dat.append([row[1], float(row[2]), float(row[3])])\n"
+            "def read_cnv(file,cnv,plot_chr):\n"
             "   with open(file, 'rb') as f:\n"
             "       reader = csv.reader(f, 'tab')\n"
             "       for row in reader:\n"
             "           chr = row[0]\n"
-            "           if chr[0]=='#': continue\n"
-            "           if chr not in cnv: cnv[chr] = []\n"
+            "           if chr != plot_chr: continue\n"
             "           row[2] = int(row[2]) + 0.5\n"
-            "           cnv[chr].append(row[1:])\n"
+            "           cnv.append(row[1:])\n"
             "def find_diffs(a,b):\n"
             "    out = []\n"
             "    diff = []\n"
@@ -465,20 +462,20 @@ static void create_plots(args_t *args)
             "    if len(diff): out.append(diff)\n"
             "    return out\n"
             "\n"
-            "control_dat = {}\n"
-            "control_cnv = {}\n"
-            "query_dat   = {}\n"
-            "query_cnv   = {}\n"
-            "read_dat('%s',control_dat)\n"
-            "read_dat('%s',query_dat)\n"
-            "read_cnv('%s',control_cnv)\n"
-            "read_cnv('%s',query_cnv)\n"
+            "for chr in sorted(plot_chroms.keys()):\n"
+            "    control_dat = []\n"
+            "    control_cnv = []\n"
+            "    query_dat   = []\n"
+            "    query_cnv   = []\n"
+            "    read_dat('%s',control_dat,chr)\n"
+            "    read_dat('%s',query_dat,chr)\n"
+            "    read_cnv('%s',control_cnv,chr)\n"
+            "    read_cnv('%s',query_cnv,chr)\n"
             "\n"
-            "for chr in query_dat:\n"
             "    fig,(ax1,ax2,ax3,ax4,ax5,ax6) = plt.subplots(6,1,figsize=(10,8),sharex=True)\n"
-            "    ax1.plot([x[0] for x in control_dat[chr]],[x[2] for x in control_dat[chr]], '.', ms=3,color='red')\n"
-            "    ax2.plot([x[0] for x in control_dat[chr]],[x[1] for x in control_dat[chr]], '.', ms=3,color='red')\n"
-            "    cn_dat = control_cnv[chr]\n"
+            "    ax1.plot([x[0] for x in control_dat],[x[2] for x in control_dat], '.', ms=3,color='red')\n"
+            "    ax2.plot([x[0] for x in control_dat],[x[1] for x in control_dat], '.', ms=3,color='red')\n"
+            "    cn_dat = control_cnv\n"
             "    xgrid = [float(x[0]) for x in cn_dat]\n"
             "    ygrid = np.linspace(0,5,6)\n"
             "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
@@ -492,9 +489,9 @@ static void create_plots(args_t *args)
             "    mesh.set_clim(vmin=-1,vmax=1)\n"
             "    ax3.plot([x[0] for x in cn_dat],[x[1] for x in cn_dat],'-',ms=3,color='black',lw=1.7)\n"
             "\n"
-            "    ax6.plot([x[0] for x in query_dat[chr]],[x[2] for x in query_dat[chr]], '.', ms=3)\n"
-            "    ax5.plot([x[0] for x in query_dat[chr]],[x[1] for x in query_dat[chr]], '.', ms=3)\n"
-            "    cn_dat = query_cnv[chr]\n"
+            "    ax6.plot([x[0] for x in query_dat],[x[2] for x in query_dat], '.', ms=3)\n"
+            "    ax5.plot([x[0] for x in query_dat],[x[1] for x in query_dat], '.', ms=3)\n"
+            "    cn_dat = query_cnv\n"
             "    xgrid = [float(x[0]) for x in cn_dat]\n"
             "    ygrid = np.linspace(0,5,6)\n"
             "    xgrid, ygrid = np.meshgrid(xgrid, ygrid)\n"
@@ -510,7 +507,7 @@ static void create_plots(args_t *args)
             "    ax3.annotate(control_sample, xy=(0.02,0.1), xycoords='axes fraction', color='red',fontsize=12, va='bottom',ha='left')\n"
             "    ax4.annotate(query_sample, xy=(0.02,0.9), xycoords='axes fraction', color='blue',fontsize=12, va='top',ha='left')\n"
             "\n"
-            "    diffs = find_diffs(control_cnv[chr],query_cnv[chr])\n"
+            "    diffs = find_diffs(control_cnv,query_cnv)\n"
             "    for diff in diffs:\n"
             "        ax3.plot([x[0] for x in diff],[x[1] for x in diff],'-',ms=3,color='blue',lw=1.7)\n"
             "        ax4.plot([x[0] for x in diff],[x[2] for x in diff],'-',ms=3,color='red',lw=1.7)\n"

From 3c4ddc79d6c8c5d99d5ef02c8d6d747692ef7fe9 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 22 Oct 2015 10:10:28 +0100
Subject: [PATCH 102/211] Added cnv and polysomy commands to the docs

---
 doc/bcftools.txt | 148 +++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 148 insertions(+)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index f485507f6..5fa963b1b 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -75,6 +75,7 @@ list of available options, run *bcftools* 'COMMAND' without arguments.
 
 - *<<annotate,annotate>>*   .. edit VCF files, add or remove annotations
 - *<<call,call>>*        ..  SNP/indel calling (former "view")
+- *<<cnv,cnv>>*          ..  Copy Number Variation caller
 - *<<concat,concat>>*    ..  concatenate VCF/BCF files from the same set of samples
 - *<<consensus,consensus>>*    ..  create consensus sequence by applying VCF variants
 - *<<convert,convert>>*  ..  convert VCF/BCF to other formats and back
@@ -85,6 +86,7 @@ list of available options, run *bcftools* 'COMMAND' without arguments.
 - *<<merge,merge>>*      ..  merge VCF/BCF files files from non-overlapping sample sets
 - *<<norm,norm>>*        ..  normalize indels
 - *<<plugin,plugin>>*    ..  run user-defined plugin
+- *<<polysomy,polysomy>>*   ..  detect contaminations and whole-chromosome aberrations
 - *<<query,query>>*      ..  transform VCF/BCF into user-defined formats
 - *<<reheader,reheader>>*   ..  modify VCF/BCF header, change sample names
 - *<<roh,roh>>*          ..  identify runs of homo/auto-zygosity
@@ -380,6 +382,91 @@ This command allows to add or remove annotations.
     bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf
 ----
 
+[[cnv]]
+=== bcftools cnv '[OPTIONS]' 'FILE'
+
+Copy number variation caller, requires a VCF annotated with the Illumina's
+B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
+considers the following copy number states: CN 2 (normal), 1 (single-copy
+loss), 0 (complete loss), 3 (single-copy gain).
+
+
+==== General Options:
+
+*-c, --control-sample* 'string'::
+    optional control sample name. If given, pairwise calling is performed
+    and the *-P*  option can be used
+
+*-f, --AF-file* 'file'::
+    read allele frequencies from  a tab-delimited file with the columns CHR,POS,REF,ALT,AF
+
+*-o, --output-dir 'path'::
+    output directory 
+
+*-p, --plot-threshold 'float'::
+    call *matplotlib* to produce plots for chromosomes with quality at least 'float',
+    useful for visual inspection of the calls. With *-p 0*, plots for all chromosomes will be 
+    generated. If not given, a *matplotlib* script will be created but not called.
+
+*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
+    see *<<common_options,Common Options>>*
+
+*-R, --regions-file* 'file'::
+    see *<<common_options,Common Options>>*
+
+*-s, --query-sample* 'string'::
+    query samply name
+
+*-t, --targets* 'LIST'::
+    see *<<common_options,Common Options>>*
+
+*-T, --targets-file* 'FILE'::
+    see *<<common_options,Common Options>>*
+
+==== HMM Options:
+
+*-a, --aberrant* 'float'[,'float']::
+    fraction of aberrant cells in query and control. The hallmark of
+    duplications and contaminations is the BAF value of heterozygous markers
+    which is dependent on the fraction of aberrant cells. Sensitivity to
+    smaller fractions of cells can be increased by setting *-a* to a lower value. Note
+    however, that this comes at the cost of increased false discovery rate.
+
+*-b, --BAF-weight* 'float'::
+    relative contribution from BAF
+
+*d, --BAF-dev* 'float'[,'float']::
+    expected BAF deviation in query and control, i.e. the noise observed
+    in the data.
+
+*-e, --err-prob* 'float'::
+    uniform error probability
+
+*-l, --LRR-weight* 'float'::
+    relative contribution from LRR. With noisy data, this option can have big effect
+    on the number of calls produced. In truly random noise (such as in simulated data),
+    the value should be set high (1.0), but in the presence of systematic noise
+    when LRR are not informative, lower values result in cleaner calls (0.2).
+
+*-L, --LRR-smooth-win* 'int'::
+    reduce LRR noise by applying moving average given this window size
+
+*-O, --optimize* 'float'::
+    iteratively estimate the fraction of aberrant cells, down to the given fraction.
+    Lowering this value from the default 1.0 to say, 0.3, can help discover more
+    events but also increases noise
+
+*-P, --same-prob* 'float'::
+    the prior probability of the query and the control sample being the same.
+    Setting to 0 calls both independently, setting to 1 forces the same copy
+    number state in both.
+
+*-x, --xy-prob* 'float'::
+    the HMM probability of transition to another copy number state. Increasing this
+    values leads to smaller and more frequent calls.
+
+
+
 
 [[call]]
 === bcftools call '[OPTIONS]' 'FILE'
@@ -1290,6 +1377,67 @@ void destroy(void);
 ----
 
 
+
+[[polysomy]]
+=== bcftools polysomy ['OPTIONS'] 'file.vcf.gz'
+Detect number of chromosomal copies in VCFs annotates with the Illumina's
+B-allele frequency (BAF) values. Note that this command is not compiled
+in by default, see the section *Optional Compilation with GSL* in the INSTALL 
+file for help.
+
+==== General options:
+
+*-o, --output-dir* 'path'::
+    output directory 
+
+*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
+    see *<<common_options,Common Options>>*
+
+*-R, --regions-file* 'file'::
+    see *<<common_options,Common Options>>*
+
+*-s, --sample* 'string'::
+    samply name
+
+*-t, --targets* 'LIST'::
+    see *<<common_options,Common Options>>*
+
+*-T, --targets-file* 'FILE'::
+    see *<<common_options,Common Options>>*
+
+*-v, --verbose*::
+    verbose debugging output which gives hints about the thresholds and decisions made
+    by the program. Note that the exact output can change between versions.
+
+==== Algorithm options:
+
+*-b, --peak-size* 'float'::
+    the minimum peak size considered as a good match can be from the interval [0,1]
+    where larger is stricter
+
+*-c, --cn-penalty* 'float'::
+    a penalty for increasing copy number state. How this works: multiple peaks
+    are always a better fit than a single peak, therefore the program prefers 
+    a single peak (normal copy number) unless the absolute deviation of the
+    multiple peaks fit is significantly smaller. Here the meaning of
+    "significant" is given by the 'float' from the interval [0,1] where
+    larger is stricter.
+    
+*-f, --fit-th* 'float'::
+    threshold for goodness of fit (normalized absolute deviation), smaller is stricter
+
+*-i, --include-aa*::
+    include also the AA peak in CN2 and CN3 evaluation. This usually requires increasing *-f*.
+
+*-m, --min-fraction* 'float'::
+    minimum distinguishable fraction of aberrant cells. The experience shows that trustworthy
+    are estimates of 20% and more.
+
+*-p, --peak-symmetry* 'float'::
+    a heuristics to filter failed fits where the expected peak symmetry is violated.
+    The 'float' is from the interval [0,1] and larger is stricter
+
+
 [[query]]
 === bcftools query ['OPTIONS'] 'file.vcf.gz' ['file.vcf.gz' [...]]
 Extracts fields from VCF or BCF files and outputs them in user-defined format.

From 649f1e23946f7a23caeb30a9b8ec0ef6ef4f3c06 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 2 Nov 2015 10:42:12 +0000
Subject: [PATCH 103/211] Expanded docs to prevent errors reported in #346 and
 #239

---
 doc/bcftools.txt | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index f485507f6..22f014628 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -235,10 +235,11 @@ specific commands to see if they apply.
 
     ::
     With the *call -C* 'alleles' command, third column of the targets file must
-    be comma-separated list of alleles, starting with the reference allele.
+    be comma-separated list of alleles, starting with the reference allele. 
+    Note that the file must be compressed and index.
     Such a file can be easily created from a VCF using:
 ----
-    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf
+    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
 ----
 
 [[annotate]]

From bca77784a8935f0fb999029d065985d58b4fb073 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 5 Nov 2015 08:57:07 +0000
Subject: [PATCH 104/211] Support for --guess GL in vcf2sex

---
 plugins/vcf2sex.c | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index 6a9a626cf..735eddd3e 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -37,6 +37,7 @@
 
 #define GUESS_GT 1
 #define GUESS_PL 2
+#define GUESS_GL 3
 
 typedef struct
 {
@@ -90,7 +91,7 @@ const char *usage(void)
         "Usage: bcftools +vcf2sex <file.vcf.gz> -- [Plugin Options]\n"
         "Plugin options:\n"
         "   -b, --background <region>   diploid region to determine normal hom/hets counts [X:60001-2699520]\n"
-        "   -g, --guess <tag>           determine ploidy by counting hom/hets (GT) or most likely genotypes (PL)\n"
+        "   -g, --guess <tag>           determine ploidy by counting hom/hets (GT) or most likely genotypes (PL or GL)\n"
         "   -m, --min-hets <float>      minimum fraction of hets in diploid regions [0.3]\n"
         "   -n, --nsites <int>          number of sites to check per region (ignored with -g) [10]\n"
         "   -p, --ploidy <file>         space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY\n"
@@ -251,7 +252,8 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
         }
         else    // use PLs to guess the ploidy
         {
-            int npl = bcf_get_format_int32(args->hdr,rec,"PL",&args->pls,&args->npls);
+            int gl2pl = args->guess & GUESS_PL ? 1 : -1;
+            int npl = bcf_get_format_int32(args->hdr,rec,args->guess&GUESS_PL?"PL":"GL",&args->pls,&args->npls);
             if ( npl<=0 ) continue;
             npl /= args->nsample;
             for (ismpl=0; ismpl<args->nsample; ismpl++)
@@ -261,11 +263,13 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
                 for (ial=0; ial<rec->n_allele; ial++)
                 {
                     if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
+                    ptr[k] *= gl2pl;
                     if ( phom > ptr[k] ) phom = ptr[k];
                     k++;
                     for (jal=0; jal<ial; jal++)
                     {
                         if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
+                        ptr[k] *= gl2pl;
                         if ( phet > ptr[k] ) phet = ptr[k];
                         k++;
                     }
@@ -377,7 +381,8 @@ int run(int argc, char **argv)
             case 'g':
                 if ( !strcasecmp(optarg,"GT") ) args->guess = GUESS_GT;
                 else if ( !strcasecmp(optarg,"PL") ) args->guess = GUESS_PL;
-                else error("The argument not recognised, expected --guess GT or --guess PL: %s\n", optarg);
+                else if ( !strcasecmp(optarg,"GL") ) args->guess = GUESS_GL;
+                else error("The argument not recognised, expected --guess GT, --guess PL or --guess GL: %s\n", optarg);
                 break;
             case 'm': 
                 args->min_hets = strtod(optarg,&tmp); 

From c30fb5fe604fc9c8ca1f083a9758c22a972e6b03 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 5 Nov 2015 10:14:32 +0000
Subject: [PATCH 105/211] Fixes in vcf2sex

- use per-sample counts to contrast haploid/diploid regions
rather than cumulative numbers
- limit the background counts to the intended region rather
than sweeping the whole chromosome
---
 plugins/vcf2sex.c | 60 +++++++++++++++++++++++++++++++++--------------
 1 file changed, 42 insertions(+), 18 deletions(-)

diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index 735eddd3e..85be9626e 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -57,7 +57,7 @@ reg_stats_t;
 typedef struct
 {
     int nsites, nsex, *sex2ploidy, dflt_ploidy, max_ploidy, guess;
-    count_t bg_counts;          // background het/hom counts for regions with the same ploidy in all sexes
+    count_t *bg_counts;         // background het/hom counts for regions with the same ploidy in all sexes
     reg_stats_t *reg_stats;     // counts for all regions, used with -g
     int nreg_stats, nsample, verbose;
     int *counts, ncounts;       // number of observed GTs with given ploidy, used when -g is not given
@@ -202,10 +202,13 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
     uint32_t start = 0, end = INT_MAX;
     reg_stats_t *stats = NULL;
 
+    // set the start and the end position
     if ( itr )
     {
         start = itr->reg[itr->i].start;
         end   = itr->reg[itr->i].end;
+
+        // flush all records with the same coordinates
         while ( itr->i+kitr<itr->n && start==itr->reg[itr->i+kitr].start && end==itr->reg[itr->i+kitr].end ) kitr++;
 
         int min,max,ret = ploidy_query(args->ploidy, seq, start, args->sex2ploidy, &min, &max);
@@ -222,6 +225,8 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
         seq = (char*) malloc(ptr - args->background + 1);
         memcpy(seq,args->background,ptr-args->background);
         seq[ptr-args->background] = 0;
+        start = spos;
+        end   = epos;
     }
 
     if ( bcf_sr_seek(args->sr,seq,start)!=0 ) 
@@ -230,6 +235,7 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
         if ( !itr ) free(seq);
         return kitr;
     }
+
     int ismpl, rid = bcf_hdr_name2id(args->hdr,seq);
     if ( !itr ) free(seq);
 
@@ -243,7 +249,7 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
             bcf_fmt_t * fmt = bcf_get_fmt(args->hdr, rec, "GT");
             for (ismpl=0; ismpl<args->nsample; ismpl++)
             {
-                count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts;
+                count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts[ismpl];
                 int gt = bcf_gt_type(fmt, ismpl, NULL,NULL);
                 if ( gt==GT_UNKN ) counts->nmiss++;
                 else if ( gt==GT_HET_RA || gt==GT_HET_AA ) counts->nhet++;
@@ -274,7 +280,7 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
                         k++;
                     }
                 }
-                count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts;
+                count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts[ismpl];
                 if ( k == rec->n_allele ) counts->nhom++;   // haploid
                 else if ( k != rec->n_allele*(rec->n_allele+1)/2 ) counts->nmiss++;
                 else if ( phet < phom ) counts->nhet++;
@@ -288,21 +294,26 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
 void sex2prob_guess(args_t *args)
 {
     int ismpl, ireg; 
-    uint64_t nhom,nhet,nmiss;
-    float bg_het = -1;
 
+    // get numbers from the background region
     if ( args->background )
     {
         process_region_guess(args, NULL, NULL);
-        nhom  = args->bg_counts.nhom;
-        nhet  = args->bg_counts.nhet;
-        nmiss = args->bg_counts.nmiss;
-        bg_het = nhom+nhet ? (float)nhet/(nhom+nhet) : 0;
 
         if ( args->verbose )
+            printf("# [1]BGR\t[2]Region\t[3]Sample\t[4]Het fraction\t[5]nHet\t[6]nHom\t[7]nMissing\n");
+
+        for (ismpl=0; ismpl<args->nsample; ismpl++)
         {
-            printf("# [1]BGR\t[2]Region\t[3]Het fraction\t[4]nHet\t[5]nHom\t[6]nMissing\n");
-            printf("BGR\t%s\t%f\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", args->background,bg_het,nhet,nhom,nmiss);
+            uint64_t nhom  = args->bg_counts[ismpl].nhom;
+            uint64_t nhet  = args->bg_counts[ismpl].nhet;
+            uint64_t nmiss = args->bg_counts[ismpl].nmiss;
+            if ( nhom+nhet==0 )
+                fprintf(stderr,"Warning: The sample %s has no variants in the background region %s\n", args->hdr->samples[ismpl],args->background);
+
+            float bg_het = (float)nhet/(nhom+nhet);
+            if ( args->verbose )
+                printf("BGR\t%s\t%s\t%f\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", args->background,args->hdr->samples[ismpl],bg_het,nhet,nhom,nmiss);
         }
     }
 
@@ -315,10 +326,18 @@ void sex2prob_guess(args_t *args)
             uint64_t nhom  = stats->counts[ismpl].nhom;
             uint64_t nhet  = stats->counts[ismpl].nhet;
             uint64_t nmiss = stats->counts[ismpl].nmiss;
-            float fhet = nhom+nhet ? (float)nhet/(nhom+nhet) : 0;
+            float fhet   = nhom+nhet ? (float)nhet/(nhom+nhet) : 0;
+
+            float bg_fhet = -1;
+            if ( args->background )
+            {
+                uint64_t bg_nhom  = args->bg_counts[ismpl].nhom;
+                uint64_t bg_nhet  = args->bg_counts[ismpl].nhet;
+                bg_fhet = bg_nhom+bg_nhet ? (float)bg_nhet/(bg_nhom+bg_nhet) : 0;
+            }
 
             if ( args->verbose )
-                printf("DBG\t%s:%d-%d\t%s\t%f\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", stats->chr,stats->start+1,stats->end+1,args->hdr->samples[ismpl],fhet,nhet,nhom,nmiss);
+                printf("REG\t%s:%d-%d\t%s\t%f\t%"PRId64"\t%"PRId64"\t%"PRId64"\n", stats->chr,stats->start+1,stats->end+1,args->hdr->samples[ismpl],fhet,nhet,nhom,nmiss);
 
             int i, ntot = nhom + nhet + nmiss;
             if ( !ntot ) continue;
@@ -333,18 +352,18 @@ void sex2prob_guess(args_t *args)
                 else if ( ploidy==1 )
                 {
                     // NB: these numbers (0.1,0.9) are made up, to be improved
-                    if ( bg_het<0 )
+                    if ( bg_fhet<0 )
                         prob = fhet > args->min_hets ? 0.1 : 0.9;
                     else
-                        prob = fhet > args->min_hets*bg_het ? 0.1 : 0.9;
+                        prob = fhet > args->min_hets*bg_fhet ? 0.1 : 0.9;
                     prob *= 1 - (float)nmiss / ntot;
                 }
                 else 
                 {
-                    if ( bg_het<0 )
+                    if ( bg_fhet<0 )
                         prob = fhet > args->min_hets ? 0.9 : 0.1;
                     else
-                        prob = fhet > args->min_hets*bg_het ? 0.9 : 0.1;
+                        prob = fhet > args->min_hets*bg_fhet ? 0.9 : 0.1;
                     prob *= 1 - (float)nmiss / ntot;
                 }
                 probs[i] *= prob;
@@ -425,14 +444,16 @@ int run(int argc, char **argv)
     if ( args->guess && args->max_ploidy > 2 ) error("Sorry, ploidy %d not supported with -g\n", args->max_ploidy);
     args->ncounts = args->nsample * ((args->max_ploidy>2 ? args->max_ploidy : 2)+1);
     args->counts = (int*) malloc(sizeof(int)*args->ncounts);
+    args->bg_counts = (count_t*) calloc(args->nsample,sizeof(count_t));
     args->sex2prob = (float*) calloc(args->nsample*args->nsex,sizeof(float));
 
     int i, nseq;
     for (i=0; i<args->nsample*args->nsex; i++) args->sex2prob[i] = 1;
 
     if ( args->verbose && args->guess )
-        printf("# [1]DBG\t[2]Region\t[3]Sample\t[4]HET fraction\t[5]nHet\t[6]nHom\t[7]nMissing\n");
+        printf("# [1]REG\t[2]Region\t[3]Sample\t[4]Het fraction\t[5]nHet\t[6]nHom\t[7]nMissing\n");
 
+    // First get the counts from expected haploid regions
     regidx_t *idx = ploidy_regions(args->ploidy);
     char **seqs = regidx_seq_names(idx, &nseq);
     for (i=0; i<nseq; i++)
@@ -447,6 +468,8 @@ int run(int argc, char **argv)
                 itr.i += process_region_precise(args, seqs[i], &itr);
         }
     }
+    // Get the counts from a PAR (the background diploid region) and see if the fraction
+    // of hets is different
     if ( args->guess ) sex2prob_guess(args);
 
     for (i=0; i<args->nsample; i++)
@@ -473,6 +496,7 @@ int run(int argc, char **argv)
     destroy_regs(args);
     free(args->sex2ploidy);
     free(args->counts);
+    free(args->bg_counts);
     free(args->gts);
     free(args->pls);
     free(args->sex2prob);

From b12ca089e6778801f4e687d6814df920dd907829 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 2 Nov 2015 08:49:02 +0000
Subject: [PATCH 106/211] More informative error msg in fill-tags plugin

---
 plugins/fill-tags.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c
index c7bd7fd24..96f5e3391 100644
--- a/plugins/fill-tags.c
+++ b/plugins/fill-tags.c
@@ -91,7 +91,7 @@ int parse_tags(args_t *args, const char *str)
         else if ( !strcasecmp(tags[i],"AC_Hemi") ) flag |= SET_AC_Hemi;
         else
         {
-            fprintf(stderr,"Unknown tag \"%s\" in \"%s\"\n", tags[i], str);
+            fprintf(stderr,"Error parsing \"--tags %s\": the tag \"%s\" is not supported\n", str,tags[i]);
             exit(1);
         }
         free(tags[i]);

From edca051a92a37da6444f4f84a84efc9e3ab545a4 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 2 Nov 2015 08:45:11 +0000
Subject: [PATCH 107/211] Expanded plugin docs: explain "+pname" vs "plugin
 name"

---
 doc/bcftools.txt | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 22f014628..570f317be 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1151,7 +1151,7 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.
 
 
 [[plugin]]
-=== bcftools plugin 'NAME' '[OPTIONS]' 'FILE' -- '[PLUGIN OPTIONS]'
+=== bcftools [plugin 'NAME'|+'NAME'] '[OPTIONS]' 'FILE' -- '[PLUGIN OPTIONS]'
 
 ==== VCF input options:
 
@@ -1241,9 +1241,13 @@ bcftools plugin
 # List available plugins
 bcftools plugin -l
 
-# One can run plugins in several ways
+# Run a plugin
 bcftools plugin counts in.vcf
+
+# Run a plugin using the abbreviated "+" notation
 bcftools +counts in.vcf
+
+# The input VCF can be streamed just like in other commands
 cat in.vcf | bcftools +counts
 
 # Print usage information of plugin "dosage"

From 7564362a16a18c89fbe305611713137d3c0a012d Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 30 Oct 2015 09:41:31 +0000
Subject: [PATCH 108/211] vcfmerge: Fix error message, correct chr name must be
 printed

See https://github.com/samtools/bcftools/issues/284#issuecomment-152362026
---
 vcfmerge.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcfmerge.c b/vcfmerge.c
index bf2de2bc2..e876cca69 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -1774,7 +1774,7 @@ void merge_buffer(args_t *args)
 
             // normalize alleles
             maux->als = merge_alleles(line->d.allele, line->n_allele, maux->d[i][j].map, maux->als, &maux->nals, &maux->mals);
-            if ( !maux->als ) error("Failed to merge alleles at %s:%d in %s\n",bcf_seqname(args->out_hdr,line),line->pos+1,reader->fname);
+            if ( !maux->als ) error("Failed to merge alleles at %s:%d in %s\n",bcf_seqname(bcf_sr_get_header(args->files,j),line),line->pos+1,reader->fname);
             hts_expand0(int, maux->nals, maux->ncnt, maux->cnt);
             for (k=1; k<line->n_allele; k++)
                 maux->cnt[ maux->d[i][j].map[k] ]++;    // how many times an allele appears in the files

From 6d12391e3d7a351ace6f5fe1b27d4ef73ad9d781 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Sat, 31 Oct 2015 09:58:20 +0000
Subject: [PATCH 109/211] gtcheck: Use also sites without DP for GT checking;
 Plot discordance in the reverse order

---
 vcfgtcheck.c | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/vcfgtcheck.c b/vcfgtcheck.c
index cbfba2510..b741ef6be 100644
--- a/vcfgtcheck.c
+++ b/vcfgtcheck.c
@@ -88,7 +88,7 @@ static void plot_check(args_t *args, char *target_sample, char *query_sample)
             "        if row[4]=='%s': tgt = 1\n"
             "        dat.append([float(row[1]), float(row[2]), float(row[3]), tgt, row[4]])\n"
             "\n"
-            "dat = sorted(dat, reverse=True)\n"
+            "dat = sorted(dat)\n"
             "\n"
             "iq = -1; dp = 0\n"
             "for i in range(len(dat)):\n"
@@ -107,6 +107,9 @@ static void plot_check(args_t *args, char *target_sample, char *query_sample)
             "   ax1.plot([iq],[dat[iq][1]],'^',color='red', ms=5)\n"
             "for tl in ax1.get_yticklabels(): tl.set_color('g')\n"
             "for tl in ax2.get_yticklabels(): tl.set_color('k'); tl.set_fontsize(9)\n"
+            "min_dp = min([x[2] for x in dat])\n"
+            "max_dp = max([x[2] for x in dat])\n"
+            "ax2.set_ylim(min_dp-1,max_dp+1)\n"
             "ax1.set_title('Discordance with %s')\n"
             "ax1.set_xlim(-0.05*len(dat),1.05*(len(dat)-1))\n"
             "ax1.set_xlabel('Sample ID')\n"
@@ -574,7 +577,8 @@ static void cross_check_gts(args_t *args)
         }
         else
             npl = fake_PLs(args, args->sm_hdr, line);
-        if ( !ignore_dp && bcf_get_format_int32(args->sm_hdr, line, "DP", &dp_arr, &ndp_arr) <= 0 ) { dp_warned++; continue; }
+        int mdp = 0;
+        if ( !ignore_dp && (mdp=bcf_get_format_int32(args->sm_hdr, line, "DP", &dp_arr, &ndp_arr)) <= 0 ) dp_warned++;
 
         if ( args->hom_only )
         {
@@ -588,14 +592,14 @@ static void cross_check_gts(args_t *args)
         {
             int *ipl = &args->pl_arr[i*npl];
             if ( *ipl==-1 ) { idx += i; continue; } // missing genotype
-            if ( !ignore_dp && (dp_arr[i]==bcf_int32_missing || !dp_arr[i]) ) { idx += i; continue; }
+            if ( mdp>0 && (dp_arr[i]==bcf_int32_missing || !dp_arr[i]) ) { idx += i; continue; }
             if ( args->hom_only && !is_hom[i] ) { idx += i; continue; }
 
             for (j=0; j<i; j++)
             {
                 int *jpl = &args->pl_arr[j*npl];
                 if ( *jpl==-1 ) { idx++; continue; } // missing genotype
-                if ( !ignore_dp && (dp_arr[j]==bcf_int32_missing || !dp_arr[j]) ) { idx++; continue; }
+                if ( mdp>0 && (dp_arr[j]==bcf_int32_missing || !dp_arr[j]) ) { idx++; continue; }
                 if ( args->hom_only && !is_hom[j] ) { idx++; continue; }
 
                 int min_pl = INT_MAX;
@@ -611,7 +615,7 @@ static void cross_check_gts(args_t *args)
                 args->lks[idx] += min_pl;
                 args->cnts[idx]++;
 
-                if ( !ignore_dp )
+                if ( mdp>0 )
                 {
                     args->dps[idx] += dp_arr[i] < dp_arr[j] ? dp_arr[i] : dp_arr[j];
                     dp[i] += dp_arr[i]; ndp[i]++;

From 6ff1c214d91c12cf9dee505ab209939cd904e636 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 27 Oct 2015 14:17:53 +0000
Subject: [PATCH 110/211] Distinguish between & and && in -i/-e FMT filtering

---
 doc/bcftools.txt |  4 ++++
 filter.c         | 29 ++++++++++++++++++++++++-----
 2 files changed, 28 insertions(+), 5 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 570f317be..d61739900 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1804,6 +1804,10 @@ not "dp" instead of "DP".
 
     MIN(DP)>10 & MIN(DV)>3
 
+    FMT/DP>10  & FMT/GQ>10 .. both conditions must be satisfied within one sample
+
+    FMT/DP>10 && FMT/GQ>10 .. the conditions can be satisfied in different samples
+
     QUAL>10 |  FMT/GQ>10   .. selects only GQ>10 samples
 
     QUAL>10 || FMT/GQ>10   .. selects all samples at QUAL>10 sites
diff --git a/filter.c b/filter.c
index 82d19f2a2..6ac4868ba 100644
--- a/filter.c
+++ b/filter.c
@@ -845,7 +845,7 @@ static void set_strlen(filter_t *flt, bcf1_t *line, token_t *tok)
     if ( !has_values ) { (atok)->nvalues = 0; (atok)->nsamples = 0; } \
 }
 
-static int vector_logic_and(token_t *atok, token_t *btok)
+static int vector_logic_and(token_t *atok, token_t *btok, int and_type)
 {
     // We are comparing either two scalars (result of INFO tag vs a threshold), two vectors (two FORMAT fields),
     // or a vector and a scalar (FORMAT field vs threshold)
@@ -858,10 +858,29 @@ static int vector_logic_and(token_t *atok, token_t *btok)
     if ( !atok->nsamples && !btok->nsamples ) return atok->pass_site && btok->pass_site;
     if ( atok->nsamples && btok->nsamples )
     {
-        for (i=0; i<atok->nsamples; i++)
+        if ( and_type==TOK_AND )
         {
-            atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_samples[i];
-            if ( !pass_site && atok->pass_samples[i] ) pass_site = 1;
+            // perform AND within a sample
+            for (i=0; i<atok->nsamples; i++)
+            {
+                atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_samples[i];
+                if ( !pass_site && atok->pass_samples[i] ) pass_site = 1;
+            }
+        }
+        else
+        {
+            // perform AND across samples
+            int pass_a = 0, pass_b = 0;
+            for (i=0; i<atok->nsamples; i++)
+            {
+                if ( atok->pass_samples[i] ) pass_a = 1;
+                atok->pass_samples[i] = atok->pass_samples[i] && btok->pass_samples[i];
+            }
+            for (i=0; i<btok->nsamples; i++)
+            {
+                if ( btok->pass_samples[i] ) { pass_b = 1; break; }
+            }
+            pass_site = pass_a && pass_b;
         }
         return pass_site;
     }
@@ -1646,7 +1665,7 @@ int filter_test(filter_t *filter, bcf1_t *line, const uint8_t **samples)
         {
             if ( filter->flt_stack[nstack-1]->pass_site<0 || filter->flt_stack[nstack-2]->pass_site<0 )
                 error("Error occurred while processing the filter \"%s\" (%d %d AND)\n", filter->str,filter->flt_stack[nstack-2]->pass_site,filter->flt_stack[nstack-1]->pass_site);
-            filter->flt_stack[nstack-2]->pass_site = vector_logic_and(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1]);
+            filter->flt_stack[nstack-2]->pass_site = vector_logic_and(filter->flt_stack[nstack-2],filter->flt_stack[nstack-1], filter->filters[i].tok_type);
             nstack--;
             continue;
         }

From 74cc328d1b9f93dc4d82cf8d4d535fdda70afc48 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 27 Oct 2015 15:44:23 +0000
Subject: [PATCH 111/211] Fix in filtering of missing values.

* previously -i'INFO/INT!="."' did not work
* values like INFO/INT=1 could sneak through due to uninitialized memory
* added more tests for missing values
---
 filter.c          | 10 +++-------
 test/missing.vcf  | 18 ++++++++++++++++++
 test/query.19.out |  1 +
 test/query.21.out |  1 +
 test/query.22.out |  2 ++
 test/query.23.out |  3 +++
 test/test.pl      | 20 ++++++++++++--------
 7 files changed, 40 insertions(+), 15 deletions(-)
 create mode 100644 test/missing.vcf
 create mode 100644 test/query.22.out
 create mode 100644 test/query.23.out

diff --git a/filter.c b/filter.c
index 6ac4868ba..924a095eb 100644
--- a/filter.c
+++ b/filter.c
@@ -1035,11 +1035,7 @@ static int vector_logic_or(token_t *atok, token_t *btok, int or_type)
         } \
         else \
         { \
-            if ( bcf_float_is_missing((atok)->values[0]) || bcf_float_is_missing((btok)->values[0]) ) \
-            { \
-                (atok)->nvalues = 0; (atok)->nsamples = 0; (ret) = 0; \
-            } \
-            else if ( (atok)->values[0] CMP_OP (btok)->values[0] ) { pass_site = 1; } \
+            if ( (atok)->values[0] CMP_OP (btok)->values[0] ) { pass_site = 1; } \
         } \
         /*fprintf(stderr,"pass=%d\n", pass_site);*/ \
         (ret) = pass_site; \
@@ -1506,8 +1502,8 @@ filter_t *filter_init(bcf_hdr_t *hdr, const char *str)
             if ( out[k].hdr_id>0 && out[j].is_str && !strcmp(".",out[j].key) )
             {
                 int type = bcf_hdr_id2type(filter->hdr,out[k].type,out[k].hdr_id);
-                if ( type==BCF_HT_INT ) { out[j].is_str = 0; out[j].is_missing = 1; }
-                if ( type==BCF_HT_REAL ) { out[j].is_str = 0; out[j].is_missing = 1; }
+                if ( type==BCF_HT_INT ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_float_set_missing(out[j].values[0]); }
+                if ( type==BCF_HT_REAL ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_float_set_missing(out[j].values[0]); }
             }
         }
         if ( out[i].tok_type==TOK_LIKE || out[i].tok_type==TOK_NLIKE )
diff --git a/test/missing.vcf b/test/missing.vcf
new file mode 100644
index 000000000..b6ca53d26
--- /dev/null
+++ b/test/missing.vcf
@@ -0,0 +1,18 @@
+##fileformat=VCFv4.1
+##contig=<ID=1,assembly=b37,length=249250621>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##INFO=<ID=FLAG,Number=0,Type=Flag,Description="Test type">
+##INFO=<ID=IINT,Number=1,Type=Integer,Description="Test type">
+##INFO=<ID=IFLT,Number=1,Type=Float,Description="Test type">
+##INFO=<ID=ISTR,Number=1,Type=String,Description="Test type">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=FINT,Number=1,Type=Integer,Description="Test type">
+##FORMAT=<ID=FFLT,Number=1,Type=Float,Description="Test type">
+##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test type">
+##FILTER=<ID=q11,Description="Quality below 10">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B	C
+1	3000001	xx	C	T	11	PASS	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0/0:11:1.1:xxx	0/0:11:1.1:x	0/0:11:1.1:x
+1	3000002	.	C	T	.	.	.	GT	.	.	.
+1	3000003	xx	C	T	11	q11	FLAG;IINT=.;IFLT=.;ISTR=.	GT:FINT:FFLT:FSTR	0/0:.:.:.	0/0:.:.:.	0/0:.:.:.
+1	3000004	xx	C	T	11	q11	FLAG;IINT=11;IFLT=1.1;ISTR=xxx	GT:FINT:FFLT:FSTR	0/0:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
+1	3000005	xx	C	T	11	q11	FLAG;IINT=1;IFLT=1;ISTR=..	GT:FINT:FFLT:FSTR	0/0:11:1.1:x	0/0:11:1.1:xxx	0/0:11:1.1:xxx
diff --git a/test/query.19.out b/test/query.19.out
index ec7168b33..f16b4abcd 100644
--- a/test/query.19.out
+++ b/test/query.19.out
@@ -1,2 +1,3 @@
 3000001 11
 3000004 11
+3000005 1
diff --git a/test/query.21.out b/test/query.21.out
index 960fc0027..ead31a1f7 100644
--- a/test/query.21.out
+++ b/test/query.21.out
@@ -1,2 +1,3 @@
 3000001 1.1
 3000004 1.1
+3000005 1
diff --git a/test/query.22.out b/test/query.22.out
new file mode 100644
index 000000000..961849857
--- /dev/null
+++ b/test/query.22.out
@@ -0,0 +1,2 @@
+3000002 .
+3000003 .
diff --git a/test/query.23.out b/test/query.23.out
new file mode 100644
index 000000000..3594a8477
--- /dev/null
+++ b/test/query.23.out
@@ -0,0 +1,3 @@
+3000001 xxx
+3000004 xxx
+3000005 ..
diff --git a/test/test.pl b/test/test.pl
index 2c56e0aea..b23296725 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -82,14 +82,18 @@
 test_vcf_query($opts,in=>'query.filter',out=>'query.15.out',args=>q[-f'%POS[ %GT]\\n' -e'GT ="1"']);
 test_vcf_query($opts,in=>'query.filter',out=>'query.16.out',args=>q[-f'%POS[ %GT]\\n' -e'GT!="1"']);
 test_vcf_query($opts,in=>'query.2',out=>'query.17.out',args=>q[-f'%XX_A %XX.A %XX.A0 %xx.a0\\n']);
-test_vcf_query($opts,in=>'annotate2',out=>'query.18.out',args=>q[-i'IINT="."'  -f'%POS %IINT\\n']);
-test_vcf_query($opts,in=>'annotate2',out=>'query.19.out',args=>q[-i'IINT!="."' -f'%POS %IINT\\n']);
-test_vcf_query($opts,in=>'annotate2',out=>'query.18.out',args=>q[-e'IINT!="."' -f'%POS %IINT\\n']);
-test_vcf_query($opts,in=>'annotate2',out=>'query.19.out',args=>q[-e'IINT="."'  -f'%POS %IINT\\n']);
-test_vcf_query($opts,in=>'annotate2',out=>'query.20.out',args=>q[-i'IFLT="."'  -f'%POS %IFLT\\n']);
-test_vcf_query($opts,in=>'annotate2',out=>'query.21.out',args=>q[-i'IFLT!="."' -f'%POS %IFLT\\n']);
-test_vcf_query($opts,in=>'annotate2',out=>'query.20.out',args=>q[-e'IFLT!="."' -f'%POS %IFLT\\n']);
-test_vcf_query($opts,in=>'annotate2',out=>'query.21.out',args=>q[-e'IFLT="."'  -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.18.out',args=>q[-i'IINT="."'  -f'%POS %IINT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.19.out',args=>q[-i'IINT!="."' -f'%POS %IINT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.18.out',args=>q[-e'IINT!="."' -f'%POS %IINT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.19.out',args=>q[-e'IINT="."'  -f'%POS %IINT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.20.out',args=>q[-i'IFLT="."'  -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.21.out',args=>q[-i'IFLT!="."' -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.20.out',args=>q[-e'IFLT!="."' -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.21.out',args=>q[-e'IFLT="."'  -f'%POS %IFLT\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.22.out',args=>q[-i'ISTR="."'  -f'%POS %ISTR\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.23.out',args=>q[-i'ISTR!="."' -f'%POS %ISTR\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.23.out',args=>q[-e'ISTR="."'  -f'%POS %ISTR\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.22.out',args=>q[-e'ISTR!="."' -f'%POS %ISTR\\n']);
 test_vcf_norm($opts,in=>'norm',out=>'norm.out',fai=>'norm');
 test_vcf_norm($opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.split.2',out=>'norm.split.2.out',args=>'-m-');

From c43c235883b2f9514a9b88133d79cd5cc14a7ecf Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 6 Nov 2015 14:46:03 +0000
Subject: [PATCH 112/211] Document requirement of compressed/indexed files when
 reading multiple VCFs simultaneously

Closes #340
---
 doc/bcftools.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index d61739900..c54ec0d25 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -38,7 +38,8 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
 Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
-work in most, but not all situations.
+work in most, but not all situations. In general, whenever multiple VCFs are 
+read simultaneously, they must be indexed and therefore also compressed.
 
 BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several

From 0b9ad1a3dfa6449f926b79386a43f1c7a391e83e Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 6 Nov 2015 15:20:24 +0000
Subject: [PATCH 113/211] document subset behaviour with regard to sample
 dependent tags

Closes #331
---
 doc/bcftools.txt | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index c54ec0d25..b04893de2 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -190,10 +190,20 @@ specific commands to see if they apply.
 *-s, --samples* \[&#94;]'LIST'::
     Comma-separated list of samples to include or exclude if prefixed
     with "&#94;".
+    Note that in general tags such as INFO/AC, INFO/AN, etc are not updated
+    to correspond to the subset samples. *<<view,bcftools view>>* is the
+    exception where some tags will be updated (unless the *-I, --no-update*
+    option is used; see *<<view,bcftools view>>* documentation). To use updated 
+    tags for the subset in another command one can pipe from *view* into
+    that command. For example:
+----
+    bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n
+----
 
 *-S, --samples-file* [&#94;]'FILE'[[samples_file]]::
     File of sample names to include or exclude if prefixed with "&#94;".
-    One sample per line.
+    One sample per line. See also the note above for the *-s, --samples*
+    option.
     The command *<<call,bcftools call>>* accepts an optional second
     column indicating ploidy (0, 1 or 2) or sex (as defined by
     *<<ploidy,--ploidy>>*, for example "F" or "M"), and can parse also PED

From 08cc3f203bee8f8eaf8baec7200905881c25037d Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 6 Nov 2015 16:13:26 +0000
Subject: [PATCH 114/211] add some missing documentation

---
 doc/bcftools.txt | 45 ++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 42 insertions(+), 3 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index b04893de2..72357d2fb 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -462,6 +462,9 @@ demand. The original calling model can be invoked with the *-c* option.
     minimum per-sample depth required to include a site in the non-variant
     block.
 
+*-i, --insert-missed* 'INT'::
+    output also sites missed by mpileup but present in *-T, --targets-file*.
+
 *-M, --keep-masked-ref*::
     output sites where REF allele is N
 
@@ -684,14 +687,31 @@ Create consensus sequence by applying VCF variants to a reference fasta file.
     convert from haps/sample format to VCF. The columns of .haps file are
     similar to .gen file above, but there are only two haplotype columns per
     sample. Note that the first column of the haps file is expected to be in
-    the form "CHR:POS_REF_ALT", for example:
+    the form "CHR:POS_REF_ALT(_END)?", with the _END being optional for
+    defining the INFO/END tag when ALT is a symbolic allele, for example:
 ----
   .haps
   ----
   1:111485207_G_A rsID1 111485207 G A 0 1 0 0
   1:111494194_C_T rsID2 111494194 C T 0 1 0 0
+  1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0
 ----
 
+*--hapsample* 'prefix' or 'haps-file','sample-file'::
+    convert from VCF to haps/sample format used by IMPUTE2 and SHAPEIT.
+    The columns of .haps file begin with ID,RSID,POS,REF,ALT. In order to 
+    prevent strand swaps, the program uses IDs of the form 
+    "CHROM:POS_REF_ALT".
+
+*--haploid2diploid*::
+    with *-h* option converts haploid genotypes to homozygous diploid
+    genotypes. For example, the program will print '0 0' instead of the 
+    default '0 -'. This is useful for programs which do not handle haploid
+    genotypes correctly.
+
+*--vcf-ids*::
+    output VCF IDs instead of "CHROM:POS_REF_ALT" IDs
+
 ==== HAPS/LEGEND/SAMPLE conversion:
 *-H, --haplegendsample2vcf* 'prefix' or 'haps-file','legend-file','sample-file'::
     convert from haps/legend/sample format used by IMPUTE2 to VCF, see
@@ -1113,8 +1133,14 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.
     can swap alleles and will update genotypes (GT) and AC counts, 
     but will not attempt to fix PL or other fields.
 
+*-d, --rm-dup* 'snps'|'indels'|'both'|'all'|'none'::
+    If a record is present in multiple files, output only the first instance,
+    see *--collapse* in *<<common_options,Common Options>>*.
+    Requires *-a, --allow-overlaps*.
+
 *-D, --remove-duplicates*::
-    remove duplicate lines of the same type
+    If a record is present in multiple files, output only the first instance.
+    Alias for *-d none*.  Requires *-a, --allow-overlaps*.
 
 *-f, --fasta-ref* 'FILE'[[fasta_ref]]::
     reference sequence. Supplying this option will turn on left-alignment
@@ -1216,6 +1242,9 @@ If htslib is not installed systemwide, set the environment variable
 *-v, --verbose*::
     print debugging information to debug plugin failure
 
+*-V, --version*::
+    print version string and exit
+
 ==== List of plugins coming with the distribution:
 
 *counts*::
@@ -1466,6 +1495,9 @@ Transition probabilities:
     be a single file or a file mask, where string "{CHROM}" is replaced with
     chromosome name.
 
+*-M, --rec-rate* 'FLOAT'::
+    constant recombination rate per bp
+
 *-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
     see *<<common_options,Common Options>>*
 
@@ -1503,7 +1535,7 @@ default only sites are compared, *-s*/*-S* must given to include also sample
 columns.
 
 *-1, --1st-allele-only*::
-    consider only 1st allele at multiallelic sites
+    consider only the 1st alternate allele at multiallelic sites
 
 *-c, --collapse* 'snps'|'indels'|'both'|'all'|'some'|'none'::
     see *<<common_options,Common Options>>*
@@ -1558,7 +1590,11 @@ columns.
 *-T, --targets-file* 'file'::
     see *<<common_options,Common Options>>*
 
+*-u, --user-tstv* '<TAG[:min:max:n]>'::
+    collect Ts/Tv stats for any tag using the given binning [0:1:100]
 
+*-v, --verbose*::
+    produce verbose per-site and per-sample output
 
 
 [[view]]
@@ -1604,6 +1640,9 @@ Convert between VCF and BCF. Former *bcftools subset*.
 *-a, --trim-alt-alleles*::
     trim alternate alleles not seen in subset. Type A, G and R INFO and FORMAT fields will also be trimmed
 
+*--force-samples*::
+    only warn about unknown subset samples
+
 *-I, --no-update*::
     do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
 

From 06ce5a11d4b3f5bf522533f43149d12c6138fbac Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 6 Nov 2015 16:14:15 +0000
Subject: [PATCH 115/211] update man and html doc from the asciidoc

---
 doc/bcftools.1    | 137 +++++++++++++++++++++++++++++++++++++++++-----
 doc/bcftools.html |  98 ++++++++++++++++++++++++++++-----
 2 files changed, 206 insertions(+), 29 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index d0e609ed1..37fbd21e0 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-09-15 11:42 BST
+.\"      Date: 2015-11-06 16:12 GMT
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-09\-15 11:42 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-11\-06 16:12 GMT" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -36,12 +36,12 @@ bcftools \- utilities for variant calling and manipulating VCFs and BCFs\&.
 .sp
 BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF\&. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF\-compressed\&.
 .sp
-Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe\&. Indexed VCF and BCF will work in all situations\&. Un\-indexed VCF and BCF and streams will work in most, but not all situations\&.
+Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe\&. Indexed VCF and BCF will work in all situations\&. Un\-indexed VCF and BCF and streams will work in most, but not all situations\&. In general, whenever multiple VCFs are read simultaneously, they must be indexed and therefore also compressed\&.
 .sp
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-09\-15 11:42 BST\fR and refers to bcftools git version \fB1\&.2\-127\-g5940dc0+\fR\&.
+This manual page was last updated \fB2015\-11\-06 16:12 GMT\fR and refers to bcftools git version \fB1\&.2\-170\-g0b9ad1a+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -404,12 +404,32 @@ cannot be used in combination with
 .PP
 \fB\-s, \-\-samples\fR [^]\fILIST\fR
 .RS 4
-Comma\-separated list of samples to include or exclude if prefixed with "^"\&.
+Comma\-separated list of samples to include or exclude if prefixed with "^"\&. Note that in general tags such as INFO/AC, INFO/AN, etc are not updated to correspond to the subset samples\&.
+\fBbcftools view\fR
+is the exception where some tags will be updated (unless the
+\fB\-I, \-\-no\-update\fR
+option is used; see
+\fBbcftools view\fR
+documentation)\&. To use updated tags for the subset in another command one can pipe from
+\fBview\fR
+into that command\&. For example:
+.RE
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    bcftools view \-Ou \-s sample1,sample2 file\&.vcf | bcftools query \-f %INFO/AC\et%INFO/AN\en
+.fi
+.if n \{\
 .RE
+.\}
 .PP
 \fB\-S, \-\-samples\-file\fR \fIFILE\fR
 .RS 4
-File of sample names to include or exclude if prefixed with "^"\&. One sample per line\&. The command
+File of sample names to include or exclude if prefixed with "^"\&. One sample per line\&. See also the note above for the
+\fB\-s, \-\-samples\fR
+option\&. The command
 \fBbcftools call\fR
 accepts an optional second column indicating ploidy (0, 1 or 2) or sex (as defined by
 \fB\-\-ploidy\fR, for example "F" or "M"), and can parse also PED files\&. If the second column is not present, the sex "F" is assumed\&. With
@@ -476,14 +496,14 @@ cannot be used in combination with
 With the
 \fBcall \-C\fR
 \fIalleles\fR
-command, third column of the targets file must be comma\-separated list of alleles, starting with the reference allele\&. Such a file can be easily created from a VCF using:
+command, third column of the targets file must be comma\-separated list of alleles, starting with the reference allele\&. Note that the file must be compressed and index\&. Such a file can be easily created from a VCF using:
 .RE
 .sp
 .if n \{\
 .RS 4
 .\}
 .nf
-    bcftools query \-f\*(Aq%CHROM\et%POS\et%REF,%ALT\en\*(Aq file\&.vcf
+    bcftools query \-f\*(Aq%CHROM\et%POS\et%REF,%ALT\en\*(Aq file\&.vcf | bgzip \-c > als\&.tsv\&.gz && tabix \-s1 \-b2 \-e2 als\&.tsv\&.gz
 .fi
 .if n \{\
 .RE
@@ -773,6 +793,12 @@ output also gVCF blocks of homozygous REF calls\&. The parameter
 is the minimum per\-sample depth required to include a site in the non\-variant block\&.
 .RE
 .PP
+\fB\-i, \-\-insert\-missed\fR \fIINT\fR
+.RS 4
+output also sites missed by mpileup but present in
+\fB\-T, \-\-targets\-file\fR\&.
+.RE
+.PP
 \fB\-M, \-\-keep\-masked\-ref\fR
 .RS 4
 output sites where REF allele is N
@@ -1156,7 +1182,7 @@ reference sequence in fasta format\&. Must be indexed with samtools faidx
 .PP
 \fB\-\-hapsample2vcf\fR \fIprefix\fR or \fIhaps\-file\fR,\fIsample\-file\fR
 .RS 4
-convert from haps/sample format to VCF\&. The columns of \&.haps file are similar to \&.gen file above, but there are only two haplotype columns per sample\&. Note that the first column of the haps file is expected to be in the form "CHR:POS_REF_ALT", for example:
+convert from haps/sample format to VCF\&. The columns of \&.haps file are similar to \&.gen file above, but there are only two haplotype columns per sample\&. Note that the first column of the haps file is expected to be in the form "CHR:POS_REF_ALT(_END)?", with the _END being optional for defining the INFO/END tag when ALT is a symbolic allele, for example:
 .RE
 .sp
 .if n \{\
@@ -1167,10 +1193,31 @@ convert from haps/sample format to VCF\&. The columns of \&.haps file are simila
   \-\-\-\-
   1:111485207_G_A rsID1 111485207 G A 0 1 0 0
   1:111494194_C_T rsID2 111494194 C T 0 1 0 0
+  1:111495231_A_<DEL>_111495784 rsID3 111495231 A <DEL> 0 0 1 0
 .fi
 .if n \{\
 .RE
 .\}
+.PP
+\fB\-\-hapsample\fR \fIprefix\fR or \fIhaps\-file\fR,\fIsample\-file\fR
+.RS 4
+convert from VCF to haps/sample format used by IMPUTE2 and SHAPEIT\&. The columns of \&.haps file begin with ID,RSID,POS,REF,ALT\&. In order to prevent strand swaps, the program uses IDs of the form "CHROM:POS_REF_ALT"\&.
+.RE
+.PP
+\fB\-\-haploid2diploid\fR
+.RS 4
+with
+\fB\-h\fR
+option converts haploid genotypes to homozygous diploid genotypes\&. For example, the program will print
+\fI0 0\fR
+instead of the default
+\fI0 \-\fR\&. This is useful for programs which do not handle haploid genotypes correctly\&.
+.RE
+.PP
+\fB\-\-vcf\-ids\fR
+.RS 4
+output VCF IDs instead of "CHROM:POS_REF_ALT" IDs
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -1803,7 +1850,9 @@ is one of
 \fIavg\fR,
 \fImin\fR,
 \fImax\fR,
-\fIjoin\fR\&.
+\fIjoin\fR\&. Default is
+\fIDP:sum,DP4:sum\fR
+if these fields exist in the input files\&. Fields with no specified rule will take the value from the first input file\&. The merged QUAL value is currently set to the maximum\&. This behaviour is not user controllable at the moment\&.
 .RE
 .PP
 \fB\-l, \-\-file\-list\fR \fIFILE\fR
@@ -1871,9 +1920,20 @@ and
 can swap alleles and will update genotypes (GT) and AC counts, but will not attempt to fix PL or other fields\&.
 .RE
 .PP
+\fB\-d, \-\-rm\-dup\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fInone\fR
+.RS 4
+If a record is present in multiple files, output only the first instance, see
+\fB\-\-collapse\fR
+in
+\fBCommon Options\fR\&. Requires
+\fB\-a, \-\-allow\-overlaps\fR\&.
+.RE
+.PP
 \fB\-D, \-\-remove\-duplicates\fR
 .RS 4
-remove duplicate lines of the same type
+If a record is present in multiple files, output only the first instance\&. Alias for
+\fB\-d none\fR\&. Requires
+\fB\-a, \-\-allow\-overlaps\fR\&.
 .RE
 .PP
 \fB\-f, \-\-fasta\-ref\fR \fIFILE\fR
@@ -1948,7 +2008,7 @@ see
 .RS 4
 maximum distance between two records to consider when locally sorting variants which changed position during the realignment
 .RE
-.SS "bcftools plugin \fINAME\fR \fI[OPTIONS]\fR \fIFILE\fR \(em \fI[PLUGIN OPTIONS]\fR"
+.SS "bcftools [plugin \fINAME\fR|+\fINAME\fR] \fI[OPTIONS]\fR \fIFILE\fR \(em \fI[PLUGIN OPTIONS]\fR"
 .sp
 .it 1 an-trap
 .nr an-no-space-flag 1
@@ -2048,6 +2108,11 @@ is located\&.
 .RS 4
 print debugging information to debug plugin failure
 .RE
+.PP
+\fB\-V, \-\-version\fR
+.RS 4
+print version string and exit
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -2117,9 +2182,13 @@ bcftools plugin
 # List available plugins
 bcftools plugin \-l
 
-# One can run plugins in several ways
+# Run a plugin
 bcftools plugin counts in\&.vcf
+
+# Run a plugin using the abbreviated "+" notation
 bcftools +counts in\&.vcf
+
+# The input VCF can be streamed just like in other commands
 cat in\&.vcf | bcftools +counts
 
 # Print usage information of plugin "dosage"
@@ -2522,6 +2591,11 @@ genetic map in the format required also by IMPUTE2\&. Only the first and third c
 can chromosome name\&.
 .RE
 .PP
+\fB\-M, \-\-rec\-rate\fR \fIFLOAT\fR
+.RS 4
+constant recombination rate per bp
+.RE
+.PP
 \fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
 .RS 4
 see
@@ -2581,7 +2655,7 @@ Parses VCF or BCF and produces text file stats which is suitable for machine pro
 .PP
 \fB\-1, \-\-1st\-allele\-only\fR
 .RS 4
-consider only 1st allele at multiallelic sites
+consider only the 1st alternate allele at multiallelic sites
 .RE
 .PP
 \fB\-c, \-\-collapse\fR \fIsnps\fR|\fIindels\fR|\fIboth\fR|\fIall\fR|\fIsome\fR|\fInone\fR
@@ -2682,6 +2756,16 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-u, \-\-user\-tstv\fR \fI<TAG[:min:max:n]>\fR
+.RS 4
+collect Ts/Tv stats for any tag using the given binning [0:1:100]
+.RE
+.PP
+\fB\-v, \-\-verbose\fR
+.RS 4
+produce verbose per\-site and per\-sample output
+.RE
 .SS "bcftools view [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR [\fIREGION\fR [\&...]]"
 .sp
 View, subset and filter VCF or BCF files by position and filtering expression\&. Convert between VCF and BCF\&. Former \fBbcftools subset\fR\&.
@@ -2762,6 +2846,11 @@ see
 trim alternate alleles not seen in subset\&. Type A, G and R INFO and FORMAT fields will also be trimmed
 .RE
 .PP
+\fB\-\-force\-samples\fR
+.RS 4
+only warn about unknown subset samples
+.RE
+.PP
 \fB\-I, \-\-no\-update\fR
 .RS 4
 do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
@@ -3297,6 +3386,26 @@ MIN(DP)>10 & MIN(DV)>3
 .RS 4
 .\}
 .nf
+FMT/DP>10  & FMT/GQ>10 \&.\&. both conditions must be satisfied within one sample
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+FMT/DP>10 && FMT/GQ>10 \&.\&. the conditions can be satisfied in different samples
+.fi
+.if n \{\
+.RE
+.\}
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
 QUAL>10 |  FMT/GQ>10   \&.\&. selects only GQ>10 samples
 .fi
 .if n \{\
diff --git a/doc/bcftools.html b/doc/bcftools.html
index 3ac3e8614..a29a9148c 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,13 +1,14 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp213264"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp152704"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
 will work in all situations. Un-indexed VCF and BCF and streams will
-work in most, but not all situations.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
+work in most, but not all situations. In general, whenever multiple VCFs are
+read simultaneously, they must be indexed and therefore also compressed.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-09-15 11:42 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-127-g5940dc0+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-11-06 16:12 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-170-g0b9ad1a+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -40,7 +41,7 @@
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#norm" title="bcftools norm [OPTIONS] file.vcf.gz">norm</a></strong></span>        ..  normalize indels
 </li><li class="listitem">
-<span class="strong"><strong><a class="link" href="#plugin" title="bcftools plugin NAME [OPTIONS] FILE — [PLUGIN OPTIONS]">plugin</a></strong></span>    ..  run user-defined plugin
+<span class="strong"><strong><a class="link" href="#plugin" title="bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]">plugin</a></strong></span>    ..  run user-defined plugin
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#query" title="bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]">query</a></strong></span>      ..  transform VCF/BCF into user-defined formats
 </li><li class="listitem">
@@ -150,11 +151,18 @@
 </span></dt><dd>
     Comma-separated list of samples to include or exclude if prefixed
     with "^".
-</dd><dt><span class="term">
+    Note that in general tags such as INFO/AC, INFO/AN, etc are not updated
+    to correspond to the subset samples. <span class="strong"><strong><a class="link" href="#view" title="bcftools view [OPTIONS] file.vcf.gz [REGION […]]">bcftools view</a></strong></span> is the
+    exception where some tags will be updated (unless the <span class="strong"><strong>-I, --no-update</strong></span>
+    option is used; see <span class="strong"><strong><a class="link" href="#view" title="bcftools view [OPTIONS] file.vcf.gz [REGION […]]">bcftools view</a></strong></span> documentation). To use updated
+    tags for the subset in another command one can pipe from <span class="strong"><strong>view</strong></span> into
+    that command. For example:
+</dd></dl></div><pre class="screen">    bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n</pre><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-S, --samples-file</strong></span> <span class="emphasis"><em><span class="^">FILE</span></em></span><a id="samples_file"></a>
 </span></dt><dd>
     File of sample names to include or exclude if prefixed with "^".
-    One sample per line.
+    One sample per line. See also the note above for the <span class="strong"><strong>-s, --samples</strong></span>
+    option.
     The command <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">bcftools call</a></strong></span> accepts an optional second
     column indicating ploidy (0, 1 or 2) or sex (as defined by
     <span class="strong"><strong><a class="link" href="#ploidy">--ploidy</a></strong></span>, for example "F" or "M"), and can parse also PED
@@ -198,8 +206,9 @@
 </span></dt><dd>
     With the <span class="strong"><strong>call -C</strong></span> <span class="emphasis"><em>alleles</em></span> command, third column of the targets file must
     be comma-separated list of alleles, starting with the reference allele.
+    Note that the file must be compressed and index.
     Such a file can be easily created from a VCF using:
-</dd></dl></div><pre class="screen">    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf</pre></div><div class="refsect2" title="bcftools annotate [OPTIONS] FILE"><a id="annotate"></a><h3>bcftools annotate <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command allows to add or remove annotations.</p><div class="variablelist"><dl><dt><span class="term">
+</dd></dl></div><pre class="screen">    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c &gt; als.tsv.gz &amp;&amp; tabix -s1 -b2 -e2 als.tsv.gz</pre></div><div class="refsect2" title="bcftools annotate [OPTIONS] FILE"><a id="annotate"></a><h3>bcftools annotate <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command allows to add or remove annotations.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-a, --annotations</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     Bgzip-compressed and tabix-indexed file with annotations. The file
@@ -403,6 +412,10 @@
     minimum per-sample depth required to include a site in the non-variant
     block.
 </dd><dt><span class="term">
+<span class="strong"><strong>-i, --insert-missed</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    output also sites missed by mpileup but present in <span class="strong"><strong>-T, --targets-file</strong></span>.
+</dd><dt><span class="term">
 <span class="strong"><strong>-M, --keep-masked-ref</strong></span>
 </span></dt><dd>
     output sites where REF allele is N
@@ -640,11 +653,31 @@
     convert from haps/sample format to VCF. The columns of .haps file are
     similar to .gen file above, but there are only two haplotype columns per
     sample. Note that the first column of the haps file is expected to be in
-    the form "CHR:POS_REF_ALT", for example:
+    the form "CHR:POS_REF_ALT(_END)?", with the _END being optional for
+    defining the INFO/END tag when ALT is a symbolic allele, for example:
 </dd></dl></div><pre class="screen">  .haps
   ----
   1:111485207_G_A rsID1 111485207 G A 0 1 0 0
-  1:111494194_C_T rsID2 111494194 C T 0 1 0 0</pre></div><div class="refsect3" title="HAPS/LEGEND/SAMPLE conversion:"><a id="_haps_legend_sample_conversion"></a><h4>HAPS/LEGEND/SAMPLE conversion:</h4><div class="variablelist"><dl><dt><span class="term">
+  1:111494194_C_T rsID2 111494194 C T 0 1 0 0
+  1:111495231_A_&lt;DEL&gt;_111495784 rsID3 111495231 A &lt;DEL&gt; 0 0 1 0</pre><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--hapsample</strong></span> <span class="emphasis"><em>prefix</em></span> or <span class="emphasis"><em>haps-file</em></span>,<span class="emphasis"><em>sample-file</em></span>
+</span></dt><dd>
+    convert from VCF to haps/sample format used by IMPUTE2 and SHAPEIT.
+    The columns of .haps file begin with ID,RSID,POS,REF,ALT. In order to
+    prevent strand swaps, the program uses IDs of the form
+    "CHROM:POS_REF_ALT".
+</dd><dt><span class="term">
+<span class="strong"><strong>--haploid2diploid</strong></span>
+</span></dt><dd>
+    with <span class="strong"><strong>-h</strong></span> option converts haploid genotypes to homozygous diploid
+    genotypes. For example, the program will print <span class="emphasis"><em>0 0</em></span> instead of the
+    default <span class="emphasis"><em>0 -</em></span>. This is useful for programs which do not handle haploid
+    genotypes correctly.
+</dd><dt><span class="term">
+<span class="strong"><strong>--vcf-ids</strong></span>
+</span></dt><dd>
+    output VCF IDs instead of "CHROM:POS_REF_ALT" IDs
+</dd></dl></div></div><div class="refsect3" title="HAPS/LEGEND/SAMPLE conversion:"><a id="_haps_legend_sample_conversion"></a><h4>HAPS/LEGEND/SAMPLE conversion:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-H, --haplegendsample2vcf</strong></span> <span class="emphasis"><em>prefix</em></span> or <span class="emphasis"><em>haps-file</em></span>,<span class="emphasis"><em>legend-file</em></span>,<span class="emphasis"><em>sample-file</em></span>
 </span></dt><dd>
     convert from haps/legend/sample format used by IMPUTE2 to VCF, see
@@ -997,7 +1030,11 @@
 <span class="strong"><strong>-i, --info-rules</strong></span> <span class="emphasis"><em>-</em></span>|<span class="emphasis"><em>TAG:METHOD</em></span>[,…]
 </span></dt><dd>
     Rules for merging INFO fields (scalars or vectors) or <span class="emphasis"><em>-</em></span> to disable the
-    default rules.  <span class="emphasis"><em>METHOD</em></span> is one of <span class="emphasis"><em>sum</em></span>, <span class="emphasis"><em>avg</em></span>, <span class="emphasis"><em>min</em></span>, <span class="emphasis"><em>max</em></span>, <span class="emphasis"><em>join</em></span>.
+    default rules. <span class="emphasis"><em>METHOD</em></span> is one of <span class="emphasis"><em>sum</em></span>, <span class="emphasis"><em>avg</em></span>, <span class="emphasis"><em>min</em></span>, <span class="emphasis"><em>max</em></span>, <span class="emphasis"><em>join</em></span>.
+    Default is <span class="emphasis"><em>DP:sum,DP4:sum</em></span> if these fields exist in the input files.
+    Fields with no specified rule will take the value from the first input file.
+    The merged QUAL value is currently set to the maximum. This behaviour is
+    not user controllable at the moment.
 </dd><dt><span class="term">
 <span class="strong"><strong>-l, --file-list</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
@@ -1039,9 +1076,16 @@
     can swap alleles and will update genotypes (GT) and AC counts,
     but will not attempt to fix PL or other fields.
 </dd><dt><span class="term">
+<span class="strong"><strong>-d, --rm-dup</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>all</em></span>|<span class="emphasis"><em>none</em></span>
+</span></dt><dd>
+    If a record is present in multiple files, output only the first instance,
+    see <span class="strong"><strong>--collapse</strong></span> in <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>.
+    Requires <span class="strong"><strong>-a, --allow-overlaps</strong></span>.
+</dd><dt><span class="term">
 <span class="strong"><strong>-D, --remove-duplicates</strong></span>
 </span></dt><dd>
-    remove duplicate lines of the same type
+    If a record is present in multiple files, output only the first instance.
+    Alias for <span class="strong"><strong>-d none</strong></span>.  Requires <span class="strong"><strong>-a, --allow-overlaps</strong></span>.
 </dd><dt><span class="term">
 <span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>FILE</em></span><a id="fasta_ref"></a>
 </span></dt><dd>
@@ -1097,7 +1141,7 @@
 </span></dt><dd>
     maximum distance between two records to consider when locally
     sorting variants which changed position during the realignment
-</dd></dl></div></div><div class="refsect2" title="bcftools plugin NAME [OPTIONS] FILE — [PLUGIN OPTIONS]"><a id="plugin"></a><h3>bcftools plugin <span class="emphasis"><em>NAME</em></span> <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span> — <span class="emphasis"><em>[PLUGIN OPTIONS]</em></span></h3><div class="refsect3" title="VCF input options:"><a id="_vcf_input_options_2"></a><h4>VCF input options:</h4><div class="variablelist"><dl><dt><span class="term">
+</dd></dl></div></div><div class="refsect2" title="bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]"><a id="plugin"></a><h3>bcftools [plugin <span class="emphasis"><em>NAME</em></span>|+<span class="emphasis"><em>NAME</em></span>] <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span> — <span class="emphasis"><em>[PLUGIN OPTIONS]</em></span></h3><div class="refsect3" title="VCF input options:"><a id="_vcf_input_options_2"></a><h4>VCF input options:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-e, --exclude</strong></span> <span class="emphasis"><em>EXPRESSION</em></span>
 </span></dt><dd>
     exclude sites for which <span class="emphasis"><em>EXPRESSION</em></span> is true. For valid expressions see
@@ -1150,6 +1194,10 @@
 <span class="strong"><strong>-v, --verbose</strong></span>
 </span></dt><dd>
     print debugging information to debug plugin failure
+</dd><dt><span class="term">
+<span class="strong"><strong>-V, --version</strong></span>
+</span></dt><dd>
+    print version string and exit
 </dd></dl></div></div><div class="refsect3" title="List of plugins coming with the distribution:"><a id="_list_of_plugins_coming_with_the_distribution"></a><h4>List of plugins coming with the distribution:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>counts</strong></span>
 </span></dt><dd>
@@ -1189,9 +1237,13 @@
 # List available plugins
 bcftools plugin -l
 
-# One can run plugins in several ways
+# Run a plugin
 bcftools plugin counts in.vcf
+
+# Run a plugin using the abbreviated "+" notation
 bcftools +counts in.vcf
+
+# The input VCF can be streamed just like in other commands
 cat in.vcf | bcftools +counts
 
 # Print usage information of plugin "dosage"
@@ -1380,6 +1432,10 @@
     third column are used (position and Genetic_Map(cM)). The <span class="emphasis"><em>FILE</em></span> can
     chromosome name.
 </dd><dt><span class="term">
+<span class="strong"><strong>-M, --rec-rate</strong></span> <span class="emphasis"><em>FLOAT</em></span>
+</span></dt><dd>
+    constant recombination rate per bp
+</dd><dt><span class="term">
 <span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1418,7 +1474,7 @@
 columns.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-1, --1st-allele-only</strong></span>
 </span></dt><dd>
-    consider only 1st allele at multiallelic sites
+    consider only the 1st alternate allele at multiallelic sites
 </dd><dt><span class="term">
 <span class="strong"><strong>-c, --collapse</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>all</em></span>|<span class="emphasis"><em>some</em></span>|<span class="emphasis"><em>none</em></span>
 </span></dt><dd>
@@ -1484,6 +1540,14 @@
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-u, --user-tstv</strong></span> <span class="emphasis"><em>&lt;TAG[:min:max:n]&gt;</em></span>
+</span></dt><dd>
+    collect Ts/Tv stats for any tag using the given binning [0:1:100]
+</dd><dt><span class="term">
+<span class="strong"><strong>-v, --verbose</strong></span>
+</span></dt><dd>
+    produce verbose per-site and per-sample output
 </dd></dl></div></div><div class="refsect2" title="bcftools view [OPTIONS] file.vcf.gz [REGION […]]"><a id="view"></a><h3>bcftools view [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span> [<span class="emphasis"><em>REGION</em></span> […]]</h3><p>View, subset and filter VCF or BCF files by position and filtering expression.
 Convert between VCF and BCF. Former <span class="strong"><strong>bcftools subset</strong></span>.</p><div class="refsect3" title="Output options"><a id="_output_options"></a><h4>Output options</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-G, --drop-genotypes</strong></span>
@@ -1528,6 +1592,10 @@
 </span></dt><dd>
     trim alternate alleles not seen in subset. Type A, G and R INFO and FORMAT fields will also be trimmed
 </dd><dt><span class="term">
+<span class="strong"><strong>--force-samples</strong></span>
+</span></dt><dd>
+    only warn about unknown subset samples
+</dd><dt><span class="term">
 <span class="strong"><strong>-I, --no-update</strong></span>
 </span></dt><dd>
     do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)
@@ -1698,7 +1766,7 @@
 Variables and function names are case-insensitive, but not tag names. For example,
 "qual" can be used instead of "QUAL", "strlen()" instead of "STRLEN()" , but
 not "dp" instead of "DP".
-</li></ul></div><p><span class="strong"><strong>Examples:</strong></span></p><pre class="literallayout">MIN(DV)&gt;5</pre><pre class="literallayout">MIN(DV/DP)&gt;0.3</pre><pre class="literallayout">MIN(DP)&gt;10 &amp; MIN(DV)&gt;3</pre><pre class="literallayout">QUAL&gt;10 |  FMT/GQ&gt;10   .. selects only GQ&gt;10 samples</pre><pre class="literallayout">QUAL&gt;10 || FMT/GQ&gt;10   .. selects all samples at QUAL&gt;10 sites</pre><pre class="literallayout">TYPE="snp" &amp;&amp; QUAL&gt;=10 &amp;&amp; (DP4[2]+DP4[3] &gt; 2)</pre><pre class="literallayout">MIN(DP)&gt;35 &amp;&amp; AVG(GQ)&gt;50</pre><pre class="literallayout">ID=@file       .. selects lines with ID present in the file</pre><pre class="literallayout">ID!=@~/file    .. skip lines with ID present in the ~/file</pre><pre class="literallayout">MAF[0]&lt;0.05    .. select rare variants at 5% cutoff</pre><p><span class="strong"><strong>Shell expansion:</strong></span></p><p>Note that expressions must often be quoted because some characters
+</li></ul></div><p><span class="strong"><strong>Examples:</strong></span></p><pre class="literallayout">MIN(DV)&gt;5</pre><pre class="literallayout">MIN(DV/DP)&gt;0.3</pre><pre class="literallayout">MIN(DP)&gt;10 &amp; MIN(DV)&gt;3</pre><pre class="literallayout">FMT/DP&gt;10  &amp; FMT/GQ&gt;10 .. both conditions must be satisfied within one sample</pre><pre class="literallayout">FMT/DP&gt;10 &amp;&amp; FMT/GQ&gt;10 .. the conditions can be satisfied in different samples</pre><pre class="literallayout">QUAL&gt;10 |  FMT/GQ&gt;10   .. selects only GQ&gt;10 samples</pre><pre class="literallayout">QUAL&gt;10 || FMT/GQ&gt;10   .. selects all samples at QUAL&gt;10 sites</pre><pre class="literallayout">TYPE="snp" &amp;&amp; QUAL&gt;=10 &amp;&amp; (DP4[2]+DP4[3] &gt; 2)</pre><pre class="literallayout">MIN(DP)&gt;35 &amp;&amp; AVG(GQ)&gt;50</pre><pre class="literallayout">ID=@file       .. selects lines with ID present in the file</pre><pre class="literallayout">ID!=@~/file    .. skip lines with ID present in the ~/file</pre><pre class="literallayout">MAF[0]&lt;0.05    .. select rare variants at 5% cutoff</pre><p><span class="strong"><strong>Shell expansion:</strong></span></p><p>Note that expressions must often be quoted because some characters
 have special meaning in the shell.
 An example of expression enclosed in single quotes which cause
 that the whole expression is passed to the program as intended:</p><pre class="literallayout">bcftools view -i '%ID!="." &amp; MAF[0]&lt;0.01'</pre><p>Please refer to the documentation of your shell for details.</p></div><div class="refsect1" title="SCRIPTS AND OPTIONS"><a id="_scripts_and_options"></a><h2>SCRIPTS AND OPTIONS</h2><div class="refsect2" title="plot-vcfstats [OPTIONS] file.vchk […]"><a id="plot-vcfstats"></a><h3>plot-vcfstats [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vchk</em></span> […]</h3><p>Script for processing output of <span class="strong"><strong><a class="link" href="#stats" title="bcftools stats [OPTIONS] A.vcf.gz [B.vcf.gz]">bcftools stats</a></strong></span>. It can merge

From 2e5fda73099ea237db5d2c0b98881509a1e81ab7 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Mon, 9 Nov 2015 16:26:31 +0000
Subject: [PATCH 116/211] Dynamically export bcftools symbols to plugins

...instead of linking the plugins against libhts.so.  This simplifies
building and installation, as plugins no longer need to be able to find
libhts.so/.dylib at runtime -- which to date has unfortunately often
been done via $LD_LIBRARY_PATH.

On OS X, build plugins as Mach-O bundles rather than shared libraries
(and ensure that bcftools is built first, so is available for use with
-bundle_loader).  Fixes #225.

(TODO) The advice in print_plugin_usage_hint() should be revisited.

When bcftools is linked to libhts.a statically, there is a small chance
that a plugin will need HTSlib functions that have not been pulled in by
the bcftools executable.  This is surely unlikely, and can be prevented
by linking bcftools or your plugin against a shared libhts.so.

Fixes #249; fixes #224; supersedes and closes #254.
---
 Makefile              | 18 +++++++++++++-----
 plugins/color-chrs.mk |  4 ++--
 plugins/fixploidy.mk  |  4 ++--
 plugins/vcf2sex.mk    |  4 ++--
 4 files changed, 19 insertions(+), 11 deletions(-)

diff --git a/Makefile b/Makefile
index d6f620f86..042149993 100644
--- a/Makefile
+++ b/Makefile
@@ -1,6 +1,6 @@
 # Makefile for bcftools, utilities for Variant Call Format VCF/BCF files.
 #
-#   Copyright (C) 2012-2014 Genome Research Ltd.
+#   Copyright (C) 2012-2015 Genome Research Ltd.
 #
 #   Author: Petr Danecek <pd3@sanger.ac.uk>
 #
@@ -113,8 +113,16 @@ PLUGINC = $(foreach dir, plugins, $(wildcard $(dir)/*.c))
 PLUGINS = $(PLUGINC:.c=.so)
 PLUGINM = $(PLUGINC:.c=.mk)
 
-%.so: %.c version.h version.c $(HTSDIR)/libhts.so
-	$(CC) -fPIC -shared $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -L$(HTSDIR) $(LDFLAGS) -o $@ version.c $< -lhts $(LIBS)
+ifeq "$(shell uname -s)" "Darwin"
+$(PLUGINS): | bcftools
+
+PLUGIN_FLAGS = -bundle -bundle_loader bcftools
+else
+PLUGIN_FLAGS = -fPIC -shared
+endif
+
+%.so: %.c version.h version.c
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(LIBS)
 
 -include $(PLUGINM)
 
@@ -170,10 +178,10 @@ version.o: version.h version.c
 test/test-rbuf.o: test/test-rbuf.c rbuf.h
 
 test/test-rbuf: test/test-rbuf.o
-	$(CC) $(LDFLAGS) -o $@ $^ -lm -ldl $(LIBS)
+	$(CC) $(LDFLAGS) -o $@ $^ -lm $(LIBS)
 
 bcftools: $(HTSLIB) $(OBJS)
-	$(CC) $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
+	$(CC) -rdynamic $(LDFLAGS) -o $@ $(OBJS) $(HTSLIB) -lpthread -lz -lm -ldl $(GSL_LIBS) $(LIBS)
 
 doc/bcftools.1: doc/bcftools.txt
 	cd doc && a2x -adate="$(DOC_DATE)" -aversion=$(DOC_VERSION) --doctype manpage --format manpage bcftools.txt
diff --git a/plugins/color-chrs.mk b/plugins/color-chrs.mk
index ca7a8a408..506b99d5a 100644
--- a/plugins/color-chrs.mk
+++ b/plugins/color-chrs.mk
@@ -1,2 +1,2 @@
-plugins/color-chrs.so: plugins/color-chrs.c version.h version.c HMM.h HMM.c $(HTSDIR)/libhts.so
-	$(CC) -fPIC -shared $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -L$(HTSDIR) $(LDFLAGS) -o $@ HMM.c version.c $< -lhts $(LIBS)
+plugins/color-chrs.so: plugins/color-chrs.c version.h version.c HMM.h HMM.c
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ HMM.c version.c $< $(LIBS)
diff --git a/plugins/fixploidy.mk b/plugins/fixploidy.mk
index 675282fe3..c476169d3 100644
--- a/plugins/fixploidy.mk
+++ b/plugins/fixploidy.mk
@@ -1,2 +1,2 @@
-plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
-	$(CC) -fPIC -shared $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -L$(HTSDIR) $(LDFLAGS) -o $@ ploidy.c version.c $< -lhts $(LIBS)
+plugins/fixploidy.so: plugins/fixploidy.c version.h version.c ploidy.h ploidy.c
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ ploidy.c version.c $< $(LIBS)
diff --git a/plugins/vcf2sex.mk b/plugins/vcf2sex.mk
index 1f12fb038..fa3d9996c 100644
--- a/plugins/vcf2sex.mk
+++ b/plugins/vcf2sex.mk
@@ -1,2 +1,2 @@
-plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c $(HTSDIR)/libhts.so
-	$(CC) -fPIC -shared $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) -L$(HTSDIR) $(LDFLAGS) -o $@ ploidy.c version.c $< -lhts $(LIBS)
+plugins/vcf2sex.so: plugins/vcf2sex.c version.h version.c ploidy.h ploidy.c
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ ploidy.c version.c $< $(LIBS)

From db3d87d21c16cada798daaf4bd8aea5e83e830c8 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Tue, 10 Nov 2015 15:37:44 +0000
Subject: [PATCH 117/211] Fix error message segfault [minor]

---
 vcfview.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcfview.c b/vcfview.c
index ed888c7c1..5727ab6d5 100644
--- a/vcfview.c
+++ b/vcfview.c
@@ -470,7 +470,7 @@ void set_allele_type (int *atype, char *atype_string)
         *atype = ALLELE_NONMAJOR;
     }
     else {
-        error("Error: allele type (%s) not recognised. Must be one of nref|alt1|minor|major|nonmajor: %s\n", atype_string);
+        error("Error: allele type not recognised. Expected one of nref|alt1|minor|major|nonmajor, got \"%s\".\n", atype_string);
     }
 }
 

From 63cffa41eae7b0349b56a44e400fe2f963e69ca2 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 12 Nov 2015 10:48:08 +0000
Subject: [PATCH 118/211] further fixes in vcf2sex

- check the return status of bcf_get_fmt to prevent segfaults when GT tag is
  not present
- fix a silly error in assigning homs and hets from likelihoods
- set to missing when most het and hom equally likely

Closes #347
---
 plugins/vcf2sex.c | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index 85be9626e..b9ce69dcc 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -246,7 +246,8 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
 
         if ( args->guess & GUESS_GT )   // use GTs to guess the ploidy
         {
-            bcf_fmt_t * fmt = bcf_get_fmt(args->hdr, rec, "GT");
+            bcf_fmt_t *fmt = bcf_get_fmt(args->hdr, rec, "GT");
+            if ( !fmt ) continue;
             for (ismpl=0; ismpl<args->nsample; ismpl++)
             {
                 count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts[ismpl];
@@ -268,10 +269,6 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
                 int phom = INT_MAX, phet = INT_MAX, ial, jal, k = 0;
                 for (ial=0; ial<rec->n_allele; ial++)
                 {
-                    if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
-                    ptr[k] *= gl2pl;
-                    if ( phom > ptr[k] ) phom = ptr[k];
-                    k++;
                     for (jal=0; jal<ial; jal++)
                     {
                         if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
@@ -279,10 +276,14 @@ int process_region_guess(args_t *args, char *seq, regitr_t *itr)
                         if ( phet > ptr[k] ) phet = ptr[k];
                         k++;
                     }
+                    if ( ptr[k] == bcf_int32_missing || ptr[k] == bcf_int32_vector_end )  break;
+                    ptr[k] *= gl2pl;
+                    if ( phom > ptr[k] ) phom = ptr[k];
+                    k++;
                 }
                 count_t *counts = stats ? &stats->counts[ismpl] : &args->bg_counts[ismpl];
                 if ( k == rec->n_allele ) counts->nhom++;   // haploid
-                else if ( k != rec->n_allele*(rec->n_allele+1)/2 ) counts->nmiss++;
+                else if ( phet == phom || k != rec->n_allele*(rec->n_allele+1)/2 ) counts->nmiss++;
                 else if ( phet < phom ) counts->nhet++;
                 else counts->nhom++;
             }

From 3eb86dca612545d97a190d412d2e3673ff0f6212 Mon Sep 17 00:00:00 2001
From: David Laehnemann <david.laehnemann@hhu.de>
Date: Thu, 12 Nov 2015 21:19:03 +0100
Subject: [PATCH 119/211] plot-vcfstats: plotting of sample names fixed

Plotting of sample names instead of sample ID numbers (flags -s/--sample-names) in plot-vcfstats did not work as the first input to plt.xticks in <prefix>-plot.py was an array of strings instead of an array of integers for all by-sample plots. A simple call of int() around the row[0] argument in the list comprehension fixes that.
---
 plot-vcfstats | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/plot-vcfstats b/plot-vcfstats
index e46b3eab8..5989062f4 100755
--- a/plot-vcfstats
+++ b/plot-vcfstats
@@ -877,7 +877,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Ts/Tv')
             \\tax1.set_ylim(min(float(row[1]) for row in dat)-0.1,max(float(row[1]) for row in dat)+0.1)
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -895,7 +895,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('nHet(RA) / nHom(AA)')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -913,7 +913,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Number of SNPs')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -931,7 +931,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Number of indels')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -949,7 +949,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Number of singletons')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -967,7 +967,7 @@ sub plot_per_sample_stats
             \\tax1.set_ylabel('Average depth')
             \\tax1.ticklabel_format(style='sci', scilimits=(0,0), axis='y')
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[7] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)
@@ -1469,7 +1469,7 @@ sub plot_concordance_by_sample
             \\tax1.set_ylabel('Non-ref discordance')
             \\tax1.set_ylim(0,)
             \\tif sample_names:
-            \\t\\t     plt.xticks([row[0] for row in dat],[row[2] for row in dat],**sample_font)
+            \\t\\t     plt.xticks([int(row[0]) for row in dat],[row[2] for row in dat],**sample_font)
             \\t\\t     plt.subplots_adjust(**sample_margins)
             \\telse:
             \\t\\t     plt.subplots_adjust(right=0.98,left=0.07,bottom=0.17)

From 459a7ab1ca94dff1d3fda324c2c657b181c214c7 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 16 Nov 2015 09:02:53 +0000
Subject: [PATCH 120/211] update docs from asciidoc

---
 doc/bcftools.1    | 252 +++++++++++++++++++++++++++++++++++++++++++++-
 doc/bcftools.html | 171 +++++++++++++++++++++++++++++--
 2 files changed, 414 insertions(+), 9 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index 37fbd21e0..ef6ae10ed 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-11-06 16:12 GMT
+.\"      Date: 2015-11-16 09:01 GMT
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-11\-06 16:12 GMT" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-11\-16 09:01 GMT" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-11\-06 16:12 GMT\fR and refers to bcftools git version \fB1\&.2\-170\-g0b9ad1a+\fR\&.
+This manual page was last updated \fB2015\-11\-16 09:01 GMT\fR and refers to bcftools git version \fB1\&.2\-182\-g6710191+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -97,6 +97,19 @@ For a full list of available commands, run \fBbcftools\fR without arguments\&. F
 .IP \(bu 2.3
 .\}
 
+\fBcnv\fR
+\&.\&. Copy Number Variation caller
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
 \fBconcat\fR
 \&.\&. concatenate VCF/BCF files from the same set of samples
 .RE
@@ -227,6 +240,19 @@ For a full list of available commands, run \fBbcftools\fR without arguments\&. F
 .IP \(bu 2.3
 .\}
 
+\fBpolysomy\fR
+\&.\&. detect contaminations and whole\-chromosome aberrations
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
 \fBquery\fR
 \&.\&. transform VCF/BCF into user\-defined formats
 .RE
@@ -682,6 +708,131 @@ List of annotations to remove\&. Use "FILTER" to remove all filters or "FILTER/S
 .if n \{\
 .RE
 .\}
+.SS "bcftools cnv \fI[OPTIONS]\fR \fIFILE\fR"
+.sp
+Copy number variation caller, requires a VCF annotated with the Illumina\(cqs B\-allele frequency (BAF) and Log R Ratio intensity (LRR) values\&. The HMM considers the following copy number states: CN 2 (normal), 1 (single\-copy loss), 0 (complete loss), 3 (single\-copy gain)\&.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBGeneral Options:\fR
+.RS 4
+.PP
+\fB\-c, \-\-control\-sample\fR \fIstring\fR
+.RS 4
+optional control sample name\&. If given, pairwise calling is performed and the
+\fB\-P\fR
+option can be used
+.RE
+.PP
+\fB\-f, \-\-AF\-file\fR \fIfile\fR
+.RS 4
+read allele frequencies from a tab\-delimited file with the columns CHR,POS,REF,ALT,AF
+.RE
+.PP
+*\-o, \-\-output\-dir \fIpath\fR
+.RS 4
+output directory
+.RE
+.PP
+*\-p, \-\-plot\-threshold \fIfloat\fR
+.RS 4
+call
+\fBmatplotlib\fR
+to produce plots for chromosomes with quality at least
+\fIfloat\fR, useful for visual inspection of the calls\&. With
+\fB\-p 0\fR, plots for all chromosomes will be generated\&. If not given, a
+\fBmatplotlib\fR
+script will be created but not called\&.
+.RE
+.PP
+\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-R, \-\-regions\-file\fR \fIfile\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-s, \-\-query\-sample\fR \fIstring\fR
+.RS 4
+query samply name
+.RE
+.PP
+\fB\-t, \-\-targets\fR \fILIST\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-T, \-\-targets\-file\fR \fIFILE\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBHMM Options:\fR
+.RS 4
+.PP
+\fB\-a, \-\-aberrant\fR \fIfloat\fR[,\fIfloat\fR]
+.RS 4
+fraction of aberrant cells in query and control\&. The hallmark of duplications and contaminations is the BAF value of heterozygous markers which is dependent on the fraction of aberrant cells\&. Sensitivity to smaller fractions of cells can be increased by setting
+\fB\-a\fR
+to a lower value\&. Note however, that this comes at the cost of increased false discovery rate\&.
+.RE
+.PP
+\fB\-b, \-\-BAF\-weight\fR \fIfloat\fR
+.RS 4
+relative contribution from BAF
+.RE
+.PP
+\fBd, \-\-BAF\-dev\fR \fIfloat\fR[,\fIfloat\fR]
+.RS 4
+expected BAF deviation in query and control, i\&.e\&. the noise observed in the data\&.
+.RE
+.PP
+\fB\-e, \-\-err\-prob\fR \fIfloat\fR
+.RS 4
+uniform error probability
+.RE
+.PP
+\fB\-l, \-\-LRR\-weight\fR \fIfloat\fR
+.RS 4
+relative contribution from LRR\&. With noisy data, this option can have big effect on the number of calls produced\&. In truly random noise (such as in simulated data), the value should be set high (1\&.0), but in the presence of systematic noise when LRR are not informative, lower values result in cleaner calls (0\&.2)\&.
+.RE
+.PP
+\fB\-L, \-\-LRR\-smooth\-win\fR \fIint\fR
+.RS 4
+reduce LRR noise by applying moving average given this window size
+.RE
+.PP
+\fB\-O, \-\-optimize\fR \fIfloat\fR
+.RS 4
+iteratively estimate the fraction of aberrant cells, down to the given fraction\&. Lowering this value from the default 1\&.0 to say, 0\&.3, can help discover more events but also increases noise
+.RE
+.PP
+\fB\-P, \-\-same\-prob\fR \fIfloat\fR
+.RS 4
+the prior probability of the query and the control sample being the same\&. Setting to 0 calls both independently, setting to 1 forces the same copy number state in both\&.
+.RE
+.PP
+\fB\-x, \-\-xy\-prob\fR \fIfloat\fR
+.RS 4
+the HMM probability of transition to another copy number state\&. Increasing this values leads to smaller and more frequent calls\&.
+.RE
+.RE
 .SS "bcftools call \fI[OPTIONS]\fR \fIFILE\fR"
 .sp
 This command replaces the former \fBbcftools view\fR caller\&. Some of the original functionality has been temporarily lost in the process of transition under htslib, but will be added back on popular demand\&. The original calling model can be invoked with the \fB\-c\fR option\&.
@@ -2324,6 +2475,101 @@ void destroy(void);
 .RE
 .\}
 .RE
+.SS "bcftools polysomy [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR"
+.sp
+Detect number of chromosomal copies in VCFs annotates with the Illumina\(cqs B\-allele frequency (BAF) values\&. Note that this command is not compiled in by default, see the section \fBOptional Compilation with GSL\fR in the INSTALL file for help\&.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBGeneral options:\fR
+.RS 4
+.PP
+\fB\-o, \-\-output\-dir\fR \fIpath\fR
+.RS 4
+output directory
+.RE
+.PP
+\fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-R, \-\-regions\-file\fR \fIfile\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-s, \-\-sample\fR \fIstring\fR
+.RS 4
+samply name
+.RE
+.PP
+\fB\-t, \-\-targets\fR \fILIST\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-T, \-\-targets\-file\fR \fIFILE\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-v, \-\-verbose\fR
+.RS 4
+verbose debugging output which gives hints about the thresholds and decisions made by the program\&. Note that the exact output can change between versions\&.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBAlgorithm options:\fR
+.RS 4
+.PP
+\fB\-b, \-\-peak\-size\fR \fIfloat\fR
+.RS 4
+the minimum peak size considered as a good match can be from the interval [0,1] where larger is stricter
+.RE
+.PP
+\fB\-c, \-\-cn\-penalty\fR \fIfloat\fR
+.RS 4
+a penalty for increasing copy number state\&. How this works: multiple peaks are always a better fit than a single peak, therefore the program prefers a single peak (normal copy number) unless the absolute deviation of the multiple peaks fit is significantly smaller\&. Here the meaning of "significant" is given by the
+\fIfloat\fR
+from the interval [0,1] where larger is stricter\&.
+.RE
+.PP
+\fB\-f, \-\-fit\-th\fR \fIfloat\fR
+.RS 4
+threshold for goodness of fit (normalized absolute deviation), smaller is stricter
+.RE
+.PP
+\fB\-i, \-\-include\-aa\fR
+.RS 4
+include also the AA peak in CN2 and CN3 evaluation\&. This usually requires increasing
+\fB\-f\fR\&.
+.RE
+.PP
+\fB\-m, \-\-min\-fraction\fR \fIfloat\fR
+.RS 4
+minimum distinguishable fraction of aberrant cells\&. The experience shows that trustworthy are estimates of 20% and more\&.
+.RE
+.PP
+\fB\-p, \-\-peak\-symmetry\fR \fIfloat\fR
+.RS 4
+a heuristics to filter failed fits where the expected peak symmetry is violated\&. The
+\fIfloat\fR
+is from the interval [0,1] and larger is stricter
+.RE
+.RE
 .SS "bcftools query [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR [\fIfile\&.vcf\&.gz\fR [\&...]]"
 .sp
 Extracts fields from VCF or BCF files and outputs them in user\-defined format\&.
diff --git a/doc/bcftools.html b/doc/bcftools.html
index a29a9148c..f3a14405a 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp152704"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25136160"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
@@ -8,7 +8,7 @@
 work in most, but not all situations. In general, whenever multiple VCFs are
 read simultaneously, they must be indexed and therefore also compressed.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-11-06 16:12 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-170-g0b9ad1a+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-11-16 09:01 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-182-g6710191+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -23,6 +23,8 @@
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#call" title="bcftools call [OPTIONS] FILE">call</a></strong></span>        ..  SNP/indel calling (former "view")
 </li><li class="listitem">
+<span class="strong"><strong><a class="link" href="#cnv" title="bcftools cnv [OPTIONS] FILE">cnv</a></strong></span>          ..  Copy Number Variation caller
+</li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#concat" title="bcftools concat [OPTIONS] FILE1 FILE2 […]">concat</a></strong></span>    ..  concatenate VCF/BCF files from the same set of samples
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#consensus" title="bcftools consensus [OPTIONS] FILE">consensus</a></strong></span>    ..  create consensus sequence by applying VCF variants
@@ -43,6 +45,8 @@
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#plugin" title="bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]">plugin</a></strong></span>    ..  run user-defined plugin
 </li><li class="listitem">
+<span class="strong"><strong><a class="link" href="#polysomy" title="bcftools polysomy [OPTIONS] file.vcf.gz">polysomy</a></strong></span>   ..  detect contaminations and whole-chromosome aberrations
+</li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#query" title="bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]">query</a></strong></span>      ..  transform VCF/BCF into user-defined formats
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#reheader" title="bcftools reheader [OPTIONS] file.vcf.gz">reheader</a></strong></span>   ..  modify VCF/BCF header, change sample names
@@ -342,7 +346,98 @@
     bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG inut.vcf
 
     # Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
-    bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf</pre></div><div class="refsect2" title="bcftools call [OPTIONS] FILE"><a id="call"></a><h3>bcftools call <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command replaces the former <span class="strong"><strong>bcftools view</strong></span> caller. Some of the original
+    bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf</pre></div><div class="refsect2" title="bcftools cnv [OPTIONS] FILE"><a id="cnv"></a><h3>bcftools cnv <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>Copy number variation caller, requires a VCF annotated with the Illumina’s
+B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
+considers the following copy number states: CN 2 (normal), 1 (single-copy
+loss), 0 (complete loss), 3 (single-copy gain).</p><div class="refsect3" title="General Options:"><a id="_general_options"></a><h4>General Options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-c, --control-sample</strong></span> <span class="emphasis"><em>string</em></span>
+</span></dt><dd>
+    optional control sample name. If given, pairwise calling is performed
+    and the <span class="strong"><strong>-P</strong></span>  option can be used
+</dd><dt><span class="term">
+<span class="strong"><strong>-f, --AF-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    read allele frequencies from  a tab-delimited file with the columns CHR,POS,REF,ALT,AF
+</dd><dt><span class="term">
+*-o, --output-dir <span class="emphasis"><em>path</em></span>
+</span></dt><dd>
+    output directory
+</dd><dt><span class="term">
+*-p, --plot-threshold <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    call <span class="strong"><strong>matplotlib</strong></span> to produce plots for chromosomes with quality at least <span class="emphasis"><em>float</em></span>,
+    useful for visual inspection of the calls. With <span class="strong"><strong>-p 0</strong></span>, plots for all chromosomes will be
+    generated. If not given, a <span class="strong"><strong>matplotlib</strong></span> script will be created but not called.
+</dd><dt><span class="term">
+<span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-s, --query-sample</strong></span> <span class="emphasis"><em>string</em></span>
+</span></dt><dd>
+    query samply name
+</dd><dt><span class="term">
+<span class="strong"><strong>-t, --targets</strong></span> <span class="emphasis"><em>LIST</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd></dl></div></div><div class="refsect3" title="HMM Options:"><a id="_hmm_options"></a><h4>HMM Options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-a, --aberrant</strong></span> <span class="emphasis"><em>float</em></span>[,<span class="emphasis"><em>float</em></span>]
+</span></dt><dd>
+    fraction of aberrant cells in query and control. The hallmark of
+    duplications and contaminations is the BAF value of heterozygous markers
+    which is dependent on the fraction of aberrant cells. Sensitivity to
+    smaller fractions of cells can be increased by setting <span class="strong"><strong>-a</strong></span> to a lower value. Note
+    however, that this comes at the cost of increased false discovery rate.
+</dd><dt><span class="term">
+<span class="strong"><strong>-b, --BAF-weight</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    relative contribution from BAF
+</dd><dt><span class="term">
+<span class="strong"><strong>d, --BAF-dev</strong></span> <span class="emphasis"><em>float</em></span>[,<span class="emphasis"><em>float</em></span>]
+</span></dt><dd>
+    expected BAF deviation in query and control, i.e. the noise observed
+    in the data.
+</dd><dt><span class="term">
+<span class="strong"><strong>-e, --err-prob</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    uniform error probability
+</dd><dt><span class="term">
+<span class="strong"><strong>-l, --LRR-weight</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    relative contribution from LRR. With noisy data, this option can have big effect
+    on the number of calls produced. In truly random noise (such as in simulated data),
+    the value should be set high (1.0), but in the presence of systematic noise
+    when LRR are not informative, lower values result in cleaner calls (0.2).
+</dd><dt><span class="term">
+<span class="strong"><strong>-L, --LRR-smooth-win</strong></span> <span class="emphasis"><em>int</em></span>
+</span></dt><dd>
+    reduce LRR noise by applying moving average given this window size
+</dd><dt><span class="term">
+<span class="strong"><strong>-O, --optimize</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    iteratively estimate the fraction of aberrant cells, down to the given fraction.
+    Lowering this value from the default 1.0 to say, 0.3, can help discover more
+    events but also increases noise
+</dd><dt><span class="term">
+<span class="strong"><strong>-P, --same-prob</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    the prior probability of the query and the control sample being the same.
+    Setting to 0 calls both independently, setting to 1 forces the same copy
+    number state in both.
+</dd><dt><span class="term">
+<span class="strong"><strong>-x, --xy-prob</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    the HMM probability of transition to another copy number state. Increasing this
+    values leads to smaller and more frequent calls.
+</dd></dl></div></div></div><div class="refsect2" title="bcftools call [OPTIONS] FILE"><a id="call"></a><h3>bcftools call <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command replaces the former <span class="strong"><strong>bcftools view</strong></span> caller. Some of the original
 functionality has been temporarily lost in the process of transition under
 <a class="ulink" href="http://github.com/samtools/htslib" target="_top">htslib</a>, but will be added back on popular
 demand. The original calling model can be invoked with the <span class="strong"><strong>-c</strong></span> option.</p><div class="refsect3" title="File format options:"><a id="_file_format_options"></a><h4>File format options:</h4><div class="variablelist"><dl><dt><span class="term">
@@ -1281,7 +1376,71 @@
 bcf1_t *process(bcf1_t *rec);
 
 // Called after all lines have been processed to clean up
-void destroy(void);</pre></div></div><div class="refsect2" title="bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]"><a id="query"></a><h3>bcftools query [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span> [<span class="emphasis"><em>file.vcf.gz</em></span> […]]</h3><p>Extracts fields from VCF or BCF files and outputs them in user-defined format.</p><div class="variablelist"><dl><dt><span class="term">
+void destroy(void);</pre></div></div><div class="refsect2" title="bcftools polysomy [OPTIONS] file.vcf.gz"><a id="polysomy"></a><h3>bcftools polysomy [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Detect number of chromosomal copies in VCFs annotates with the Illumina’s
+B-allele frequency (BAF) values. Note that this command is not compiled
+in by default, see the section <span class="strong"><strong>Optional Compilation with GSL</strong></span> in the INSTALL
+file for help.</p><div class="refsect3" title="General options:"><a id="_general_options_2"></a><h4>General options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-o, --output-dir</strong></span> <span class="emphasis"><em>path</em></span>
+</span></dt><dd>
+    output directory
+</dd><dt><span class="term">
+<span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-s, --sample</strong></span> <span class="emphasis"><em>string</em></span>
+</span></dt><dd>
+    samply name
+</dd><dt><span class="term">
+<span class="strong"><strong>-t, --targets</strong></span> <span class="emphasis"><em>LIST</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-v, --verbose</strong></span>
+</span></dt><dd>
+    verbose debugging output which gives hints about the thresholds and decisions made
+    by the program. Note that the exact output can change between versions.
+</dd></dl></div></div><div class="refsect3" title="Algorithm options:"><a id="_algorithm_options"></a><h4>Algorithm options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-b, --peak-size</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    the minimum peak size considered as a good match can be from the interval [0,1]
+    where larger is stricter
+</dd><dt><span class="term">
+<span class="strong"><strong>-c, --cn-penalty</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    a penalty for increasing copy number state. How this works: multiple peaks
+    are always a better fit than a single peak, therefore the program prefers
+    a single peak (normal copy number) unless the absolute deviation of the
+    multiple peaks fit is significantly smaller. Here the meaning of
+    "significant" is given by the <span class="emphasis"><em>float</em></span> from the interval [0,1] where
+    larger is stricter.
+</dd><dt><span class="term">
+<span class="strong"><strong>-f, --fit-th</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    threshold for goodness of fit (normalized absolute deviation), smaller is stricter
+</dd><dt><span class="term">
+<span class="strong"><strong>-i, --include-aa</strong></span>
+</span></dt><dd>
+    include also the AA peak in CN2 and CN3 evaluation. This usually requires increasing <span class="strong"><strong>-f</strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>-m, --min-fraction</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    minimum distinguishable fraction of aberrant cells. The experience shows that trustworthy
+    are estimates of 20% and more.
+</dd><dt><span class="term">
+<span class="strong"><strong>-p, --peak-symmetry</strong></span> <span class="emphasis"><em>float</em></span>
+</span></dt><dd>
+    a heuristics to filter failed fits where the expected peak symmetry is violated.
+    The <span class="emphasis"><em>float</em></span> is from the interval [0,1] and larger is stricter
+</dd></dl></div></div></div><div class="refsect2" title="bcftools query [OPTIONS] file.vcf.gz [file.vcf.gz […]]"><a id="query"></a><h3>bcftools query [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span> [<span class="emphasis"><em>file.vcf.gz</em></span> […]]</h3><p>Extracts fields from VCF or BCF files and outputs them in user-defined format.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-c, --collapse</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>|<span class="emphasis"><em>both</em></span>|<span class="emphasis"><em>all</em></span>|<span class="emphasis"><em>some</em></span>|<span class="emphasis"><em>none</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1389,7 +1548,7 @@
   HWi = P_i(HW)
 
   P_{i+1}(AZ) = oAZ * max[(1 - tAZ * ci) * AZ{i-1} , tAZ * ci * (1-AZ{i-1})]
-  P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]</pre></div><div class="refsect3" title="General Options:"><a id="_general_options"></a><h4>General Options:</h4><div class="variablelist"><dl><dt><span class="term">
+  P_{i+1}(HW) = oHW * max[(1 - tHW * ci) * (1-AZ{i-1}) , tHW * ci * AZ{i-1}]</pre></div><div class="refsect3" title="General Options:"><a id="_general_options_3"></a><h4>General Options:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>--AF-dflt</strong></span> <span class="emphasis"><em>FLOAT</em></span>
 </span></dt><dd>
     in case allele frequency is not known, use the <span class="emphasis"><em>FLOAT</em></span>. By default, sites where
@@ -1455,7 +1614,7 @@
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
-</dd></dl></div></div><div class="refsect3" title="HMM Options:"><a id="_hmm_options"></a><h4>HMM Options:</h4><div class="variablelist"><dl><dt><span class="term">
+</dd></dl></div></div><div class="refsect3" title="HMM Options:"><a id="_hmm_options_2"></a><h4>HMM Options:</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-a, --hw-to-az</strong></span> <span class="emphasis"><em>FLOAT</em></span>
 </span></dt><dd>
     P(AZ|HW) transition probability from AZ (autozygous) to HW (Hardy-Weinberg) state

From 37b0ddc34ba17fbf58bdb96a19f4af14e7d158c5 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 16 Nov 2015 16:09:40 +0000
Subject: [PATCH 121/211] add *.dSYM to .gitignore

These files are generated on Mac OS X after 2e5fda73099ea237db5d2c0b98881509a1e81ab7
---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 21e4d81fb..b251ae6ab 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,7 @@ bcftools
 *.o
 /version.h
 plugins/*.so
+plugins/*.dSYM
 plugins/*.P
 
 /test/test-rbuf

From 8e8679d28a2bde33cc3a67c7afbde10b81f0b8c1 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 18 Nov 2015 13:57:25 +0000
Subject: [PATCH 122/211] Prevent empty PL fields on BCF output with "call -C
 alleles"

---
 mcall.c | 1 +
 1 file changed, 1 insertion(+)

diff --git a/mcall.c b/mcall.c
index 67ae04482..70d617c79 100644
--- a/mcall.c
+++ b/mcall.c
@@ -1332,6 +1332,7 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
                 if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(unseen,unseen);
                 new_pl[k] = ori_pl[k_ori];
             }
+            if ( !k && new_pl[k]==bcf_int32_vector_end ) new_pl[k]=bcf_int32_missing;
         }
         ori_pl += npls_ori;
         new_pl += npls_new;

From 03c60cfd3c3ad5715f3795faa1101d58281a2d86 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 19 Nov 2015 11:57:38 +0000
Subject: [PATCH 123/211] add POS as a filter column

---
 doc/bcftools.txt   |  4 +++-
 filter.c           | 14 +++++++++++++-
 test/filter.11.out | 26 ++++++++++++++++++++++++++
 test/test.pl       |  3 ++-
 4 files changed, 44 insertions(+), 3 deletions(-)
 create mode 100644 test/filter.11.out

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 9e4ea0d2d..9498e14a1 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1945,7 +1945,7 @@ These filtering expressions are accepted by *<<annotate,annotate>>*,
 
         INFO/DP or DP
         FORMAT/DV, FMT/DV, or DV
-        FILTER, QUAL, ID, REF, ALT[0]
+        FILTER, QUAL, ID, POS, REF, ALT[0]
 
 * 1 (or 0) to test the presence (or absence) of a flag
 
@@ -2020,6 +2020,8 @@ not "dp" instead of "DP".
 
     MAF[0]<0.05    .. select rare variants at 5% cutoff
 
+    POS>=100   .. restrict your range query, e.g. 20:100-200 to strictly sites with POS in that range.
+
 --
 
 *Shell expansion:*
diff --git a/filter.c b/filter.c
index 924a095eb..c56ae6d12 100644
--- a/filter.c
+++ b/filter.c
@@ -1,6 +1,6 @@
 /*  filter.c -- filter expressions.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2015 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -364,6 +364,12 @@ static int bcf_get_info_value(bcf1_t *line, int info_id, int ivec, void *value)
     return -1;  // this shouldn't happen
 }
 
+static void filters_set_pos(filter_t *flt, bcf1_t *line, token_t *tok)
+{
+    tok->values[0] = line->pos+1;
+    tok->nvalues = 1;
+}
+
 static void filters_set_info_int(filter_t *flt, bcf1_t *line, token_t *tok)
 {
     if ( tok->idx==-2 )
@@ -1206,6 +1212,12 @@ static int filters_init1(filter_t *filter, char *str, int len, token_t *tok)
             tok->tag = strdup("ID");
             return 0;
         }
+        else if ( !strncasecmp(str,"POS",len) )
+        {
+            tok->setter = &filters_set_pos;
+            tok->tag = strdup("POS");
+            return 0;
+        }
         else if ( !strncasecmp(str,"REF",len) )
         {
             tok->setter = &filters_set_ref_string;
diff --git a/test/filter.11.out b/test/filter.11.out
new file mode 100644
index 000000000..8b58d6322
--- /dev/null
+++ b/test/filter.11.out
@@ -0,0 +1,26 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
+##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=test,Description="Testing filter">
+##contig=<ID=1,assembly=b37,length=249250621>
+##contig=<ID=2,assembly=b37,length=249250621>
+##contig=<ID=3,assembly=b37,length=198022430>
+##contig=<ID=4,assembly=b37,length=191154276>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##readme=AAAAAA
+##readme=BBBBBB
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	3106154	.	CAAA	C	342	PASS	AN=4;AC=2	GT:GQ:DP	0/1:245:32	0/1:25:300
+1	3106154	.	C	CT	59.2	PASS	AN=4;AC=2	GT:GQ:DP	0/1:25:12	0/1:245:310
+1	3157410	.	GA	G	90.6	q10	AN=4;AC=4	GT:GQ:DP	1/1:21:21	1/1:21:21
diff --git a/test/test.pl b/test/test.pl
index b23296725..b5b12e337 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 #
-#   Copyright (C) 2012-2014 Genome Research Ltd.
+#   Copyright (C) 2012-2015 Genome Research Ltd.
 #
 #   Author: Petr Danecek <pd3@sanger.ac.uk>
 #
@@ -126,6 +126,7 @@
 test_vcf_view($opts,in=>'view.filter',out=>'view.filter.4.out',args=>q[-H -i'FMT/FRS[1]="BB"'],reg=>'');
 test_vcf_view($opts,in=>'view.filter',out=>'view.filter.5.out',args=>q[-H -i'TXT0="text"'],reg=>'');
 test_vcf_view($opts,in=>'view.chrs',out=>'view.chrs.out',args=>'',reg=>'',tgts=>'view.chrs.tab');
+test_vcf_view($opts,in=>'filter.2',out=>'filter.11.out',args=>q[-i 'POS>=3062917'],reg=>'1:3062917-3157410');
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.6.out',args=>q[-S. -e'TXT0="text"'],reg=>'');
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.7.out',args=>q[-S. -e'FMT/FRS[1]="BB"'],reg=>'');
 test_vcf_filter($opts,in=>'view.filter',out=>'view.filter.8.out',args=>q[-S. -e'FMT/FGS[0]="AAAAAA"'],reg=>'');

From 3aa989e2191f68441f6be8d07d99d3160442f65a Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 30 Nov 2015 12:34:00 +0000
Subject: [PATCH 124/211] Fix typo: annotate -x ^FORMAT/TAG did not work

---
 vcfannotate.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcfannotate.c b/vcfannotate.c
index 621da5739..d653bcd4d 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -310,7 +310,7 @@ static void init_remove_annots(args_t *args)
         ss = *se ? se+1 : se;
     }
     free(str.s);
-    if ( keep_flt || keep_info || keep_flt )
+    if ( keep_flt || keep_info || keep_fmt )
     {
         int j;
         for (j=0; j<args->hdr->nhrec; j++)

From 5d90843e0b271233a42fbf2579c4daa324f4dd30 Mon Sep 17 00:00:00 2001
From: mcshane <sm15@sanger.ac.uk>
Date: Mon, 7 Dec 2015 21:24:44 +0000
Subject: [PATCH 125/211] split out test input files for -c and -m calling

this is to allow pulling in the bugfix from pd3/bcftools@47ab239744ab2aaf2165d1542010ba7e6ba7dafd
the `-c' calling mode is not ready for PLs with missing values
etc yet that are added to the test files in that commit.
---
 test/mpileup.c.X.vcf | 4127 ++++++++++++++++++++++++++++++++++++++++++
 test/mpileup.c.vcf   | 4127 ++++++++++++++++++++++++++++++++++++++++++
 test/test.pl         |    8 +-
 3 files changed, 8258 insertions(+), 4 deletions(-)
 create mode 100644 test/mpileup.c.X.vcf
 create mode 100644 test/mpileup.c.vcf

diff --git a/test/mpileup.c.X.vcf b/test/mpileup.c.X.vcf
new file mode 100644
index 000000000..ea2983a3b
--- /dev/null
+++ b/test/mpileup.c.X.vcf
@@ -0,0 +1,4127 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	1	.	A	<*>	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	2	.	A	<*>	0	.	DP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	3	.	G	<*>	0	.	DP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	4	.	C	<*>	0	.	DP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,71:3:0
+X	5	.	T	<*>	0	.	DP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	6	.	T	<*>	0	.	DP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	7	.	C	<*>	0	.	DP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	8	.	T	<*>	0	.	DP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	9	.	C	<*>	0	.	DP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	10	.	A	<*>	0	.	DP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,69:3:0
+X	11	.	C	<*>	0	.	DP=11;I16=11,0,0,0,413,15603,0,0,319,9251,0,0,241,5495,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	12	.	C	<*>	0	.	DP=11;I16=11,0,0,0,438,17506,0,0,319,9251,0,0,242,5562,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	13	.	C	<*>	0	.	DP=11;I16=11,0,0,0,437,17463,0,0,319,9251,0,0,243,5639,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	14	.	T	<*>	0	.	DP=11;I16=11,0,0,0,453,18715,0,0,319,9251,0,0,242,5628,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	15	.	G	<*>	0	.	DP=11;I16=11,0,0,0,439,17599,0,0,319,9251,0,0,240,5580,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	16	.	T	<*>	0	.	DP=11;I16=11,0,0,0,426,16546,0,0,319,9251,0,0,238,5544,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	17	.	T	<*>	0	.	DP=11;I16=11,0,0,0,407,15195,0,0,319,9251,0,0,235,5469,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+X	18	.	C	<*>	0	.	DP=12;I16=12,0,0,0,450,17136,0,0,379,12851,0,0,231,5353,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,113:6:0	0,9,72:3:0	0,9,72:3:0
+X	19	.	C	<*>	0	.	DP=13;I16=13,0,0,0,502,19652,0,0,439,16451,0,0,228,5246,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,112:6:0	0,12,89:4:0	0,9,72:3:0
+X	20	.	T	<*>	0	.	DP=13;I16=13,0,0,0,532,21878,0,0,439,16451,0,0,226,5150,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,116:6:0	0,12,98:4:0	0,9,72:3:0
+X	21	.	G	<*>	0	.	DP=13;I16=13,0,0,0,498,19254,0,0,439,16451,0,0,224,5066,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,117:6:0	0,12,94:4:0	0,9,72:3:0
+X	22	.	C	<*>	0	.	DP=13;I16=13,0,0,0,511,20289,0,0,470,19210,0,0,223,4993,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,115:6:0	0,12,91:4:0	0,9,76:3:0
+X	23	.	A	<*>	0	.	DP=14;I16=14,0,0,0,513,19399,0,0,530,22810,0,0,223,4931,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,133:7:0	0,12,82:4:0	0,9,82:3:0
+X	24	.	T	<*>	0	.	DP=14;I16=14,0,0,0,534,20540,0,0,530,22810,0,0,224,4882,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,131:7:0	0,12,96:4:0	0,9,80:3:0
+X	25	.	A	<*>	0	.	DP=15;I16=15,0,0,0,561,21133,0,0,590,26410,0,0,225,4847,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,140:8:0	0,12,96:4:0	0,9,81:3:0
+X	26	.	G	<*>	0	.	DP=15;I16=15,0,0,0,591,23429,0,0,590,26410,0,0,227,4827,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,96:4:0	0,9,81:3:0
+X	27	.	A	<*>	0	.	DP=15;I16=15,0,0,0,588,23120,0,0,590,26410,0,0,229,4823,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,12,98:4:0	0,9,83:3:0
+X	28	.	T	<*>	0	.	DP=16;I16=16,0,0,0,605,23001,0,0,650,30010,0,0,231,4835,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,147:8:0	0,12,97:4:0	0,12,101:4:0
+X	29	.	A	<*>	0	.	DP=17;I16=17,0,0,0,615,22533,0,0,710,33610,0,0,234,4864,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,15,102:5:0	0,12,104:4:0
+X	30	.	A	<*>	0	.	DP=17;I16=17,0,0,0,660,25914,0,0,710,33610,0,0,238,4912,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,149:8:0	0,15,115:5:0	0,12,108:4:0
+X	31	.	T	<*>	0	.	DP=17;I16=17,0,0,0,656,25392,0,0,710,33610,0,0,242,4980,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,150:8:0	0,15,113:5:0	0,12,105:4:0
+X	32	.	T	<*>	0	.	DP=17;I16=17,0,0,0,605,21789,0,0,741,36369,0,0,247,5067,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,143:8:0	0,15,104:5:0	0,12,104:4:0
+X	33	.	G	<*>	0	.	DP=17;I16=17,0,0,0,659,25757,0,0,741,36369,0,0,252,5124,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,158:8:0	0,15,118:5:0	0,12,105:4:0
+X	34	.	C	<*>	0	.	DP=17;I16=17,0,0,0,658,25704,0,0,741,36369,0,0,257,5203,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,15,121:5:0	0,12,106:4:0
+X	35	.	A	<*>	0	.	DP=18;I16=18,0,0,0,677,25881,0,0,801,39969,0,0,262,5304,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,152:8:0	0,15,109:5:0	0,15,121:5:0
+X	36	.	T	<*>	0	.	DP=18;I16=18,0,0,0,678,25796,0,0,801,39969,0,0,268,5428,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,15,114:5:0	0,15,125:5:0
+X	37	.	G	<*>	0	.	DP=18;I16=18,0,0,0,685,26291,0,0,801,39969,0,0,274,5576,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,157:8:0	0,15,116:5:0	0,15,126:5:0
+X	38	.	A	<*>	0	.	DP=18;I16=18,0,0,0,697,27245,0,0,801,39969,0,0,280,5748,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,152:8:0	0,15,116:5:0	0,15,129:5:0
+X	39	.	C	<*>	0	.	DP=16;I16=16,0,0,0,591,22311,0,0,743,38287,0,0,288,5942,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,148:7:0	0,12,94:4:0	0,15,123:5:0
+X	40	.	A	<*>	0	.	DP=16;I16=16,0,0,0,630,24896,0,0,743,38287,0,0,295,6107,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,146:7:0	0,12,104:4:0	0,15,127:5:0
+X	41	.	A	<*>	0	.	DP=17;I16=17,0,0,0,645,24685,0,0,803,41887,0,0,302,6294,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,104:4:0	0,15,131:5:0
+X	42	.	T	<*>	0	.	DP=17;I16=17,0,0,0,618,23118,0,0,803,41887,0,0,310,6504,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,155:8:0	0,12,82:4:0	0,15,127:5:0
+X	43	.	T	<*>	0	.	DP=17;I16=17,0,0,0,631,23689,0,0,803,41887,0,0,318,6738,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,101:4:0	0,15,129:5:0
+X	44	.	G	<*>	0	.	DP=17;I16=17,0,0,0,664,26162,0,0,803,41887,0,0,324,6896,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,164:8:0	0,12,100:4:0	0,15,129:5:0
+X	45	.	C	<*>	0	.	DP=17;I16=17,0,0,0,657,25525,0,0,803,41887,0,0,329,7027,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,163:8:0	0,12,108:4:0	0,15,125:5:0
+X	46	.	C	<*>	0	.	DP=17;I16=17,0,0,0,646,25244,0,0,803,41887,0,0,334,7180,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,161:8:0	0,12,98:4:0	0,15,131:5:0
+X	47	.	T	<*>	0	.	DP=17;I16=17,0,0,0,700,28998,0,0,803,41887,0,0,339,7355,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,165:8:0	0,12,110:4:0	0,15,136:5:0
+X	48	.	T	<*>	0	.	DP=17;I16=17,0,0,0,648,25020,0,0,803,41887,0,0,343,7501,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,155:8:0	0,12,105:4:0	0,15,131:5:0
+X	49	.	G	<*>	0	.	DP=18;I16=18,0,0,0,686,26674,0,0,832,42728,0,0,346,7616,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,158:8:0	0,15,119:5:0	0,15,128:5:0
+X	50	.	T	<*>	0	.	DP=18;I16=17,0,0,0,650,24972,0,0,772,39128,0,0,332,7426,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,155:8:0	0,12,101:4:0	0,15,128:5:0
+X	51	.	C	<*>	0	.	DP=18;I16=18,0,0,0,681,26529,0,0,832,42728,0,0,353,7853,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,167:8:0	0,15,99:5:0	0,15,127:5:0
+X	52	.	C	<*>	0	.	DP=18;I16=17,0,0,0,645,24983,0,0,803,41887,0,0,353,7965,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,164:8:0	0,12,99:4:0	0,15,128:5:0
+X	53	.	C	<*>	0	.	DP=18;I16=18,0,0,0,687,26735,0,0,832,42728,0,0,359,8113,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,164:8:0	0,15,113:5:0	0,15,132:5:0
+X	54	.	T	<*>	0	.	DP=18;I16=18,0,0,0,736,30194,0,0,832,42728,0,0,361,8219,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,163:8:0	0,15,128:5:0	0,15,136:5:0
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+X	1111	.	T	<*>	0	.	DP=29;I16=22,6,0,0,1025,37919,0,0,1680,100800,0,0,552,12470,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,30,227:10:0	0,24,227:8:0	0,30,211:10:0
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+X	1933	.	T	<*>	0	.	DP=27;I16=14,13,0,0,962,35344,0,0,1546,91130,0,0,542,12602,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,142:5:0	0,15,158:5:0
+X	1934	.	G	<*>	0	.	DP=27;I16=13,13,0,0,987,38219,0,0,1529,90841,0,0,543,12569,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,15,134:5:0	0,15,143:5:0
+X	1935	.	C	<*>	0	.	DP=27;I16=14,12,0,0,963,36627,0,0,1529,90841,0,0,520,11930,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,162:6:0	0,15,154:5:0
+X	1936	.	C	<*>	0	.	DP=27;I16=14,13,0,0,1018,39406,0,0,1589,94441,0,0,547,12561,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,177:6:0	0,15,159:5:0
+X	1937	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1036,40636,0,0,1589,94441,0,0,547,12489,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,182:6:0	0,15,170:5:0
+X	1938	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1001,38377,0,0,1589,94441,0,0,546,12392,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,166:6:0	0,15,155:5:0
+X	1939	.	T	<*>	0	.	DP=27;I16=14,12,0,0,964,36430,0,0,1560,93600,0,0,525,11909,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,167:6:0	0,12,144:4:0
+X	1940	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1003,37937,0,0,1589,94441,0,0,542,12172,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,159:6:0	0,15,155:5:0
+X	1941	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1004,38072,0,0,1589,94441,0,0,540,12098,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,176:6:0	0,15,156:5:0
+X	1942	.	C	<*>	0	.	DP=27;I16=14,12,0,0,996,38790,0,0,1560,93600,0,0,516,11564,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,174:6:0	0,12,140:4:0
+X	1943	.	T	<*>	0	.	DP=27;I16=14,13,0,0,1044,40952,0,0,1589,94441,0,0,536,12022,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,184:6:0	0,15,167:5:0
+X	1944	.	T	<*>	0	.	DP=27;I16=14,13,0,0,987,37237,0,0,1589,94441,0,0,533,11971,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,15,170:5:0
+X	1945	.	T	<*>	0	.	DP=27;I16=14,13,0,0,993,37067,0,0,1589,94441,0,0,530,11946,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,174:6:0	0,15,171:5:0
+X	1946	.	G	<*>	0	.	DP=27;I16=14,13,0,0,1013,38617,0,0,1589,94441,0,0,526,11896,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,162:6:0	0,15,162:5:0
+X	1947	.	A	<*>	0	.	DP=26;I16=13,13,0,0,950,35522,0,0,1529,90841,0,0,522,11818,0,0;QS=3,0;MQSB=0.945959;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,167:6:0	0,15,160:5:0
+X	1948	.	G	C,<*>	0	.	DP=27;I16=14,12,0,1,966,36912,16,256,1560,93600,29,841,493,11135,25,625;QS=2.90361,0.0963855,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.94394;BQB=1;MQ0F=0	PL:DP:DV	0,45,255,45,255,255:15:0	0,21,190,21,190,190:7:0	1,0,123,13,126,132:5:1
+X	1949	.	A	<*>	0	.	DP=26;I16=14,11,0,0,871,31325,0,0,1469,87241,0,0,490,11048,0,0;QS=3,0;MQSB=0.929204;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,174:7:0	0,15,155:5:0
+X	1950	.	A	<*>	0	.	DP=27;I16=14,13,0,0,1007,38049,0,0,1589,94441,0,0,511,11559,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,205:7:0	0,18,176:6:0
+X	1951	.	G	<*>	0	.	DP=27;I16=14,13,0,0,960,35536,0,0,1589,94441,0,0,509,11469,0,0;QS=3,0;MQSB=0.94394;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,180:7:0	0,18,181:6:0
+X	1952	.	A	<*>	0	.	DP=27;I16=14,12,0,0,924,33366,0,0,1529,90841,0,0,483,10779,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,184:7:0	0,18,182:6:0
+X	1953	.	A	<*>	0	.	DP=28;I16=15,12,0,0,925,32719,0,0,1589,94441,0,0,482,10740,0,0;QS=3,0;MQSB=0.935229;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,189:7:0	0,18,168:6:0
+X	1954	.	A	C,<*>	0	.	DP=29;I16=14,13,0,1,929,33219,18,324,1620,97200,29,841,475,10679,25,625;QS=2.90217,0.0978261,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.949591;BQB=1;MQ0F=0	PL:DP:DV	0,45,255,45,255,255:15:0	0,21,198,21,198,198:7:0	0,0,130,15,133,141:6:1
+X	1955	.	C	<*>	0	.	DP=29;I16=14,12,0,0,961,36067,0,0,1560,93600,0,0,451,10035,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,206:7:0	0,15,165:5:0
+X	1956	.	C	<*>	0	.	DP=29;I16=14,13,0,0,964,35402,0,0,1620,97200,0,0,475,10573,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,15,164:5:0
+X	1957	.	C	<*>	0	.	DP=29;I16=14,13,0,0,980,36212,0,0,1620,97200,0,0,472,10420,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,183:7:0	0,15,167:5:0
+X	1958	.	C	<*>	0	.	DP=29;I16=15,13,0,0,1003,37293,0,0,1649,98041,0,0,493,10825,0,0;QS=3,0;MQSB=0.942064;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,191:7:0	0,18,190:6:0
+X	1959	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1112,43258,0,0,1709,101641,0,0,491,10593,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,213:7:0	0,18,193:6:0
+X	1960	.	T	<*>	0	.	DP=30;I16=17,13,0,0,1053,37939,0,0,1769,105241,0,0,485,10339,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,196:7:0	0,18,186:6:0
+X	1961	.	C	<*>	0	.	DP=30;I16=17,13,0,0,1101,41737,0,0,1769,105241,0,0,480,10122,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,195:7:0	0,18,183:6:0
+X	1962	.	T	<*>	0	.	DP=29;I16=17,12,0,0,1134,44582,0,0,1709,101641,0,0,477,9941,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,208:7:0	0,18,198:6:0
+X	1963	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1066,41050,0,0,1649,98041,0,0,476,9794,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,192:7:0	0,18,188:6:0
+X	1964	.	G	<*>	0	.	DP=28;I16=16,12,0,0,970,34764,0,0,1649,98041,0,0,475,9681,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,178:7:0	0,18,169:6:0
+X	1965	.	T	<*>	0	.	DP=29;I16=16,12,0,0,964,34772,0,0,1649,98041,0,0,449,8977,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,18,171:6:0
+X	1966	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1029,37027,0,0,1709,101641,0,0,474,9558,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,191:7:0	0,18,181:6:0
+X	1967	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1030,37234,0,0,1709,101641,0,0,474,9550,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,187:7:0	0,18,182:6:0
+X	1968	.	T	<*>	0	.	DP=29;I16=16,13,0,0,1075,40173,0,0,1709,101641,0,0,474,9578,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,195:7:0	0,18,190:6:0
+X	1969	.	A	<*>	0	.	DP=28;I16=16,12,0,0,992,35828,0,0,1649,98041,0,0,474,9592,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,18,186:6:0
+X	1970	.	C	<*>	0	.	DP=28;I16=16,12,0,0,1015,37503,0,0,1649,98041,0,0,474,9642,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,170:6:0	0,18,180:6:0
+X	1971	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1073,40273,0,0,1709,101641,0,0,474,9728,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,178:6:0	0,21,206:7:0
+X	1972	.	T	<*>	0	.	DP=30;I16=16,14,0,0,1068,38978,0,0,1769,105241,0,0,475,9851,0,0;QS=3,0;MQSB=0.946202;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,176:6:0	0,21,203:7:0
+X	1973	.	A	<*>	0	.	DP=30;I16=16,13,0,0,1046,38070,0,0,1740,104400,0,0,452,9388,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,172:6:0	0,18,196:6:0
+X	1974	.	A	<*>	0	.	DP=29;I16=16,13,0,0,1086,41474,0,0,1709,101641,0,0,477,10065,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,157:5:0	0,21,214:7:0
+X	1975	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1067,41171,0,0,1649,98041,0,0,478,10156,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,133:4:0	0,21,195:7:0
+X	1976	.	A	<*>	0	.	DP=28;I16=16,12,0,0,981,34839,0,0,1649,98041,0,0,478,10234,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,125:4:0	0,21,199:7:0
+X	1977	.	C	<*>	0	.	DP=28;I16=16,12,0,0,1009,37471,0,0,1649,98041,0,0,477,10297,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,132:4:0	0,21,194:7:0
+X	1978	.	A	<*>	0	.	DP=28;I16=16,12,0,0,1082,42132,0,0,1649,98041,0,0,476,10394,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,144:4:0	0,21,220:7:0
+X	1979	.	G	<*>	0	.	DP=28;I16=16,11,0,0,1019,38927,0,0,1589,94441,0,0,454,10064,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,12,122:4:0	0,21,208:7:0
+X	1980	.	C	<*>	0	.	DP=27;I16=16,10,0,0,932,34456,0,0,1529,90841,0,0,452,10114,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,107:3:0	0,21,197:7:0
+X	1981	.	C	<*>	0	.	DP=28;I16=16,12,0,0,998,36510,0,0,1649,98041,0,0,469,10479,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,9,101:3:0	0,24,219:8:0
+X	1982	.	A	<*>	0	.	DP=29;I16=16,12,0,0,1035,38815,0,0,1649,98041,0,0,472,10548,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,110:3:0	0,27,254:9:0
+X	1983	.	G	<*>	0	.	DP=28;I16=16,12,0,0,1048,40322,0,0,1649,98041,0,0,477,10599,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,96:3:0	0,27,249:9:0
+X	1984	.	A	<*>	0	.	DP=27;I16=16,11,0,0,1024,39232,0,0,1589,94441,0,0,482,10632,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,70:2:0	0,27,255:9:0
+X	1985	.	G	<*>	0	.	DP=27;I16=16,11,0,0,1009,38449,0,0,1589,94441,0,0,487,10695,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,66:2:0	0,27,231:9:0
+X	1986	.	A	<*>	0	.	DP=27;I16=16,10,0,0,926,33696,0,0,1560,93600,0,0,466,10112,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,76:2:0	0,24,223:8:0
+X	1987	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1034,39088,0,0,1649,98041,0,0,495,10807,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,78:2:0	0,27,247:9:0
+X	1988	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1050,39980,0,0,1649,98041,0,0,499,10855,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,63:2:0	0,27,239:9:0
+X	1989	.	G	<*>	0	.	DP=28;I16=17,10,0,0,994,37610,0,0,1589,94441,0,0,493,10801,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,73:2:0	0,27,237:9:0
+X	1990	.	G	T,<*>	0	.	DP=28;I16=17,9,0,1,965,36359,33,1089,1560,93600,29,841,472,10250,25,625;QS=2.90675,0.0932476,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.912952;BQB=1;MQ0F=0	PL:DP:DV	0,48,255,48,255,255:16:0	0,6,71,6,71,71:2:0	2,0,195,26,198,215:9:1
+X	1991	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1017,38203,0,0,1649,98041,0,0,507,10975,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,60:2:0	0,27,250:9:0
+X	1992	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1028,38852,0,0,1649,98041,0,0,509,11039,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,62:2:0	0,27,231:9:0
+X	1993	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1015,37325,0,0,1649,98041,0,0,511,11131,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,59:2:0	0,27,243:9:0
+X	1994	.	T	<*>	0	.	DP=27;I16=16,11,0,0,942,33698,0,0,1589,94441,0,0,514,11250,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,54:2:0	0,24,216:8:0
+X	1995	.	G	<*>	0	.	DP=28;I16=16,11,0,0,960,35432,0,0,1620,97200,0,0,492,10770,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,66:2:0	0,21,188:7:0
+X	1996	.	C	<*>	0	.	DP=29;I16=17,12,0,0,1022,37426,0,0,1709,101641,0,0,519,11469,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,64:2:0	0,24,192:8:0
+X	1997	.	C	<*>	0	.	DP=29;I16=17,11,0,0,934,32858,0,0,1649,98041,0,0,520,11524,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,70:2:0	0,24,193:8:0
+X	1998	.	C	<*>	0	.	DP=29;I16=17,12,0,0,1027,37843,0,0,1709,101641,0,0,522,11562,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,69:2:0	0,24,222:8:0
+X	1999	.	A	<*>	0	.	DP=28;I16=17,11,0,0,1073,41493,0,0,1649,98041,0,0,525,11627,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,21,206:7:0
+X	2000	.	G	<*>	0	.	DP=28;I16=16,11,0,0,1036,40576,0,0,1589,94441,0,0,511,11395,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,18,168:6:0
+X	2001	.	G	<*>	0	.	DP=28;I16=15,11,0,0,955,35661,0,0,1529,90841,0,0,489,10853,0,0;QS=3,0;MQSB=0.927041;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,62:2:0	0,18,172:6:0
+X	2002	.	G	<*>	0	.	DP=28;I16=17,10,0,0,907,32227,0,0,1620,97200,0,0,519,11663,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,53:2:0	0,18,163:6:0
+X	2003	.	T	<*>	0	.	DP=28;I16=17,11,0,0,920,31866,0,0,1649,98041,0,0,541,12163,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,49:2:0	0,21,190:7:0
+X	2004	.	G	<*>	0	.	DP=27;I16=16,10,0,0,970,36928,0,0,1560,93600,0,0,530,12110,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,57:2:0	0,18,178:6:0
+X	2005	.	G	<*>	0	.	DP=27;I16=16,10,0,0,868,30936,0,0,1560,93600,0,0,536,12370,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,59:2:0	0,18,153:6:0
+X	2006	.	C	<*>	0	.	DP=27;I16=16,10,0,0,968,37046,0,0,1560,93600,0,0,541,12605,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,73:2:0	0,18,166:6:0
+X	2007	.	A	<*>	0	.	DP=27;I16=16,11,0,0,1000,37396,0,0,1589,94441,0,0,556,12882,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,76:2:0	0,21,193:7:0
+X	2008	.	C	<*>	0	.	DP=26;I16=16,10,0,0,964,36892,0,0,1529,90841,0,0,555,12833,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,21,183:7:0
+X	2009	.	A	<*>	0	.	DP=26;I16=16,10,0,0,997,38955,0,0,1529,90841,0,0,554,12802,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,21,210:7:0
+X	2010	.	G	<*>	0	.	DP=26;I16=16,9,0,0,936,36208,0,0,1500,90000,0,0,542,12640,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,18,169:6:0
+X	2011	.	C	<*>	0	.	DP=26;I16=16,9,0,0,966,37960,0,0,1500,90000,0,0,541,12617,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,18,175:6:0
+X	2012	.	A	<*>	0	.	DP=27;I16=16,11,0,0,956,35018,0,0,1589,94441,0,0,548,12676,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,74:2:0	0,21,189:7:0
+X	2013	.	C	<*>	0	.	DP=27;I16=15,10,0,0,876,31370,0,0,1500,90000,0,0,514,11950,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,69:2:0	0,18,160:6:0
+X	2014	.	G	<*>	0	.	DP=27;I16=17,10,0,0,903,31239,0,0,1589,94441,0,0,545,12591,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,80:3:0	0,18,160:6:0
+X	2015	.	T	<*>	0	.	DP=27;I16=17,10,0,0,999,37507,0,0,1589,94441,0,0,545,12577,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,95:3:0	0,18,178:6:0
+X	2016	.	T	<*>	0	.	DP=27;I16=17,10,0,0,971,35649,0,0,1589,94441,0,0,545,12583,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,93:3:0	0,18,178:6:0
+X	2017	.	G	<*>	0	.	DP=28;I16=17,11,0,0,1013,37849,0,0,1649,98041,0,0,545,12609,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,91:3:0	0,18,172:6:0
+X	2018	.	C	<*>	0	.	DP=28;I16=17,11,0,0,1060,41414,0,0,1649,98041,0,0,546,12656,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,97:3:0	0,18,169:6:0
+X	2019	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1083,42253,0,0,1649,98041,0,0,547,12725,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,106:3:0	0,18,187:6:0
+X	2020	.	G	<*>	0	.	DP=29;I16=18,11,0,0,1095,42063,0,0,1678,98882,0,0,548,12816,0,0;QS=3,0;MQSB=0.987702;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,85:3:0	0,18,175:6:0
+X	2021	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1081,41535,0,0,1709,101641,0,0,551,12877,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,97:3:0	0,15,167:5:0
+X	2022	.	C	<*>	0	.	DP=30;I16=19,11,0,0,1115,42003,0,0,1769,105241,0,0,555,12907,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,18,177:6:0
+X	2023	.	A	<*>	0	.	DP=30;I16=19,10,0,0,1063,39991,0,0,1709,101641,0,0,549,12837,0,0;QS=3,0;MQSB=0.974027;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,18,186:6:0
+X	2024	.	G	<*>	0	.	DP=32;I16=20,12,0,0,1168,43872,0,0,1889,112441,0,0,564,12982,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,24,203:8:0
+X	2025	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1150,42122,0,0,1889,112441,0,0,569,12981,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,87:3:0	0,24,226:8:0
+X	2026	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1130,40724,0,0,1889,112441,0,0,572,12908,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,208:8:0
+X	2027	.	A	<*>	0	.	DP=32;I16=19,12,0,0,1121,40871,0,0,1829,108841,0,0,550,12240,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,84:3:0	0,21,207:7:0
+X	2028	.	C	<*>	0	.	DP=32;I16=20,12,0,0,1242,48548,0,0,1889,112441,0,0,577,12803,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,228:8:0
+X	2029	.	T	<*>	0	.	DP=32;I16=20,12,0,0,1229,47605,0,0,1889,112441,0,0,578,12724,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,102:3:0	0,24,236:8:0
+X	2030	.	G	<*>	0	.	DP=32;I16=20,12,0,0,1222,47140,0,0,1889,112441,0,0,579,12679,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,93:3:0	0,24,216:8:0
+X	2031	.	C	<*>	0	.	DP=31;I16=19,12,0,0,1150,43656,0,0,1829,108841,0,0,581,12667,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,24,204:8:0
+X	2032	.	C	<*>	0	.	DP=31;I16=19,12,0,0,1157,44035,0,0,1829,108841,0,0,583,12687,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,90:3:0	0,24,210:8:0
+X	2033	.	A	<*>	0	.	DP=30;I16=19,11,0,0,1091,40223,0,0,1769,105241,0,0,585,12689,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,93:3:0	0,21,203:7:0
+X	2034	.	T	<*>	0	.	DP=30;I16=19,11,0,0,1104,41498,0,0,1769,105241,0,0,587,12723,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,91:3:0	0,21,208:7:0
+X	2035	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1084,41024,0,0,1709,101641,0,0,589,12739,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,211:7:0
+X	2036	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1080,40612,0,0,1709,101641,0,0,591,12787,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,67:2:0	0,21,216:7:0
+X	2037	.	T	<*>	0	.	DP=29;I16=18,11,0,0,1082,40956,0,0,1709,101641,0,0,592,12818,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,217:7:0
+X	2038	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1117,43573,0,0,1709,101641,0,0,592,12832,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,211:7:0
+X	2039	.	A	<*>	0	.	DP=29;I16=18,11,0,0,1067,39581,0,0,1709,101641,0,0,592,12878,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,72:2:0	0,21,212:7:0
+X	2040	.	C	<*>	0	.	DP=29;I16=18,11,0,0,1077,40469,0,0,1709,101641,0,0,590,12856,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,69:2:0	0,21,196:7:0
+X	2041	.	G	A,<*>	0	.	DP=31;I16=6,5,12,7,389,14023,721,28149,660,39600,1109,65641,235,5607,353,7259;QS=0.917304,2.0827,0;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0	PL:DP:DV	229,0,212,255,245,255:21:11	32,0,24,35,27,59:2:1	223,21,0,223,21,223:7:7
+X	2042	.	G	<*>	0	.	DP=32;I16=18,14,0,0,1189,45617,0,0,1889,112441,0,0,588,12910,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,86:3:0	0,21,206:7:0
+X	2043	.	G	<*>	0	.	DP=32;I16=17,14,0,0,1115,41585,0,0,1829,108841,0,0,581,12891,0,0;QS=3,0;MQSB=0.962133;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,90:3:0	0,21,197:7:0
+X	2044	.	C	<*>	0	.	DP=32;I16=18,14,0,0,1213,47029,0,0,1889,112441,0,0,588,13006,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,85:3:0	0,21,207:7:0
+X	2045	.	A	<*>	0	.	DP=32;I16=18,14,0,0,1181,44527,0,0,1889,112441,0,0,588,13108,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,83:3:0	0,21,213:7:0
+X	2046	.	T	<*>	0	.	DP=32;I16=18,14,0,0,1197,45135,0,0,1889,112441,0,0,587,13195,0,0;QS=3,0;MQSB=0.965264;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,9,103:3:0	0,21,216:7:0
+X	2047	.	G	<*>	0	.	DP=34;I16=17,16,0,0,1248,47798,0,0,1949,116041,0,0,557,12491,0,0;QS=3,0;MQSB=0.959328;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,9,88:3:0	0,18,195:6:0
+X	2048	.	A	<*>	0	.	DP=34;I16=18,16,0,0,1230,45184,0,0,2009,119641,0,0,578,13022,0,0;QS=3,0;MQSB=0.962621;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,9,87:3:0	0,21,206:7:0
+X	2049	.	A	<*>	0	.	DP=33;I16=17,16,0,0,1207,44567,0,0,1949,116041,0,0,575,12963,0,0;QS=3,0;MQSB=0.959328;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,6,74:2:0	0,21,208:7:0
+X	2050	.	A	<*>	0	.	DP=33;I16=16,16,0,0,1169,43313,0,0,1889,112441,0,0,545,12211,0,0;QS=3,0;MQSB=0.955563;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,6,77:2:0	0,18,188:6:0
+X	2051	.	T	<*>	0	.	DP=31;I16=16,15,0,0,1134,42164,0,0,1829,108841,0,0,567,12737,0,0;QS=3,0;MQSB=0.957006;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,6,69:2:0	0,18,170:6:0
+X	2052	.	G	<*>	0	.	DP=31;I16=16,15,0,0,1180,45546,0,0,1829,108841,0,0,564,12664,0,0;QS=3,0;MQSB=0.957006;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,6,74:2:0	0,18,175:6:0
+X	2053	.	G	T,<*>	0	.	DP=31;I16=15,15,0,1,1126,42672,23,529,1769,105241,60,3600,537,11991,25,625;QS=2.97307,0.0269321,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.951229;BQB=1;MQ0F=0	PL:DP:DV	0,46,255,66,255,255:23:1	0,6,71,6,71,71:2:0	0,18,180,18,180,180:6:0
+X	2054	.	A	<*>	0	.	DP=30;I16=15,15,0,0,1123,43027,0,0,1769,105241,0,0,562,12592,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,6,78:2:0	0,18,171:6:0
+X	2055	.	G	<*>	0	.	DP=30;I16=15,15,0,0,1156,45206,0,0,1769,105241,0,0,562,12592,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,6,66:2:0	0,18,168:6:0
+X	2056	.	A	<*>	0	.	DP=30;I16=15,15,0,0,1124,42416,0,0,1769,105241,0,0,560,12518,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,6,71:2:0	0,18,179:6:0
+X	2057	.	T	<*>	0	.	DP=30;I16=15,15,0,0,1094,40082,0,0,1769,105241,0,0,556,12374,0,0;QS=3,0;MQSB=0.952765;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,6,72:2:0	0,18,178:6:0
+X	2058	.	A	<*>	0	.	DP=29;I16=14,15,0,0,1035,37517,0,0,1709,101641,0,0,552,12212,0,0;QS=3,0;MQSB=0.947838;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,6,57:2:0	0,18,179:6:0
+X	2059	.	A	<*>	0	.	DP=29;I16=14,15,0,0,1063,39615,0,0,1709,101641,0,0,548,12082,0,0;QS=3,0;MQSB=0.947838;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,6,66:2:0	0,18,188:6:0
+X	2060	.	C	<*>	0	.	DP=28;I16=12,15,0,0,1015,39057,0,0,1589,94441,0,0,523,11499,0,0;QS=3,0;MQSB=0.935229;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,6,62:2:0	0,15,143:5:0
+X	2061	.	A	<*>	0	.	DP=27;I16=12,14,0,0,950,35084,0,0,1529,90841,0,0,501,11073,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,3,41:1:0	0,15,163:5:0
+X	2062	.	A	<*>	0	.	DP=26;I16=11,15,0,0,973,37349,0,0,1529,90841,0,0,519,11425,0,0;QS=3,0;MQSB=0.927041;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,57:2:0	0,15,164:5:0
+X	2063	.	C	<*>	0	.	DP=26;I16=11,15,0,0,1017,40149,0,0,1529,90841,0,0,517,11405,0,0;QS=3,0;MQSB=0.927041;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,74:2:0	0,15,158:5:0
+X	2064	.	A	<*>	0	.	DP=26;I16=11,15,0,0,1002,38980,0,0,1529,90841,0,0,515,11413,0,0;QS=3,0;MQSB=0.927041;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,75:2:0	0,15,164:5:0
+X	2065	.	G	<*>	0	.	DP=26;I16=12,14,0,0,1030,41232,0,0,1529,90841,0,0,514,11448,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,78:2:0	0,18,167:6:0
+X	2066	.	G	<*>	0	.	DP=26;I16=12,14,0,0,973,37055,0,0,1529,90841,0,0,514,11510,0,0;QS=3,0;MQSB=0.937241;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,75:2:0	0,18,152:6:0
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+X	3689	.	T	<*>	0	.	DP=28;I16=17,11,0,0,1042,39780,0,0,1629,95763,0,0,535,11919,0,0;QS=3,0;MQSB=0.995584;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,15,162:5:0	0,24,233:8:0
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+X	3812	.	T	<*>	0	.	DP=23;I16=10,11,0,0,802,32860,0,0,1084,60066,0,0,405,9447,0,0;QS=3,0;MQSB=0.187115;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,114:4:0	0,12,160:4:0
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+X	3818	.	T	<*>	0	.	DP=20;I16=8,11,0,0,728,30466,0,0,1010,57328,0,0,391,8749,0,0;QS=3,0;MQSB=0.373354;MQ0F=0	PL:DP:DV	0,33,252:11:0	0,12,115:4:0	0,12,160:4:0
+X	3819	.	A	<*>	0	.	DP=21;I16=9,11,0,0,790,34094,0,0,1039,58169,0,0,389,8681,0,0;QS=3,0;MQSB=0.247381;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,121:4:0	0,12,167:4:0
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+X	3822	.	G	<*>	0	.	DP=22;I16=10,11,0,0,810,33228,0,0,1099,61769,0,0,386,8532,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,103:4:0	0,12,157:4:0
+X	3823	.	T	<*>	0	.	DP=22;I16=9,11,0,0,753,30705,0,0,1042,58520,0,0,380,8460,0,0;QS=3,0;MQSB=0.434285;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,12,102:4:0	0,12,163:4:0
+X	3824	.	C	<*>	0	.	DP=22;I16=10,11,0,0,802,32368,0,0,1099,61769,0,0,384,8456,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,105:4:0	0,12,159:4:0
+X	3825	.	C	<*>	0	.	DP=23;I16=10,11,0,0,813,33955,0,0,1079,59889,0,0,379,8387,0,0;QS=3,0;MQSB=0.317882;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,130:5:0	0,12,157:4:0
+X	3826	.	T	<*>	0	.	DP=23;I16=11,11,0,0,827,34611,0,0,1136,63138,0,0,381,8357,0,0;QS=3,0;MQSB=0.232836;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,15,133:5:0	0,12,155:4:0
+X	3827	.	G	<*>	0	.	DP=23;I16=11,10,0,0,820,34130,0,0,1076,59538,0,0,355,7715,0,0;QS=3,0;MQSB=0.269397;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,121:4:0	0,12,162:4:0
+X	3828	.	C	<*>	0	.	DP=23;I16=11,10,0,0,805,33147,0,0,1076,59538,0,0,354,7720,0,0;QS=3,0;MQSB=0.269397;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,12,114:4:0	0,12,157:4:0
+X	3829	.	A	<*>	0	.	DP=22;I16=9,11,0,0,763,31295,0,0,1069,59789,0,0,369,8241,0,0;QS=3,0;MQSB=0.477679;MQ0F=0	PL:DP:DV	0,33,255:11:0	0,15,132:5:0	0,12,158:4:0
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+X	3831	.	C	A,<*>	0	.	DP=23;I16=10,11,1,0,802,32198,14,196,1126,63038,10,100,370,8294,7,49;QS=2.97758,0.0224215,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.232836;BQB=1;MQ0F=0	PL:DP:DV	0,27,255,36,255,255:13:1	0,15,134,15,134,134:5:0	0,12,149,12,149,149:4:0
+X	3832	.	A	<*>	0	.	DP=24;I16=12,11,0,0,836,32436,0,0,1196,66738,0,0,377,8389,0,0;QS=3,0;MQSB=0.291845;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,15,136:5:0	0,12,139:4:0
+X	3833	.	C	<*>	0	.	DP=23;I16=10,11,0,0,690,24938,0,0,1076,59538,0,0,377,8409,0,0;QS=3,0;MQSB=0.175325;MQ0F=0	PL:DP:DV	0,36,249:12:0	0,15,113:5:0	0,12,131:4:0
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+X	3835	.	T	<*>	0	.	DP=22;I16=10,11,0,0,773,30373,0,0,1076,59538,0,0,381,8475,0,0;QS=3,0;MQSB=0.175325;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,15,140:5:0	0,12,153:4:0
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+X	3838	.	C	<*>	0	.	DP=24;I16=10,14,0,0,817,28975,0,0,1202,65348,0,0,409,8945,0,0;QS=3,0;MQSB=0.122456;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,18,143:6:0	0,15,148:5:0
+X	3839	.	C	<*>	0	.	DP=23;I16=9,13,0,0,688,22248,0,0,1132,61648,0,0,386,8238,0,0;QS=3,0;MQSB=0.248197;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,123:6:0	0,12,112:4:0
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+X	3841	.	T	<*>	0	.	DP=23;I16=9,14,0,0,867,33103,0,0,1192,65248,0,0,414,8734,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,167:6:0	0,15,162:5:0
+X	3842	.	C	<*>	0	.	DP=23;I16=9,14,0,0,890,34728,0,0,1192,65248,0,0,415,8689,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,167:6:0	0,15,159:5:0
+X	3843	.	T	<*>	0	.	DP=24;I16=9,14,0,0,896,35122,0,0,1192,65248,0,0,416,8674,0,0;QS=3,0;MQSB=0.211072;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,164:6:0	0,15,159:5:0
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+X	3845	.	T	<*>	0	.	DP=26;I16=10,16,0,0,970,36442,0,0,1372,76048,0,0,444,9310,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,186:7:0	0,18,166:6:0
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+X	3847	.	T	<*>	0	.	DP=27;I16=10,16,0,0,952,35268,0,0,1372,76048,0,0,423,8723,0,0;QS=3,0;MQSB=0.220358;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,18,170:6:0	0,21,189:7:0
+X	3848	.	C	<*>	0	.	DP=27;I16=10,17,0,0,1025,39533,0,0,1432,79648,0,0,449,9341,0,0;QS=3,0;MQSB=0.195223;MQ0F=0	PL:DP:DV	0,39,255:13:0	0,21,177:7:0	0,21,188:7:0
+X	3849	.	T	<*>	0	.	DP=27;I16=9,17,0,0,987,37685,0,0,1395,78279,0,0,450,9368,0,0;QS=3,0;MQSB=0.282527;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,21,179:7:0	0,21,190:7:0
+X	3850	.	G	<*>	0	.	DP=26;I16=9,17,0,0,957,35751,0,0,1395,78279,0,0,452,9428,0,0;QS=3,0;MQSB=0.282527;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,21,179:7:0	0,21,182:7:0
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+X	3852	.	C	<*>	0	.	DP=26;I16=9,16,0,0,921,34525,0,0,1335,74679,0,0,444,9440,0,0;QS=3,0;MQSB=0.310905;MQ0F=0	PL:DP:DV	0,36,255:12:0	0,18,163:6:0	0,21,179:7:0
+X	3853	.	T	<*>	0	.	DP=28;I16=10,18,0,0,1050,40222,0,0,1484,82720,0,0,455,9641,0,0;QS=3,0;MQSB=0.515783;MQ0F=0	PL:DP:DV	0,42,255:14:0	0,21,185:7:0	0,21,192:7:0
+X	3854	.	T	<*>	0	.	DP=28;I16=10,17,0,0,955,34605,0,0,1455,81879,0,0,451,9709,0,0;QS=3,0;MQSB=0.359211;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,171:6:0	0,18,178:6:0
+X	3855	.	C	<*>	0	.	DP=29;I16=10,18,0,0,992,36040,0,0,1515,85479,0,0,438,9264,0,0;QS=3,0;MQSB=0.331344;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,15,139:5:0	0,21,175:7:0
+X	3856	.	T	<*>	0	.	DP=30;I16=10,18,0,0,1033,38725,0,0,1546,88238,0,0,464,9982,0,0;QS=3,0;MQSB=0.190183;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,18,163:6:0	0,21,185:7:0
+X	3857	.	C	<*>	0	.	DP=30;I16=10,19,0,0,1077,40979,0,0,1575,89079,0,0,447,9505,0,0;QS=3,0;MQSB=0.306875;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,15,154:5:0	0,24,194:8:0
+X	3858	.	T	<*>	0	.	DP=31;I16=10,21,0,0,1141,42567,0,0,1695,96279,0,0,477,10255,0,0;QS=3,0;MQSB=0.266219;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,171:6:0	0,24,208:8:0
+X	3859	.	C	<*>	0	.	DP=32;I16=10,21,0,0,950,30078,0,0,1695,96279,0,0,484,10416,0,0;QS=3,0;MQSB=0.266219;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,136:6:0	0,24,156:8:0
+X	3860	.	G	<*>	0	.	DP=32;I16=10,22,0,0,1070,37794,0,0,1755,99879,0,0,516,11240,0,0;QS=3,0;MQSB=0.249261;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,154:6:0	0,27,209:9:0
+X	3861	.	C	<*>	0	.	DP=33;I16=11,20,0,0,1133,42547,0,0,1672,94048,0,0,517,11391,0,0;QS=3,0;MQSB=0.19205;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,162:6:0	0,24,199:8:0
+X	3862	.	T	<*>	0	.	DP=34;I16=11,22,0,0,1241,47443,0,0,1792,101248,0,0,526,11518,0,0;QS=3,0;MQSB=0.161533;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,185:7:0	0,27,221:9:0
+X	3863	.	T	<*>	0	.	DP=34;I16=12,22,0,0,1200,43542,0,0,1852,104848,0,0,541,11685,0,0;QS=3,0;MQSB=0.210327;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,199:7:0	0,27,213:9:0
+X	3864	.	A	<*>	0	.	DP=33;I16=11,22,0,0,1238,47448,0,0,1792,101248,0,0,550,11790,0,0;QS=3,0;MQSB=0.161533;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,210:7:0	0,27,230:9:0
+X	3865	.	G	<*>	0	.	DP=34;I16=11,23,0,0,1251,47113,0,0,1852,104848,0,0,559,11933,0,0;QS=3,0;MQSB=0.149071;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,200:7:0	0,27,212:9:0
+X	3866	.	C	<*>	0	.	DP=33;I16=11,21,0,0,1165,43545,0,0,1732,97648,0,0,545,11489,0,0;QS=3,0;MQSB=0.175751;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,189:7:0	0,24,197:8:0
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+X	3877	.	C	<*>	0	.	DP=37;I16=13,24,0,0,1363,51201,0,0,2029,115297,0,0,681,14765,0,0;QS=3,0;MQSB=0.117872;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,217:8:0	0,24,196:8:0
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+X	3882	.	T	<*>	0	.	DP=37;I16=14,21,0,0,1192,42352,0,0,1886,105866,0,0,684,15348,0,0;QS=3,0;MQSB=0.105399;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,21,189:7:0	0,21,178:7:0
+X	3883	.	C	<*>	0	.	DP=38;I16=15,22,0,0,1295,46659,0,0,2006,113066,0,0,717,16279,0,0;QS=3,0;MQSB=0.124405;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,205:8:0	0,24,171:8:0
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+X	3885	.	T	<*>	0	.	DP=40;I16=16,24,0,0,1445,53663,0,0,2163,121635,0,0,754,17262,0,0;QS=3,0;MQSB=0.0679472;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,24,219:8:0	0,27,214:9:0
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+X	3887	.	C	<*>	0	.	DP=39;I16=16,23,0,0,1364,49222,0,0,2103,118035,0,0,767,17567,0,0;QS=3,0;MQSB=0.0760633;MQ0F=0	PL:DP:DV	0,69,255:23:0	0,24,194:8:0	0,24,201:8:0
+X	3888	.	C	<*>	0	.	DP=39;I16=15,23,0,0,1387,51885,0,0,2043,114435,0,0,747,17073,0,0;QS=3,0;MQSB=0.0555905;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,195:8:0	0,24,208:8:0
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+X	3890	.	C	<*>	0	.	DP=38;I16=14,23,0,0,1362,51064,0,0,2006,113066,0,0,757,17329,0,0;QS=3,0;MQSB=0.0844255;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,24,203:8:0	0,24,216:8:0
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+X	3893	.	T	<*>	0	.	DP=39;I16=15,24,0,0,1348,48170,0,0,2126,120266,0,0,798,18404,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,196:8:0	0,27,212:9:0
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+X	3895	.	T	<*>	0	.	DP=39;I16=15,24,0,0,1375,49773,0,0,2126,120266,0,0,810,18752,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,24,202:8:0	0,27,225:9:0
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+X	3898	.	C	<*>	0	.	DP=40;I16=15,23,0,0,1487,59351,0,0,2066,116666,0,0,813,19023,0,0;QS=3,0;MQSB=0.112471;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,18,186:6:0	0,30,238:10:0
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+X	3900	.	T	<*>	0	.	DP=40;I16=15,24,0,0,1458,55516,0,0,2126,120266,0,0,833,19417,0,0;QS=3,0;MQSB=0.102114;MQ0F=0	PL:DP:DV	0,66,255:22:0	0,21,197:7:0	0,30,240:10:0
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+X	3920	.	T	<*>	0	.	DP=42;I16=15,26,0,0,1605,64327,0,0,2232,126450,0,0,825,18691,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,207:7:0	0,30,251:10:0
+X	3921	.	T	<*>	0	.	DP=42;I16=15,26,0,0,1519,58507,0,0,2232,126450,0,0,824,18630,0,0;QS=3,0;MQSB=0.110793;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,21,201:7:0	0,30,242:10:0
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+X	3927	.	T	<*>	0	.	DP=41;I16=14,26,0,0,1512,59566,0,0,2195,125081,0,0,808,18384,0,0;QS=3,0;MQSB=0.168991;MQ0F=0	PL:DP:DV	0,72,255:24:0	0,18,160:6:0	0,30,237:10:0
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+X	4073	.	G	<*>	0	.	DP=5;I16=3,2,0,0,156,5082,0,0,254,13538,0,0,60,994,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,136:5:0	0,0,0:0:0	0,0,0:0:0
+X	4074	.	C	<*>	0	.	DP=5;I16=3,2,0,0,160,5602,0,0,254,13538,0,0,56,928,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,142:5:0	0,0,0:0:0	0,0,0:0:0
+X	4075	.	T	<*>	0	.	DP=5;I16=3,2,0,0,187,7069,0,0,254,13538,0,0,52,870,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,155:5:0	0,0,0:0:0	0,0,0:0:0
+X	4076	.	G	<*>	0	.	DP=5;I16=3,2,0,0,174,6298,0,0,254,13538,0,0,48,820,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,149:5:0	0,0,0:0:0	0,0,0:0:0
+X	4077	.	A	<*>	0	.	DP=4;I16=3,1,0,0,138,4810,0,0,194,9938,0,0,44,728,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,121:4:0	0,0,0:0:0	0,0,0:0:0
+X	4078	.	T	<*>	0	.	DP=4;I16=3,1,0,0,143,5173,0,0,194,9938,0,0,40,644,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,124:4:0	0,0,0:0:0	0,0,0:0:0
+X	4079	.	A	<*>	0	.	DP=4;I16=3,1,0,0,121,3847,0,0,194,9938,0,0,36,568,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,107:4:0	0,0,0:0:0	0,0,0:0:0
+X	4080	.	T	<*>	0	.	DP=4;I16=3,0,0,0,106,3778,0,0,134,6338,0,0,25,451,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,9,87:3:0	0,0,0:0:0	0,0,0:0:0
+X	4081	.	T	<*>	0	.	DP=4;I16=3,1,0,0,106,2934,0,0,194,9938,0,0,28,440,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,94:4:0	0,0,0:0:0	0,0,0:0:0
+X	4082	.	C	<*>	0	.	DP=3;I16=2,1,0,0,110,4042,0,0,134,6338,0,0,25,387,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,9,103:3:0	0,0,0:0:0	0,0,0:0:0
+X	4083	.	C	<*>	0	.	DP=3;I16=2,1,0,0,104,3648,0,0,134,6338,0,0,22,340,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,9,98:3:0	0,0,0:0:0	0,0,0:0:0
+X	4084	.	A	<*>	0	.	DP=2;I16=1,1,0,0,78,3050,0,0,97,4969,0,0,20,298,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,74:2:0	0,0,0:0:0	0,0,0:0:0
+X	4085	.	C	<*>	0	.	DP=2;I16=1,1,0,0,62,1940,0,0,97,4969,0,0,18,260,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,62:2:0	0,0,0:0:0	0,0,0:0:0
+X	4086	.	G	<*>	0	.	DP=2;I16=1,1,0,0,56,1640,0,0,97,4969,0,0,16,226,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,56:2:0	0,0,0:0:0	0,0,0:0:0
+X	4087	.	C	<*>	0	.	DP=2;I16=1,1,0,0,69,2405,0,0,97,4969,0,0,14,196,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,68:2:0	0,0,0:0:0	0,0,0:0:0
+X	4088	.	A	<*>	0	.	DP=1;I16=1,0,0,0,39,1521,0,0,37,1369,0,0,13,169,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4089	.	C	<*>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,12,144,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+X	4090	.	C	<*>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,37,1369,0,0,11,121,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,33:1:0	0,0,0:0:0	0,0,0:0:0
+X	4091	.	T	<*>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,10,100,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+X	4092	.	G	<*>	0	.	DP=1;I16=1,0,0,0,37,1369,0,0,37,1369,0,0,9,81,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4093	.	C	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,8,64,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4094	.	T	<*>	0	.	DP=1;I16=1,0,0,0,40,1600,0,0,37,1369,0,0,7,49,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+X	4095	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,6,36,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4096	.	C	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,5,25,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+X	4097	.	A	<*>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,4,16,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+X	4098	.	C	<*>	0	.	DP=1;I16=1,0,0,0,31,961,0,0,37,1369,0,0,3,9,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,31:1:0	0,0,0:0:0	0,0,0:0:0
+X	4099	.	T	<*>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,2,4,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+X	4100	.	C	<*>	0	.	DP=1;I16=1,0,0,0,27,729,0,0,37,1369,0,0,1,1,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,27:1:0	0,0,0:0:0	0,0,0:0:0
+X	4101	.	C	<*>	0	.	DP=1;I16=1,0,0,0,26,676,0,0,37,1369,0,0,0,0,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,26:1:0	0,0,0:0:0	0,0,0:0:0
diff --git a/test/mpileup.c.vcf b/test/mpileup.c.vcf
new file mode 100644
index 000000000..13c013225
--- /dev/null
+++ b/test/mpileup.c.vcf
@@ -0,0 +1,4127 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=17,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	1	.	A	<X>	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	2	.	A	<X>	0	.	DP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	3	.	G	<X>	0	.	DP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	4	.	C	<X>	0	.	DP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,71:3:0
+17	5	.	T	<X>	0	.	DP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	6	.	T	<X>	0	.	DP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	7	.	C	<X>	0	.	DP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	8	.	T	<X>	0	.	DP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	9	.	C	<X>	0	.	DP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	10	.	A	<X>	0	.	DP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,69:3:0
+17	11	.	C	<X>	0	.	DP=11;I16=11,0,0,0,413,15603,0,0,319,9251,0,0,241,5495,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	12	.	C	<X>	0	.	DP=11;I16=11,0,0,0,438,17506,0,0,319,9251,0,0,242,5562,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	13	.	C	<X>	0	.	DP=11;I16=11,0,0,0,437,17463,0,0,319,9251,0,0,243,5639,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	14	.	T	<X>	0	.	DP=11;I16=11,0,0,0,453,18715,0,0,319,9251,0,0,242,5628,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	15	.	G	<X>	0	.	DP=11;I16=11,0,0,0,439,17599,0,0,319,9251,0,0,240,5580,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	16	.	T	<X>	0	.	DP=11;I16=11,0,0,0,426,16546,0,0,319,9251,0,0,238,5544,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	17	.	T	<X>	0	.	DP=11;I16=11,0,0,0,407,15195,0,0,319,9251,0,0,235,5469,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	18	.	C	<X>	0	.	DP=12;I16=12,0,0,0,450,17136,0,0,379,12851,0,0,231,5353,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,113:6:0	0,9,72:3:0	0,9,72:3:0
+17	19	.	C	<X>	0	.	DP=13;I16=13,0,0,0,502,19652,0,0,439,16451,0,0,228,5246,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,112:6:0	0,12,89:4:0	0,9,72:3:0
+17	20	.	T	<X>	0	.	DP=13;I16=13,0,0,0,532,21878,0,0,439,16451,0,0,226,5150,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,116:6:0	0,12,98:4:0	0,9,72:3:0
+17	21	.	G	<X>	0	.	DP=13;I16=13,0,0,0,498,19254,0,0,439,16451,0,0,224,5066,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,117:6:0	0,12,94:4:0	0,9,72:3:0
+17	22	.	C	<X>	0	.	DP=13;I16=13,0,0,0,511,20289,0,0,470,19210,0,0,223,4993,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,18,115:6:0	0,12,91:4:0	0,9,76:3:0
+17	23	.	A	<X>	0	.	DP=14;I16=14,0,0,0,513,19399,0,0,530,22810,0,0,223,4931,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,133:7:0	0,12,82:4:0	0,9,82:3:0
+17	24	.	T	<X>	0	.	DP=14;I16=14,0,0,0,534,20540,0,0,530,22810,0,0,224,4882,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,21,131:7:0	0,12,96:4:0	0,9,80:3:0
+17	25	.	A	<X>	0	.	DP=15;I16=15,0,0,0,561,21133,0,0,590,26410,0,0,225,4847,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,140:8:0	0,12,96:4:0	0,9,81:3:0
+17	26	.	G	<X>	0	.	DP=15;I16=15,0,0,0,591,23429,0,0,590,26410,0,0,227,4827,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,151:8:0	0,12,96:4:0	0,9,81:3:0
+17	27	.	A	<X>	0	.	DP=15;I16=15,0,0,0,588,23120,0,0,590,26410,0,0,229,4823,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,146:8:0	0,12,98:4:0	0,9,83:3:0
+17	28	.	T	<X>	0	.	DP=16;I16=16,0,0,0,605,23001,0,0,650,30010,0,0,231,4835,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,147:8:0	0,12,97:4:0	0,12,101:4:0
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+17	1960	.	T	<X>	0	.	DP=30;I16=17,13,0,0,1053,37939,0,0,1769,105241,0,0,485,10339,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,196:7:0	0,18,186:6:0
+17	1961	.	C	<X>	0	.	DP=30;I16=17,13,0,0,1101,41737,0,0,1769,105241,0,0,480,10122,0,0;QS=3,0;MQSB=0.938685;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,195:7:0	0,18,183:6:0
+17	1962	.	T	<X>	0	.	DP=29;I16=17,12,0,0,1134,44582,0,0,1709,101641,0,0,477,9941,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,208:7:0	0,18,198:6:0
+17	1963	.	G	<X>	0	.	DP=28;I16=16,12,0,0,1066,41050,0,0,1649,98041,0,0,476,9794,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,192:7:0	0,18,188:6:0
+17	1964	.	G	<X>	0	.	DP=28;I16=16,12,0,0,970,34764,0,0,1649,98041,0,0,475,9681,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,178:7:0	0,18,169:6:0
+17	1965	.	T	<X>	0	.	DP=29;I16=16,12,0,0,964,34772,0,0,1649,98041,0,0,449,8977,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,45,255:15:0	0,21,196:7:0	0,18,171:6:0
+17	1966	.	T	<X>	0	.	DP=29;I16=16,13,0,0,1029,37027,0,0,1709,101641,0,0,474,9558,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,191:7:0	0,18,181:6:0
+17	1967	.	A	<X>	0	.	DP=29;I16=16,13,0,0,1030,37234,0,0,1709,101641,0,0,474,9550,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,187:7:0	0,18,182:6:0
+17	1968	.	T	<X>	0	.	DP=29;I16=16,13,0,0,1075,40173,0,0,1709,101641,0,0,474,9578,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,21,195:7:0	0,18,190:6:0
+17	1969	.	A	<X>	0	.	DP=28;I16=16,12,0,0,992,35828,0,0,1649,98041,0,0,474,9592,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,175:6:0	0,18,186:6:0
+17	1970	.	C	<X>	0	.	DP=28;I16=16,12,0,0,1015,37503,0,0,1649,98041,0,0,474,9642,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,170:6:0	0,18,180:6:0
+17	1971	.	A	<X>	0	.	DP=29;I16=16,13,0,0,1073,40273,0,0,1709,101641,0,0,474,9728,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,18,178:6:0	0,21,206:7:0
+17	1972	.	T	<X>	0	.	DP=30;I16=16,14,0,0,1068,38978,0,0,1769,105241,0,0,475,9851,0,0;QS=3,0;MQSB=0.946202;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,176:6:0	0,21,203:7:0
+17	1973	.	A	<X>	0	.	DP=30;I16=16,13,0,0,1046,38070,0,0,1740,104400,0,0,452,9388,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,172:6:0	0,18,196:6:0
+17	1974	.	A	<X>	0	.	DP=29;I16=16,13,0,0,1086,41474,0,0,1709,101641,0,0,477,10065,0,0;QS=3,0;MQSB=0.940317;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,15,157:5:0	0,21,214:7:0
+17	1975	.	G	<X>	0	.	DP=28;I16=16,12,0,0,1067,41171,0,0,1649,98041,0,0,478,10156,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,133:4:0	0,21,195:7:0
+17	1976	.	A	<X>	0	.	DP=28;I16=16,12,0,0,981,34839,0,0,1649,98041,0,0,478,10234,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,125:4:0	0,21,199:7:0
+17	1977	.	C	<X>	0	.	DP=28;I16=16,12,0,0,1009,37471,0,0,1649,98041,0,0,477,10297,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,132:4:0	0,21,194:7:0
+17	1978	.	A	<X>	0	.	DP=28;I16=16,12,0,0,1082,42132,0,0,1649,98041,0,0,476,10394,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,12,144:4:0	0,21,220:7:0
+17	1979	.	G	<X>	0	.	DP=28;I16=16,11,0,0,1019,38927,0,0,1589,94441,0,0,454,10064,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,12,122:4:0	0,21,208:7:0
+17	1980	.	C	<X>	0	.	DP=27;I16=16,10,0,0,932,34456,0,0,1529,90841,0,0,452,10114,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,107:3:0	0,21,197:7:0
+17	1981	.	C	<X>	0	.	DP=28;I16=16,12,0,0,998,36510,0,0,1649,98041,0,0,469,10479,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,9,101:3:0	0,24,219:8:0
+17	1982	.	A	<X>	0	.	DP=29;I16=16,12,0,0,1035,38815,0,0,1649,98041,0,0,472,10548,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,110:3:0	0,27,254:9:0
+17	1983	.	G	<X>	0	.	DP=28;I16=16,12,0,0,1048,40322,0,0,1649,98041,0,0,477,10599,0,0;QS=3,0;MQSB=0.933359;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,9,96:3:0	0,27,249:9:0
+17	1984	.	A	<X>	0	.	DP=27;I16=16,11,0,0,1024,39232,0,0,1589,94441,0,0,482,10632,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,70:2:0	0,27,255:9:0
+17	1985	.	G	<X>	0	.	DP=27;I16=16,11,0,0,1009,38449,0,0,1589,94441,0,0,487,10695,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,66:2:0	0,27,231:9:0
+17	1986	.	A	<X>	0	.	DP=27;I16=16,10,0,0,926,33696,0,0,1560,93600,0,0,466,10112,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,76:2:0	0,24,223:8:0
+17	1987	.	A	<X>	0	.	DP=28;I16=17,11,0,0,1034,39088,0,0,1649,98041,0,0,495,10807,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,78:2:0	0,27,247:9:0
+17	1988	.	G	<X>	0	.	DP=28;I16=17,11,0,0,1050,39980,0,0,1649,98041,0,0,499,10855,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,63:2:0	0,27,239:9:0
+17	1989	.	G	<X>	0	.	DP=28;I16=17,10,0,0,994,37610,0,0,1589,94441,0,0,493,10801,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,48,255:16:0	0,6,73:2:0	0,27,237:9:0
+17	1990	.	G	T,<X>	0	.	DP=28;I16=17,9,0,1,965,36359,33,1089,1560,93600,29,841,472,10250,25,625;QS=2.90675,0.0932476,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.912952;BQB=1;MQ0F=0	PL:DP:DV	0,48,255,48,255,255:16:0	0,6,71,6,71,71:2:0	2,0,195,26,198,215:9:1
+17	1991	.	A	<X>	0	.	DP=28;I16=17,11,0,0,1017,38203,0,0,1649,98041,0,0,507,10975,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,60:2:0	0,27,250:9:0
+17	1992	.	G	<X>	0	.	DP=28;I16=17,11,0,0,1028,38852,0,0,1649,98041,0,0,509,11039,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,62:2:0	0,27,231:9:0
+17	1993	.	T	<X>	0	.	DP=28;I16=17,11,0,0,1015,37325,0,0,1649,98041,0,0,511,11131,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,59:2:0	0,27,243:9:0
+17	1994	.	T	<X>	0	.	DP=27;I16=16,11,0,0,942,33698,0,0,1589,94441,0,0,514,11250,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,54:2:0	0,24,216:8:0
+17	1995	.	G	<X>	0	.	DP=28;I16=16,11,0,0,960,35432,0,0,1620,97200,0,0,492,10770,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,66:2:0	0,21,188:7:0
+17	1996	.	C	<X>	0	.	DP=29;I16=17,12,0,0,1022,37426,0,0,1709,101641,0,0,519,11469,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,64:2:0	0,24,192:8:0
+17	1997	.	C	<X>	0	.	DP=29;I16=17,11,0,0,934,32858,0,0,1649,98041,0,0,520,11524,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,70:2:0	0,24,193:8:0
+17	1998	.	C	<X>	0	.	DP=29;I16=17,12,0,0,1027,37843,0,0,1709,101641,0,0,522,11562,0,0;QS=3,0;MQSB=0.931617;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,69:2:0	0,24,222:8:0
+17	1999	.	A	<X>	0	.	DP=28;I16=17,11,0,0,1073,41493,0,0,1649,98041,0,0,525,11627,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,21,206:7:0
+17	2000	.	G	<X>	0	.	DP=28;I16=16,11,0,0,1036,40576,0,0,1589,94441,0,0,511,11395,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,72:2:0	0,18,168:6:0
+17	2001	.	G	<X>	0	.	DP=28;I16=15,11,0,0,955,35661,0,0,1529,90841,0,0,489,10853,0,0;QS=3,0;MQSB=0.927041;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,62:2:0	0,18,172:6:0
+17	2002	.	G	<X>	0	.	DP=28;I16=17,10,0,0,907,32227,0,0,1620,97200,0,0,519,11663,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,53:2:0	0,18,163:6:0
+17	2003	.	T	<X>	0	.	DP=28;I16=17,11,0,0,920,31866,0,0,1649,98041,0,0,541,12163,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,6,49:2:0	0,21,190:7:0
+17	2004	.	G	<X>	0	.	DP=27;I16=16,10,0,0,970,36928,0,0,1560,93600,0,0,530,12110,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,57:2:0	0,18,178:6:0
+17	2005	.	G	<X>	0	.	DP=27;I16=16,10,0,0,868,30936,0,0,1560,93600,0,0,536,12370,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,59:2:0	0,18,153:6:0
+17	2006	.	C	<X>	0	.	DP=27;I16=16,10,0,0,968,37046,0,0,1560,93600,0,0,541,12605,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,73:2:0	0,18,166:6:0
+17	2007	.	A	<X>	0	.	DP=27;I16=16,11,0,0,1000,37396,0,0,1589,94441,0,0,556,12882,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,76:2:0	0,21,193:7:0
+17	2008	.	C	<X>	0	.	DP=26;I16=16,10,0,0,964,36892,0,0,1529,90841,0,0,555,12833,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,21,183:7:0
+17	2009	.	A	<X>	0	.	DP=26;I16=16,10,0,0,997,38955,0,0,1529,90841,0,0,554,12802,0,0;QS=3,0;MQSB=0.914947;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,21,210:7:0
+17	2010	.	G	<X>	0	.	DP=26;I16=16,9,0,0,936,36208,0,0,1500,90000,0,0,542,12640,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,73:2:0	0,18,169:6:0
+17	2011	.	C	<X>	0	.	DP=26;I16=16,9,0,0,966,37960,0,0,1500,90000,0,0,541,12617,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,74:2:0	0,18,175:6:0
+17	2012	.	A	<X>	0	.	DP=27;I16=16,11,0,0,956,35018,0,0,1589,94441,0,0,548,12676,0,0;QS=3,0;MQSB=0.925036;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,6,74:2:0	0,21,189:7:0
+17	2013	.	C	<X>	0	.	DP=27;I16=15,10,0,0,876,31370,0,0,1500,90000,0,0,514,11950,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,6,69:2:0	0,18,160:6:0
+17	2014	.	G	<X>	0	.	DP=27;I16=17,10,0,0,903,31239,0,0,1589,94441,0,0,545,12591,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,80:3:0	0,18,160:6:0
+17	2015	.	T	<X>	0	.	DP=27;I16=17,10,0,0,999,37507,0,0,1589,94441,0,0,545,12577,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,95:3:0	0,18,178:6:0
+17	2016	.	T	<X>	0	.	DP=27;I16=17,10,0,0,971,35649,0,0,1589,94441,0,0,545,12583,0,0;QS=3,0;MQSB=0.912952;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,9,93:3:0	0,18,178:6:0
+17	2017	.	G	<X>	0	.	DP=28;I16=17,11,0,0,1013,37849,0,0,1649,98041,0,0,545,12609,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,91:3:0	0,18,172:6:0
+17	2018	.	C	<X>	0	.	DP=28;I16=17,11,0,0,1060,41414,0,0,1649,98041,0,0,546,12656,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,97:3:0	0,18,169:6:0
+17	2019	.	T	<X>	0	.	DP=28;I16=17,11,0,0,1083,42253,0,0,1649,98041,0,0,547,12725,0,0;QS=3,0;MQSB=0.923174;MQ0F=0	PL:DP:DV	0,57,255:19:0	0,9,106:3:0	0,18,187:6:0
+17	2020	.	G	<X>	0	.	DP=29;I16=18,11,0,0,1095,42063,0,0,1678,98882,0,0,548,12816,0,0;QS=3,0;MQSB=0.987702;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,85:3:0	0,18,175:6:0
+17	2021	.	C	<X>	0	.	DP=29;I16=18,11,0,0,1081,41535,0,0,1709,101641,0,0,551,12877,0,0;QS=3,0;MQSB=0.969907;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,97:3:0	0,15,167:5:0
+17	2022	.	C	<X>	0	.	DP=30;I16=19,11,0,0,1115,42003,0,0,1769,105241,0,0,555,12907,0,0;QS=3,0;MQSB=0.972375;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,18,177:6:0
+17	2023	.	A	<X>	0	.	DP=30;I16=19,10,0,0,1063,39991,0,0,1709,101641,0,0,549,12837,0,0;QS=3,0;MQSB=0.974027;MQ0F=0	PL:DP:DV	0,60,255:20:0	0,9,96:3:0	0,18,186:6:0
+17	2024	.	G	<X>	0	.	DP=32;I16=20,12,0,0,1168,43872,0,0,1889,112441,0,0,564,12982,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,92:3:0	0,24,203:8:0
+17	2025	.	T	<X>	0	.	DP=32;I16=20,12,0,0,1150,42122,0,0,1889,112441,0,0,569,12981,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,87:3:0	0,24,226:8:0
+17	2026	.	T	<X>	0	.	DP=32;I16=20,12,0,0,1130,40724,0,0,1889,112441,0,0,572,12908,0,0;QS=3,0;MQSB=0.973096;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,94:3:0	0,24,208:8:0
+17	2027	.	A	<X>	0	.	DP=32;I16=19,12,0,0,1121,40871,0,0,1829,108841,0,0,550,12240,0,0;QS=3,0;MQSB=0.970829;MQ0F=0	PL:DP:DV	0,63,255:21:0	0,9,84:3:0	0,21,207:7:0
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+17	4072	.	G	<X>	0	.	DP=5;I16=2,2,0,0,138,4974,0,0,194,9938,0,0,55,987,0,0;QS=1,0;MQSB=0;MQ0F=0	PL:DP:DV	0,12,122:4:0	0,0,0:0:0	0,0,0:0:0
+17	4073	.	G	<X>	0	.	DP=5;I16=3,2,0,0,156,5082,0,0,254,13538,0,0,60,994,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,136:5:0	0,0,0:0:0	0,0,0:0:0
+17	4074	.	C	<X>	0	.	DP=5;I16=3,2,0,0,160,5602,0,0,254,13538,0,0,56,928,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,142:5:0	0,0,0:0:0	0,0,0:0:0
+17	4075	.	T	<X>	0	.	DP=5;I16=3,2,0,0,187,7069,0,0,254,13538,0,0,52,870,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,155:5:0	0,0,0:0:0	0,0,0:0:0
+17	4076	.	G	<X>	0	.	DP=5;I16=3,2,0,0,174,6298,0,0,254,13538,0,0,48,820,0,0;QS=1,0;MQSB=0.333333;MQ0F=0	PL:DP:DV	0,15,149:5:0	0,0,0:0:0	0,0,0:0:0
+17	4077	.	A	<X>	0	.	DP=4;I16=3,1,0,0,138,4810,0,0,194,9938,0,0,44,728,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,121:4:0	0,0,0:0:0	0,0,0:0:0
+17	4078	.	T	<X>	0	.	DP=4;I16=3,1,0,0,143,5173,0,0,194,9938,0,0,40,644,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,124:4:0	0,0,0:0:0	0,0,0:0:0
+17	4079	.	A	<X>	0	.	DP=4;I16=3,1,0,0,121,3847,0,0,194,9938,0,0,36,568,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,107:4:0	0,0,0:0:0	0,0,0:0:0
+17	4080	.	T	<X>	0	.	DP=4;I16=3,0,0,0,106,3778,0,0,134,6338,0,0,25,451,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,9,87:3:0	0,0,0:0:0	0,0,0:0:0
+17	4081	.	T	<X>	0	.	DP=4;I16=3,1,0,0,106,2934,0,0,194,9938,0,0,28,440,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,12,94:4:0	0,0,0:0:0	0,0,0:0:0
+17	4082	.	C	<X>	0	.	DP=3;I16=2,1,0,0,110,4042,0,0,134,6338,0,0,25,387,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,9,103:3:0	0,0,0:0:0	0,0,0:0:0
+17	4083	.	C	<X>	0	.	DP=3;I16=2,1,0,0,104,3648,0,0,134,6338,0,0,22,340,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,9,98:3:0	0,0,0:0:0	0,0,0:0:0
+17	4084	.	A	<X>	0	.	DP=2;I16=1,1,0,0,78,3050,0,0,97,4969,0,0,20,298,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,74:2:0	0,0,0:0:0	0,0,0:0:0
+17	4085	.	C	<X>	0	.	DP=2;I16=1,1,0,0,62,1940,0,0,97,4969,0,0,18,260,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,62:2:0	0,0,0:0:0	0,0,0:0:0
+17	4086	.	G	<X>	0	.	DP=2;I16=1,1,0,0,56,1640,0,0,97,4969,0,0,16,226,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,56:2:0	0,0,0:0:0	0,0,0:0:0
+17	4087	.	C	<X>	0	.	DP=2;I16=1,1,0,0,69,2405,0,0,97,4969,0,0,14,196,0,0;QS=1,0;MQSB=1;MQ0F=0	PL:DP:DV	0,6,68:2:0	0,0,0:0:0	0,0,0:0:0
+17	4088	.	A	<X>	0	.	DP=1;I16=1,0,0,0,39,1521,0,0,37,1369,0,0,13,169,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+17	4089	.	C	<X>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,12,144,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+17	4090	.	C	<X>	0	.	DP=1;I16=1,0,0,0,33,1089,0,0,37,1369,0,0,11,121,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,33:1:0	0,0,0:0:0	0,0,0:0:0
+17	4091	.	T	<X>	0	.	DP=1;I16=1,0,0,0,36,1296,0,0,37,1369,0,0,10,100,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,36:1:0	0,0,0:0:0	0,0,0:0:0
+17	4092	.	G	<X>	0	.	DP=1;I16=1,0,0,0,37,1369,0,0,37,1369,0,0,9,81,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+17	4093	.	C	<X>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,8,64,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+17	4094	.	T	<X>	0	.	DP=1;I16=1,0,0,0,40,1600,0,0,37,1369,0,0,7,49,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,37:1:0	0,0,0:0:0	0,0,0:0:0
+17	4095	.	A	<X>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,6,36,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+17	4096	.	C	<X>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,5,25,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+17	4097	.	A	<X>	0	.	DP=1;I16=1,0,0,0,35,1225,0,0,37,1369,0,0,4,16,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,35:1:0	0,0,0:0:0	0,0,0:0:0
+17	4098	.	C	<X>	0	.	DP=1;I16=1,0,0,0,31,961,0,0,37,1369,0,0,3,9,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,31:1:0	0,0,0:0:0	0,0,0:0:0
+17	4099	.	T	<X>	0	.	DP=1;I16=1,0,0,0,32,1024,0,0,37,1369,0,0,2,4,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,32:1:0	0,0,0:0:0	0,0,0:0:0
+17	4100	.	C	<X>	0	.	DP=1;I16=1,0,0,0,27,729,0,0,37,1369,0,0,1,1,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,27:1:0	0,0,0:0:0	0,0,0:0:0
+17	4101	.	C	<X>	0	.	DP=1;I16=1,0,0,0,26,676,0,0,37,1369,0,0,0,0,0,0;QS=1,0;MQ0F=0	PL:DP:DV	0,3,26:1:0	0,0,0:0:0	0,0,0:0:0
diff --git a/test/test.pl b/test/test.pl
index b5b12e337..899ea169a 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -144,10 +144,10 @@
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_call_cAls($opts,in=>'mpileup',out=>'mpileup.cAls.out',tab=>'mpileup');
-test_vcf_call($opts,in=>'mpileup',out=>'mpileup.c.1.out',args=>'-cv');
-# test_vcf_call($opts,in=>'mpileup',out=>'mpileup.c.2.out',args=>'-cg0');
-test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
-test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
+test_vcf_call($opts,in=>'mpileup.c',out=>'mpileup.c.1.out',args=>'-cv');
+# test_vcf_call($opts,in=>'mpileup.c',out=>'mpileup.c.2.out',args=>'-cg0');
+test_vcf_call($opts,in=>'mpileup.c.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
+test_vcf_call($opts,in=>'mpileup.c.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
 test_vcf_filter($opts,in=>'filter.1',out=>'filter.1.out',args=>'-mx -g2 -G2');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.2.out',args=>q[-e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S.]);
 test_vcf_filter($opts,in=>'filter.3',out=>'filter.3.out',args=>q[-e'DP=19'],fmt=>'%POS\\t%FILTER\\t%DP[\\t%GT]\\n');

From 71921ca39706fb7b15165ed76729c24a6b89e8cf Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 30 Nov 2015 09:58:36 +0000
Subject: [PATCH 126/211] call -mC alleles fix: Do not take X as last in ALT
 list for granted

---
 mcall.c               | 29 ++++++++++++++++++++++-------
 test/mpileup.2.out    |  2 +-
 test/mpileup.cAls.out |  7 +++++++
 test/mpileup.tab      |  7 +++++++
 test/mpileup.vcf      | 14 +++++++-------
 5 files changed, 44 insertions(+), 15 deletions(-)

diff --git a/mcall.c b/mcall.c
index 70d617c79..495f849a8 100644
--- a/mcall.c
+++ b/mcall.c
@@ -1255,7 +1255,11 @@ void mcall_trim_numberR(call_t *call, bcf1_t *rec, int nals, int nout_als, int o
     }
 }
 
-static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
+
+// NB: in this function we temporarily use calls->als_map for a different
+// purpose to store mapping from new (target) alleles to original alleles.
+//
+static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int *unseen)
 {
     bcf_sr_regions_t *tgt = call->srs->targets;
     if ( tgt->nals>5 ) error("Maximum accepted number of alleles is 5, got %d\n", tgt->nals);
@@ -1278,6 +1282,8 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
         call->als[nals] = tgt->als[i];
         j = vcmp_find_allele(call->vcmp, rec->d.allele+1, rec->n_allele - 1, tgt->als[i]);
 
+        if ( j+1==*unseen ) error("Cannot constrain to %s\n",tgt->als[i]);
+        
         if ( j>=0 )
         {
             // existing allele
@@ -1290,11 +1296,18 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
             // present at multiallelic indels sites. In that case we use the
             // last allele anyway, because the least likely allele comes last
             // in mpileup's ALT output.
-            call->als_map[nals] = unseen>=0 ? unseen : rec->n_allele - 1;
+            call->als_map[nals] = (*unseen)>=0 ? *unseen : rec->n_allele - 1;
             has_new = 1;
         }
         nals++;
     }
+    if ( *unseen )
+    {
+        call->als_map[nals] = *unseen;
+        call->als[nals] = rec->d.allele[*unseen];
+        nals++;
+    }
+
     if ( !has_new && nals==rec->n_allele ) return;
     bcf_update_alleles(call->hdr, rec, (const char**)call->als, nals);
 
@@ -1321,15 +1334,15 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
         for (k=0; k<npls_new; k++)
         {
             new_pl[k] = ori_pl[call->pl_map[k]];
-            if ( new_pl[k]==bcf_int32_missing && unseen>=0 )
+            if ( new_pl[k]==bcf_int32_missing && *unseen>=0 )
             {
                 // missing value, and there is an unseen allele: identify the
                 // alleles and use the lk of either AX or XX
                 int k_ori = call->pl_map[k], ia, ib;
                 bcf_gt2alleles(k_ori, &ia, &ib);
-                k_ori = bcf_alleles2gt(ia,unseen);
-                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(ib,unseen);
-                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(unseen,unseen);
+                k_ori = bcf_alleles2gt(ia,*unseen);
+                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(ib,*unseen);
+                if ( ori_pl[k_ori]==bcf_int32_missing ) k_ori = bcf_alleles2gt(*unseen,*unseen);
                 new_pl[k] = ori_pl[k_ori];
             }
             if ( !k && new_pl[k]==bcf_int32_vector_end ) new_pl[k]=bcf_int32_missing;
@@ -1345,6 +1358,8 @@ static void mcall_constrain_alleles(call_t *call, bcf1_t *rec, int unseen)
     for (i=0; i<nals; i++)
         qsum[i] = call->als_map[i]<nqs ? call->qsum[call->als_map[i]] : 0;
     bcf_update_info_float(call->hdr, rec, "QS", qsum, nals);
+
+    if ( *unseen ) *unseen = nals-1;
 }
 
 
@@ -1359,7 +1374,7 @@ int mcall(call_t *call, bcf1_t *rec)
     int i, unseen = call->unseen;
 
     // Force alleles when calling genotypes given alleles was requested
-    if ( call->flag & CALL_CONSTR_ALLELES ) mcall_constrain_alleles(call, rec, unseen);
+    if ( call->flag & CALL_CONSTR_ALLELES ) mcall_constrain_alleles(call, rec, &unseen);
 
     int nsmpl = bcf_hdr_nsamples(call->hdr);
     int nals  = rec->n_allele;
diff --git a/test/mpileup.2.out b/test/mpileup.2.out
index 1090fbd52..d6571607a 100644
--- a/test/mpileup.2.out
+++ b/test/mpileup.2.out
@@ -29,7 +29,7 @@
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
-17	1	.	A	.	.	.	END=301;MinDP=1	GT:DP	0/0:5	0/0:1	0/0:3
+17	1	.	A	.	.	.	END=301;MinDP=1	GT:DP	./.:5	./.:1	./.:3
 17	302	.	T	TA	488	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=49	GT:PL:DP:DV	0/1:167,0,96:11:6	0/1:157,0,9:7:6	1/1:201,21,0:7:7
 17	303	.	G	.	.	.	END=827;MinDP=2	GT:DP	0/0:9	0/0:2	0/0:3
 17	828	.	T	C	409	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	0/1:116,0,91:9:5	1/1:120,12,0:4:4
diff --git a/test/mpileup.cAls.out b/test/mpileup.cAls.out
index 660e7f5a2..105f2944a 100644
--- a/test/mpileup.cAls.out
+++ b/test/mpileup.cAls.out
@@ -27,6 +27,13 @@
 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
 ##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	1	.	A	G,T	0	.	DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0,0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	2	.	A	T,G	0	.	DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0,0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	3	.	A	C	0	.	DP=11;MQ0F=0;AC=0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	4	.	A	G,T,C	21.815	.	DP=11;MQ0F=0;AC=0,0,0;AN=2;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	0/0:1,2,3,7,8,10,11,12,14,15:5:0	./.:.:3:0	./.:.:3:0
+17	5	.	A	G,T	0	.	DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0,0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	6	.	A	T,G	0	.	DP=11;MQ0F=0;AC=0,0;AN=0;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	./.:0,0,0,0,0,0:5:0	./.:.:3:0	./.:.:3:0
+17	7	.	A	T,G,C	21.5769	.	DP=11;MQ0F=0;AC=0,0,0;AN=2;DP4=11,0,0,0;MQ=29	GT:PL:DP:DV	0/0:1,2,3,4,5,6,2,3,5,3:5:0	./.:.:3:0	./.:.:3:0
 17	828	.	T	C	409	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.8;HOB=0.222222;AC=4;AN=6;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	0/1:116,0,91:9:5	1/1:120,12,0:4:4
 17	1665	.	T	C	3.10665	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.128205;HOB=0.0555556;AC=1;AN=6;DP4=7,11,1,1;MQ=55	GT:PL:DP:DV	0/0:0,21,185:7:0	0/0:0,27,222:9:0	0/1:35,0,51:4:2
 17	2220	.	G	C	999	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AC=0;AN=6;DP4=6,2,1,11;MQ=58	GT:PL:DP:DV	0/0:139,157,255:12:6	0/0:69,75,119:4:2	0/0:131,131,131:4:4
diff --git a/test/mpileup.tab b/test/mpileup.tab
index c585dadf5..1930ea004 100644
--- a/test/mpileup.tab
+++ b/test/mpileup.tab
@@ -1,3 +1,10 @@
+17	1	A,G,T
+17	2	A,T,G
+17	3	A,C
+17	4	A,C,T,G
+17	5	A,G,T
+17	6	A,T,G
+17	7	A,T,G,C
 17	828	T,C
 17	1665	T,C
 17	2220	G,C
diff --git a/test/mpileup.vcf b/test/mpileup.vcf
index 13c013225..155af1ba2 100644
--- a/test/mpileup.vcf
+++ b/test/mpileup.vcf
@@ -22,13 +22,13 @@
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
 ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
-17	1	.	A	<X>	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	2	.	A	<X>	0	.	DP=11;I16=11,0,0,0,439,17587,0,0,319,9251,0,0,226,5030,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	3	.	G	<X>	0	.	DP=11;I16=11,0,0,0,431,16971,0,0,319,9251,0,0,229,5111,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	4	.	C	<X>	0	.	DP=11;I16=11,0,0,0,423,16417,0,0,319,9251,0,0,232,5202,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,71:3:0
-17	5	.	T	<X>	0	.	DP=11;I16=11,0,0,0,450,18520,0,0,319,9251,0,0,234,5252,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	6	.	T	<X>	0	.	DP=11;I16=11,0,0,0,403,14847,0,0,319,9251,0,0,236,5310,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
-17	7	.	C	<X>	0	.	DP=11;I16=11,0,0,0,446,18114,0,0,319,9251,0,0,237,5327,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
+17	1	.	A	G,X,T,C	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,1,0,1,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0,.,.,.,.,.,.,.,.,.:5:0	.:3:0	.:3:0
+17	2	.	A	G,X,T,C	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,1,0,1,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0,.,.,.,.,.,.,.,.,.:5:0	.:3:0	.:3:0
+17	3	.	A	G,X,T,C	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,1,0,1,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0,.,.,.,.,.,.,.,.,.:5:0	.:3:0	.:3:0
+17	4	.	A	G,X,T,C	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,1,0,1,1;MQ0F=0	PL:DP:DV	1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:5:0	.:3:0	.:3:0
+17	5	.	A	X,G	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,0,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0:5:0	.:3:0	.:3:0
+17	6	.	A	X,G	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,0,1;MQ0F=0	PL:DP:DV	0,0,0,0,0,0:5:0	.:3:0	.:3:0
+17	7	.	A	X,G	0	.	DP=11;I16=11,0,0,0,452,18594,0,0,319,9251,0,0,223,4959,0,0;QS=1,0,1;MQ0F=0	PL:DP:DV	1,2,3,4,5,6:5:0	.:3:0	.:3:0
 17	8	.	T	<X>	0	.	DP=11;I16=11,0,0,0,465,19677,0,0,319,9251,0,0,238,5354,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
 17	9	.	C	<X>	0	.	DP=11;I16=11,0,0,0,447,18205,0,0,319,9251,0,0,239,5391,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,72:3:0
 17	10	.	A	<X>	0	.	DP=11;I16=11,0,0,0,426,16756,0,0,319,9251,0,0,240,5438,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,15,100:5:0	0,9,72:3:0	0,9,69:3:0

From 6737c5c8074943b51e18fd53458f41a30d623fb7 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 9 Nov 2015 18:28:42 +0000
Subject: [PATCH 127/211] add --threads option for output compression threads

* `--threads` option added to commands that output VCF/BCF
* add this new option to the docs
---
 doc/bcftools.txt | 34 +++++++++++++++++++--
 vcfannotate.c    | 39 +++++++++++++-----------
 vcfcall.c        | 63 ++++++++++++++++++++------------------
 vcfconcat.c      | 31 +++++++++++--------
 vcfconvert.c     | 22 +++++++++++---
 vcffilter.c      | 35 ++++++++++++---------
 vcfisec.c        | 40 +++++++++++++-----------
 vcfmerge.c       | 33 +++++++++++---------
 vcfnorm.c        | 39 +++++++++++++-----------
 vcfplugin.c      | 33 +++++++++++---------
 vcfview.c        | 79 +++++++++++++++++++++++++-----------------------
 11 files changed, 268 insertions(+), 180 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 9498e14a1..e26692dbd 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -255,6 +255,11 @@ specific commands to see if they apply.
     bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
 ----
 
+*--threads* 'INT'::
+    Number of output compression threads to use in addition to main thread. 
+    Only used when '--output-type' is 'b' or 'z'. Default: 0.
+
+
 [[annotate]]
 === bcftools annotate '[OPTIONS]' 'FILE'
 
@@ -359,6 +364,9 @@ This command allows to add or remove annotations.
     given as "src_name dst_name\n", separated by whitespaces, each pair on a
     separate line.
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 *-x, --remove* 'list'::
     List of annotations to remove. Use "FILTER" to remove all filters or
     "FILTER/SomeFilter" to remove a specific filter. Similarly, "INFO" can
@@ -490,6 +498,9 @@ demand. The original calling model can be invoked with the *-c* option.
 
 ==== File format options:
 
+*-o, --output* 'FILE'::
+    see *<<common_options,Common Options>>*
+
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
@@ -533,6 +544,9 @@ demand. The original calling model can be invoked with the *-c* option.
 *-T, --targets-file* 'FILE'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 ==== Input/output options:
 
 *-A, --keep-alts*::
@@ -555,9 +569,6 @@ demand. The original calling model can be invoked with the *-c* option.
 *-M, --keep-masked-ref*::
     output sites where REF allele is N
 
-*-o, --output* 'FILE'::
-    see *<<common_options,Common Options>>*
-
 *-V, --skip-variants* 'snps'|'indels'::
     skip indel/SNP sites
 
@@ -655,6 +666,9 @@ the *-a, --allow-overlaps* option is specified.
 *-R, --regions-file* 'FILE'::
     see *<<common_options,Common Options>>*. Requires *-a, --allow-overlaps*.
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 
 [[consensus]]
 === bcftools consensus '[OPTIONS]' 'FILE'
@@ -731,6 +745,9 @@ Create consensus sequence by applying VCF variants to a reference fasta file.
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 ==== GEN/SAMPLE conversion:
 *-G, --gensample2vcf* 'prefix' or 'gen-file','sample-file'::
     convert IMPUTE2 output to VCF. The second column must be of the form
@@ -1204,6 +1221,8 @@ For "vertical" merge take a look at *<<norm,bcftools norm>>* instead.
 *-R, --regions-file* 'file'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
 
 
 [[norm]]
@@ -1269,6 +1288,9 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.
 *-T, --targets-file* 'FILE'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 *-w, --site-win* 'INT'::
     maximum distance between two records to consider when locally
     sorting variants which changed position during the realignment
@@ -1307,6 +1329,9 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 ==== Plugin options:
 
 *-h, --help*::
@@ -1783,6 +1808,9 @@ Convert between VCF and BCF. Former *bcftools subset*.
 *-T, --targets-file* 'file'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 
 ==== Subset options:
 *-a, --trim-alt-alleles*::
diff --git a/vcfannotate.c b/vcfannotate.c
index d653bcd4d..96a1649c5 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -87,7 +87,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr, *hdr_out;
     htsFile *out_fh;
-    int output_type;
+    int output_type, n_threads;
     bcf_sr_regions_t *tgts;
 
     filter_t *filter;
@@ -1426,6 +1426,7 @@ static void init_data(args_t *args)
 
         args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
         if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+        if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
         bcf_hdr_write(args->out_fh, args->hdr_out);
     }
 }
@@ -1634,6 +1635,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -s, --samples [^]<list>        comma separated list of samples to annotate (or exclude with \"^\" prefix)\n");
     fprintf(stderr, "   -S, --samples-file [^]<file>   file of samples to annotate (or exclude with \"^\" prefix)\n");
     fprintf(stderr, "   -x, --remove <list>            list of annotations to remove (e.g. ID,INFO/DP,FORMAT/DP,FILTER). See man page for details\n");
+    fprintf(stderr, "       --threads <int>            number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -1646,28 +1648,30 @@ int main_vcfannotate(int argc, char *argv[])
     args->files   = bcf_sr_init();
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->ref_idx = args->alt_idx = args->chr_idx = args->from_idx = args->to_idx = -1;
     args->set_ids_replace = 1;
     int regions_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"mark-sites",1,0,'m'},
-        {"set-id",1,0,'I'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"annotations",1,0,'a'},
-        {"include",1,0,'i'},
-        {"exclude",1,0,'e'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"remove",1,0,'x'},
-        {"columns",1,0,'c'},
-        {"rename-chrs",1,0,1},
-        {"header-lines",1,0,'h'},
-        {"samples",1,0,'s'},
-        {"samples-file",1,0,'S'},
-        {0,0,0,0}
+        {"mark-sites",required_argument,NULL,'m'},
+        {"set-id",required_argument,NULL,'I'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"annotations",required_argument,NULL,'a'},
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"remove",required_argument,NULL,'x'},
+        {"columns",required_argument,NULL,'c'},
+        {"rename-chrs",required_argument,NULL,1},
+        {"header-lines",required_argument,NULL,'h'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "h:?o:O:r:R:a:x:c:i:e:S:s:I:m:",loptions,NULL)) >= 0)
     {
@@ -1700,6 +1704,7 @@ int main_vcfannotate(int argc, char *argv[])
             case 'R': args->regions_list = optarg; regions_is_file = 1; break;
             case 'h': args->header_fname = optarg; break;
             case  1 : args->rename_chrs = optarg; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case '?': usage(args); break;
             default: error("Unknown argument: %s\n", optarg);
         }
diff --git a/vcfcall.c b/vcfcall.c
index 2287936bc..a28caee6a 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -68,7 +68,7 @@ void error(const char *format, ...);
 typedef struct
 {
     int flag;   // combination of CF_* flags above
-    int output_type;
+    int output_type, n_threads;
     htsFile *bcf_in, *out_fh;
     char *bcf_fname, *output_fname;
     char **samples;             // for subsampling and ploidy
@@ -425,6 +425,7 @@ static void init_data(args_t *args)
 
     args->out_fh = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
 
     if ( args->flag & CF_QCALL )
         return;
@@ -588,6 +589,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -S, --samples-file <file>       PED file or a file with an optional column with sex (see man page for details) [all samples]\n");
     fprintf(stderr, "   -t, --targets <region>          similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "   -T, --targets-file <file>       similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "       --threads <int>             number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Input/output options:\n");
     fprintf(stderr, "   -A, --keep-alts                 keep all possible alternate alleles at variant sites\n");
@@ -631,40 +633,42 @@ int main_vcfcall(int argc, char *argv[])
     args.flag           = CF_ACGT_ONLY;
     args.output_fname   = "-";
     args.output_type    = FT_VCF;
+    args.n_threads = 0;
     args.aux.trio_Pm_SNPs = 1 - 1e-8;
     args.aux.trio_Pm_ins  = args.aux.trio_Pm_del  = 1 - 1e-9;
 
     int c;
     static struct option loptions[] =
     {
-        {"help",0,0,'h'},
-        {"format-fields",1,0,'f'},
-        {"gvcf",1,0,'g'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"samples",1,0,'s'},
-        {"samples-file",1,0,'S'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"keep-alts",0,0,'A'},
-        {"insert-missed",0,0,'i'},
-        {"skip-Ns",0,0,'N'},            // now the new default
-        {"keep-masked-refs",0,0,'M'},
-        {"skip-variants",1,0,'V'},
-        {"variants-only",0,0,'v'},
-        {"consensus-caller",0,0,'c'},
-        {"constrain",1,0,'C'},
-        {"multiallelic-caller",0,0,'m'},
-        {"pval-threshold",1,0,'p'},
-        {"prior",1,0,'P'},
-        {"novel-rate",1,0,'n'},
-        {"ploidy",1,0,1},
-        {"ploidy-file",1,0,2},
-        {"chromosome-X",1,0,'X'},
-        {"chromosome-Y",1,0,'Y'},
-        {0,0,0,0}
+        {"help",no_argument,NULL,'h'},
+        {"format-fields",required_argument,NULL,'f'},
+        {"gvcf",required_argument,NULL,'g'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"threads",required_argument,NULL,9},
+        {"keep-alts",no_argument,NULL,'A'},
+        {"insert-missed",no_argument,NULL,'i'},
+        {"skip-Ns",no_argument,NULL,'N'},            // now the new default
+        {"keep-masked-refs",no_argument,NULL,'M'},
+        {"skip-variants",required_argument,NULL,'V'},
+        {"variants-only",no_argument,NULL,'v'},
+        {"consensus-caller",no_argument,NULL,'c'},
+        {"constrain",required_argument,NULL,'C'},
+        {"multiallelic-caller",no_argument,NULL,'m'},
+        {"pval-threshold",required_argument,NULL,'p'},
+        {"prior",required_argument,NULL,'P'},
+        {"novel-rate",required_argument,NULL,'n'},
+        {"ploidy",required_argument,NULL,1},
+        {"ploidy-file",required_argument,NULL,2},
+        {"chromosome-X",no_argument,NULL,'X'},
+        {"chromosome-Y",no_argument,NULL,'Y'},
+        {NULL,0,NULL,0}
     };
 
     char *tmp = NULL;
@@ -722,6 +726,7 @@ int main_vcfcall(int argc, char *argv[])
             case 'T': args.targets = optarg; args.targets_is_file = 1; break;
             case 's': args.samples_fname = optarg; break;
             case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break;
+            case  9 : args.n_threads = strtol(optarg, 0, 0); break;
             default: usage(&args);
         }
     }
diff --git a/vcfconcat.c b/vcfconcat.c
index f5370f1ba..cfec7c01a 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -37,7 +37,7 @@ typedef struct _args_t
 {
     bcf_srs_t *files;
     htsFile *out_fh;
-    int output_type;
+    int output_type, n_threads;
     bcf_hdr_t *out_hdr;
     int *seen_seq;
 
@@ -109,6 +109,7 @@ static void init_data(args_t *args)
     bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat");
     args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
 
     bcf_hdr_write(args->out_fh, args->out_hdr);
 
@@ -572,6 +573,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -q, --min-PQ <int>             Break phase set if phasing quality is lower than <int> [30]\n");
     fprintf(stderr, "   -r, --regions <region>         Restrict to comma-separated list of regions\n");
     fprintf(stderr, "   -R, --regions-file <file>      Restrict to regions listed in a file\n");
+    fprintf(stderr, "       --threads <int>            Number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -583,22 +585,24 @@ int main_vcfconcat(int argc, char *argv[])
     args->argc    = argc; args->argv = argv;
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->min_PQ  = 30;
 
     static struct option loptions[] =
     {
-        {"compact-PS",0,0,'c'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"remove-duplicates",0,0,'D'},
-        {"rm-dups",1,0,'d'},
-        {"allow-overlaps",0,0,'a'},
-        {"ligate",0,0,'l'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"file-list",1,0,'f'},
-        {"min-PQ",1,0,'q'},
-        {0,0,0,0}
+        {"compact-PS",no_argument,NULL,'c'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"remove-duplicates",no_argument,NULL,'D'},
+        {"rm-dups",required_argument,NULL,'d'},
+        {"allow-overlaps",no_argument,NULL,'a'},
+        {"ligate",no_argument,NULL,'l'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"file-list",required_argument,NULL,'f'},
+        {"min-PQ",required_argument,NULL,'q'},
+        {NULL,0,NULL,0}
     };
     char *tmp;
     while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:r:R:c",loptions,NULL)) >= 0)
@@ -626,6 +630,7 @@ int main_vcfconcat(int argc, char *argv[])
                     default: error("The output type \"%s\" not recognised\n", optarg);
                 };
                 break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage(args); break;
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfconvert.c b/vcfconvert.c
index 54d066602..26166dfad 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -66,7 +66,7 @@ struct _args_t
     int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type;
     char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns;
     char *outfname, *infname, *ref_fname;
-    int argc;
+    int argc, n_threads;
 };
 
 static void destroy_data(args_t *args)
@@ -383,6 +383,8 @@ static void gensample_to_vcf(args_t *args)
     free(samples);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
     bcf_hdr_write(out_fh,args->header);
     bcf1_t *rec = bcf_init();
 
@@ -506,6 +508,8 @@ static void haplegendsample_to_vcf(args_t *args)
     free(samples);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
     bcf_hdr_write(out_fh,args->header);
     bcf1_t *rec = bcf_init();
 
@@ -617,6 +621,8 @@ static void hapsample_to_vcf(args_t *args)
     free(samples);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
     bcf_hdr_write(out_fh,args->header);
     bcf1_t *rec = bcf_init();
 
@@ -1152,6 +1158,8 @@ static void tsv_to_vcf(args_t *args)
     args->gts = (int32_t *) malloc(sizeof(int32_t)*n*2);
 
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
     bcf_hdr_write(out_fh,args->header);
 
     tsv_t *tsv = tsv_init(args->columns ? args->columns : "ID,CHROM,POS,AA");
@@ -1200,7 +1208,8 @@ static void vcf_to_vcf(args_t *args)
 {
     open_vcf(args,NULL);
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
-    if ( !out_fh ) error("Failed to open: %s\n", args->outfname);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
 
     bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
     bcf_hdr_write(out_fh,hdr);
@@ -1228,7 +1237,8 @@ static void gvcf_to_vcf(args_t *args)
 
     open_vcf(args,NULL);
     htsFile *out_fh = hts_open(args->outfname,hts_bcf_wmode(args->output_type));
-    if ( !out_fh ) error("Failed to open: %s\n", args->outfname);
+    if ( out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->outfname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
 
     bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
     bcf_hdr_append_version(hdr, args->argc, args->argv, "bcftools_convert");
@@ -1294,6 +1304,7 @@ static void usage(void)
     fprintf(stderr, "   -S, --samples-file <file>   file of samples to include\n");
     fprintf(stderr, "   -t, --targets <region>      similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "   -T, --targets-file <file>   similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "       --threads <int>         number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "VCF output options:\n");
     fprintf(stderr, "   -o, --output <file>            output file name [stdout]\n");
@@ -1347,6 +1358,7 @@ int main_vcfconvert(int argc, char *argv[])
     args->argc   = argc; args->argv = argv;
     args->outfname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
 
     static struct option loptions[] =
     {
@@ -1354,6 +1366,7 @@ int main_vcfconvert(int argc, char *argv[])
         {"exclude",required_argument,NULL,'e'},
         {"output",required_argument,NULL,'o'},
         {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
         {"regions",required_argument,NULL,'r'},
         {"regions-file",required_argument,NULL,'R'},
         {"targets",required_argument,NULL,'t'},
@@ -1374,7 +1387,7 @@ int main_vcfconvert(int argc, char *argv[])
         {"haplegendsample2vcf",required_argument,NULL,'H'},
         {"columns",required_argument,NULL,'c'},
         {"fasta-ref",required_argument,NULL,'f'},
-        {0,0,0,0}
+        {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "?h:r:R:s:S:t:T:i:e:g:G:o:O:c:f:H:",loptions,NULL)) >= 0) {
         switch (c) {
@@ -1410,6 +1423,7 @@ int main_vcfconvert(int argc, char *argv[])
                 }
                 break;
             case 'h': args->convert_func = vcf_to_haplegendsample; args->outfname = optarg; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
         }
diff --git a/vcffilter.c b/vcffilter.c
index f2abf0f4b..ac4c3a32e 100644
--- a/vcffilter.c
+++ b/vcffilter.c
@@ -68,7 +68,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr;
     htsFile *out_fh;
-    int output_type;
+    int output_type, n_threads;
 
     char **argv, *output_fname, *targets_list, *regions_list;
     int argc;
@@ -79,6 +79,7 @@ static void init_data(args_t *args)
 {
     args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
 
     args->hdr = args->files->readers[0].header;
     args->flt_pass = bcf_hdr_id2int(args->hdr,BCF_DT_ID,"PASS"); assert( !args->flt_pass );  // sanity check: required by BCF spec
@@ -415,6 +416,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -S, --set-GTs <.|0>           set genotypes of failed samples to missing (.) or ref (0)\n");
     fprintf(stderr, "    -t, --targets <region>        similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>     similar to -R but streams rather than index-jumps\n");
+    fprintf(stderr, "        --threads <int>           number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -427,24 +429,26 @@ int main_vcffilter(int argc, char *argv[])
     args->files   = bcf_sr_init();
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     int regions_is_file = 0, targets_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"set-GTs",1,0,'S'},
-        {"mode",1,0,'m'},
-        {"soft-filter",1,0,'s'},
-        {"exclude",1,0,'e'},
-        {"include",1,0,'i'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"SnpGap",1,0,'g'},
-        {"IndelGap",1,0,'G'},
-        {0,0,0,0}
+        {"set-GTs",required_argument,NULL,'S'},
+        {"mode",required_argument,NULL,'m'},
+        {"soft-filter",required_argument,NULL,'s'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"SnpGap",required_argument,NULL,'g'},
+        {"IndelGap",required_argument,NULL,'G'},
+        {NULL,0,NULL,0}
     };
     char *tmp;
     while ((c = getopt_long(argc, argv, "e:i:t:T:r:R:h?s:m:o:O:g:G:S:",loptions,NULL)) >= 0) {
@@ -483,6 +487,7 @@ int main_vcffilter(int argc, char *argv[])
                 else if ( !strcmp("0",optarg) ) args->set_gts = SET_GTS_REF;
                 else error("The argument to -S not recognised: %s\n", optarg);
                 break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage(args);
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfisec.c b/vcfisec.c
index c082d68d0..611514685 100644
--- a/vcfisec.c
+++ b/vcfisec.c
@@ -49,7 +49,7 @@ THE SOFTWARE.  */
 
 typedef struct
 {
-    int isec_op, isec_n, *write, iwrite, nwrite, output_type;
+    int isec_op, isec_n, *write, iwrite, nwrite, output_type, n_threads;
     int nflt, *flt_logic;
     filter_t **flt;
     char **flt_expr;
@@ -142,6 +142,7 @@ void isec_vcf(args_t *args)
     {
         out_fh = hts_open(args->output_fname? args->output_fname : "-",hts_bcf_wmode(args->output_type));
         if ( out_fh == NULL ) error("Can't write to %s: %s\n", args->output_fname? args->output_fname : "standard output", strerror(errno));
+        if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
         bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
         bcf_hdr_write(out_fh, files->readers[args->iwrite].header);
     }
@@ -349,6 +350,7 @@ static void init_data(args_t *args)
                 open_file(&args->fnames[i], NULL, "%s/%04d.%s", args->prefix, i, suffix); \
                 args->fh_out[i] = hts_open(args->fnames[i], hts_bcf_wmode(args->output_type));  \
                 if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \
+                if ( args->n_threads ) hts_set_threads(args->fh_out[i], args->n_threads); \
                 bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \
                 bcf_hdr_write(args->fh_out[i], args->files->readers[j].header); \
             }
@@ -463,6 +465,7 @@ static void usage(void)
     fprintf(stderr, "    -t, --targets <region>        similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>     similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "    -w, --write <list>            list of files to write with -p given as 1-based indexes. By default, all files are written\n");
+    fprintf(stderr, "        --threads <int>           number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Examples:\n");
     fprintf(stderr, "   # Create intersection and complements of two sets saving the output in dir/*\n");
@@ -488,26 +491,28 @@ int main_vcfisec(int argc, char *argv[])
     args->argc   = argc; args->argv = argv;
     args->output_fname = NULL;
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     int targets_is_file = 0, regions_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"help",0,0,'h'},
-        {"exclude",1,0,'e'},
-        {"include",1,0,'i'},
-        {"collapse",1,0,'c'},
-        {"complement",0,0,'C'},
-        {"apply-filters",1,0,'f'},
-        {"nfiles",1,0,'n'},
-        {"prefix",1,0,'p'},
-        {"write",1,0,'w'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {0,0,0,0}
+        {"help",no_argument,NULL,'h'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"collapse",required_argument,NULL,'c'},
+        {"complement",no_argument,NULL,'C'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"nfiles",required_argument,NULL,'n'},
+        {"prefix",required_argument,NULL,'p'},
+        {"write",required_argument,NULL,'w'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:",loptions,NULL)) >= 0) {
         switch (c) {
@@ -554,6 +559,7 @@ int main_vcfisec(int argc, char *argv[])
                     else if ( sscanf(p,"%d",&args->isec_n)!=1 ) error("Could not parse --nfiles %s\n", optarg);
                 }
                 break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfmerge.c b/vcfmerge.c
index e876cca69..0517bd56c 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -118,7 +118,7 @@ typedef struct
     htsFile *out_fh;
     bcf_hdr_t *out_hdr;
     char **argv;
-    int argc;
+    int argc, n_threads;
 }
 args_t;
 
@@ -1898,6 +1898,7 @@ void merge_vcf(args_t *args)
 {
     args->out_fh  = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
     args->out_hdr = bcf_hdr_init("w");
 
     if ( args->header_fname )
@@ -1965,6 +1966,7 @@ static void usage(void)
     fprintf(stderr, "    -O, --output-type <b|u|z|v>        'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
     fprintf(stderr, "    -r, --regions <region>             restrict to comma-separated list of regions\n");
     fprintf(stderr, "    -R, --regions-file <file>          restrict to regions listed in a file\n");
+    fprintf(stderr, "        --threads <int>                number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -1977,24 +1979,26 @@ int main_vcfmerge(int argc, char *argv[])
     args->argc   = argc; args->argv = argv;
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->collapse = COLLAPSE_BOTH;
     int regions_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"help",0,0,'h'},
-        {"merge",1,0,'m'},
-        {"file-list",1,0,'l'},
-        {"apply-filters",1,0,'f'},
-        {"use-header",1,0,1},
-        {"print-header",0,0,2},
-        {"force-samples",0,0,3},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"info-rules",1,0,'i'},
-        {0,0,0,0}
+        {"help",no_argument,NULL,'h'},
+        {"merge",required_argument,NULL,'m'},
+        {"file-list",required_argument,NULL,'l'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"use-header",required_argument,NULL,1},
+        {"print-header",no_argument,NULL,2},
+        {"force-samples",no_argument,NULL,3},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"info-rules",required_argument,NULL,'i'},
+        {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:l:",loptions,NULL)) >= 0) {
         switch (c) {
@@ -2027,6 +2031,7 @@ int main_vcfmerge(int argc, char *argv[])
             case  1 : args->header_fname = optarg; break;
             case  2 : args->header_only = 1; break;
             case  3 : args->force_samples = 1; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfnorm.c b/vcfnorm.c
index 9bffddbb3..732eca903 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -74,7 +74,7 @@ typedef struct
     faidx_t *fai;
     struct { int tot, set, swap; } nref;
     char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets;
-    int argc, rmdup, output_type, check_ref, strict_filter, do_indels;
+    int argc, rmdup, output_type, n_threads, check_ref, strict_filter, do_indels;
     int nchanged, nskipped, nsplit, ntotal, mrows_op, mrows_collapse, parsimonious;
 }
 args_t;
@@ -1580,6 +1580,7 @@ static void normalize_vcf(args_t *args)
 {
     htsFile *out = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
     if ( out == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+    if ( args->n_threads ) hts_set_threads(out, args->n_threads);
     bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_norm");
     bcf_hdr_write(out, args->hdr);
 
@@ -1674,6 +1675,7 @@ static void usage(void)
     fprintf(stderr, "    -t, --targets <region>            similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>         similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "    -w, --site-win <int>              buffer for sorting lines which changed position during realignment [1000]\n");
+    fprintf(stderr, "        --threads <int>               number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -1686,6 +1688,7 @@ int main_vcfnorm(int argc, char *argv[])
     args->files   = bcf_sr_init();
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->aln_win = 100;
     args->buf_win = 1000;
     args->mrows_collapse = COLLAPSE_BOTH;
@@ -1695,22 +1698,23 @@ int main_vcfnorm(int argc, char *argv[])
 
     static struct option loptions[] =
     {
-        {"help",0,0,'h'},
-        {"fasta-ref",1,0,'f'},
-        {"do-not-normalize",0,0,'N'},
-        {"multiallelics",1,0,'m'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"site-win",1,0,'w'},
-        {"remove-duplicates",0,0,'D'},
-        {"rm-dup",1,0,'d'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"check-ref",1,0,'c'},
-        {"strict-filter",0,0,'s'},
-        {0,0,0,0}
+        {"help",no_argument,NULL,'h'},
+        {"fasta-ref",required_argument,NULL,'f'},
+        {"do-not-normalize",no_argument,NULL,'N'},
+        {"multiallelics",required_argument,NULL,'m'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"site-win",required_argument,NULL,'w'},
+        {"remove-duplicates",no_argument,NULL,'D'},
+        {"rm-dup",required_argument,NULL,'d'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"check-ref",required_argument,NULL,'c'},
+        {"strict-filter",no_argument,NULL,'s'},
+        {NULL,0,NULL,0}
     };
     char *tmp;
     while ((c = getopt_long(argc, argv, "hr:R:f:w:Dd:o:O:c:m:t:T:sN",loptions,NULL)) >= 0) {
@@ -1766,6 +1770,7 @@ int main_vcfnorm(int argc, char *argv[])
                 args->buf_win = strtol(optarg,&tmp,10);
                 if ( *tmp ) error("Could not parse argument: --site-win %s\n", optarg);
                 break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfplugin.c b/vcfplugin.c
index 1c2921c65..e2ca04a8e 100644
--- a/vcfplugin.c
+++ b/vcfplugin.c
@@ -129,7 +129,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr, *hdr_out;
     htsFile *out_fh;
-    int output_type;
+    int output_type, n_threads;
 
     filter_t *filter;
     char *filter_str;
@@ -423,6 +423,7 @@ static void init_data(args_t *args)
     {
         args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
         if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
+        if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
         bcf_hdr_write(args->out_fh, args->hdr_out);
     }
 }
@@ -461,6 +462,7 @@ static void usage(args_t *args)
     fprintf(stderr, "VCF output options:\n");
     fprintf(stderr, "   -o, --output <file>         write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <type>    'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
+    fprintf(stderr, "       --threads <int>         number of extra output compression threads [0]\n");
     fprintf(stderr, "Plugin options:\n");
     fprintf(stderr, "   -h, --help                  list plugin's options\n");
     fprintf(stderr, "   -l, --list-plugins          list available plugins. See BCFTOOLS_PLUGINS environment variable and man page for details\n");
@@ -477,6 +479,7 @@ int main_plugin(int argc, char *argv[])
     args->argc    = argc; args->argv = argv;
     args->output_fname = "-";
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     args->nplugin_paths = -1;
     int regions_is_file = 0, targets_is_file = 0, plist_only = 0, usage_only = 0, version_only = 0;
 
@@ -486,19 +489,20 @@ int main_plugin(int argc, char *argv[])
 
     static struct option loptions[] =
     {
-        {"version",0,0,'V'},
-        {"verbose",0,0,'v'},
-        {"help",0,0,'h'},
-        {"list-plugins",0,0,'l'},
-        {"output",1,0,'o'},
-        {"output-type",1,0,'O'},
-        {"include",1,0,'i'},
-        {"exclude",1,0,'e'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {0,0,0,0}
+        {"version",no_argument,NULL,'V'},
+        {"verbose",no_argument,NULL,'v'},
+        {"help",no_argument,NULL,'h'},
+        {"list-plugins",no_argument,NULL,'l'},
+        {"output",required_argument,NULL,'o'},
+        {"output-type",required_argument,NULL,'O'},
+        {"threads",required_argument,NULL,9},
+        {"include",required_argument,NULL,'i'},
+        {"exclude",required_argument,NULL,'e'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vV",loptions,NULL)) >= 0)
     {
@@ -522,6 +526,7 @@ int main_plugin(int argc, char *argv[])
             case 't': args->targets_list = optarg; break;
             case 'T': args->targets_list = optarg; targets_is_file = 1; break;
             case 'l': plist_only = 1; break;
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case '?':
             case 'h': usage_only = 1; break;
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfview.c b/vcfview.c
index 5727ab6d5..ed415950b 100644
--- a/vcfview.c
+++ b/vcfview.c
@@ -63,7 +63,7 @@ typedef struct _args_t
     bcf_srs_t *files;
     bcf_hdr_t *hdr, *hnull, *hsub; // original header, sites-only header, subset header
     char **argv, *format, *sample_names, *subset_fname, *targets_list, *regions_list;
-    int argc, clevel, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac;
+    int argc, clevel, n_threads, output_type, print_header, update_info, header_only, n_samples, *imap, calc_ac;
     int trim_alts, sites_only, known, novel, min_alleles, max_alleles, private_vars, uncalled, phased;
     int min_ac, min_ac_type, max_ac, max_ac_type, min_af_type, max_af_type, gt_type;
     int *ac, mac;
@@ -218,6 +218,7 @@ static void init_data(args_t *args)
     else if (args->output_type & FT_GZ) strcat(modew,"z");      // compressed VCF
     args->out = hts_open(args->fn_out ? args->fn_out : "-", modew);
     if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
+    if ( args->n_threads ) hts_set_threads(args->out, args->n_threads);
 
     // headers: hdr=full header, hsub=subset header, hnull=sites only header
     if (args->sites_only){
@@ -490,6 +491,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -R, --regions-file <file>           restrict to regions listed in a file\n");
     fprintf(stderr, "    -t, --targets [^]<region>           similar to -r but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
     fprintf(stderr, "    -T, --targets-file [^]<file>        similar to -R but streams rather than index-jumps. Exclude regions with \"^\" prefix\n");
+    fprintf(stderr, "        --threads <int>                 number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Subset options:\n");
     fprintf(stderr, "    -a, --trim-alt-alleles        trim alternate alleles not seen in the subset\n");
@@ -526,46 +528,48 @@ int main_vcfview(int argc, char *argv[])
     args->print_header = 1;
     args->update_info = 1;
     args->output_type = FT_VCF;
+    args->n_threads = 0;
     int targets_is_file = 0, regions_is_file = 0;
 
     static struct option loptions[] =
     {
-        {"genotype",1,0,'g'},
-        {"compression-level",1,0,'l'},
-        {"header-only",0,0,'h'},
-        {"no-header",0,0,'H'},
-        {"exclude",1,0,'e'},
-        {"include",1,0,'i'},
-        {"trim-alt-alleles",0,0,'a'},
-        {"no-update",0,0,'I'},
-        {"drop-genotypes",0,0,'G'},
-        {"private",0,0,'x'},
-        {"exclude-private",0,0,'X'},
-        {"uncalled",0,0,'u'},
-        {"exclude-uncalled",0,0,'U'},
-        {"apply-filters",1,0,'f'},
-        {"known",0,0,'k'},
-        {"novel",0,0,'n'},
-        {"min-alleles",1,0,'m'},
-        {"max-alleles",1,0,'M'},
-        {"samples",1,0,'s'},
-        {"samples-file",1,0,'S'},
-        {"force-samples",0,0,1},
-        {"output-type",1,0,'O'},
-        {"output-file",1,0,'o'},
-        {"types",1,0,'v'},
-        {"exclude-types",1,0,'V'},
-        {"targets",1,0,'t'},
-        {"targets-file",1,0,'T'},
-        {"regions",1,0,'r'},
-        {"regions-file",1,0,'R'},
-        {"min-ac",1,0,'c'},
-        {"max-ac",1,0,'C'},
-        {"min-af",1,0,'q'},
-        {"max-af",1,0,'Q'},
-        {"phased",0,0,'p'},
-        {"exclude-phased",0,0,'P'},
-        {0,0,0,0}
+        {"genotype",required_argument,NULL,'g'},
+        {"compression-level",required_argument,NULL,'l'},
+        {"threads",required_argument,NULL,9},
+        {"header-only",no_argument,NULL,'h'},
+        {"no-header",no_argument,NULL,'H'},
+        {"exclude",required_argument,NULL,'e'},
+        {"include",required_argument,NULL,'i'},
+        {"trim-alt-alleles",no_argument,NULL,'a'},
+        {"no-update",no_argument,NULL,'I'},
+        {"drop-genotypes",no_argument,NULL,'G'},
+        {"private",no_argument,NULL,'x'},
+        {"exclude-private",no_argument,NULL,'X'},
+        {"uncalled",no_argument,NULL,'u'},
+        {"exclude-uncalled",no_argument,NULL,'U'},
+        {"apply-filters",required_argument,NULL,'f'},
+        {"known",no_argument,NULL,'k'},
+        {"novel",no_argument,NULL,'n'},
+        {"min-alleles",required_argument,NULL,'m'},
+        {"max-alleles",required_argument,NULL,'M'},
+        {"samples",required_argument,NULL,'s'},
+        {"samples-file",required_argument,NULL,'S'},
+        {"force-samples",no_argument,NULL,1},
+        {"output-type",required_argument,NULL,'O'},
+        {"output-file",required_argument,NULL,'o'},
+        {"types",required_argument,NULL,'v'},
+        {"exclude-types",required_argument,NULL,'V'},
+        {"targets",required_argument,NULL,'t'},
+        {"targets-file",required_argument,NULL,'T'},
+        {"regions",required_argument,NULL,'r'},
+        {"regions-file",required_argument,NULL,'R'},
+        {"min-ac",required_argument,NULL,'c'},
+        {"max-ac",required_argument,NULL,'C'},
+        {"min-af",required_argument,NULL,'q'},
+        {"max-af",required_argument,NULL,'Q'},
+        {"phased",no_argument,NULL,'p'},
+        {"exclude-phased",no_argument,NULL,'P'},
+        {NULL,0,NULL,0}
     };
     char *tmp;
     while ((c = getopt_long(argc, argv, "l:t:T:r:R:o:O:s:S:Gf:knv:V:m:M:auUhHc:C:Ii:e:xXpPq:Q:g:",loptions,NULL)) >= 0)
@@ -673,6 +677,7 @@ int main_vcfview(int argc, char *argv[])
                 else error("The argument to -g not recognised. Expected one of hom/het/miss/^hom/^het/^miss, got \"%s\".\n", optarg);
                 break;
             }
+            case  9 : args->n_threads = strtol(optarg, 0, 0); break;
             case '?': usage(args);
             default: error("Unknown argument: %s\n", optarg);
         }

From 5c0d8117b42db02aa4f4638c2b00a5505ed80460 Mon Sep 17 00:00:00 2001
From: mcshane <sm15@sanger.ac.uk>
Date: Tue, 15 Dec 2015 14:04:48 +0000
Subject: [PATCH 128/211] update manpage docs after adding --threads options

---
 doc/bcftools.1    | 88 +++++++++++++++++++++++++++++++++++++++++------
 doc/bcftools.html | 55 ++++++++++++++++++++++++-----
 2 files changed, 124 insertions(+), 19 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index ef6ae10ed..d2783d499 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-11-16 09:01 GMT
+.\"      Date: 2015-12-15 14:02 GMT
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-11\-16 09:01 GMT" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2015\-12\-15 14:02 GMT" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-11\-16 09:01 GMT\fR and refers to bcftools git version \fB1\&.2\-182\-g6710191+\fR\&.
+This manual page was last updated \fB2015\-12\-15 14:02 GMT\fR and refers to bcftools git version \fB1\&.2\-191\-g6737c5c+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -534,6 +534,16 @@ command, third column of the targets file must be comma\-separated list of allel
 .if n \{\
 .RE
 .\}
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+Number of output compression threads to use in addition to main thread\&. Only used when
+\fI\-\-output\-type\fR
+is
+\fIb\fR
+or
+\fIz\fR\&. Default: 0\&.
+.RE
 .SS "bcftools annotate \fI[OPTIONS]\fR \fIFILE\fR"
 .sp
 This command allows to add or remove annotations\&.
@@ -670,6 +680,12 @@ subset of samples to annotate\&. If the samples are named differently in the tar
 VCF, the name mapping can be given as "src_name dst_name\en", separated by whitespaces, each pair on a separate line\&.
 .RE
 .PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-x, \-\-remove\fR \fIlist\fR
 .RS 4
 List of annotations to remove\&. Use "FILTER" to remove all filters or "FILTER/SomeFilter" to remove a specific filter\&. Similarly, "INFO" can be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags except GT\&. To remove all INFO tags except "FOO" and "BAR", use "^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER)\&. "INFO" can be abbreviated to "INF" and "FORMAT" to "FMT"\&.
@@ -845,6 +861,12 @@ This command replaces the former \fBbcftools view\fR caller\&. Some of the origi
 \fBFile format options:\fR
 .RS 4
 .PP
+\fB\-o, \-\-output\fR \fIFILE\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
 .RS 4
 see
@@ -917,6 +939,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -955,12 +983,6 @@ output also sites missed by mpileup but present in
 output sites where REF allele is N
 .RE
 .PP
-\fB\-o, \-\-output\fR \fIFILE\fR
-.RS 4
-see
-\fBCommon Options\fR
-.RE
-.PP
 \fB\-V, \-\-skip\-variants\fR \fIsnps\fR|\fIindels\fR
 .RS 4
 skip indel/SNP sites
@@ -1119,6 +1141,12 @@ see
 \fBCommon Options\fR\&. Requires
 \fB\-a, \-\-allow\-overlaps\fR\&.
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .SS "bcftools consensus \fI[OPTIONS]\fR \fIFILE\fR"
 .sp
 Create consensus sequence by applying VCF variants to a reference fasta file\&.
@@ -1256,6 +1284,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -2055,6 +2089,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .SS "bcftools norm [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR"
 .sp
 Left\-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows\&. Left\-alignment and normalization will only be applied if the \fB\-\-fasta\-ref\fR option is supplied\&.
@@ -2155,6 +2195,12 @@ see
 \fBCommon Options\fR
 .RE
 .PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-w, \-\-site\-win\fR \fIINT\fR
 .RS 4
 maximum distance between two records to consider when locally sorting variants which changed position during the realignment
@@ -2229,6 +2275,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -3077,6 +3129,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .RE
 .sp
 .it 1 an-trap
@@ -3405,7 +3463,7 @@ INFO tags, FORMAT tags, column names
 .nf
 INFO/DP or DP
 FORMAT/DV, FMT/DV, or DV
-FILTER, QUAL, ID, REF, ALT[0]
+FILTER, QUAL, ID, POS, REF, ALT[0]
 .fi
 .if n \{\
 .RE
@@ -3718,6 +3776,16 @@ MAF[0]<0\&.05    \&.\&. select rare variants at 5% cutoff
 .RE
 .\}
 .sp
+.if n \{\
+.RS 4
+.\}
+.nf
+POS>=100   \&.\&. restrict your range query, e\&.g\&. 20:100\-200 to strictly sites with POS in that range\&.
+.fi
+.if n \{\
+.RE
+.\}
+.sp
 \fBShell expansion:\fR
 .sp
 Note that expressions must often be quoted because some characters have special meaning in the shell\&. An example of expression enclosed in single quotes which cause that the whole expression is passed to the program as intended:
diff --git a/doc/bcftools.html b/doc/bcftools.html
index f3a14405a..012d67017 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25136160"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp1931920"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
@@ -8,7 +8,7 @@
 work in most, but not all situations. In general, whenever multiple VCFs are
 read simultaneously, they must be indexed and therefore also compressed.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-11-16 09:01 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-182-g6710191+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-12-15 14:02 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-191-g6737c5c+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -212,7 +212,12 @@
     be comma-separated list of alleles, starting with the reference allele.
     Note that the file must be compressed and index.
     Such a file can be easily created from a VCF using:
-</dd></dl></div><pre class="screen">    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c &gt; als.tsv.gz &amp;&amp; tabix -s1 -b2 -e2 als.tsv.gz</pre></div><div class="refsect2" title="bcftools annotate [OPTIONS] FILE"><a id="annotate"></a><h3>bcftools annotate <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command allows to add or remove annotations.</p><div class="variablelist"><dl><dt><span class="term">
+</dd></dl></div><pre class="screen">    bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c &gt; als.tsv.gz &amp;&amp; tabix -s1 -b2 -e2 als.tsv.gz</pre><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Number of output compression threads to use in addition to main thread.
+    Only used when <span class="emphasis"><em>--output-type</em></span> is <span class="emphasis"><em>b</em></span> or <span class="emphasis"><em>z</em></span>. Default: 0.
+</dd></dl></div></div><div class="refsect2" title="bcftools annotate [OPTIONS] FILE"><a id="annotate"></a><h3>bcftools annotate <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command allows to add or remove annotations.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-a, --annotations</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     Bgzip-compressed and tabix-indexed file with annotations. The file
@@ -316,6 +321,10 @@
     given as "src_name dst_name\n", separated by whitespaces, each pair on a
     separate line.
 </dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-x, --remove</strong></span> <span class="emphasis"><em>list</em></span>
 </span></dt><dd>
     List of annotations to remove. Use "FILTER" to remove all filters or
@@ -441,6 +450,10 @@
 functionality has been temporarily lost in the process of transition under
 <a class="ulink" href="http://github.com/samtools/htslib" target="_top">htslib</a>, but will be added back on popular
 demand. The original calling model can be invoked with the <span class="strong"><strong>-c</strong></span> option.</p><div class="refsect3" title="File format options:"><a id="_file_format_options"></a><h4>File format options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -487,6 +500,10 @@
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="Input/output options:"><a id="_input_output_options"></a><h4>Input/output options:</h4><div class="variablelist"><dl><dt><span class="term">
@@ -515,10 +532,6 @@
 </span></dt><dd>
     output sites where REF allele is N
 </dd><dt><span class="term">
-<span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
-</span></dt><dd>
-    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
-</dd><dt><span class="term">
 <span class="strong"><strong>-V, --skip-variants</strong></span> <span class="emphasis"><em>snps</em></span>|<span class="emphasis"><em>indels</em></span>
 </span></dt><dd>
     skip indel/SNP sites
@@ -630,6 +643,10 @@
 <span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>. Requires <span class="strong"><strong>-a, --allow-overlaps</strong></span>.
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect2" title="bcftools consensus [OPTIONS] FILE"><a id="consensus"></a><h3>bcftools consensus <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>Create consensus sequence by applying VCF variants to a reference fasta file.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
@@ -702,6 +719,10 @@
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
 <span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="GEN/SAMPLE conversion:"><a id="_gen_sample_conversion"></a><h4>GEN/SAMPLE conversion:</h4><div class="variablelist"><dl><dt><span class="term">
@@ -1157,6 +1178,10 @@
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
 <span class="strong"><strong>-R, --regions-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect2" title="bcftools norm [OPTIONS] file.vcf.gz"><a id="norm"></a><h3>bcftools norm [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Left-align and normalize indels, check if REF alleles match the reference,
@@ -1232,6 +1257,10 @@
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-w, --site-win</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     maximum distance between two records to consider when locally
@@ -1268,6 +1297,10 @@
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
 <span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="Plugin options:"><a id="_plugin_options"></a><h4>Plugin options:</h4><div class="variablelist"><dl><dt><span class="term">
@@ -1744,6 +1777,10 @@
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="Subset options:"><a id="_subset_options"></a><h4>Subset options:</h4><div class="variablelist"><dl><dt><span class="term">
@@ -1895,7 +1932,7 @@
 INFO tags, FORMAT tags, column names
 </p><pre class="literallayout">INFO/DP or DP
 FORMAT/DV, FMT/DV, or DV
-FILTER, QUAL, ID, REF, ALT[0]</pre></li><li class="listitem"><p class="simpara">
+FILTER, QUAL, ID, POS, REF, ALT[0]</pre></li><li class="listitem"><p class="simpara">
 1 (or 0) to test the presence (or absence) of a flag
 </p><pre class="literallayout">FlagA=1 &amp;&amp; FlagB=0</pre></li><li class="listitem"><p class="simpara">
 "." to test missing values
@@ -1925,7 +1962,7 @@
 Variables and function names are case-insensitive, but not tag names. For example,
 "qual" can be used instead of "QUAL", "strlen()" instead of "STRLEN()" , but
 not "dp" instead of "DP".
-</li></ul></div><p><span class="strong"><strong>Examples:</strong></span></p><pre class="literallayout">MIN(DV)&gt;5</pre><pre class="literallayout">MIN(DV/DP)&gt;0.3</pre><pre class="literallayout">MIN(DP)&gt;10 &amp; MIN(DV)&gt;3</pre><pre class="literallayout">FMT/DP&gt;10  &amp; FMT/GQ&gt;10 .. both conditions must be satisfied within one sample</pre><pre class="literallayout">FMT/DP&gt;10 &amp;&amp; FMT/GQ&gt;10 .. the conditions can be satisfied in different samples</pre><pre class="literallayout">QUAL&gt;10 |  FMT/GQ&gt;10   .. selects only GQ&gt;10 samples</pre><pre class="literallayout">QUAL&gt;10 || FMT/GQ&gt;10   .. selects all samples at QUAL&gt;10 sites</pre><pre class="literallayout">TYPE="snp" &amp;&amp; QUAL&gt;=10 &amp;&amp; (DP4[2]+DP4[3] &gt; 2)</pre><pre class="literallayout">MIN(DP)&gt;35 &amp;&amp; AVG(GQ)&gt;50</pre><pre class="literallayout">ID=@file       .. selects lines with ID present in the file</pre><pre class="literallayout">ID!=@~/file    .. skip lines with ID present in the ~/file</pre><pre class="literallayout">MAF[0]&lt;0.05    .. select rare variants at 5% cutoff</pre><p><span class="strong"><strong>Shell expansion:</strong></span></p><p>Note that expressions must often be quoted because some characters
+</li></ul></div><p><span class="strong"><strong>Examples:</strong></span></p><pre class="literallayout">MIN(DV)&gt;5</pre><pre class="literallayout">MIN(DV/DP)&gt;0.3</pre><pre class="literallayout">MIN(DP)&gt;10 &amp; MIN(DV)&gt;3</pre><pre class="literallayout">FMT/DP&gt;10  &amp; FMT/GQ&gt;10 .. both conditions must be satisfied within one sample</pre><pre class="literallayout">FMT/DP&gt;10 &amp;&amp; FMT/GQ&gt;10 .. the conditions can be satisfied in different samples</pre><pre class="literallayout">QUAL&gt;10 |  FMT/GQ&gt;10   .. selects only GQ&gt;10 samples</pre><pre class="literallayout">QUAL&gt;10 || FMT/GQ&gt;10   .. selects all samples at QUAL&gt;10 sites</pre><pre class="literallayout">TYPE="snp" &amp;&amp; QUAL&gt;=10 &amp;&amp; (DP4[2]+DP4[3] &gt; 2)</pre><pre class="literallayout">MIN(DP)&gt;35 &amp;&amp; AVG(GQ)&gt;50</pre><pre class="literallayout">ID=@file       .. selects lines with ID present in the file</pre><pre class="literallayout">ID!=@~/file    .. skip lines with ID present in the ~/file</pre><pre class="literallayout">MAF[0]&lt;0.05    .. select rare variants at 5% cutoff</pre><pre class="literallayout">POS&gt;=100   .. restrict your range query, e.g. 20:100-200 to strictly sites with POS in that range.</pre><p><span class="strong"><strong>Shell expansion:</strong></span></p><p>Note that expressions must often be quoted because some characters
 have special meaning in the shell.
 An example of expression enclosed in single quotes which cause
 that the whole expression is passed to the program as intended:</p><pre class="literallayout">bcftools view -i '%ID!="." &amp; MAF[0]&lt;0.01'</pre><p>Please refer to the documentation of your shell for details.</p></div><div class="refsect1" title="SCRIPTS AND OPTIONS"><a id="_scripts_and_options"></a><h2>SCRIPTS AND OPTIONS</h2><div class="refsect2" title="plot-vcfstats [OPTIONS] file.vchk […]"><a id="plot-vcfstats"></a><h3>plot-vcfstats [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vchk</em></span> […]</h3><p>Script for processing output of <span class="strong"><strong><a class="link" href="#stats" title="bcftools stats [OPTIONS] A.vcf.gz [B.vcf.gz]">bcftools stats</a></strong></span>. It can merge

From 9e33c258658d5d9d3144bcc1880bf08b314e7e3b Mon Sep 17 00:00:00 2001
From: mcshane <sm15@sanger.ac.uk>
Date: Mon, 11 Jan 2016 16:15:16 +0000
Subject: [PATCH 129/211] Happy New Year

---
 main.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/main.c b/main.c
index f08b5c7e1..1892c1de5 100644
--- a/main.c
+++ b/main.c
@@ -1,6 +1,6 @@
 /*  main.c -- main bcftools command front-end.
 
-    Copyright (C) 2012-2015 Genome Research Ltd.
+    Copyright (C) 2012-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -219,7 +219,7 @@ int main(int argc, char *argv[])
     if (argc < 2) { usage(stderr); return 1; }
 
     if (strcmp(argv[1], "version") == 0 || strcmp(argv[1], "--version") == 0 || strcmp(argv[1], "-v") == 0) {
-        printf("bcftools %s\nUsing htslib %s\nCopyright (C) 2015 Genome Research Ltd.\n", bcftools_version(), hts_version());
+        printf("bcftools %s\nUsing htslib %s\nCopyright (C) 2016 Genome Research Ltd.\n", bcftools_version(), hts_version());
 #if USE_GPL
         printf("License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>\n");
 #else

From 781e0498dbafe8a695275ca7f742b851a9060405 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 11 Jan 2016 13:00:42 +0000
Subject: [PATCH 130/211] annotate: print more informative error message,
 resolves #365

---
 vcfannotate.c | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/vcfannotate.c b/vcfannotate.c
index 96a1649c5..2f8aa8247 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -1,6 +1,6 @@
 /*  vcfannotate.c -- Annotate and edit VCF/BCF files.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -1517,8 +1517,10 @@ static void buffer_annot_lines(args_t *args, bcf1_t *line, int start_pos, int en
         }
         if ( args->ref_idx != -1 )
         {
-            assert( args->ref_idx < tmp->ncols );
-            assert( args->alt_idx < tmp->ncols );
+            if ( args->ref_idx >= tmp->ncols ) 
+                error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->ref_idx+1,tmp->ncols,args->tgts->line.s);
+            if ( args->alt_idx >= tmp->ncols )
+                error("Could not parse the line, expected %d+ columns, found %d:\n\t%s\n",args->alt_idx+1,tmp->ncols,args->tgts->line.s);
             tmp->nals = 2;
             hts_expand(char*,tmp->nals,tmp->mals,tmp->als);
             tmp->als[0] = tmp->cols[args->ref_idx];

From bbe1543ec463fb750d643d9c8297a573f660361f Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 11 Jan 2016 14:54:32 +0000
Subject: [PATCH 131/211] call: improvements in "bcftools call --ploidy" when
 all samples haploid

Previously samples of unknown sex were assigned the
default ploidy of 2 and the only way to override the
default was to create a sample file. This is not required
any more, one can assign the default ploidy for all
sexes using the "* * * * <int>" rule.

If all samples are haploid, run with "--ploidy 1".

Resolves #366.
---
 ploidy.c  | 30 ++++++++++++++++++++++--------
 vcfcall.c | 33 ++++++++++++++++++++++++++++-----
 2 files changed, 50 insertions(+), 13 deletions(-)

diff --git a/ploidy.c b/ploidy.c
index 160bc3eae..719e1753c 100644
--- a/ploidy.c
+++ b/ploidy.c
@@ -1,5 +1,5 @@
-/* 
-    Copyright (C) 2014 Genome Research Ltd.
+/*
+    Copyright (C) 2014-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -98,7 +98,7 @@ int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, v
         ploidy->id2sex[ploidy->nsex-1] = strdup(ploidy->tmp_str.s);
         sp->sex = khash_str2int_inc(ploidy->sex2id, ploidy->id2sex[ploidy->nsex-1]);
         ploidy->sex2dflt = (int*) realloc(ploidy->sex2dflt,sizeof(int)*ploidy->nsex);
-        ploidy->sex2dflt[ploidy->nsex-1] = ploidy->dflt;
+        ploidy->sex2dflt[ploidy->nsex-1] = -1;
     }
 
     ss = se;
@@ -106,8 +106,8 @@ int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, v
     if ( !*se ) error("Could not parse: %s\n", line);
     sp->ploidy = strtol(ss,&se,10);
     if ( ss==se ) error("Could not parse: %s\n", line);
-    if ( sp->ploidy < ploidy->min ) ploidy->min = sp->ploidy;
-    if ( sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy;
+    if ( ploidy->min<0 || sp->ploidy < ploidy->min ) ploidy->min = sp->ploidy;
+    if ( ploidy->max<0 || sp->ploidy > ploidy->max ) ploidy->max = sp->ploidy;
 
     // Special case, chr="*" stands for a default value
     if ( default_ploidy_def )
@@ -119,19 +119,32 @@ int ploidy_parse(const char *line, char **chr_beg, char **chr_end, reg_t *reg, v
     return 0;
 }
 
+static void _set_defaults(ploidy_t *ploidy, int dflt)
+{
+    int i;
+    if ( khash_str2int_get(ploidy->sex2id, "*", &i) == 0 ) dflt = ploidy->sex2dflt[i];
+    for (i=0; i<ploidy->nsex; i++)
+        if ( ploidy->sex2dflt[i]==-1 ) ploidy->sex2dflt[i] = dflt;
+
+    ploidy->dflt = dflt;
+    if ( ploidy->min<0 || dflt < ploidy->min ) ploidy->min = dflt;
+    if ( ploidy->max<0 || dflt > ploidy->max ) ploidy->max = dflt;
+}
+
 ploidy_t *ploidy_init(const char *fname, int dflt)
 {
     ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t));
     if ( !pld ) return NULL;
 
-    pld->dflt = pld->min = pld->max = dflt;
+    pld->min = pld->max = -1;
     pld->sex2id = khash_str2int_init();
     pld->idx = regidx_init(fname,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld);
     if ( !pld->idx )
     {
         ploidy_destroy(pld);
-        pld = NULL;
+        return NULL;
     }
+    _set_defaults(pld,dflt);
     return pld;
 }
 
@@ -140,7 +153,7 @@ ploidy_t *ploidy_init_string(const char *str, int dflt)
     ploidy_t *pld = (ploidy_t*) calloc(1,sizeof(ploidy_t));
     if ( !pld ) return NULL;
 
-    pld->dflt = pld->min = pld->max = dflt;
+    pld->min = pld->max = -1;
     pld->sex2id = khash_str2int_init();
     pld->idx = regidx_init(NULL,ploidy_parse,NULL,sizeof(sex_ploidy_t),pld);
 
@@ -160,6 +173,7 @@ ploidy_t *ploidy_init_string(const char *str, int dflt)
     regidx_insert(pld->idx,NULL);
     free(tmp.s);
 
+    _set_defaults(pld,dflt);
     return pld;
 }
 
diff --git a/vcfcall.c b/vcfcall.c
index a28caee6a..0755e6742 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -1,6 +1,6 @@
 /*  vcfcall.c -- SNP/indel variant calling from VCF/BCF.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -175,6 +175,11 @@ static ploidy_predef_t ploidy_predefs[] =
           "*  * *     M 1\n"
           "*  * *     F 0\n"
     },
+    { .alias  = "1",
+      .about  = "Treat all samples as haploid",
+      .ploidy =
+          "*  * *     * 1\n"
+    },
     {
         .alias  = NULL,
         .about  = NULL,
@@ -396,9 +401,21 @@ static void init_data(args_t *args)
             if ( 3*args->aux.nfams!=args->nsamples ) error("Expected only trios in %s, sorry!\n", args->samples_fname);
             fprintf(stderr,"Detected %d samples in %d trio families\n", args->nsamples,args->aux.nfams);
         }
+    }
+    if ( args->ploidy  )
+    {
         args->nsex = ploidy_nsex(args->ploidy);
         args->sex2ploidy = (int*) calloc(args->nsex,sizeof(int));
         args->sex2ploidy_prev = (int*) calloc(args->nsex,sizeof(int));
+        if ( !args->nsamples )
+        {
+            args->nsamples = bcf_hdr_nsamples(args->aux.hdr);
+            args->sample2sex = (int*) malloc(sizeof(int)*args->nsamples);
+            for (i=0; i<args->nsamples; i++) args->sample2sex[i] = 0;
+        }
+    }
+    if ( args->nsamples )
+    {
         args->aux.ploidy = (uint8_t*) malloc(args->nsamples);
         for (i=0; i<args->nsamples; i++) args->aux.ploidy[i] = 2;
         for (i=0; i<args->nsex; i++) args->sex2ploidy_prev[i] = 2;
@@ -418,9 +435,12 @@ static void init_data(args_t *args)
     else
     {
         args->aux.hdr = bcf_hdr_dup(bcf_sr_get_header(args->aux.srs,0));
-        for (i=0; i<args->nsamples; i++)
-            if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 )
-                error("No such sample: %s\n", args->samples[i]);
+        if ( args->samples )
+        {
+            for (i=0; i<args->nsamples; i++)
+                if ( bcf_hdr_id2int(args->aux.hdr,BCF_DT_SAMPLE,args->samples[i])<0 )
+                    error("No such sample: %s\n", args->samples[i]);
+        }
     }
 
     args->out_fh = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
@@ -451,7 +471,10 @@ static void destroy_data(args_t *args)
     else if ( args->flag & CF_MCALL ) mcall_destroy(&args->aux);
     else if ( args->flag & CF_QCALL ) qcall_destroy(&args->aux);
     int i;
-    for (i=0; i<args->nsamples; i++) free(args->samples[i]);
+    if ( args->samples )
+    {
+        for (i=0; i<args->nsamples; i++) free(args->samples[i]);
+    }
     if ( args->aux.fams )
     {
         for (i=0; i<args->aux.nfams; i++) free(args->aux.fams[i].name);

From cba6e327b6dceec04df400788fc95dce84519b23 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 11 Jan 2016 15:09:51 +0000
Subject: [PATCH 132/211] index: do not segfault when indexing non-existent
 files. Fixes #367

---
 vcfindex.c | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/vcfindex.c b/vcfindex.c
index e40fab52c..d1e9179e4 100644
--- a/vcfindex.c
+++ b/vcfindex.c
@@ -1,7 +1,7 @@
 
 /*  vcfindex.c -- Index bgzip compressed VCF/BCF files for random access.
 
-    Copyright (C) 2014 Genome Research Ltd.
+    Copyright (C) 2014-2016 Genome Research Ltd.
 
     Author: Shane McCarthy <sm15@sanger.ac.uk>
 
@@ -177,6 +177,7 @@ int main_vcfindex(int argc, char *argv[])
     if (stats) return vcf_index_stats(fname, stats);
 
     htsFile *fp = hts_open(fname,"r"); 
+    if ( !fp ) error("Failed to read %s\n", fname);
     htsFormat type = *hts_get_format(fp);
     hts_close(fp);
 

From 3138e74c6958704be96807cb4f3f617db05237a3 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 11 Jan 2016 15:48:57 +0000
Subject: [PATCH 133/211] norm: remove forced flush, forgotten when fixing
 #336. Fixes #368

---
 vcfnorm.c | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/vcfnorm.c b/vcfnorm.c
index 732eca903..a59854ae0 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -1,6 +1,6 @@
 /*  vcfnorm.c -- Left-align and normalize indels.
 
-    Copyright (C) 2013-2014 Genome Research Ltd.
+    Copyright (C) 2013-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -1641,7 +1641,6 @@ static void normalize_vcf(args_t *args)
             if ( args->lines[ilast]->pos - args->lines[i]->pos < args->buf_win ) break;
             j++;
         }
-        if ( args->rbuf.n==args->rbuf.m ) j = 1;
         if ( j>0 ) flush_buffer(args, out, j);
     }
     flush_buffer(args, out, args->rbuf.n);

From 611297e88188c776021af612776364ee5e62b14b Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 12 Jan 2016 10:36:54 +0000
Subject: [PATCH 134/211] reheader: support spaces in sample names

- spaces can be escaped with a backslash
- document this behaviour
- add tests

Resolves the issue brought up under #93.
---
 doc/bcftools.txt       |  7 +++---
 khash_str2str.h        | 19 ++++++++++++++-
 reheader.c             | 39 ++++++++++++++++++++++--------
 test/reheader.3.out    | 55 ++++++++++++++++++++++++++++++++++++++++++
 test/reheader.4.out    | 55 ++++++++++++++++++++++++++++++++++++++++++
 test/reheader.samples3 |  2 ++
 test/reheader.samples4 |  1 +
 test/test.pl           |  2 ++
 8 files changed, 166 insertions(+), 14 deletions(-)
 create mode 100644 test/reheader.3.out
 create mode 100644 test/reheader.4.out
 create mode 100644 test/reheader.samples3
 create mode 100644 test/reheader.samples4

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index e26692dbd..4f32b7e39 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1594,9 +1594,10 @@ Modify header of VCF/BCF files, change sample names.
 *-s, --samples* 'FILE'::
     new sample names, one name per line, in the same order as they appear
     in the VCF file. Alternatively, only samples which need to be renamed
-    can be listed as "old_name new_name\n" pairs separated by
-    whitespaces, each on separate line.
-
+    can be listed as "old_name new_name\n" pairs separated by whitespaces,
+    each on a separate line. If a sample name contains spaces, the
+    spaces can be escaped using the backslash character, for example
+    "Not\ a\ good\ sample\ name".
 
 
 [[roh]]
diff --git a/khash_str2str.h b/khash_str2str.h
index ecf4e0b46..4a5bd1278 100644
--- a/khash_str2str.h
+++ b/khash_str2str.h
@@ -1,6 +1,6 @@
 /*  khash_str2str.h -- C-string to C-string hash table.
 
-    Copyright (C) 2014 Genome Research Ltd.
+    Copyright (C) 2014,2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -60,6 +60,23 @@ static inline void khash_str2str_destroy_free(void *_hash)
     kh_destroy(str2str, hash);
 }
 
+/*
+ *  Destroys the hash structure, the keys and the values
+ */
+static inline void khash_str2str_destroy_free_all(void *_hash)
+{
+    khash_t(str2str) *hash = (khash_t(str2str)*)_hash;
+    khint_t k;
+    if (hash == 0) return;
+    for (k = 0; k < kh_end(hash); ++k)
+        if (kh_exist(hash, k))
+        {
+            free((char*)kh_key(hash, k));
+            free((char*)kh_val(hash, k));
+        }
+    kh_destroy(str2str, hash);
+}
+
 /*
  *  Returns value if key exists or NULL if not
  */
diff --git a/reheader.c b/reheader.c
index f32518871..132b968c5 100644
--- a/reheader.c
+++ b/reheader.c
@@ -1,6 +1,6 @@
 /*  reheader.c -- reheader subcommand.
 
-    Copyright (C) 2014 Genome Research Ltd.
+    Copyright (C) 2014,2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -69,22 +69,41 @@ static void read_header_file(char *fname, kstring_t *hdr)
 static int set_sample_pairs(char **samples, int nsamples, kstring_t *hdr, int idx)
 {
     int i, j, n;
+    kstring_t key = {0,0,0};
+    kstring_t val = {0,0,0};
 
     // Are these samples "old-name new-name" pairs?
     void *hash = khash_str2str_init();
     for (i=0; i<nsamples; i++)
     {
-        char *key, *value;
-        key = value = samples[i];
-        while ( *value && !isspace(*value) ) value++;
-        if ( !*value ) break;
-        *value = 0; value++;
-        while ( isspace(*value) ) value++;
-        khash_str2str_set(hash,key,value);
+        char *ptr = samples[i];
+        key.l = val.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &key);
+            escaped = 0;
+            ptr++;
+        }
+        if ( !*ptr ) break;
+        ptr++;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &val);
+            escaped = 0;
+            ptr++;
+        }
+        khash_str2str_set(hash,strdup(key.s),strdup(val.s));
     }
+    free(key.s);
+    free(val.s);
     if ( i!=nsamples )  // not "old-name new-name" pairs
     {
-        khash_str2str_destroy(hash);
+        khash_str2str_destroy_free_all(hash);
         return 0;
     }
 
@@ -117,7 +136,7 @@ static int set_sample_pairs(char **samples, int nsamples, kstring_t *hdr, int id
     char *ori = khash_str2str_get(hash,hdr->s+idx+j);
     kputs(ori ? ori : hdr->s+idx+j, &tmp);
 
-    if ( hash ) khash_str2str_destroy(hash);
+    khash_str2str_destroy_free_all(hash);
 
     hdr->l = idx;
     kputs(tmp.s, hdr);
diff --git a/test/reheader.3.out b/test/reheader.3.out
new file mode 100644
index 000000000..c5207468e
--- /dev/null
+++ b/test/reheader.3.out
@@ -0,0 +1,55 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
+##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
+##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=3,length=2147483647>
+##contig=<ID=4,length=2147483647>
+##contig=<ID=5,length=2147483647>
+##contig=<ID=20,length=2147483647>
+##FILTER=<ID=Test,Description="Test Filter">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A AA	BB B
+2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+2	114	.	TC	TTCC,TTC	999	PASS	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
+2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+20	3	.	G	CT	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
+20	3	.	GATG	GACT	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0
+20	5	.	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1
+20	59	.	AG	.	999	PASS	AN=4	GT:PL:DP	0/0:0:4	0/0:0:4
+20	80	.	CACAG	CACAT	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	81	.	A	C	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	95	.	TCACCG	ACACCG	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	95	.	TCACCG	AAAAAA	999	Test	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	273	.	CAAAAAAAAAAAAAAAAAAAAA	CAAAAAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=4;AC=2,2	GT:PL:DP	1/2:0,3,5,3,5,5:1	1/2:0,3,5,3,5,5:1
+20	274	.	AAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	278	.	AAAAAAAAAAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+3	10	.	GTGGAC	GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+3	15	.	CACA	CAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+4	21	.	ATTTTTTTTTTTTTTTC	ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+5	22	.	A	AGA	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
diff --git a/test/reheader.4.out b/test/reheader.4.out
new file mode 100644
index 000000000..8b7c1ed2e
--- /dev/null
+++ b/test/reheader.4.out
@@ -0,0 +1,55 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO">
+##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO">
+##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO">
+##FORMAT=<ID=FRF,Number=R,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAF,Number=A,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGF,Number=G,Type=Float,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRI,Number=R,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAI,Number=A,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGI,Number=G,Type=Integer,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FRS,Number=R,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FAS,Number=A,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FGS,Number=G,Type=String,Description="Test Number=AGR in FORMAT">
+##FORMAT=<ID=FSTR,Number=1,Type=String,Description="Test String in FORMAT">
+##INFO=<ID=ISTR,Number=1,Type=String,Description="Test String in INFO">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled likelihood">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Depth">
+##contig=<ID=1,length=2147483647>
+##contig=<ID=2,length=2147483647>
+##contig=<ID=3,length=2147483647>
+##contig=<ID=4,length=2147483647>
+##contig=<ID=5,length=2147483647>
+##contig=<ID=20,length=2147483647>
+##FILTER=<ID=Test,Description="Test Filter">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	XY00001	BB
+2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+2	114	.	TC	TTCC,TTC	999	PASS	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
+2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
+20	3	.	G	CT	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
+20	3	.	GATG	GACT	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0
+20	5	.	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1	1/2:1,2,3,4,5,6,7,8,9,10,11,12,13,14,15:1
+20	59	.	AG	.	999	PASS	AN=4	GT:PL:DP	0/0:0:4	0/0:0:4
+20	80	.	CACAG	CACAT	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	81	.	A	C	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	95	.	TCACCG	ACACCG	999	PASS	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	95	.	TCACCG	AAAAAA	999	Test	AN=4;AC=2	GT:PL:DP	0/1:255,0,255:13	0/1:255,0,255:13
+20	273	.	CAAAAAAAAAAAAAAAAAAAAA	CAAAAAAAAAAAAAAAAAAAAAAA,CAAAAAAAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=4;AC=2,2	GT:PL:DP	1/2:0,3,5,3,5,5:1	1/2:0,3,5,3,5,5:1
+20	274	.	AAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+20	278	.	AAAAAAAAAAAAAAAAA	AAAAAAAAAAAAAAAAAAA	999	PASS	INDEL;AN=0;AC=0	GT:PL:DP	./.:0,0,0:0	./.:0,0,0:0
+3	10	.	GTGGAC	GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+3	15	.	CACA	CAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+4	21	.	ATTTTTTTTTTTTTTTC	ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+5	22	.	A	AGA	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
diff --git a/test/reheader.samples3 b/test/reheader.samples3
new file mode 100644
index 000000000..b8f870021
--- /dev/null
+++ b/test/reheader.samples3
@@ -0,0 +1,2 @@
+XY00002 BB\ B
+XY00001 A\ AA
diff --git a/test/reheader.samples4 b/test/reheader.samples4
new file mode 100644
index 000000000..dcda975da
--- /dev/null
+++ b/test/reheader.samples4
@@ -0,0 +1 @@
+XY00002 BB
diff --git a/test/test.pl b/test/test.pl
index 899ea169a..5154a0d1e 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -197,6 +197,8 @@
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.1.out',header=>'reheader.hdr');
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.2.out',samples=>'reheader.samples');
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.2.out',samples=>'reheader.samples2');
+test_vcf_reheader($opts,in=>'reheader',out=>'reheader.3.out',samples=>'reheader.samples3');
+test_vcf_reheader($opts,in=>'reheader',out=>'reheader.4.out',samples=>'reheader.samples4');
 test_rename_chrs($opts,in=>'annotate');
 test_vcf_convert($opts,in=>'convert',out=>'convert.gs.gt.gen',args=>'-g -,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.gs.gt.samples',args=>'-g .,-');

From c0b49dcef7d09c387c2f123f3787a2914de2a8a2 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 6 Oct 2015 09:38:54 +0100
Subject: [PATCH 135/211] annotate: add to FORMAT fields from a tab-delimited
 file

---
 test/annotate10.hdr |   3 +
 test/annotate10.out |  18 +++++
 test/annotate10.vcf |  17 ++++
 test/annots10.tab   |   4 +
 test/test.pl        |   1 +
 vcfannotate.c       | 192 +++++++++++++++++++++++++++++++++++++-------
 6 files changed, 208 insertions(+), 27 deletions(-)
 create mode 100644 test/annotate10.hdr
 create mode 100644 test/annotate10.out
 create mode 100644 test/annotate10.vcf
 create mode 100644 test/annots10.tab

diff --git a/test/annotate10.hdr b/test/annotate10.hdr
new file mode 100644
index 000000000..2162e9dd5
--- /dev/null
+++ b/test/annotate10.hdr
@@ -0,0 +1,3 @@
+##FORMAT=<ID=FINT,Number=.,Type=Integer,Description="Test type">
+##FORMAT=<ID=FFLT,Number=.,Type=Float,Description="Test type">
+##FORMAT=<ID=FSTR,Number=.,Type=String,Description="Test type">
diff --git a/test/annotate10.out b/test/annotate10.out
new file mode 100644
index 000000000..c7f393b4d
--- /dev/null
+++ b/test/annotate10.out
@@ -0,0 +1,18 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=q99,Description="Quality below 10">
+##contig=<ID=1,assembly=b37,length=249250621>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##INFO=<ID=FLAG,Number=0,Type=Flag,Description="Test type">
+##INFO=<ID=IINT,Number=.,Type=Integer,Description="Test type">
+##INFO=<ID=IFLT,Number=.,Type=Float,Description="Test type">
+##INFO=<ID=ISTR,Number=.,Type=String,Description="Test type">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=FINT,Number=.,Type=Integer,Description="Test type">
+##FORMAT=<ID=FFLT,Number=.,Type=Float,Description="Test type">
+##FORMAT=<ID=FSTR,Number=.,Type=String,Description="Test type">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	B	A
+1	3000001	.	C	T	.	.	.	GT:FINT:FFLT:FSTR	.:.:.:.	.:.:.:.
+1	3000002	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	1|1:88,99:8.8,9.9:888,999	0|1:77:7.7:77
+1	3000003	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	1|1:88,99:8.8,9.9:888,999	0|1:77:7.7:77
+1	3000004	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT:FINT:FFLT:FSTR	1|1:88,99:8.8,9.9:888,999	0|1:77:7.7:77
diff --git a/test/annotate10.vcf b/test/annotate10.vcf
new file mode 100644
index 000000000..0557da6b1
--- /dev/null
+++ b/test/annotate10.vcf
@@ -0,0 +1,17 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##FILTER=<ID=q99,Description="Quality below 10">
+##contig=<ID=1,assembly=b37,length=249250621>
+##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
+##INFO=<ID=FLAG,Number=0,Type=Flag,Description="Test type">
+##INFO=<ID=IINT,Number=.,Type=Integer,Description="Test type">
+##INFO=<ID=IFLT,Number=.,Type=Float,Description="Test type">
+##INFO=<ID=ISTR,Number=.,Type=String,Description="Test type">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##bcftools_annotateVersion=1.2-207-g2038312-dirty+htslib-1.2.1-158-g6876a07-dirty
+##bcftools_annotateCommand=annotate -x FMT test/annots2.vcf
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	B	A
+1	3000001	.	C	T	.	.	.	GT	.	.
+1	3000002	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT	1|1	0|1
+1	3000003	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT	1|1	0|1
+1	3000004	id	C	T	99	q99	FLAG;IINT=88,99;IFLT=8.8,9.9;ISTR=888,999	GT	1|1	0|1
diff --git a/test/annots10.tab b/test/annots10.tab
new file mode 100644
index 000000000..5128f3c56
--- /dev/null
+++ b/test/annots10.tab
@@ -0,0 +1,4 @@
+1	3000001	.	.	.	.	.	.
+1	3000002	88,99	77	8.8,9.9	7.7	888,999	77
+1	3000003	88,99	77	8.8,9.9	7.7	888,999	77
+1	3000004	88,99	77	8.8,9.9	7.7	888,999	77
diff --git a/test/test.pl b/test/test.pl
index 5154a0d1e..48ec9db08 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -175,6 +175,7 @@
 test_vcf_annotate($opts,in=>'annotate3',out=>'annotate7.out',args=>'-x FORMAT');
 test_vcf_annotate($opts,in=>'annotate4',vcf=>'annots4',out=>'annotate8.out',args=>'-c +INFO');
 test_vcf_annotate($opts,in=>'annotate4',tab=>'annots4',out=>'annotate8.out',args=>'-c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR');
+test_vcf_annotate($opts,in=>'annotate10',tab=>'annots10',out=>'annotate10.out',args=>'-c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR');
 test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+missing2ref');
 test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+setGT',args=>'-- -t . -n 0');
 test_vcf_annotate($opts,in=>'annotate9',tab=>'annots9',out=>'annotate9.out',args=>'-c CHROM,POS,REF,ALT,+ID');
diff --git a/vcfannotate.c b/vcfannotate.c
index 2f8aa8247..fe09f9f7b 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -809,6 +809,135 @@ static int vcf_setter_format_gt(args_t *args, bcf1_t *line, annot_col_t *col, vo
         return bcf_update_genotypes(args->hdr_out,line,args->tmpi3,nsrc*bcf_hdr_nsamples(args->hdr_out));
     }
 }
+static int count_vals(annot_line_t *tab, int icol_beg, int icol_end)
+{
+    int i, nmax = 0;
+    for (i=icol_beg; i<icol_end; i++)
+    {
+        char *str = tab->cols[i], *end = str;
+        if ( str[0]=='.' && !str[1] ) 
+        {
+            // missing value
+            if ( !nmax ) nmax = 1;
+            continue;
+        }
+        int n = 1;
+        while ( *end )
+        {
+            if ( *end==',' ) n++;
+            end++;
+        }
+        if ( nmax<n ) nmax = n;
+    }
+    return nmax;
+}
+static int setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+    int nsmpl = bcf_hdr_nsamples(args->hdr_out);
+    assert( col->icol+nsmpl <= tab->ncols );
+    int nvals = count_vals(tab,col->icol,col->icol+nsmpl);
+    assert( nvals>0 );
+    hts_expand(int32_t,nvals*nsmpl,args->mtmpi,args->tmpi);
+
+    int icol = col->icol, ismpl;
+    for (ismpl=0; ismpl<nsmpl; ismpl++)
+    {
+        int32_t *ptr = args->tmpi + ismpl*nvals;
+        int ival = 0;
+
+        char *str = tab->cols[icol];
+        while ( *str )
+        {
+            if ( str[0]=='.' && (!str[1] || str[1]==',') )  // missing value
+            {
+                ptr[ival++] = bcf_int32_missing;
+                str += str[1] ? 2 : 1;
+                continue;
+            }
+
+            char *end = str;
+            ptr[ival] = strtol(str, &end, 10); 
+            if ( end==str )
+                error("Could not parse %s at %s:%d .. [%s]\n", col->hdr_key,bcf_seqname(args->hdr,line),line->pos+1,tab->cols[col->icol]);
+
+            ival++;
+            str = *end ? end+1 : end;
+        }
+        while ( ival<nvals ) ptr[ival++] = bcf_int32_vector_end;
+        icol++;
+    }
+    return bcf_update_format_int32(args->hdr_out,line,col->hdr_key,args->tmpi,nsmpl*nvals);
+}
+static int setter_format_real(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+    int nsmpl = bcf_hdr_nsamples(args->hdr_out);
+    assert( col->icol+nsmpl <= tab->ncols );
+    int nvals = count_vals(tab,col->icol,col->icol+nsmpl);
+    assert( nvals>0 );
+    hts_expand(float,nvals*nsmpl,args->mtmpf,args->tmpf);
+
+    int icol = col->icol, ismpl;
+    for (ismpl=0; ismpl<nsmpl; ismpl++)
+    {
+        float *ptr = args->tmpf + ismpl*nvals;
+        int ival = 0;
+
+        char *str = tab->cols[icol];
+        while ( *str )
+        {
+            if ( str[0]=='.' && (!str[1] || str[1]==',') )  // missing value
+            {
+                bcf_float_set_missing(ptr[ival]); 
+                ival++;
+                str += str[1] ? 2 : 1;
+                continue;
+            }
+
+            char *end = str;
+            ptr[ival] = strtod(str, &end); 
+            if ( end==str )
+                error("Could not parse %s at %s:%d .. [%s]\n", col->hdr_key,bcf_seqname(args->hdr,line),line->pos+1,tab->cols[col->icol]);
+
+            ival++;
+            str = *end ? end+1 : end;
+        }
+        while ( ival<nvals ) { bcf_float_set_vector_end(ptr[ival]); ival++; }
+        icol++;
+    }
+    return bcf_update_format_float(args->hdr_out,line,col->hdr_key,args->tmpf,nsmpl*nvals);
+}
+static int setter_format_str(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
+{
+    annot_line_t *tab = (annot_line_t*) data;
+    int nsmpl = bcf_hdr_nsamples(args->hdr_out);
+    assert( col->icol+nsmpl <= tab->ncols );
+
+    int i, max_len = 0;
+    for (i=col->icol; i<col->icol+nsmpl; i++)
+    {
+        int len = strlen(tab->cols[i]);
+        if ( max_len < len ) max_len = len;
+    }
+    hts_expand(char,max_len*nsmpl,args->mtmps,args->tmps);
+
+    int icol = col->icol, ismpl;
+    for (ismpl=0; ismpl<nsmpl; ismpl++)
+    {
+        char *ptr = args->tmps + ismpl*max_len;
+        char *str = tab->cols[icol];
+        i = 0;
+        while ( str[i] )
+        {
+            ptr[i] = str[i];
+            i++;
+        }
+        while ( i<max_len ) ptr[i++] = 0;
+        icol++;
+    }
+    return bcf_update_format_char(args->hdr_out,line,col->hdr_key,args->tmps,nsmpl*max_len);
+}
 static int vcf_setter_format_int(args_t *args, bcf1_t *line, annot_col_t *col, void *data)
 {
     bcf1_t *rec = (bcf1_t*) data;
@@ -1127,7 +1256,7 @@ static void init_columns(args_t *args)
     kstring_t str = {0,0,0}, tmp = {0,0,0};
     char *ss = args->columns, *se = ss;
     args->ncols = 0;
-    int i = -1, has_fmt_str = 0, force_samples = -1;
+    int icol = -1, has_fmt_str = 0, force_samples = -1;
     while ( *ss )
     {
         if ( *se && *se!=',' ) { se++; continue; }
@@ -1135,22 +1264,22 @@ static void init_columns(args_t *args)
         if ( *ss=='+' ) { replace = REPLACE_MISSING; ss++; }
         else if ( *ss=='-' ) { replace = REPLACE_EXISTING; ss++; }
         else if ( *ss=='=' ) { replace = SET_OR_APPEND; ss++; }
-        i++;
+        icol++;
         str.l = 0;
         kputsn(ss, se-ss, &str);
         if ( !str.s[0] || !strcasecmp("-",str.s) ) ;
-        else if ( !strcasecmp("CHROM",str.s) ) args->chr_idx = i;
-        else if ( !strcasecmp("POS",str.s) ) args->from_idx = i;
-        else if ( !strcasecmp("FROM",str.s) ) args->from_idx = i;
-        else if ( !strcasecmp("TO",str.s) ) args->to_idx = i;
-        else if ( !strcasecmp("REF",str.s) ) args->ref_idx = i;
-        else if ( !strcasecmp("ALT",str.s) ) args->alt_idx = i;
+        else if ( !strcasecmp("CHROM",str.s) ) args->chr_idx = icol;
+        else if ( !strcasecmp("POS",str.s) ) args->from_idx = icol;
+        else if ( !strcasecmp("FROM",str.s) ) args->from_idx = icol;
+        else if ( !strcasecmp("TO",str.s) ) args->to_idx = icol;
+        else if ( !strcasecmp("REF",str.s) ) args->ref_idx = icol;
+        else if ( !strcasecmp("ALT",str.s) ) args->alt_idx = icol;
         else if ( !strcasecmp("ID",str.s) )
         {
             if ( replace==REPLACE_EXISTING ) error("Apologies, the -ID feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
-            col->icol = i;
+            col->icol = icol;
             col->replace = replace;
             col->setter = args->tgts_is_vcf ? vcf_setter_id : setter_id;
             col->hdr_key = strdup(str.s);
@@ -1160,7 +1289,7 @@ static void init_columns(args_t *args)
             if ( replace==REPLACE_EXISTING ) error("Apologies, the -FILTER feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
-            col->icol = i;
+            col->icol = icol;
             col->replace = replace;
             col->setter = args->tgts_is_vcf ? vcf_setter_filter : setter_filter;
             col->hdr_key = strdup(str.s);
@@ -1187,7 +1316,7 @@ static void init_columns(args_t *args)
             if ( replace==SET_OR_APPEND ) error("Apologies, the =QUAL feature has not been implemented yet.\n");
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
-            col->icol = i;
+            col->icol = icol;
             col->replace = replace;
             col->setter = args->tgts_is_vcf ? vcf_setter_qual : setter_qual;
             col->hdr_key = strdup(str.s);
@@ -1262,30 +1391,38 @@ static void init_columns(args_t *args)
         }
         else if ( !strncasecmp("FORMAT/",str.s, 7) || !strncasecmp("FMT/",str.s,4) )
         {
-            if ( !args->tgts_is_vcf )
-                error("Error: FORMAT fields can be carried over from a VCF file only.\n");
-
             char *key = str.s + (!strncasecmp("FMT/",str.s,4) ? 4 : 7);
             if ( force_samples<0 ) force_samples = replace;
-            if ( force_samples>=0 && replace!=REPLACE_ALL ) force_samples = replace;;
-            bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key, NULL);
-            tmp.l = 0;
-            bcf_hrec_format(hrec, &tmp);
-            bcf_hdr_append(args->hdr_out, tmp.s);
-            bcf_hdr_sync(args->hdr_out);
+            if ( force_samples>=0 && replace!=REPLACE_ALL ) force_samples = replace;
+            if ( args->tgts_is_vcf )
+            {
+                bcf_hrec_t *hrec = bcf_hdr_get_hrec(args->files->readers[1].header, BCF_HL_FMT, "ID", key, NULL);
+                tmp.l = 0;
+                bcf_hrec_format(hrec, &tmp);
+                bcf_hdr_append(args->hdr_out, tmp.s);
+                bcf_hdr_sync(args->hdr_out);
+            }
             int hdr_id = bcf_hdr_id2int(args->hdr_out, BCF_DT_ID, key);
+            if ( !bcf_hdr_idinfo_exists(args->hdr_out,BCF_HL_FMT,hdr_id) )
+                error("The tag \"%s\" is not defined in %s\n", str.s, args->targets_fname);
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
-            col->icol = -1;
+            if ( !args->tgts_is_vcf )
+            {
+                col->icol = icol;
+                icol += bcf_hdr_nsamples(args->hdr_out) - 1;
+            }
+            else
+                col->icol = -1;
             col->replace = replace;
             col->hdr_key = strdup(key);
             if ( !strcasecmp("GT",key) ) col->setter = vcf_setter_format_gt;
             else
                 switch ( bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id) )
                 {
-                    case BCF_HT_INT:    col->setter = vcf_setter_format_int; break;
-                    case BCF_HT_REAL:   col->setter = vcf_setter_format_real; break;
-                    case BCF_HT_STR:    col->setter = vcf_setter_format_str; has_fmt_str = 1; break;
+                    case BCF_HT_INT:    col->setter = args->tgts_is_vcf ? vcf_setter_format_int  : setter_format_int; break;
+                    case BCF_HT_REAL:   col->setter = args->tgts_is_vcf ? vcf_setter_format_real : setter_format_real; break;
+                    case BCF_HT_STR:    col->setter = args->tgts_is_vcf ? vcf_setter_format_str  : setter_format_str; has_fmt_str = 1; break;
                     default: error("The type of %s not recognised (%d)\n", str.s,bcf_hdr_id2type(args->hdr_out,BCF_HL_FMT,hdr_id));
                 }
         }
@@ -1314,7 +1451,7 @@ static void init_columns(args_t *args)
 
             args->ncols++; args->cols = (annot_col_t*) realloc(args->cols,sizeof(annot_col_t)*args->ncols);
             annot_col_t *col = &args->cols[args->ncols-1];
-            col->icol = i;
+            col->icol = icol;
             col->replace = replace;
             col->hdr_key = strdup(str.s);
             col->number  = bcf_hdr_id2length(args->hdr_out,BCF_HL_INFO,hdr_id);
@@ -1338,11 +1475,12 @@ static void init_columns(args_t *args)
     if ( skip_fmt ) khash_str2int_destroy_free(skip_fmt);
     if ( has_fmt_str )
     {
-        int n = bcf_hdr_nsamples(args->hdr_out) > bcf_hdr_nsamples(args->files->readers[1].header) ? bcf_hdr_nsamples(args->hdr_out) : bcf_hdr_nsamples(args->files->readers[1].header);
+        int n = bcf_hdr_nsamples(args->hdr_out);
+        if ( args->tgts_is_vcf && n<bcf_hdr_nsamples(args->files->readers[1].header) ) n = bcf_hdr_nsamples(args->files->readers[1].header);
         args->tmpp  = (char**)malloc(sizeof(char*)*n);
         args->tmpp2 = (char**)malloc(sizeof(char*)*n);
     }
-    if ( force_samples>=0 )
+    if ( force_samples>=0 && args->tgts_is_vcf )
         set_samples(args, args->files->readers[1].header, args->hdr, force_samples==REPLACE_ALL ? 0 : 1);
 }
 

From ba58f21511e9c7c34eee7dbcdc440ca4cd7982ea Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 29 Oct 2015 19:28:34 +0000
Subject: [PATCH 136/211] The fill-tags plugin can add AF. Resolves #345

---
 plugins/fill-tags.c | 33 ++++++++++++++++++++++++++++-----
 1 file changed, 28 insertions(+), 5 deletions(-)

diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c
index 96f5e3391..1d2892981 100644
--- a/plugins/fill-tags.c
+++ b/plugins/fill-tags.c
@@ -37,6 +37,7 @@
 #define SET_AC_Hom  (1<<2)
 #define SET_AC_Het  (1<<3)
 #define SET_AC_Hemi (1<<4)
+#define SET_AF      (1<<5)
 
 typedef struct
 {
@@ -47,8 +48,9 @@ counts_t;
 typedef struct
 {
     bcf_hdr_t *in_hdr, *out_hdr;
-    int tags, marr, mcounts, gt_id;
+    int tags, marr, mfarr, mcounts, gt_id;
     int32_t *arr;
+    float *farr;
     counts_t *counts;
 }
 args_t;
@@ -57,14 +59,14 @@ static args_t args;
 
 const char *about(void)
 {
-    return "Set INFO tags AN, AC, AC_Hom, AC_Het, AC_Hemi.\n";
+    return "Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi.\n";
 }
 
 const char *usage(void)
 {
     return 
         "\n"
-        "About: Set INFO tags AN, AC, AC_Hom, AC_Het, AC_Hemi.\n"
+        "About: Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi.\n"
         "Usage: bcftools +fill-tags [General Options] -- [Plugin Options]\n"
         "Options:\n"
         "   run \"bcftools plugin\" for a list of common options\n"
@@ -89,6 +91,7 @@ int parse_tags(args_t *args, const char *str)
         else if ( !strcasecmp(tags[i],"AC_Hom") ) flag |= SET_AC_Hom;
         else if ( !strcasecmp(tags[i],"AC_Het") ) flag |= SET_AC_Het;
         else if ( !strcasecmp(tags[i],"AC_Hemi") ) flag |= SET_AC_Hemi;
+        else if ( !strcasecmp(tags[i],"AF") ) flag |= SET_AF;
         else
         {
             fprintf(stderr,"Error parsing \"--tags %s\": the tag \"%s\" is not supported\n", str,tags[i]);
@@ -124,7 +127,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         }
     }
     if ( optind != argc ) error(usage());
-    if ( !args.tags ) args.tags |= SET_AN|SET_AC|SET_AC_Hom|SET_AC_Het|SET_AC_Hemi;
+    if ( !args.tags ) args.tags |= SET_AN|SET_AC|SET_AC_Hom|SET_AC_Het|SET_AC_Hemi|SET_AF;
     
     args.gt_id = bcf_hdr_id2int(args.in_hdr,BCF_DT_ID,"GT");
     if ( args.gt_id<0 ) error("Error: GT field is not present\n");
@@ -134,6 +137,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
     if ( args.tags&SET_AC_Hom ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Hom,Number=A,Type=Integer,Description=\"Allele counts in homozygous genotypes\">");
     if ( args.tags&SET_AC_Het ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Het,Number=A,Type=Integer,Description=\"Allele counts in heterozygous genotypes\">");
     if ( args.tags&SET_AC_Hemi ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Hemi,Number=A,Type=Integer,Description=\"Allele counts in hemizygous genotypes\">");
+    if ( args.tags&SET_AF ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele frequency\">");
 
     return 0;
 }
@@ -149,6 +153,7 @@ bcf1_t *process(bcf1_t *rec)
     if ( !fmt_gt ) return rec;    // no GT tag
 
     hts_expand(int32_t,rec->n_allele,args.marr,args.arr);
+    hts_expand(float,rec->n_allele,args.mfarr,args.farr);
     hts_expand(counts_t,rec->n_allele,args.mcounts,args.counts);
     memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
     memset(args.counts,0,sizeof(*args.counts)*rec->n_allele);
@@ -201,6 +206,23 @@ bcf1_t *process(bcf1_t *rec)
         if ( bcf_update_info_int32(args.out_hdr,rec,"AN",args.arr,1)!=0 )
             error("Error occurred while updating AN at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
     }
+    if ( args.tags&SET_AF )
+    {
+        int n = rec->n_allele-1;
+        if ( n>0 )
+        {
+            args.arr[0] = 0;
+            for (i=0; i<rec->n_allele; i++)
+                args.arr[0] += args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
+            for (i=1; i<rec->n_allele; i++)
+                args.farr[i] = (args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi)*1.0/args.arr[0];
+        }
+        if ( args.arr[0] )
+        {
+            if ( bcf_update_info_float(args.out_hdr,rec,"AF",args.farr+1,n)!=0 )
+                error("Error occurred while updating AF at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+        }
+    }
     if ( args.tags&SET_AC )
     {
         int n = rec->n_allele-1;
@@ -208,7 +230,7 @@ bcf1_t *process(bcf1_t *rec)
         {
             memset(args.arr,0,sizeof(*args.arr)*rec->n_allele);
             for (i=1; i<rec->n_allele; i++)
-                args.arr[i] += args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
+                args.arr[i] = args.counts[i].nhet + args.counts[i].nhom + args.counts[i].nhemi;
         }
         if ( bcf_update_info_int32(args.out_hdr,rec,"AC",args.arr+1,n)!=0 )
             error("Error occurred while updating AC at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
@@ -256,6 +278,7 @@ void destroy(void)
 {
     free(args.counts);
     free(args.arr);
+    free(args.farr);
 }
 
 

From 820e1d612adfcf063ef855be6510e18a4af58022 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 17 Dec 2015 07:58:56 +0000
Subject: [PATCH 137/211] roh: Viterbi training fixed, resolves #328

---
 vcfroh.c | 43 +++++++++++++++++++++++++++++++++----------
 1 file changed, 33 insertions(+), 10 deletions(-)

diff --git a/vcfroh.c b/vcfroh.c
index fa64b798e..95605592f 100644
--- a/vcfroh.c
+++ b/vcfroh.c
@@ -368,14 +368,31 @@ static void flush_viterbi(args_t *args)
             }
         }
 
-        // update the transition matrix tprob
+        // update the transition matrix
+        int n = 1;
         for (i=0; i<2; i++)
         {
-            int n = 0;
             for (j=0; j<2; j++) n += MAT(tcounts,2,i,j);
-            if ( !n) error("fixme: state %d not observed\n", i+1);
-            for (j=0; j<2; j++) MAT(tcounts,2,i,j) /= n;
         }
+        for (i=0; i<2; i++)
+        {
+            for (j=0; j<2; j++)
+            {
+                // no transition to i-th state was observed, set to a small number
+                if ( !MAT(tcounts,2,i,j) ) MAT(tcounts,2,i,j) = 0.1/n;
+                else MAT(tcounts,2,i,j) /= n;
+            }
+        }
+
+        // normalize
+        for (i=0; i<2; i++)
+        {
+            double norm = 0;
+            for (j=0; j<2; j++) norm += MAT(tcounts,2,j,i);
+            assert( norm!=0 );
+            for (j=0; j<2; j++) MAT(tcounts,2,j,i) /= norm;
+        }
+
         if ( args->genmap_fname || args->rec_rate > 0 )
             hmm_set_tprob(args->hmm, tcounts, 0);
         else
@@ -385,14 +402,16 @@ static void flush_viterbi(args_t *args)
         deltaz = fabs(MAT(tprob_arr,2,1,0)-t2az_prev);
         delthw = fabs(MAT(tprob_arr,2,0,1)-t2hw_prev);
         niter++;
-
-        fprintf(stderr,"%d: %f %f\n", niter,deltaz,delthw);
+        fprintf(stderr,"Viterbi training, iteration %d: dAZ=%e dHW=%e\tP(HW|HW)=%e  P(AZ|HW)=%e  P(AZ|AZ)=%e  P(HW|AZ)=%e\n", 
+            niter,deltaz,delthw,
+            MAT(tprob_arr,2,STATE_HW,STATE_HW),MAT(tprob_arr,2,STATE_AZ,STATE_HW),
+            MAT(tprob_arr,2,STATE_AZ,STATE_AZ),MAT(tprob_arr,2,STATE_HW,STATE_AZ));
     }
     while ( deltaz > 0.0 || delthw > 0.0 );
-    fprintf(stderr, "Viterbi training converged in %d iterations to", niter);
     double *tprob_arr = hmm_get_tprob(args->hmm);
-    for (i=0; i<2; i++) for (j=0; j<2; j++) fprintf(stderr, " %f", MAT(tprob_arr,2,i,j));
-    fprintf(stderr, "\n");
+    fprintf(stderr, "Viterbi training converged in %d iterations to P(HW|HW)=%e  P(AZ|HW)=%e  P(AZ|AZ)=%e  P(HW|AZ)=%e\n", niter,
+            MAT(tprob_arr,2,STATE_HW,STATE_HW),MAT(tprob_arr,2,STATE_AZ,STATE_HW),
+            MAT(tprob_arr,2,STATE_AZ,STATE_AZ),MAT(tprob_arr,2,STATE_HW,STATE_AZ));
     
     // output the results
     for (i=0; i<args->nrids; i++)
@@ -400,12 +419,16 @@ static void flush_viterbi(args_t *args)
         int ioff = args->rid_offs[i];
         int nsites = (i+1==args->nrids ? args->nsites : args->rid_offs[i+1]) - ioff;
         hmm_run_viterbi(args->hmm, nsites, args->eprob+ioff*2, args->sites+ioff);
+        hmm_run_fwd_bwd(args->hmm, nsites, args->eprob+ioff*2, args->sites+ioff);
         uint8_t *vpath = hmm_get_viterbi_path(args->hmm);
+        double  *fwd   = hmm_get_fwd_bwd_prob(args->hmm);
 
         const char *chr = bcf_hdr_id2name(args->hdr,args->rids[i]);
         for (j=0; j<nsites; j++)
         {
-            printf("%s\t%d\t%d\t..\n", chr,args->sites[ioff+j]+1,vpath[j*2]==STATE_AZ ? 1 : 0);
+            int state = vpath[j*2];
+            double pval = fwd[j*2 + state];
+            printf("%s\t%d\t%d\t%e\n", chr,args->sites[ioff+j]+1,state==STATE_AZ ? 1 : 0, pval);
         }
     }
 }

From 36036cf14684f9f7d21f88b7565b890329e6eb2d Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 20 Nov 2015 15:18:37 +0000
Subject: [PATCH 138/211] concat: new --naive option for fast operations on
 large BCFs

---
 Makefile         |   4 +-
 doc/bcftools.txt |  12 ++++-
 reheader.c       |  11 ++--
 vcfconcat.c      | 131 +++++++++++++++++++++++++++++++++++++++++++++--
 4 files changed, 143 insertions(+), 15 deletions(-)

diff --git a/Makefile b/Makefile
index 4357d7c7f..b84556523 100644
--- a/Makefile
+++ b/Makefile
@@ -143,7 +143,7 @@ main.o: main.c $(htslib_hts_h) version.h $(bcftools_h)
 vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
 vcfplugin.o: vcfplugin.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
 vcfcall.o: vcfcall.c $(htslib_vcf_h) $(HTSDIR)/htslib/kfunc.h $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/khash_str2int.h $(bcftools_h) $(call_h) $(prob1_h) $(ploidy_h)
-vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h)
+vcfconcat.o: vcfconcat.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(htslib_bgzf_h) $(htslib_tbx_h) $(bcftools_h)
 vcfconvert.o: vcfconvert.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) $(convert_h) $(tsv2vcf_h)
 vcffilter.o: vcffilter.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h) rbuf.h
 vcfgtcheck.o: vcfgtcheck.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h)
@@ -157,7 +157,7 @@ vcfcnv.o: vcfcnv.c $(cnv_h)
 vcfsom.o: vcfsom.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h)
 vcfstats.o: vcfstats.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(htslib_faidx_h) $(bcftools_h)
 vcfview.o: vcfview.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(filter_h)
-reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h)
+reheader.o: reheader.c $(htslib_vcf_h) $(htslib_bgzf_h) $(htslib_tbx_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h)
 tabix.o: tabix.c $(htslib_bgzf_h) $(htslib_tbx_h)
 ccall.o: ccall.c $(HTSDIR)/htslib/kfunc.h $(call_h) kmin.h $(prob1_h)
 convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfutils_h) $(bcftools_h) $(convert_h)
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 4f32b7e39..baa5b0d5d 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -630,7 +630,10 @@ columns appearing in the same order. Can be used, for example, to
 concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel
 VCF into one. The input files must be sorted by chr and position. The files
 must be given in the correct order to produce sorted VCF on output unless
-the *-a, --allow-overlaps* option is specified.
+the *-a, --allow-overlaps* option is specified. With the --naive option, the files
+are concatenated without being recompressed, which is very fast but dangerous
+if the BCF headers differ.
+
 
 *-a, --allow-overlaps*::
     First coordinate of the next file can precede last record of the current file.
@@ -651,6 +654,13 @@ the *-a, --allow-overlaps* option is specified.
 *-l, --ligate*::
     Ligate phased VCFs by matching phase at overlapping haplotypes
 
+*-n, --naive*::
+    Concatenate BCF files without recompression. This is very fast but requires
+    that all files have the same headers. This is because all tags and
+    chromosome names in the BCF body rely on the implicit order of the contig
+    and tag definitions in the header. Currently no sanity checks
+    are in place and only works for compressed BCF files. Dangerous, use with caution. 
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
diff --git a/reheader.c b/reheader.c
index 132b968c5..73123f942 100644
--- a/reheader.c
+++ b/reheader.c
@@ -34,6 +34,7 @@ THE SOFTWARE.  */
 #include <math.h>
 #include <htslib/vcf.h>
 #include <htslib/bgzf.h>
+#include <htslib/tbx.h> // for hts_get_bgzfp()
 #include <htslib/kseq.h>
 #include "bcftools.h"
 #include "khash_str2str.h"
@@ -239,11 +240,7 @@ static void reheader_vcf_gz(args_t *args)
     }
 
     // Output the modified header
-    BGZF *bgzf_out;
-    if ( args->output_fname )
-        bgzf_out = bgzf_open(args->output_fname,"w");
-    else
-        bgzf_out = bgzf_dopen(fileno(stdout), "w");
+    BGZF *bgzf_out = bgzf_open(args->output_fname ? args->output_fname : "-","w");;
     bgzf_write(bgzf_out, hdr.s, hdr.l);
     free(hdr.s);
 
@@ -256,8 +253,8 @@ static void reheader_vcf_gz(args_t *args)
 
     // Stream the rest of the file without as it is, without decompressing
     ssize_t nread;
-    int page_size = getpagesize();
-    char *buf = (char*) valloc(page_size);
+    const size_t page_size = 32768;
+    char *buf = (char*) malloc(page_size);
     while (1)
     {
         nread = bgzf_raw_read(fp, buf, page_size);
diff --git a/vcfconcat.c b/vcfconcat.c
index cfec7c01a..8cc177b33 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -31,6 +31,8 @@ THE SOFTWARE.  */
 #include <htslib/vcf.h>
 #include <htslib/synced_bcf_reader.h>
 #include <htslib/kseq.h>
+#include <htslib/bgzf.h>
+#include <htslib/tbx.h> // for hts_get_bgzfp()
 #include "bcftools.h"
 
 typedef struct _args_t
@@ -50,7 +52,7 @@ typedef struct _args_t
 
     char **argv, *output_fname, *file_list, **fnames, *remove_dups, *regions_list;
     int argc, nfnames, allow_overlaps, phased_concat, regions_is_file;
-    int compact_PS, phase_set_changed;
+    int compact_PS, phase_set_changed, naive_concat;
 }
 args_t;
 
@@ -176,8 +178,11 @@ static void destroy_data(args_t *args)
     for (i=0; i<args->nfnames; i++) free(args->fnames[i]);
     free(args->fnames);
     if ( args->files ) bcf_sr_destroy(args->files);
-    if ( hts_close(args->out_fh)!=0 ) error("hts_close error\n");
-    bcf_hdr_destroy(args->out_hdr);
+    if ( args->out_fh )
+    {
+        if ( hts_close(args->out_fh)!=0 ) error("hts_close error\n");
+    }
+    if ( args->out_hdr ) bcf_hdr_destroy(args->out_hdr);
     free(args->seen_seq);
     free(args->start_pos);
     free(args->swap_phase);
@@ -550,6 +555,108 @@ static void concat(args_t *args)
     }
 }
 
+static void naive_concat(args_t *args)
+{
+    // only compressed BCF atm
+    BGZF *bgzf_out = bgzf_open(args->output_fname,"w");;
+
+    const size_t page_size = 32768;
+    char *buf = (char*) malloc(page_size);
+    kstring_t tmp = {0,0,0};
+    int i;
+    for (i=0; i<args->nfnames; i++)
+    {
+        htsFile *hts_fp = hts_open(args->fnames[i],"r");
+        if ( !hts_fp ) error("Failed to open: %s\n", args->fnames[i]);
+        htsFormat type = *hts_get_format(hts_fp);
+
+        if ( type.format==vcf ) error("The --naive option currently works only for compressed BCFs, sorry :-/\n");
+        if ( type.compression!=bgzf ) error("The --naive option currently works only for compressed BCFs, sorry :-/\n");
+
+        BGZF *fp = hts_get_bgzfp(hts_fp);
+        if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length )
+            error("Failed to read %s: %s\n", args->fnames[i], strerror(errno));
+
+        uint8_t magic[5];
+        if ( bgzf_read(fp, magic, 5)<0 ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
+        if (strncmp((char*)magic, "BCF\2\2", 5) != 0) error("Invalid BCF magic string in %s\n", args->fnames[i]);
+
+        bgzf_read(fp, &tmp.l, 4);
+        hts_expand(char,tmp.l,tmp.m,tmp.s);
+        bgzf_read(fp, tmp.s, tmp.l);
+
+        // write only the first header
+        if ( i==0 )
+        {
+            if ( bgzf_write(bgzf_out, "BCF\2\2", 5) !=5 ) error("Failed to write %d bytes to %s\n", 5,args->output_fname);
+            if ( bgzf_write(bgzf_out, &tmp.l, 4) !=4 ) error("Failed to write %d bytes to %s\n", 4,args->output_fname);
+            if ( bgzf_write(bgzf_out, tmp.s, tmp.l) != tmp.l) error("Failed to write %d bytes to %s\n", tmp.l,args->output_fname);
+        }
+
+        // Output all non-header data that were read together with the header block
+        int nskip = fp->block_offset;
+        if ( fp->block_length - nskip > 0 )
+        {
+            if ( bgzf_write(bgzf_out, fp->uncompressed_block+nskip, fp->block_length-nskip)<0 ) error("Error: %d\n",fp->errcode);
+        }
+        if ( bgzf_flush(bgzf_out)<0 ) error("Error: %d\n",bgzf_out->errcode);
+
+
+        // Stream the rest of the file as it is, without recompressing, but remove BGZF EOF blocks
+        ssize_t nread, ncached = 0, nwr;
+        const int neof = 28;
+        char cached[neof];
+        while (1)
+        {
+            nread = bgzf_raw_read(fp, buf, page_size);
+
+            // page_size boundary may occur in the middle of the EOF block, so we need to cache the blocks' ends
+            if ( nread<=0 ) break;
+            if ( nread<=neof )      // last block
+            {
+                if ( ncached )
+                {
+                    // flush the part of the cache that won't be needed
+                    nwr = bgzf_raw_write(bgzf_out, cached, nread);
+                    if (nwr != nread) error("Write failed, wrote %d instead of %d bytes.\n", nwr,(int)nread);
+
+                    // make space in the cache so that we can append to the end
+                    if ( nread!=neof ) memmove(cached,cached+nread,neof-nread);
+                }
+
+                // fill the cache and check for eof outside this loop
+                memcpy(cached+neof-nread,buf,nread);
+                break;
+            }
+
+            // not the last block, flush the cache if full
+            if ( ncached )
+            {
+                nwr = bgzf_raw_write(bgzf_out, cached, ncached);
+                if (nwr != ncached) error("Write failed, wrote %d instead of %d bytes.\n", nwr,(int)ncached);
+                ncached = 0;
+            }
+
+            // fill the cache
+            nread -= neof;
+            memcpy(cached,buf+nread,neof);
+            ncached = neof;
+
+            nwr = bgzf_raw_write(bgzf_out, buf, nread);
+            if (nwr != nread) error("Write failed, wrote %d instead of %d bytes.\n", nwr,(int)nread);
+        }
+        if ( ncached && memcmp(cached,"\037\213\010\4\0\0\0\0\0\377\6\0\102\103\2\0\033\0\3\0\0\0\0\0\0\0\0\0",neof) )
+        {
+            nwr = bgzf_raw_write(bgzf_out, cached, neof);
+            if (nwr != neof) error("Write failed, wrote %d instead of %d bytes.\n", nwr,(int)neof);
+        }
+        if (hts_close(hts_fp)) error("Close failed: %s\n",args->fnames[i]);
+    }
+    free(buf);
+    free(tmp.s);
+    if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
+}
+
 static void usage(args_t *args)
 {
     fprintf(stderr, "\n");
@@ -558,7 +665,9 @@ static void usage(args_t *args)
     fprintf(stderr, "         concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel\n");
     fprintf(stderr, "         VCF into one. The input files must be sorted by chr and position. The files\n");
     fprintf(stderr, "         must be given in the correct order to produce sorted VCF on output unless\n");
-    fprintf(stderr, "         the -a, --allow-overlaps option is specified.\n");
+    fprintf(stderr, "         the -a, --allow-overlaps option is specified. With the --naive option, the files\n");
+    fprintf(stderr, "         are concatenated without being recompressed, which is very fast but dangerous\n");
+    fprintf(stderr, "         if the BCF headers differ.\n");
     fprintf(stderr, "Usage:   bcftools concat [options] <A.vcf.gz> [<B.vcf.gz> [...]]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Options:\n");
@@ -568,6 +677,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -D, --remove-duplicates        Alias for -d none\n");
     fprintf(stderr, "   -f, --file-list <file>         Read the list of files from a file.\n");
     fprintf(stderr, "   -l, --ligate                   Ligate phased VCFs by matching phase at overlapping haplotypes\n");
+    fprintf(stderr, "   -n, --naive                    Concatenate BCF files without recompression (dangerous, use with caution)\n");
     fprintf(stderr, "   -o, --output <file>            Write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
     fprintf(stderr, "   -q, --min-PQ <int>             Break phase set if phasing quality is lower than <int> [30]\n");
@@ -590,6 +700,7 @@ int main_vcfconcat(int argc, char *argv[])
 
     static struct option loptions[] =
     {
+        {"naive",no_argument,NULL,'n'},
         {"compact-PS",no_argument,NULL,'c'},
         {"regions",required_argument,NULL,'r'},
         {"regions-file",required_argument,NULL,'R'},
@@ -605,7 +716,7 @@ int main_vcfconcat(int argc, char *argv[])
         {NULL,0,NULL,0}
     };
     char *tmp;
-    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:r:R:c",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h:?o:O:f:alq:Dd:r:R:cn",loptions,NULL)) >= 0)
     {
         switch (c) {
             case 'c': args->compact_PS = 1; break;
@@ -617,6 +728,7 @@ int main_vcfconcat(int argc, char *argv[])
                 args->min_PQ = strtol(optarg,&tmp,10);
                 if ( *tmp ) error("Could not parse argument: --min-PQ %s\n", optarg);
                 break;
+            case 'n': args->naive_concat = 1; break;
             case 'a': args->allow_overlaps = 1; break;
             case 'l': args->phased_concat = 1; break;
             case 'f': args->file_list = optarg; break;
@@ -654,6 +766,15 @@ int main_vcfconcat(int argc, char *argv[])
     if ( !args->nfnames ) usage(args);
     if ( args->remove_dups && !args->allow_overlaps ) error("The -D option is supported only with -a\n");
     if ( args->regions_list && !args->allow_overlaps ) error("The -r/-R option is supported only with -a\n");
+    if ( args->naive_concat )
+    {
+        if ( args->allow_overlaps ) error("The option --naive cannot be combined with --allow-overlaps\n");
+        if ( args->phased_concat ) error("The option --naive cannot be combined with --ligate\n");
+        naive_concat(args);
+        destroy_data(args);
+        free(args);
+        return 0;
+    }
     init_data(args);
     concat(args);
     destroy_data(args);

From 2cd6f08753fb2fdd45c2116fae7e129bb83351b9 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 18 Nov 2015 13:49:08 +0000
Subject: [PATCH 139/211] Pass unchanged argc,argv to plugins with run()
 implemented.

This allows to get rid of the cumbersome "--" in command line
options.

Updated print_plugin_usage_hint() following 5f1756ace.
---
 plugins/vcf2sex.c |  8 ++++----
 vcfplugin.c       | 33 +++++++++++++++------------------
 2 files changed, 19 insertions(+), 22 deletions(-)

diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index b9ce69dcc..ddba74c4d 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -105,8 +105,8 @@ const char *usage(void)
         "   Y 1 59373566 F 0\n"
         "   \n"
         "   bcftools +vcf2sex in.vcf.gz\n"
-        "   bcftools +vcf2sex in.vcf.gz -- -n 10\n"
-        "   bcftools +vcf2sex in.vcf.gz -- -g GT\n"
+        "   bcftools +vcf2sex -n 10 in.vcf.gz\n"
+        "   bcftools +vcf2sex -g GT in.vcf.gz\n"
         "\n";
 }
 
@@ -420,8 +420,8 @@ int run(int argc, char **argv)
 
     args->sr = bcf_sr_init();
     args->sr->require_index = 1;
-    if ( !argv[0] ) error("%s", usage());
-    if ( !bcf_sr_add_reader(args->sr,argv[0]) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum));
+    if ( optind==argc ) error("%s", usage());
+    if ( !bcf_sr_add_reader(args->sr,argv[optind]) ) error("Error: %s\n", bcf_sr_strerror(args->sr->errnum));
     args->hdr = args->sr->readers[0].header;
     args->nsample = bcf_hdr_nsamples(args->hdr);
  
diff --git a/vcfplugin.c b/vcfplugin.c
index e2ca04a8e..ad73734bb 100644
--- a/vcfplugin.c
+++ b/vcfplugin.c
@@ -239,13 +239,6 @@ static void print_plugin_usage_hint(void)
         fprintf(stderr,
                 " in\n\tBCFTOOLS_PLUGINS=\"%s\".\n\n"
                 "- Is the plugin path correct?\n\n"
-                "- Are all shared libraries, namely libhts.so, accessible? Verify with\n"
-                "   on Mac OS X: `otool -L your/plugin.so` and set DYLD_LIBRARY_PATH if they are not\n"
-                "   on Linux:    `ldd your/plugin.so` and set LD_LIBRARY_PATH if they are not\n"
-                "\n"
-                "- If not installed systemwide, set the environment variable LD_LIBRARY_PATH (linux) or\n"
-                "DYLD_LIBRARY_PATH (mac) to include directory where *libhts.so* is located.\n"
-                "\n"
                 "- Run \"bcftools plugin -lv\" for more detailed error output.\n"
                 "\n",
                 getenv("BCFTOOLS_PLUGINS")
@@ -484,8 +477,22 @@ int main_plugin(int argc, char *argv[])
     int regions_is_file = 0, targets_is_file = 0, plist_only = 0, usage_only = 0, version_only = 0;
 
     if ( argc==1 ) usage(args);
+
     char *plugin_name = NULL;
-    if ( argv[1][0]!='-' ) { plugin_name = argv[1]; argc--; argv++; }
+    if ( argv[1][0]!='-' )
+    {
+        plugin_name = argv[1]; 
+        argc--; 
+        argv++; 
+        load_plugin(args, plugin_name, 1, &args->plugin);
+        if ( args->plugin.run )
+        {
+            int ret = args->plugin.run(argc, argv);
+            destroy_data(args);
+            free(args);
+            return ret;
+        }
+    }
 
     static struct option loptions[] =
     {
@@ -535,7 +542,6 @@ int main_plugin(int argc, char *argv[])
     if ( plist_only )  return list_plugins(args);
     if ( usage_only && ! plugin_name ) usage(args);
 
-    load_plugin(args, plugin_name, 1, &args->plugin);
     if ( version_only )
     {
         const char *bver, *hver;
@@ -554,15 +560,6 @@ int main_plugin(int argc, char *argv[])
         return 0;
     }
 
-    if ( args->plugin.run )
-    {
-        int iopt = optind; optind = 0;
-        int ret = args->plugin.run(argc-iopt, argv+iopt);
-        destroy_data(args);
-        free(args);
-        return ret;
-    }
-
     char *fname = NULL;
     if ( optind>=argc || argv[optind][0]=='-' )
     {

From 9cf0d82493db16f74e9ff278f0d5573c50694b90 Mon Sep 17 00:00:00 2001
From: mcshane <sm15@sanger.ac.uk>
Date: Thu, 21 Jan 2016 14:20:49 +0000
Subject: [PATCH 140/211] add --no-version option to suppress appending of
 version and command line to output headers

---
 doc/bcftools.txt    | 33 ++++++++++++++++++++++++++++++++-
 test/concat.1.a.vcf |  2 --
 test/concat.1.b.vcf |  2 --
 test/test.pl        | 32 ++++++++++++++++----------------
 vcfannotate.c       |  8 ++++++--
 vcfcall.c           |  8 ++++++--
 vcfconcat.c         |  8 ++++++--
 vcfconvert.c        | 18 +++++++++++-------
 vcffilter.c         |  8 ++++++--
 vcfisec.c           | 12 ++++++++----
 vcfmerge.c          |  8 ++++++--
 vcfnorm.c           |  9 +++++++--
 vcfplugin.c         |  8 ++++++--
 vcfview.c           |  8 +++++++-
 14 files changed, 117 insertions(+), 47 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index baa5b0d5d..6b771dfe7 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -159,6 +159,9 @@ specific commands to see if they apply.
     in 'LIST'. For example, to include only sites which have no filters set,
     use *-f* '.,PASS'.
 
+*--no-version*::
+    Do not append version and command line information to the output VCF header.
+
 *-o, --output* 'FILE'::
     When output consists of a single stream, write it to 'FILE' rather than
     to standard output, where it is written by default.
@@ -337,6 +340,9 @@ This command allows to add or remove annotations.
 *-m, --mark-sites* [+-]'TAG'::
     annotate sites which are present ("+") or absent ("-") in the *-a* file with a new INFO/TAG flag
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
@@ -498,6 +504,9 @@ demand. The original calling model can be invoked with the *-c* option.
 
 ==== File format options:
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
@@ -654,6 +663,9 @@ if the BCF headers differ.
 *-l, --ligate*::
     Ligate phased VCFs by matching phase at overlapping haplotypes
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-n, --naive*::
     Concatenate BCF files without recompression. This is very fast but requires
     that all files have the same headers. This is because all tags and
@@ -749,6 +761,9 @@ Create consensus sequence by applying VCF variants to a reference fasta file.
 
 ==== VCF output options:
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
@@ -946,6 +961,9 @@ And similarly here, the second is filtered:
     strings of failed sites instead of replacing them. The "x" mode resets
     filters of sites which pass to "PASS". Modes "+" and "x" can both be set.
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
@@ -971,7 +989,8 @@ And similarly here, the second is filtered:
 *-T, --targets-file* 'file'::
     see *<<common_options,Common Options>>*
 
-
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
 
 
 
@@ -1219,6 +1238,9 @@ For "vertical" merge take a look at *<<norm,bcftools norm>>* instead.
 -m id     ..  merge by ID
 ----
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
@@ -1272,6 +1294,9 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.
     'both'; if SNPs and indels should be merged into a single record, specify
     'any'.
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-N, --do-not-normalize*[[do_not_normalize]]::
     the '-c s' option can be used to fix or set the REF allele from the 
     reference '-f'. The '-N' option will not turn on indel normalisation
@@ -1333,6 +1358,9 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.
 
 ==== VCF output options:
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-o, --output* 'FILE'::
     see *<<common_options,Common Options>>*
 
@@ -1801,6 +1829,9 @@ Convert between VCF and BCF. Former *bcftools subset*.
     compression level. 0 stands for uncompressed, 1 for best speed and 9 for
     best compression.
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
diff --git a/test/concat.1.a.vcf b/test/concat.1.a.vcf
index 4e9f2f0f8..77912a6ac 100644
--- a/test/concat.1.a.vcf
+++ b/test/concat.1.a.vcf
@@ -11,8 +11,6 @@
 ##samtoolsVersion=0.2.0-rc10+htslib-0.2.0-rc10
 ##samtoolsCommand=samtools mpileup -t INFO/DPR -C50 -pm3 -F0.2 -d10000 -ug -r 1:1-1000000 -b mpileup.2014-07-03//lists/chr1-pooled.list -f human_g1k_v37.fasta
 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
-##bcftools_callVersion=0.2.0-rc10-2-gcd94fde+htslib-0.2.0-rc10
-##bcftools_callCommand=call -vm -f GQ -S mpileup.2014-07-03//pooled/1/1:1-1000000.samples -
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
 1	100	.	GTTT	G	1806	q10	XX=11;DP=35	GT:GQ:DP	0/1:409:35
 1	110	.	C	T,G	1792	Fail	DP=32	GT:GQ:DP	0/1:245:32
diff --git a/test/concat.1.b.vcf b/test/concat.1.b.vcf
index f21547e1f..4bb26e46e 100644
--- a/test/concat.1.b.vcf
+++ b/test/concat.1.b.vcf
@@ -2,8 +2,6 @@
 ##samtoolsVersion=0.2.0-rc10+htslib-0.2.0-rc10
 ##samtoolsCommand=samtools mpileup -t INFO/DPR -C50 -pm3 -F0.2 -d10000 -ug -r 1:1-1000000 -b mpileup.2014-07-03//lists/chr1-pooled.list -f human_g1k_v37.fasta
 ##ALT=<ID=X,Description="Represents allele(s) other than observed.">
-##bcftools_callVersion=0.2.0-rc10-2-gcd94fde+htslib-0.2.0-rc10
-##bcftools_callCommand=call -vm -f GQ -S mpileup.2014-07-03//pooled/1/1:1-1000000.samples -
 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
diff --git a/test/test.pl b/test/test.pl
index 48ec9db08..7491147b9 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -483,7 +483,7 @@ sub test_vcf_merge
     }
     my $args  = exists($args{args}) ? $args{args} : '';
     my $files = join(' ',@files);
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools merge $args $files | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools merge --no-version $args $files");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools merge -Ob $args $files | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_isec
@@ -510,7 +510,7 @@ sub test_vcf_isec2
     }
     my $files = join(' ',@files);
     bgzip_tabix($opts,file=>$args{tab_in},suffix=>'tab',args=>'-s 1 -b 2 -e 3');
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec $args{args} -T $$opts{tmp}/$args{tab_in}.tab.gz $files 2>/dev/null | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec --no-version  $args{args} -T $$opts{tmp}/$args{tab_in}.tab.gz $files 2>/dev/null");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec -Ob $args{args} -T $$opts{tmp}/$args{tab_in}.tab.gz $files 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_query
@@ -545,7 +545,7 @@ sub test_vcf_convert_gvcf
 {
     my ($opts,%args) = @_;
     bgzip_tabix_vcf($opts,$args{in});
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} $$opts{tmp}/$args{in}.vcf.gz | grep -v ^##bcftools");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert --no-version $args{args} -f $$opts{path}/$args{fa} $$opts{tmp}/$args{in}.vcf.gz");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} | grep -v ^##bcftools");
 }
 sub test_vcf_convert_tsv2vcf
@@ -554,7 +554,7 @@ sub test_vcf_convert_tsv2vcf
     my $params = '';
     if ( exists($args{args}) ) { $params .= " $args{args}"; }
     if ( exists($args{fai} ) ) { $params .= " -f $$opts{path}/$args{fai}.fa"; }
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $params --tsv2vcf $$opts{path}/$args{in} | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert --no-version $params --tsv2vcf $$opts{path}/$args{in}");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert -Ou $params --tsv2vcf $$opts{path}/$args{in} | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_norm
@@ -564,7 +564,7 @@ sub test_vcf_norm
     my $params = '';
     if ( exists($args{args}) ) { $params .= " $args{args}"; }
     if ( exists($args{fai} ) ) { $params .= " -f $$opts{path}/$args{fai}.fa"; }
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools norm $params $$opts{tmp}/$args{in}.vcf.gz | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools norm --no-version $params $$opts{tmp}/$args{in}.vcf.gz");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools norm -Ob $params $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_view
@@ -574,7 +574,7 @@ sub test_vcf_view
 
     if ( !exists($args{args}) ) { $args{args} = ''; }
     if ( exists($args{tgts}) ) { $args{args} .= "-T $$opts{path}/$args{tgts}"; }
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view $args{args} $$opts{tmp}/$args{in}.vcf.gz $args{reg} | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view --no-version $args{args} $$opts{tmp}/$args{in}.vcf.gz $args{reg}");
     unless ($args{args} =~ /-H/) {
         test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $args{args} $$opts{tmp}/$args{in}.vcf.gz $args{reg} | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
     }
@@ -583,14 +583,14 @@ sub test_vcf_call
 {
     my ($opts,%args) = @_;
     $args{args} =~ s/{PATH}/$$opts{path}/g;
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call $args{args} $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call --no-version $args{args} $$opts{path}/$args{in}.vcf");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob $args{args} $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_call_cAls
 {
     my ($opts,%args) = @_;
     bgzip_tabix($opts,file=>$args{tab},suffix=>'tab',args=>'-s1 -b2 -e2');
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -mA -C alleles -T $$opts{tmp}/$args{tab}.tab.gz $$opts{path}/$args{in}.vcf | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call --no-version -mA -C alleles -T $$opts{tmp}/$args{tab}.tab.gz $$opts{path}/$args{in}.vcf");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob -mA -C alleles -T $$opts{tmp}/$args{tab}.tab.gz $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_filter
@@ -767,11 +767,11 @@ sub test_vcf_plugin
     if ( !exists($args{args}) ) { $args{args} = ''; }
     $args{args} =~ s/{PATH}/$$opts{path}/g;
     bgzip_tabix_vcf($opts,"$args{in}");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools $args{cmd} $$opts{tmp}/$args{in}.vcf.gz $args{args} | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools $args{cmd} --no-version $$opts{tmp}/$args{in}.vcf.gz $args{args}");
 
     cmd("$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.bcf");
     cmd("$$opts{bin}/bcftools index -f $$opts{tmp}/$args{in}.bcf");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools $args{cmd} $$opts{tmp}/$args{in}.bcf $args{args} | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools $args{cmd} --no-version $$opts{tmp}/$args{in}.bcf $args{args} | grep -v ^##bcftools_");
 }
 sub test_vcf_concat
 {
@@ -781,7 +781,7 @@ sub test_vcf_concat
     {
         if ( $args{do_bcf} )
         {
-            cmd("$$opts{bin}/bcftools view -Ob $$opts{tmp}/$file.vcf.gz > $$opts{tmp}/$file.bcf");
+            cmd("$$opts{bin}/bcftools view --no-version -Ob $$opts{tmp}/$file.vcf.gz > $$opts{tmp}/$file.bcf");
             cmd("$$opts{bin}/bcftools index -f $$opts{tmp}/$file.bcf");
             $files .= " $$opts{tmp}/$file.bcf";
         }
@@ -791,14 +791,14 @@ sub test_vcf_concat
             $files .= " $$opts{tmp}/$file.vcf.gz";
         }
     }
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools concat $args{args} $files | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools concat --no-version $args{args} $files");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools concat -Ob $args{args} $files | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_reheader
 {
     my ($opts,%args) = @_;
-    cmd("$$opts{bin}/bcftools view -Ob $$opts{path}/$args{in}.vcf > $$opts{tmp}/$args{in}.bcf");
-    cmd("$$opts{bin}/bcftools view -Oz $$opts{path}/$args{in}.vcf > $$opts{tmp}/$args{in}.vcf.gz");
+    cmd("$$opts{bin}/bcftools view --no-version -Ob $$opts{path}/$args{in}.vcf > $$opts{tmp}/$args{in}.bcf");
+    cmd("$$opts{bin}/bcftools view --no-version -Oz $$opts{path}/$args{in}.vcf > $$opts{tmp}/$args{in}.vcf.gz");
 
     my $arg = exists($args{header}) ? "-h $$opts{path}/$args{header}" : "-s $$opts{path}/$args{samples}";
     for my $file ("$$opts{path}/$args{in}.vcf","$$opts{tmp}/$args{in}.bcf","$$opts{tmp}/$args{in}.vcf.gz")
@@ -806,8 +806,8 @@ sub test_vcf_reheader
         # bcf header lines can come in different order
         my %bcf_args = ();
         if ( $file=~/\.bcf$/ && -e "$$opts{path}/$args{out}.bcf" ) { %bcf_args = ( out=>"$args{out}.bcf" ); }
-        test_cmd($opts,%args,%bcf_args,cmd=>"$$opts{bin}/bcftools reheader $arg $file | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
-        test_cmd($opts,%args,%bcf_args,cmd=>"cat $file | $$opts{bin}/bcftools reheader $arg | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
+        test_cmd($opts,%args,%bcf_args,cmd=>"$$opts{bin}/bcftools reheader $arg $file | $$opts{bin}/bcftools view --no-version");
+        test_cmd($opts,%args,%bcf_args,cmd=>"cat $file | $$opts{bin}/bcftools reheader $arg | $$opts{bin}/bcftools view --no-version");
     }
 }
 sub test_rename_chrs
diff --git a/vcfannotate.c b/vcfannotate.c
index fe09f9f7b..8e9ba3a42 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -120,7 +120,7 @@ typedef struct _args_t
 
     char **argv, *output_fname, *targets_fname, *regions_list, *header_fname;
     char *remove_annots, *columns, *rename_chrs, *sample_names, *mark_sites;
-    int argc, drop_header, tgts_is_vcf, mark_sites_logic;
+    int argc, drop_header, record_cmd_line, tgts_is_vcf, mark_sites_logic;
 }
 args_t;
 
@@ -1557,7 +1557,7 @@ static void init_data(args_t *args)
             args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites);
     }
 
-    bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_annotate");
+     if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_annotate");
     if ( !args->drop_header )
     {
         if ( args->rename_chrs ) rename_chrs(args, args->rename_chrs);
@@ -1767,6 +1767,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -I, --set-id [+]<format>       set ID column, see man pagee for details\n");
     fprintf(stderr, "   -i, --include <expr>           select sites for which the expression is true (see man pagee for details)\n");
     fprintf(stderr, "   -m, --mark-sites [+-]<tag>     add INFO/tag flag to sites which are (\"+\") or are not (\"-\") listed in the -a file\n");
+    fprintf(stderr, "       --no-version               do not append version and command line to the header\n");
     fprintf(stderr, "   -o, --output <file>            write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
     fprintf(stderr, "   -r, --regions <region>         restrict to comma-separated list of regions\n");
@@ -1789,6 +1790,7 @@ int main_vcfannotate(int argc, char *argv[])
     args->output_fname = "-";
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
     args->ref_idx = args->alt_idx = args->chr_idx = args->from_idx = args->to_idx = -1;
     args->set_ids_replace = 1;
     int regions_is_file = 0;
@@ -1811,6 +1813,7 @@ int main_vcfannotate(int argc, char *argv[])
         {"header-lines",required_argument,NULL,'h'},
         {"samples",required_argument,NULL,'s'},
         {"samples-file",required_argument,NULL,'S'},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "h:?o:O:r:R:a:x:c:i:e:S:s:I:m:",loptions,NULL)) >= 0)
@@ -1845,6 +1848,7 @@ int main_vcfannotate(int argc, char *argv[])
             case 'h': args->header_fname = optarg; break;
             case  1 : args->rename_chrs = optarg; break;
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
             case '?': usage(args); break;
             default: error("Unknown argument: %s\n", optarg);
         }
diff --git a/vcfcall.c b/vcfcall.c
index 0755e6742..d4a19d99e 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -68,7 +68,7 @@ void error(const char *format, ...);
 typedef struct
 {
     int flag;   // combination of CF_* flags above
-    int output_type, n_threads;
+    int output_type, n_threads, record_cmd_line;
     htsFile *bcf_in, *out_fh;
     char *bcf_fname, *output_fname;
     char **samples;             // for subsampling and ploidy
@@ -459,7 +459,7 @@ static void init_data(args_t *args)
     bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "QS");
     bcf_hdr_remove(args->aux.hdr, BCF_HL_INFO, "I16");
 
-    bcf_hdr_append_version(args->aux.hdr, args->argc, args->argv, "bcftools_call");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->aux.hdr, args->argc, args->argv, "bcftools_call");
     bcf_hdr_write(args->out_fh, args->aux.hdr);
 
     if ( args->flag&CF_INS_MISSED ) init_missed_line(args);
@@ -602,6 +602,7 @@ static void usage(args_t *args)
     fprintf(stderr, "Usage:   bcftools call [options] <in.vcf.gz>\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "File format options:\n");
+    fprintf(stderr, "       --no-version                do not append version and command line to the header\n");
     fprintf(stderr, "   -o, --output <file>             write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>     output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
     fprintf(stderr, "       --ploidy <assembly>[?]      predefined ploidy, 'list' to print available settings, append '?' for details\n");
@@ -657,6 +658,7 @@ int main_vcfcall(int argc, char *argv[])
     args.output_fname   = "-";
     args.output_type    = FT_VCF;
     args.n_threads = 0;
+    args.record_cmd_line = 1;
     args.aux.trio_Pm_SNPs = 1 - 1e-8;
     args.aux.trio_Pm_ins  = args.aux.trio_Pm_del  = 1 - 1e-9;
 
@@ -691,6 +693,7 @@ int main_vcfcall(int argc, char *argv[])
         {"ploidy-file",required_argument,NULL,2},
         {"chromosome-X",no_argument,NULL,'X'},
         {"chromosome-Y",no_argument,NULL,'Y'},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
 
@@ -750,6 +753,7 @@ int main_vcfcall(int argc, char *argv[])
             case 's': args.samples_fname = optarg; break;
             case 'S': args.samples_fname = optarg; args.samples_is_file = 1; break;
             case  9 : args.n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args.record_cmd_line = 0; break;
             default: usage(&args);
         }
     }
diff --git a/vcfconcat.c b/vcfconcat.c
index 8cc177b33..32421378c 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -39,7 +39,7 @@ typedef struct _args_t
 {
     bcf_srs_t *files;
     htsFile *out_fh;
-    int output_type, n_threads;
+    int output_type, n_threads, record_cmd_line;
     bcf_hdr_t *out_hdr;
     int *seen_seq;
 
@@ -108,7 +108,7 @@ static void init_data(args_t *args)
         bcf_hdr_append(args->out_hdr,"##FORMAT=<ID=PQ,Number=1,Type=Integer,Description=\"Phasing Quality (bigger is better)\">");
         bcf_hdr_append(args->out_hdr,"##FORMAT=<ID=PS,Number=1,Type=Integer,Description=\"Phase Set\">");
     }
-    bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_concat");
     args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
     if ( args->n_threads ) hts_set_threads(args->out_fh, args->n_threads);
@@ -677,6 +677,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -D, --remove-duplicates        Alias for -d none\n");
     fprintf(stderr, "   -f, --file-list <file>         Read the list of files from a file.\n");
     fprintf(stderr, "   -l, --ligate                   Ligate phased VCFs by matching phase at overlapping haplotypes\n");
+    fprintf(stderr, "       --no-version               do not append version and command line to the header\n");
     fprintf(stderr, "   -n, --naive                    Concatenate BCF files without recompression (dangerous, use with caution)\n");
     fprintf(stderr, "   -o, --output <file>            Write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
@@ -696,6 +697,7 @@ int main_vcfconcat(int argc, char *argv[])
     args->output_fname = "-";
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
     args->min_PQ  = 30;
 
     static struct option loptions[] =
@@ -713,6 +715,7 @@ int main_vcfconcat(int argc, char *argv[])
         {"threads",required_argument,NULL,9},
         {"file-list",required_argument,NULL,'f'},
         {"min-PQ",required_argument,NULL,'q'},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
     char *tmp;
@@ -743,6 +746,7 @@ int main_vcfconcat(int argc, char *argv[])
                 };
                 break;
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
             case 'h':
             case '?': usage(args); break;
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfconvert.c b/vcfconvert.c
index 26166dfad..94e90e88f 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -66,7 +66,7 @@ struct _args_t
     int nsamples, *samples, sample_is_file, targets_is_file, regions_is_file, output_type;
     char **argv, *sample_list, *targets_list, *regions_list, *tag, *columns;
     char *outfname, *infname, *ref_fname;
-    int argc, n_threads;
+    int argc, n_threads, record_cmd_line;
 };
 
 static void destroy_data(args_t *args)
@@ -369,7 +369,7 @@ static void gensample_to_vcf(args_t *args)
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GP,Number=G,Type=Float,Description=\"Genotype Probabilities\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
-    bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
 
     int i, nsamples;
     char **samples = hts_readlist(sample_fname, 1, &nsamples);
@@ -489,7 +489,7 @@ static void haplegendsample_to_vcf(args_t *args)
     bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
-    bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
 
     int i, nrows, nsamples;
     char **samples = hts_readlist(sample_fname, 1, &nrows);
@@ -606,7 +606,7 @@ static void hapsample_to_vcf(args_t *args)
     bcf_hdr_append(args->header, "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End position of the variant described in this record\">");
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
     bcf_hdr_printf(args->header, "##contig=<ID=%s,length=%d>", args->str.s,0x7fffffff);   // MAX_CSI_COOR
-    bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
 
     int i, nsamples;
     char **samples = hts_readlist(sample_fname, 1, &nsamples);
@@ -1143,7 +1143,7 @@ static void tsv_to_vcf(args_t *args)
     args->header = bcf_hdr_init("w");
     bcf_hdr_set_chrs(args->header, args->ref);
     bcf_hdr_append(args->header, "##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
-    bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->header, args->argc, args->argv, "bcftools_convert");
 
     int i, n;
     char **smpls = hts_readlist(args->sample_list, args->sample_is_file, &n);
@@ -1241,7 +1241,7 @@ static void gvcf_to_vcf(args_t *args)
     if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
 
     bcf_hdr_t *hdr = bcf_sr_get_header(args->files,0);
-    bcf_hdr_append_version(hdr, args->argc, args->argv, "bcftools_convert");
+    if (args->record_cmd_line) bcf_hdr_append_version(hdr, args->argc, args->argv, "bcftools_convert");
     bcf_hdr_write(out_fh,hdr);
 
     int32_t *itmp = NULL, nitmp = 0;
@@ -1304,11 +1304,12 @@ static void usage(void)
     fprintf(stderr, "   -S, --samples-file <file>   file of samples to include\n");
     fprintf(stderr, "   -t, --targets <region>      similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "   -T, --targets-file <file>   similar to -R but streams rather than index-jumps\n");
-    fprintf(stderr, "       --threads <int>         number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "VCF output options:\n");
+    fprintf(stderr, "       --no-version               do not append version and command line to the header\n");
     fprintf(stderr, "   -o, --output <file>            output file name [stdout]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
+    fprintf(stderr, "       --threads <int>         number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "GEN/SAMPLE conversion (input/output from IMPUTE2):\n");
     fprintf(stderr, "   -G, --gensample2vcf <...>   <prefix>|<gen-file>,<sample-file>\n");
@@ -1359,6 +1360,7 @@ int main_vcfconvert(int argc, char *argv[])
     args->outfname = "-";
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
 
     static struct option loptions[] =
     {
@@ -1387,6 +1389,7 @@ int main_vcfconvert(int argc, char *argv[])
         {"haplegendsample2vcf",required_argument,NULL,'H'},
         {"columns",required_argument,NULL,'c'},
         {"fasta-ref",required_argument,NULL,'f'},
+        {"no-version",no_argument,NULL,10},
         {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "?h:r:R:s:S:t:T:i:e:g:G:o:O:c:f:H:",loptions,NULL)) >= 0) {
@@ -1424,6 +1427,7 @@ int main_vcfconvert(int argc, char *argv[])
                 break;
             case 'h': args->convert_func = vcf_to_haplegendsample; args->outfname = optarg; break;
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case 10 : args->record_cmd_line = 0; break;
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
         }
diff --git a/vcffilter.c b/vcffilter.c
index ac4c3a32e..f979d77f3 100644
--- a/vcffilter.c
+++ b/vcffilter.c
@@ -71,7 +71,7 @@ typedef struct _args_t
     int output_type, n_threads;
 
     char **argv, *output_fname, *targets_list, *regions_list;
-    int argc;
+    int argc, record_cmd_line;
 }
 args_t;
 
@@ -149,7 +149,7 @@ static void init_data(args_t *args)
         }
     }
 
-    bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_filter");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_filter");
 
     if ( args->filter_str )
         args->filter = filter_init(args->hdr, args->filter_str);
@@ -408,6 +408,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -G, --IndelGap <int>          filter clusters of indels separated by <int> or fewer base pairs allowing only one to pass\n");
     fprintf(stderr, "    -i, --include <expr>          include only sites for which the expression is true (see man page for details\n");
     fprintf(stderr, "    -m, --mode [+x]               \"+\": do not replace but add to existing FILTER; \"x\": reset filters at sites which pass\n");
+    fprintf(stderr, "        --no-version              do not append version and command line to the header\n");
     fprintf(stderr, "    -o, --output <file>           write output to a file [standard output]\n");
     fprintf(stderr, "    -O, --output-type <b|u|z|v>   b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
     fprintf(stderr, "    -r, --regions <region>        restrict to comma-separated list of regions\n");
@@ -430,6 +431,7 @@ int main_vcffilter(int argc, char *argv[])
     args->output_fname = "-";
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
     int regions_is_file = 0, targets_is_file = 0;
 
     static struct option loptions[] =
@@ -448,6 +450,7 @@ int main_vcffilter(int argc, char *argv[])
         {"threads",required_argument,NULL,9},
         {"SnpGap",required_argument,NULL,'g'},
         {"IndelGap",required_argument,NULL,'G'},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
     char *tmp;
@@ -488,6 +491,7 @@ int main_vcffilter(int argc, char *argv[])
                 else error("The argument to -S not recognised: %s\n", optarg);
                 break;
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
             case 'h':
             case '?': usage(args);
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfisec.c b/vcfisec.c
index 611514685..9afe62009 100644
--- a/vcfisec.c
+++ b/vcfisec.c
@@ -58,7 +58,7 @@ typedef struct
     htsFile **fh_out;
     char **argv, *prefix, *output_fname, **fnames, *write_files, *targets_list, *regions_list;
     char *isec_exact;
-    int argc;
+    int argc, record_cmd_line;
 }
 args_t;
 
@@ -143,7 +143,7 @@ void isec_vcf(args_t *args)
         out_fh = hts_open(args->output_fname? args->output_fname : "-",hts_bcf_wmode(args->output_type));
         if ( out_fh == NULL ) error("Can't write to %s: %s\n", args->output_fname? args->output_fname : "standard output", strerror(errno));
         if ( args->n_threads ) hts_set_threads(out_fh, args->n_threads);
-        bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
+        if (args->record_cmd_line) bcf_hdr_append_version(files->readers[args->iwrite].header,args->argc,args->argv,"bcftools_isec");
         bcf_hdr_write(out_fh, files->readers[args->iwrite].header);
     }
     if ( !args->nwrite && !out_std && !args->prefix )
@@ -351,7 +351,7 @@ static void init_data(args_t *args)
                 args->fh_out[i] = hts_open(args->fnames[i], hts_bcf_wmode(args->output_type));  \
                 if ( !args->fh_out[i] ) error("Could not open %s\n", args->fnames[i]); \
                 if ( args->n_threads ) hts_set_threads(args->fh_out[i], args->n_threads); \
-                bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \
+                if (args->record_cmd_line) bcf_hdr_append_version(args->files->readers[j].header,args->argc,args->argv,"bcftools_isec"); \
                 bcf_hdr_write(args->fh_out[i], args->files->readers[j].header); \
             }
             if ( !args->nwrite || args->write[0] )
@@ -456,6 +456,7 @@ static void usage(void)
     fprintf(stderr, "    -e, --exclude <expr>          exclude sites for which the expression is true\n");
     fprintf(stderr, "    -f, --apply-filters <list>    require at least one of the listed FILTER strings (e.g. \"PASS,.\")\n");
     fprintf(stderr, "    -i, --include <expr>          include only sites for which the expression is true\n");
+    fprintf(stderr, "        --no-version                  do not append version and command line to the header\n");
     fprintf(stderr, "    -n, --nfiles [+-=~]<int>      output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files\n");
     fprintf(stderr, "    -o, --output <file>           write output to a file [standard output]\n");
     fprintf(stderr, "    -O, --output-type <b|u|z|v>   b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
@@ -464,8 +465,8 @@ static void usage(void)
     fprintf(stderr, "    -R, --regions-file <file>     restrict to regions listed in a file\n");
     fprintf(stderr, "    -t, --targets <region>        similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>     similar to -R but streams rather than index-jumps\n");
-    fprintf(stderr, "    -w, --write <list>            list of files to write with -p given as 1-based indexes. By default, all files are written\n");
     fprintf(stderr, "        --threads <int>           number of extra output compression threads [0]\n");
+    fprintf(stderr, "    -w, --write <list>            list of files to write with -p given as 1-based indexes. By default, all files are written\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "Examples:\n");
     fprintf(stderr, "   # Create intersection and complements of two sets saving the output in dir/*\n");
@@ -492,6 +493,7 @@ int main_vcfisec(int argc, char *argv[])
     args->output_fname = NULL;
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
     int targets_is_file = 0, regions_is_file = 0;
 
     static struct option loptions[] =
@@ -512,6 +514,7 @@ int main_vcfisec(int argc, char *argv[])
         {"output",required_argument,NULL,'o'},
         {"output-type",required_argument,NULL,'O'},
         {"threads",required_argument,NULL,9},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "hc:r:R:p:n:w:t:T:Cf:o:O:i:e:",loptions,NULL)) >= 0) {
@@ -560,6 +563,7 @@ int main_vcfisec(int argc, char *argv[])
                 }
                 break;
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfmerge.c b/vcfmerge.c
index 0517bd56c..3ab1f51ea 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -118,7 +118,7 @@ typedef struct
     htsFile *out_fh;
     bcf_hdr_t *out_hdr;
     char **argv;
-    int argc, n_threads;
+    int argc, n_threads, record_cmd_line;
 }
 args_t;
 
@@ -1913,7 +1913,7 @@ void merge_vcf(args_t *args)
             char buf[10]; snprintf(buf,10,"%d",i+1);
             merge_headers(args->out_hdr, args->files->readers[i].header,buf,args->force_samples);
         }
-        bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_merge");
+        if (args->record_cmd_line) bcf_hdr_append_version(args->out_hdr, args->argc, args->argv, "bcftools_merge");
         bcf_hdr_sync(args->out_hdr);
     }
     info_rules_init(args);
@@ -1962,6 +1962,7 @@ static void usage(void)
     fprintf(stderr, "    -i, --info-rules <tag:method,..>   rules for merging INFO fields (method is one of sum,avg,min,max,join) or \"-\" to turn off the default [DP:sum,DP4:sum]\n");
     fprintf(stderr, "    -l, --file-list <file>             read file names from the file\n");
     fprintf(stderr, "    -m, --merge <string>               allow multiallelic records for <snps|indels|both|all|none|id>, see man page for details [both]\n");
+    fprintf(stderr, "        --no-version                   do not append version and command line to the header\n");
     fprintf(stderr, "    -o, --output <file>                write output to a file [standard output]\n");
     fprintf(stderr, "    -O, --output-type <b|u|z|v>        'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
     fprintf(stderr, "    -r, --regions <region>             restrict to comma-separated list of regions\n");
@@ -1980,6 +1981,7 @@ int main_vcfmerge(int argc, char *argv[])
     args->output_fname = "-";
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
     args->collapse = COLLAPSE_BOTH;
     int regions_is_file = 0;
 
@@ -1998,6 +2000,7 @@ int main_vcfmerge(int argc, char *argv[])
         {"regions",required_argument,NULL,'r'},
         {"regions-file",required_argument,NULL,'R'},
         {"info-rules",required_argument,NULL,'i'},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:l:",loptions,NULL)) >= 0) {
@@ -2032,6 +2035,7 @@ int main_vcfmerge(int argc, char *argv[])
             case  2 : args->header_only = 1; break;
             case  3 : args->force_samples = 1; break;
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfnorm.c b/vcfnorm.c
index a59854ae0..f473fe158 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -76,6 +76,7 @@ typedef struct
     char **argv, *output_fname, *ref_fname, *vcf_fname, *region, *targets;
     int argc, rmdup, output_type, n_threads, check_ref, strict_filter, do_indels;
     int nchanged, nskipped, nsplit, ntotal, mrows_op, mrows_collapse, parsimonious;
+    int record_cmd_line;
 }
 args_t;
 
@@ -1581,7 +1582,7 @@ static void normalize_vcf(args_t *args)
     htsFile *out = hts_open(args->output_fname, hts_bcf_wmode(args->output_type));
     if ( out == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
     if ( args->n_threads ) hts_set_threads(out, args->n_threads);
-    bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_norm");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_norm");
     bcf_hdr_write(out, args->hdr);
 
     int prev_rid = -1, prev_pos = -1, prev_type = 0;
@@ -1665,6 +1666,7 @@ static void usage(void)
     fprintf(stderr, "    -d, --rm-dup <type>               remove duplicate snps|indels|both|any\n");
     fprintf(stderr, "    -f, --fasta-ref <file>            reference sequence\n");
     fprintf(stderr, "    -m, --multiallelics <-|+>[type]   split multiallelics (-) or join biallelics (+), type: snps|indels|both|any [both]\n");
+    fprintf(stderr, "        --no-version                  do not append version and command line to the header\n");
     fprintf(stderr, "    -N, --do-not-normalize            do not normalize indels (with -m or -c s)\n");
     fprintf(stderr, "    -o, --output <file>               write output to a file [standard output]\n");
     fprintf(stderr, "    -O, --output-type <type>          'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
@@ -1673,8 +1675,8 @@ static void usage(void)
     fprintf(stderr, "    -s, --strict-filter               when merging (-m+), merged site is PASS only if all sites being merged PASS\n");
     fprintf(stderr, "    -t, --targets <region>            similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "    -T, --targets-file <file>         similar to -R but streams rather than index-jumps\n");
-    fprintf(stderr, "    -w, --site-win <int>              buffer for sorting lines which changed position during realignment [1000]\n");
     fprintf(stderr, "        --threads <int>               number of extra output compression threads [0]\n");
+    fprintf(stderr, "    -w, --site-win <int>              buffer for sorting lines which changed position during realignment [1000]\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -1688,6 +1690,7 @@ int main_vcfnorm(int argc, char *argv[])
     args->output_fname = "-";
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
     args->aln_win = 100;
     args->buf_win = 1000;
     args->mrows_collapse = COLLAPSE_BOTH;
@@ -1713,6 +1716,7 @@ int main_vcfnorm(int argc, char *argv[])
         {"threads",required_argument,NULL,9},
         {"check-ref",required_argument,NULL,'c'},
         {"strict-filter",no_argument,NULL,'s'},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
     char *tmp;
@@ -1770,6 +1774,7 @@ int main_vcfnorm(int argc, char *argv[])
                 if ( *tmp ) error("Could not parse argument: --site-win %s\n", optarg);
                 break;
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
             case 'h':
             case '?': usage();
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfplugin.c b/vcfplugin.c
index ad73734bb..87a773f50 100644
--- a/vcfplugin.c
+++ b/vcfplugin.c
@@ -140,7 +140,7 @@ typedef struct _args_t
     char **plugin_paths;
 
     char **argv, *output_fname, *regions_list, *targets_list;
-    int argc, drop_header, verbose;
+    int argc, drop_header, verbose, record_cmd_line;
 }
 args_t;
 
@@ -411,7 +411,7 @@ static void init_data(args_t *args)
     if ( args->filter_str )
         args->filter = filter_init(args->hdr, args->filter_str);
 
-    bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_plugin");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr_out, args->argc, args->argv, "bcftools_plugin");
     if ( !args->drop_header )
     {
         args->out_fh = hts_open(args->output_fname,hts_bcf_wmode(args->output_type));
@@ -453,6 +453,7 @@ static void usage(args_t *args)
     fprintf(stderr, "   -t, --targets <region>      similar to -r but streams rather than index-jumps\n");
     fprintf(stderr, "   -T, --targets-file <file>   similar to -R but streams rather than index-jumps\n");
     fprintf(stderr, "VCF output options:\n");
+    fprintf(stderr, "       --no-version            do not append version and command line to the header\n");
     fprintf(stderr, "   -o, --output <file>         write output to a file [standard output]\n");
     fprintf(stderr, "   -O, --output-type <type>    'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v]\n");
     fprintf(stderr, "       --threads <int>         number of extra output compression threads [0]\n");
@@ -473,6 +474,7 @@ int main_plugin(int argc, char *argv[])
     args->output_fname = "-";
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
     args->nplugin_paths = -1;
     int regions_is_file = 0, targets_is_file = 0, plist_only = 0, usage_only = 0, version_only = 0;
 
@@ -509,6 +511,7 @@ int main_plugin(int argc, char *argv[])
         {"regions-file",required_argument,NULL,'R'},
         {"targets",required_argument,NULL,'t'},
         {"targets-file",required_argument,NULL,'T'},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
     while ((c = getopt_long(argc, argv, "h?o:O:r:R:t:T:li:e:vV",loptions,NULL)) >= 0)
@@ -534,6 +537,7 @@ int main_plugin(int argc, char *argv[])
             case 'T': args->targets_list = optarg; targets_is_file = 1; break;
             case 'l': plist_only = 1; break;
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
             case '?':
             case 'h': usage_only = 1; break;
             default: error("Unknown argument: %s\n", optarg);
diff --git a/vcfview.c b/vcfview.c
index ed415950b..c14075d63 100644
--- a/vcfview.c
+++ b/vcfview.c
@@ -72,6 +72,7 @@ typedef struct _args_t
     int sample_is_file, force_samples;
     char *include_types, *exclude_types;
     int include, exclude;
+    int record_cmd_line;
     htsFile *out;
 }
 args_t;
@@ -86,7 +87,8 @@ static void init_data(args_t *args)
         bcf_hdr_append(args->hdr,"##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">");
         bcf_hdr_append(args->hdr,"##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
     }
-    bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_view");
+    if (args->record_cmd_line) bcf_hdr_append_version(args->hdr, args->argc, args->argv, "bcftools_view");
+    else bcf_hdr_sync(args->hdr);
 
     // setup sample data
     if (args->sample_names)
@@ -485,6 +487,7 @@ static void usage(args_t *args)
     fprintf(stderr, "    -G,   --drop-genotypes              drop individual genotype information (after subsetting if -s option set)\n");
     fprintf(stderr, "    -h/H, --header-only/--no-header     print the header only/suppress the header in VCF output\n");
     fprintf(stderr, "    -l,   --compression-level [0-9]     compression level: 0 uncompressed, 1 best speed, 9 best compression [%d]\n", args->clevel);
+    fprintf(stderr, "          --no-version                  do not append version and command line to the header\n");
     fprintf(stderr, "    -o,   --output-file <file>          output file name [stdout]\n");
     fprintf(stderr, "    -O,   --output-type <b|u|z|v>       b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
     fprintf(stderr, "    -r, --regions <region>              restrict to comma-separated list of regions\n");
@@ -529,6 +532,7 @@ int main_vcfview(int argc, char *argv[])
     args->update_info = 1;
     args->output_type = FT_VCF;
     args->n_threads = 0;
+    args->record_cmd_line = 1;
     int targets_is_file = 0, regions_is_file = 0;
 
     static struct option loptions[] =
@@ -569,6 +573,7 @@ int main_vcfview(int argc, char *argv[])
         {"max-af",required_argument,NULL,'Q'},
         {"phased",no_argument,NULL,'p'},
         {"exclude-phased",no_argument,NULL,'P'},
+        {"no-version",no_argument,NULL,8},
         {NULL,0,NULL,0}
     };
     char *tmp;
@@ -678,6 +683,7 @@ int main_vcfview(int argc, char *argv[])
                 break;
             }
             case  9 : args->n_threads = strtol(optarg, 0, 0); break;
+            case  8 : args->record_cmd_line = 0; break;
             case '?': usage(args);
             default: error("Unknown argument: %s\n", optarg);
         }

From e0890a1c47d0e8608b5f35e67a0ef4e3a1590baa Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 22 Jan 2016 16:21:52 +0000
Subject: [PATCH 141/211] reheader: allow empty body with vcf.gz. Fixes #356

---
 reheader.c              | 10 ++++++----
 test/reheader.empty.hdr |  7 +++++++
 test/reheader.empty.out |  8 ++++++++
 test/test.pl            |  1 +
 4 files changed, 22 insertions(+), 4 deletions(-)
 create mode 100644 test/reheader.empty.hdr
 create mode 100644 test/reheader.empty.out

diff --git a/reheader.c b/reheader.c
index 73123f942..7248cbb4b 100644
--- a/reheader.c
+++ b/reheader.c
@@ -203,7 +203,8 @@ static void reheader_vcf_gz(args_t *args)
             if ( skip_until>=fp->block_length )
             {
                 kputsn(buffer,skip_until,&hdr);
-                if ( bgzf_read_block(fp) != 0 || !fp->block_length ) error("FIXME: No body in the file: %s\n", args->fname);
+                if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname);
+                if ( !fp->block_length ) break;
                 skip_until = 0;
             }
             // The header has finished
@@ -217,7 +218,8 @@ static void reheader_vcf_gz(args_t *args)
         if ( skip_until>=fp->block_length )
         {
             kputsn(buffer,fp->block_length,&hdr);
-            if (bgzf_read_block(fp) != 0 || !fp->block_length) error("FIXME: No body in the file: %s\n", args->fname);
+            if ( bgzf_read_block(fp) != 0 ) error("Error reading %s\n", args->fname);
+            if ( !fp->block_length ) break;
             skip_until = 0;
         }
     }
@@ -263,8 +265,8 @@ static void reheader_vcf_gz(args_t *args)
         int count = bgzf_raw_write(bgzf_out, buf, nread);
         if (count != nread) error("Write failed, wrote %d instead of %d bytes.\n", count,(int)nread);
     }
-    if (bgzf_close(bgzf_out) < 0) error("Error: %d\n",bgzf_out->errcode);
-    if (bgzf_close(fp) < 0) error("Error: %d\n",fp->errcode);
+    if (bgzf_close(bgzf_out) < 0) error("Error closing %s: %d\n",args->output_fname ? args->output_fname : "-",bgzf_out->errcode);
+    if (hts_close(args->fp)) error("Error closing %s: %d\n",args->fname,fp->errcode);
     free(buf);
 }
 static void reheader_vcf(args_t *args)
diff --git a/test/reheader.empty.hdr b/test/reheader.empty.hdr
new file mode 100644
index 000000000..cd5a018c5
--- /dev/null
+++ b/test/reheader.empty.hdr
@@ -0,0 +1,7 @@
+##fileformat=VCFv4.1
+##contig=<ID=11,length=135006516>
+##contig=<ID=20,length=63025520>
+##contig=<ID=X,length=155270560>
+##contig=<ID=Y,length=59373566>
+##contig=<ID=Z,length=59373566>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
diff --git a/test/reheader.empty.out b/test/reheader.empty.out
new file mode 100644
index 000000000..cbc236bf0
--- /dev/null
+++ b/test/reheader.empty.out
@@ -0,0 +1,8 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=11,length=135006516>
+##contig=<ID=20,length=63025520>
+##contig=<ID=X,length=155270560>
+##contig=<ID=Y,length=59373566>
+##contig=<ID=Z,length=59373566>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
diff --git a/test/test.pl b/test/test.pl
index 48ec9db08..80ecacd9a 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -200,6 +200,7 @@
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.2.out',samples=>'reheader.samples2');
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.3.out',samples=>'reheader.samples3');
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.4.out',samples=>'reheader.samples4');
+test_vcf_reheader($opts,in=>'empty',out=>'reheader.empty.out',header=>'reheader.empty.hdr');
 test_rename_chrs($opts,in=>'annotate');
 test_vcf_convert($opts,in=>'convert',out=>'convert.gs.gt.gen',args=>'-g -,.');
 test_vcf_convert($opts,in=>'convert',out=>'convert.gs.gt.samples',args=>'-g .,-');

From 5d252954d950230408781a0627e1ed08e95d9c09 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Mon, 1 Feb 2016 16:02:41 +0000
Subject: [PATCH 142/211] Fix merging of Number=G format strings

Format strings appear to be adjacently-placed-in-memory fixed-length
(max_len, src_len, etc) optionally-NUL-terminated arrays, i.e., the same
sort of variable-up-to-a-fixed-length strings as operated on by strncpy().

In copy_string_field(), don't copy trailing NULs.
In merge_format_string(), pad the *output* string with NULs.
---
 test/norm.merge.out        | 2 +-
 test/norm.merge.strict.out | 2 +-
 test/norm.merge.vcf        | 4 ++--
 vcfmerge.c                 | 2 +-
 vcfnorm.c                  | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/test/norm.merge.out b/test/norm.merge.out
index f5b1092ff..449daba01 100644
--- a/test/norm.merge.out
+++ b/test/norm.merge.out
@@ -36,7 +36,7 @@
 1	105	.	TAAACCCTAAA	TAA,TAACCCTAAA	999	PASS	INDEL;AN=4;AC=2,2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	1/2:1,2,3,4,.,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF	1/2:1,2,3,4,.,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF
 2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT	ACGT	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
 2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
-2	114	.	TC	TTCC,TTC	999	FAIL1	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
+2	114	.	TC	TTCC,TTC	999	FAIL1	INDEL;AN=4;AC=2,2	GT:DP:FGS	1/2:1:A,BB,CCC,EEEE,.,FFFFF	1/2:1:AA,BB,CCC,EEEE,.,FFFFF
 2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
 20	3	.	GATG	CTATG,GACT	999	PASS	INDEL;AN=4;AC=2,2	GT	2/1	2/1
 20	5	id0001;id0002	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,.,6,7,.,.,10,11,.,.,.,15:1	1/2:1,2,3,4,.,6,7,.,.,10,11,.,.,.,15:1
diff --git a/test/norm.merge.strict.out b/test/norm.merge.strict.out
index 1395d2224..92f6f8826 100644
--- a/test/norm.merge.strict.out
+++ b/test/norm.merge.strict.out
@@ -36,7 +36,7 @@
 1	105	.	TAAACCCTAAA	TAA,TAACCCTAAA	999	PASS	INDEL;AN=4;AC=2,2;DP=19;ISTR=SomeString;XRF=1e+06,2e+06,500000;XRI=1111,2222,5555;XRS=AAA,BBB,DDD;XAF=1e+06,500000;XAI=1111,5555;XAS=AAA,DDD;XGF=1e+06,2e+06,3e+06,500000,.,9e+09;XGI=1111,2222,3333,5555,.,9999;XGS=A,B,C,E,.,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	1/2:1,2,3,4,.,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF	1/2:1,2,3,4,.,6:1:1e+06,2e+06,500000:1111,2222,5555:AAAA,BBB,CC:1e+06,500000:1111,5555:A,BB:1e+06,2e+06,3e+06,500000,.,9e+09:1111,2222,3333,5555,.,9999:A,BB,CCC,EEEE,.,FFFFF
 2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT	ACGT	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
 2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
-2	114	.	TC	TTCC,TTC	999	PASS	INDEL;AN=4;AC=2,2	GT:DP	1/2:1	1/2:1
+2	114	.	TC	TTCC,TTC	999	PASS	INDEL;AN=4;AC=2,2	GT:DP:FGS	1/2:1:A,BB,CCC,EEEE,.,FFFFF	1/2:1:AA,BB,CCC,EEEE,.,FFFFF
 2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
 20	3	.	GATG	CTATG,GACT	999	PASS	INDEL;AN=4;AC=2,2	GT	2/1	2/1
 20	5	id0001;id0002	TGGG	TAC,TG,TGGGG,AC	.	PASS	INDEL;AN=4;AC=2,2,0,0	GT:PL:DP	1/2:1,2,3,4,.,6,7,.,.,10,11,.,.,.,15:1	1/2:1,2,3,4,.,6,7,.,.,10,11,.,.,.,15:1
diff --git a/test/norm.merge.vcf b/test/norm.merge.vcf
index e89178e78..c702f6d91 100644
--- a/test/norm.merge.vcf
+++ b/test/norm.merge.vcf
@@ -37,8 +37,8 @@
 1	105	.	TAAACCCTAAA	TAACCCTAAA	999	PASS	INDEL;AN=4;AC=2;DP=19;ISTR=SomeString;XRF=1e+06,500000;XRI=1111,5555;XRS=AAA,DDD;XAF=500000;XAI=5555;XAS=DDD;XGF=1e+06,500000,9e+09;XGI=1111,5555,9999;XGS=A,E,F	GT:PL:DP:FRF:FRI:FRS:FAF:FAI:FAS:FGF:FGI:FGS	0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF	0/1:1,4,6:1:1e+06,500000:1111,5555:AAAA,CC:500000:5555:BB:1e+06,500000,9e+09:1111,5555,9999:A,EEEE,FFFFF
 2	1	.	GGGCGTCTCATAGCTGGAGCAATGGCGAGCGCCTGGACAAGGGAGGGGAAGGGGTTCTTATTACTGACGCGGGTAGCCCCTACTGCTGTGTGGTTCCCCTATTTTTTTTTTTTTCTTTTTGAGACGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACAATCTCGGCTCACTGCAAGCTCCACCT	ACGT	999	PASS	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
 2	101	.	ATTTTTTTTTTTTT	ATTTTTTTTTTTTTTT	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
-2	114	.	TC	TTCC	999	FAIL1	INDEL;AN=4;AC=2	GT:DP	1/0:1	1/0:1
-2	114	.	TC	TTC	999	PASS	INDEL;AN=4;AC=2	GT:DP	0/1:1	0/1:1
+2	114	.	TC	TTCC	999	FAIL1	INDEL;AN=4;AC=2	GT:DP:FGS	1/0:1:A,BB,CCC	1/0:1:AA,BB,CCC
+2	114	.	TC	TTC	999	PASS	INDEL;AN=4;AC=2	GT:DP:FGS	0/1:1:A,EEEE,FFFFF	0/1:1:AA,EEEE,FFFFF
 2	115	.	C	T	999	PASS	INDEL;AN=4;AC=4	GT:DP	1/1:1	1/1:1
 20	3	.	G	CT	999	PASS	INDEL;AN=4;AC=2	GT	0/1	0/1
 20	3	.	GATG	GACT	999	PASS	INDEL;AN=4;AC=2	GT	1/0	1/0
diff --git a/vcfmerge.c b/vcfmerge.c
index 0517bd56c..5b610fba8 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -858,7 +858,7 @@ int copy_string_field(char *src, int isrc, int src_len, kstring_t *dst, int idst
     }
     if ( ith_src!=isrc ) return -1; // requested field not found
     int end_src = start_src;
-    while ( end_src<src_len && src[end_src]!=',' ) end_src++;
+    while ( end_src<src_len && src[end_src] && src[end_src]!=',' ) end_src++;
 
     int nsrc_cpy = end_src - start_src;
     if ( nsrc_cpy==1 && src[start_src]=='.' ) return 0;   // don't write missing values, dst is already initialized
diff --git a/vcfnorm.c b/vcfnorm.c
index a59854ae0..384cece5f 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -1287,7 +1287,7 @@ static void merge_format_string(args_t *args, bcf1_t **lines, int nlines, bcf_fm
     {
         kstring_t *tmp = &args->tmp_str[i];
         kputsn(tmp->s,tmp->l,&str);
-        for (j=tmp->l; j<max_len; j++) kputc(0,tmp);
+        for (j=tmp->l; j<max_len; j++) kputc('\0',&str);
     }
     args->ntmp_arr2 = str.m;
     args->tmp_arr2  = (uint8_t*)str.s;

From 4e041a4fd0ff31939333f94ec935d96f32a303e8 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 10 Feb 2016 22:05:45 +0000
Subject: [PATCH 143/211] remove some chatter from test suite

---
 test/test.pl                 | 50 +++++++++++++++++++-----------------
 test/view.filter.annovar.vcf |  1 +
 2 files changed, 27 insertions(+), 24 deletions(-)

diff --git a/test/test.pl b/test/test.pl
index 9108fb772..68226c7c2 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 #
-#   Copyright (C) 2012-2015 Genome Research Ltd.
+#   Copyright (C) 2012-2016 Genome Research Ltd.
 #
 #   Author: Petr Danecek <pd3@sanger.ac.uk>
 #
@@ -435,8 +435,10 @@ sub test_vcf_idxstats
     cmd("$$opts{bin}/bcftools view -Oz $$opts{path}/$args{in}.vcf > $$opts{tmp}/$args{in}.vcf.gz");
     cmd("$$opts{bin}/bcftools index --tbi -f $$opts{tmp}/$args{in}.vcf.gz");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools index $args{args} $$opts{tmp}/$args{in}.vcf.gz");
+    unlink("$$opts{tmp}/$args{in}.vcf.gz.tbi");
     cmd("$$opts{bin}/bcftools index --csi -f $$opts{tmp}/$args{in}.vcf.gz");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools index $args{args} $$opts{tmp}/$args{in}.vcf.gz");
+    unlink("$$opts{tmp}/$args{in}.vcf.gz.csi");
 
     cmd("$$opts{bin}/bcftools view -Ob $$opts{path}/$args{in}.vcf > $$opts{tmp}/$args{in}.bcf");
     cmd("$$opts{bin}/bcftools index -f $$opts{tmp}/$args{in}.bcf");
@@ -459,7 +461,7 @@ sub test_vcf_check_merge
     cmd("$$opts{bin}/bcftools stats -r 2 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.2.chk");
     cmd("$$opts{bin}/bcftools stats -r 3 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.3.chk");
     cmd("$$opts{bin}/bcftools stats -r 4 $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.4.chk");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/plot-vcfstats -m $$opts{tmp}/$args{in}.1.chk $$opts{tmp}/$args{in}.2.chk $$opts{tmp}/$args{in}.3.chk $$opts{tmp}/$args{in}.4.chk | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID\t'");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/plot-vcfstats -m $$opts{tmp}/$args{in}.1.chk $$opts{tmp}/$args{in}.2.chk $$opts{tmp}/$args{in}.3.chk $$opts{tmp}/$args{in}.4.chk 2>/dev/null | grep -v 'plot-vcfstats' | grep -v '^# The command' | grep -v '^# This' | grep -v '^ID\t'");
 }
 
 sub test_vcf_stats
@@ -497,8 +499,8 @@ sub test_vcf_isec
         push @files, "$$opts{tmp}/$file.vcf.gz";
     }
     my $files = join(' ',@files);
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec $args{args} $files");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec -Ob $args{args} $files");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec $args{args} $files 2>/dev/null");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools isec -Ob $args{args} $files 2>/dev/null");
 }
 sub test_vcf_isec2
 {
@@ -525,29 +527,29 @@ sub test_vcf_convert
 {
     my ($opts,%args) = @_;
     bgzip_tabix_vcf($opts,$args{in});
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $$opts{tmp}/$args{in}.vcf.gz");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args}");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $$opts{tmp}/$args{in}.vcf.gz 2>/dev/null");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} 2>/dev/null");
 }
 sub test_vcf_convert_hls2vcf
 {
     my ($opts,%args) = @_;
     my $hls = join(',', map { "$$opts{path}/$_" }( $args{h}, $args{l}, $args{s} ) );
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls | grep -v ^##");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls -Ou | $$opts{bin}/bcftools view | grep -v ^##");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls 2>/dev/null | grep -v ^##");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hls -Ou 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##");
 }
 sub test_vcf_convert_hs2vcf
 {
     my ($opts,%args) = @_;
     my $hs = join(',', map { "$$opts{path}/$_" }( $args{h}, $args{s} ) );
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hs | grep -v ^##");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hs -Ou | $$opts{bin}/bcftools view | grep -v ^##");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hs 2>/dev/null | grep -v ^##");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert $args{args} $hs -Ou 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##");
 }
 sub test_vcf_convert_gvcf
 {
     my ($opts,%args) = @_;
     bgzip_tabix_vcf($opts,$args{in});
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert --no-version $args{args} -f $$opts{path}/$args{fa} $$opts{tmp}/$args{in}.vcf.gz");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} | grep -v ^##bcftools");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert --no-version $args{args} -f $$opts{path}/$args{fa} $$opts{tmp}/$args{in}.vcf.gz 2>/dev/null");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} 2>/dev/null | grep -v ^##bcftools");
 }
 sub test_vcf_convert_tsv2vcf
 {
@@ -555,8 +557,8 @@ sub test_vcf_convert_tsv2vcf
     my $params = '';
     if ( exists($args{args}) ) { $params .= " $args{args}"; }
     if ( exists($args{fai} ) ) { $params .= " -f $$opts{path}/$args{fai}.fa"; }
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert --no-version $params --tsv2vcf $$opts{path}/$args{in}");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert -Ou $params --tsv2vcf $$opts{path}/$args{in} | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert --no-version $params --tsv2vcf $$opts{path}/$args{in} 2>/dev/null");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert -Ou $params --tsv2vcf $$opts{path}/$args{in} 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_norm
 {
@@ -565,8 +567,8 @@ sub test_vcf_norm
     my $params = '';
     if ( exists($args{args}) ) { $params .= " $args{args}"; }
     if ( exists($args{fai} ) ) { $params .= " -f $$opts{path}/$args{fai}.fa"; }
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools norm --no-version $params $$opts{tmp}/$args{in}.vcf.gz");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools norm -Ob $params $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools norm --no-version $params $$opts{tmp}/$args{in}.vcf.gz 2>/dev/null");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools norm -Ob $params $$opts{tmp}/$args{in}.vcf.gz 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_view
 {
@@ -584,15 +586,15 @@ sub test_vcf_call
 {
     my ($opts,%args) = @_;
     $args{args} =~ s/{PATH}/$$opts{path}/g;
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call --no-version $args{args} $$opts{path}/$args{in}.vcf");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob $args{args} $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call --no-version $args{args} $$opts{path}/$args{in}.vcf 2>/dev/null");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob $args{args} $$opts{path}/$args{in}.vcf 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_call_cAls
 {
     my ($opts,%args) = @_;
     bgzip_tabix($opts,file=>$args{tab},suffix=>'tab',args=>'-s1 -b2 -e2');
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call --no-version -mA -C alleles -T $$opts{tmp}/$args{tab}.tab.gz $$opts{path}/$args{in}.vcf");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob -mA -C alleles -T $$opts{tmp}/$args{tab}.tab.gz $$opts{path}/$args{in}.vcf | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call --no-version -mA -C alleles -T $$opts{tmp}/$args{tab}.tab.gz $$opts{path}/$args{in}.vcf 2>/dev/null");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools call -Ob -mA -C alleles -T $$opts{tmp}/$args{tab}.tab.gz $$opts{path}/$args{in}.vcf 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_filter
 {
@@ -757,8 +759,8 @@ sub test_vcf_annotate
         $annot_fname = '';
         $hdr = '';
     }
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools annotate $annot_fname $hdr $args{args} $in_fname | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools annotate -Ob $annot_fname $hdr $args{args} $in_fname | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools annotate $annot_fname $hdr $args{args} $in_fname 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools annotate -Ob $annot_fname $hdr $args{args} $in_fname 2>/dev/null | $$opts{bin}/bcftools view | grep -v ^##bcftools_");
 }
 sub test_vcf_plugin
 {
@@ -831,7 +833,7 @@ sub test_vcf_consensus
     bgzip_tabix_vcf($opts,$args{in});
     my $mask = $args{mask} ? "-m $$opts{path}/$args{mask}" : '';
     my $chain = $args{chain} ? "-c $$opts{tmp}/$args{chain}" : '';
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools consensus $$opts{tmp}/$args{in}.vcf.gz -f $$opts{path}/$args{fa} $args{args} $mask $chain");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools consensus $$opts{tmp}/$args{in}.vcf.gz -f $$opts{path}/$args{fa} $args{args} $mask $chain 2>/dev/null");
 }
 sub test_vcf_consensus_chain
 {
@@ -839,6 +841,6 @@ sub test_vcf_consensus_chain
     bgzip_tabix_vcf($opts,$args{in});
     my $mask = $args{mask} ? "-m $$opts{path}/$args{mask}" : '';
     my $chain = $args{chain} ? "-c $$opts{tmp}/$args{chain}.new" : '';
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools consensus $$opts{tmp}/$args{in}.vcf.gz -f $$opts{path}/$args{fa} $args{args} $mask $chain > /dev/null; cat $$opts{tmp}/$args{chain}.new");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools consensus $$opts{tmp}/$args{in}.vcf.gz -f $$opts{path}/$args{fa} $args{args} $mask $chain > /dev/null 2>/dev/null; cat $$opts{tmp}/$args{chain}.new");
 }
 
diff --git a/test/view.filter.annovar.vcf b/test/view.filter.annovar.vcf
index 7613667ad..c19aa25f9 100644
--- a/test/view.filter.annovar.vcf
+++ b/test/view.filter.annovar.vcf
@@ -18,6 +18,7 @@
 ##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele">
 ##INFO=<ID=Gene.refGene,Number=.,Type=String,Description="Gene.refGene annotation provided by ANNOVAR">
 ##INFO=<ID=GeneDetail.refGene,Number=.,Type=String,Description="GeneDetail.refGene annotation provided by ANNOVAR">
+##INFO=<ID=Func.refGene,Number=.,Type=String,Description="Func.refGene annotation provided by ANNOVAR">
 ##INFO=<ID=ExonicFunc.refGene,Number=.,Type=String,Description="ExonicFunc.refGene annotation provided by ANNOVAR">
 ##INFO=<ID=AAChange.refGene,Number=.,Type=String,Description="AAChange.refGene annotation provided by ANNOVAR">
 ##INFO=<ID=Func.ensGene,Number=.,Type=String,Description="Func.ensGene annotation provided by ANNOVAR">

From e915fd6baba32691c8336288419a501d6c627528 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 12 Feb 2016 14:42:19 +0000
Subject: [PATCH 144/211] fill-tags plugin: add NS tag

also fix some tests so that make test-plugins no passes
---
 plugins/fill-tags.c  | 17 +++++++++++----
 test/fill-tags.2.out | 49 ++++++++++++++++++++++++++++++++++++++++++++
 test/test.pl         | 17 +++++++--------
 3 files changed, 71 insertions(+), 12 deletions(-)
 create mode 100644 test/fill-tags.2.out

diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c
index 1d2892981..2fff25803 100644
--- a/plugins/fill-tags.c
+++ b/plugins/fill-tags.c
@@ -38,6 +38,7 @@
 #define SET_AC_Het  (1<<3)
 #define SET_AC_Hemi (1<<4)
 #define SET_AF      (1<<5)
+#define SET_NS      (1<<6)
 
 typedef struct
 {
@@ -59,14 +60,14 @@ static args_t args;
 
 const char *about(void)
 {
-    return "Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi.\n";
+    return "Set INFO tags AF, AN, AC, NS, AC_Hom, AC_Het, AC_Hemi.\n";
 }
 
 const char *usage(void)
 {
     return 
         "\n"
-        "About: Set INFO tags AF, AN, AC, AC_Hom, AC_Het, AC_Hemi.\n"
+        "About: Set INFO tags AF, AN, AC, NS, AC_Hom, AC_Het, AC_Hemi.\n"
         "Usage: bcftools +fill-tags [General Options] -- [Plugin Options]\n"
         "Options:\n"
         "   run \"bcftools plugin\" for a list of common options\n"
@@ -88,6 +89,7 @@ int parse_tags(args_t *args, const char *str)
     {
         if ( !strcasecmp(tags[i],"AN") ) flag |= SET_AN;
         else if ( !strcasecmp(tags[i],"AC") ) flag |= SET_AC;
+        else if ( !strcasecmp(tags[i],"NS") ) flag |= SET_NS;
         else if ( !strcasecmp(tags[i],"AC_Hom") ) flag |= SET_AC_Hom;
         else if ( !strcasecmp(tags[i],"AC_Het") ) flag |= SET_AC_Het;
         else if ( !strcasecmp(tags[i],"AC_Hemi") ) flag |= SET_AC_Hemi;
@@ -127,13 +129,14 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         }
     }
     if ( optind != argc ) error(usage());
-    if ( !args.tags ) args.tags |= SET_AN|SET_AC|SET_AC_Hom|SET_AC_Het|SET_AC_Hemi|SET_AF;
+    if ( !args.tags ) args.tags |= SET_AN|SET_AC|SET_NS|SET_AC_Hom|SET_AC_Het|SET_AC_Hemi|SET_AF;
     
     args.gt_id = bcf_hdr_id2int(args.in_hdr,BCF_DT_ID,"GT");
     if ( args.gt_id<0 ) error("Error: GT field is not present\n");
 
     if ( args.tags&SET_AN ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AN,Number=1,Type=Integer,Description=\"Total number of alleles in called genotypes\">");
     if ( args.tags&SET_AC ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC,Number=A,Type=Integer,Description=\"Allele count in genotypes\">");
+    if ( args.tags&SET_NS ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=NS,Number=1,Type=Integer,Description=\"Number of samples with data\">");
     if ( args.tags&SET_AC_Hom ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Hom,Number=A,Type=Integer,Description=\"Allele counts in homozygous genotypes\">");
     if ( args.tags&SET_AC_Het ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Het,Number=A,Type=Integer,Description=\"Allele counts in heterozygous genotypes\">");
     if ( args.tags&SET_AC_Hemi ) bcf_hdr_append(args.out_hdr, "##INFO=<ID=AC_Hemi,Number=A,Type=Integer,Description=\"Allele counts in hemizygous genotypes\">");
@@ -144,7 +147,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
 
 bcf1_t *process(bcf1_t *rec)
 {
-    int i;
+    int i, ns = 0;
 
     bcf_unpack(rec, BCF_UN_FMT);
     bcf_fmt_t *fmt_gt = NULL;
@@ -174,6 +177,7 @@ bcf1_t *process(bcf1_t *rec)
                 als |= (1<<idx);  /* this breaks with too many alleles */ \
             } \
             if ( ial==0 ) continue; /* missing alleles */ \
+            ns++; \
             int is_hom  = als && !(als & (als-1)); /* only one bit is set */ \
             int is_hemi = ial==1; \
             for (ial=0; als; ial++) \
@@ -198,6 +202,11 @@ bcf1_t *process(bcf1_t *rec)
         default: error("The GT type is not recognised: %d at %s:%d\n",fmt_gt->type, bcf_seqname(args.in_hdr,rec),rec->pos+1); break;
     }
     #undef BRANCH_INT
+    if ( args.tags&SET_NS )
+    {
+        if ( bcf_update_info_int32(args.out_hdr,rec,"NS",&ns,1)!=0 )
+            error("Error occurred while updating NS at %s:%d\n", bcf_seqname(args.in_hdr,rec),rec->pos+1);
+    }
     if ( args.tags&SET_AN )
     {
         args.arr[0] = 0;
diff --git a/test/fill-tags.2.out b/test/fill-tags.2.out
new file mode 100644
index 000000000..01fe9c965
--- /dev/null
+++ b/test/fill-tags.2.out
@@ -0,0 +1,49 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##reference=file:///seq/references/1000Genomes-NCBI37.fasta
+##contig=<ID=11,length=135006516>
+##contig=<ID=20,length=63025520>
+##contig=<ID=X,length=155270560>
+##contig=<ID=Y,length=59373566>
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of reads containing spanning deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest contiguous homopolymer run of variant allele in either direction">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Hardy-Weinberg equilibrium test (PMID:15789306)">
+##INFO=<ID=ICF,Number=1,Type=Float,Description="Inbreeding coefficient F">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total mapping quality zero reads">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant confidence/quality by depth">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
+##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
+##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
+##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele frequency">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
+11	2343543	.	A	.	999	PASS	DP=100223;NS=3;AN=6	GT:PL:DP:GQ	0/0:0,255,255:193:99	0/0:0,255,255:211:99	0/0:0,255,255:182:99
+11	5464562	.	C	T	999	PASS	DP=0;NS=0;AN=0;AC=0	GT:PL:DP:GQ	./.:0,0,0:.:.	./.:0,0,0:.:.	./.:0,0,0:.:.
+20	76962	rs6111385	T	C	999	PASS	DP4=110138,70822,421911,262673;DP=911531;Dels=0;FS=21.447;HWE=0.491006;ICF=-0.01062;MQ0=1;MQ=46;PV4=2.5e-09,0,0,1;QD=22.31;NS=3;AN=6;AF=0.833333;AC=5	GT:PL:DP:GQ	0/1:255,0,255:193:99	1/1:255,255,0:211:99	1/1:255,255,0:182:99
+20	126310	.	ACC	A	999	StrandBias;EndDistBias	DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=6;AC=4;NS=3;AF=0.666667	GT:DP:GQ:PL	0/1:117:99:255,0,132	0/1:111:99:255,0,139	1/1:78:99:255,213,0
+20	138125	rs2298108	G	T	999	PASS	DP4=174391,20849,82080,4950;DP=286107;Dels=0;FS=3200;HWE=0.199462;ICF=0.01858;MQ0=0;MQ=46;PV4=0,0,0,1;QD=17.22;AN=6;AC=4;NS=3;AF=0.666667	GT:PL:DP:GQ	0/1:135,0,163:66:99	0/1:140,0,255:71:99	1/1:255,199,0:66:99
+20	138148	rs2298109	C	T	999	PASS	DP4=194136,45753,94945,14367;DP=356657;Dels=0;FS=3200;HWE=0.177865;ICF=0.0198;MQ0=0;MQ=47;PV4=0,0,0,1;QD=14.57;AN=6;AC=4;NS=3;AF=0.666667	GT:PL:DP:GQ	0/1:195,0,255:87:99	0/1:192,0,255:82:99	1/1:255,235,0:78:99
+20	271225	.	T	TTTA,TA	999	StrandBias	DP4=29281,42401,27887,29245;DP=272732;INDEL;IS=95,0.748031;MQ=47;PV4=0,1,0,1;QD=0.0948;AN=6;AC=2,2;NS=3;AF=0.333333,0.333333	GT:DP:GQ:PL	0/2:33:49:151,53,203,0,52,159	0/1:51:99:255,0,213,255,255,255	1/2:47:99:255,255,255,255,0,241
+20	304568	.	C	T	999	PASS	DP4=16413,4543,945,156;DP=43557;Dels=0;FS=3200;HWE=0.076855;ICF=0.0213;MQ0=0;MQ=50;PV4=0,0,0,1;QD=15.45;AN=6;AC=4;NS=3;AF=0.666667	GT:PL:DP:GQ	0|1:95,0,255:90:99	0|1:192,0,255:13:99	1|1:255,95,0:60:99
+20	326891	.	A	AC	999	PASS	DP4=125718,95950,113812,80890;DP=461867;HWE=0.24036;ICF=0.01738;INDEL;IS=374,0.937343;MQ=49;PV4=9e-30,1,0,3.8e-13;QD=0.0172;AN=4;AC=2;NS=2;AF=0.5	GT:DP:GQ:PL	0|1:117:99:255,0,132	0|1:111:99:255,0,139	./.:.:.:.,.,.
+X	2928329	rs62584840	C	T	999	PASS	DP4=302,9137,32,1329;DP=11020;Dels=0;FS=13.38;HWE=0.284332;ICF=0.0253;MQ0=0;MQ=49;PV4=0.094,0,0,1;QD=18.61;AN=4;AC=1;NS=3;AF=0.25	GT:PL:DP:GQ	0:0,56:2:73	0:0,81:3:98	0/1:73,0,19:4:30
+X	2933066	rs61746890	G	C	999	PASS	DP4=69865,100561,461,783;DP=173729;Dels=0;FS=10.833;MQ0=0;MQ=50;PV4=0.005,3.6e-14,0,1;QD=15.33;AN=4;AC=1;NS=3;AF=0.25	GT:PL:DP:GQ	0:0,255:39:99	0:0,255:37:99	0/1:255,255,255:62:99
+X	2942109	rs5939407	T	C	999	PASS	DP4=23273,27816,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=3;NS=3;AF=0.75	GT:PL:DP:GQ	0:0,255:20:99	1:255,0:33:99	1/1:255,157,0:52:99
+X	3048719	.	T	C	999	PASS	DP4=13263,27466,40128,48208;DP=146673;Dels=0;FS=43.639;HWE=0.622715;ICF=-0.01176;MQ0=1;MQ=46;PV4=0.65,1,0,1;QD=14.81;AN=4;AC=2;NS=3;AF=0.5	GT:PL:DP:GQ	0:0,255:20:99	1:255,0:33:99	0|1:255,0,157:52:99
+Y	8657215	.	C	A	999	PASS	DP4=74915,114274,1948,2955;DP=195469;Dels=0;FS=3.181;MQ0=0;MQ=50;PV4=0.86,1,0,1;QD=33.77;AN=2;AC=1;NS=2;AF=0.5	GT:PL:DP:GQ	0:0,255:47:99	1:255,0:64:99	.:.:.:.
+Y	10011673	rs78249411	G	A	999	MinAB	DP4=47351,30839,178796,279653;DP=550762;Dels=0;FS=41.028;MQ0=37362;MQ=26;PV4=0,0,0,1;QD=17.45;AN=2;AC=2;NS=2;AF=1	GT:PL:DP:GQ	1:126,101:146:37	1:95,0:130:99	.:.:.:.
diff --git a/test/test.pl b/test/test.pl
index 68226c7c2..7a54de292 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -176,17 +176,18 @@
 test_vcf_annotate($opts,in=>'annotate4',vcf=>'annots4',out=>'annotate8.out',args=>'-c +INFO');
 test_vcf_annotate($opts,in=>'annotate4',tab=>'annots4',out=>'annotate8.out',args=>'-c CHROM,POS,REF,ALT,+FA,+FR,+IA,+IR,+SA,+SR');
 test_vcf_annotate($opts,in=>'annotate10',tab=>'annots10',out=>'annotate10.out',args=>'-c CHROM,POS,FMT/FINT,FMT/FFLT,FMT/FSTR');
-test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+missing2ref');
-test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+setGT',args=>'-- -t . -n 0');
+test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+missing2ref --no-version');
+test_vcf_plugin($opts,in=>'plugin1',out=>'missing2ref.out',cmd=>'+setGT --no-version',args=>'-- -t . -n 0');
 test_vcf_annotate($opts,in=>'annotate9',tab=>'annots9',out=>'annotate9.out',args=>'-c CHROM,POS,REF,ALT,+ID');
-test_vcf_plugin($opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC');
+test_vcf_plugin($opts,in=>'plugin1',out=>'fill-AN-AC.out',cmd=>'+fill-AN-AC --no-version');
 test_vcf_plugin($opts,in=>'plugin1',out=>'dosage.out',cmd=>'+dosage');
-test_vcf_plugin($opts,in=>'fixploidy',out=>'fixploidy.out',cmd=>'+fixploidy',args=>'-- -s {PATH}/fixploidy.samples -p {PATH}/fixploidy.ploidy');
+test_vcf_plugin($opts,in=>'fixploidy',out=>'fixploidy.out',cmd=>'+fixploidy --no-version',args=>'-- -s {PATH}/fixploidy.samples -p {PATH}/fixploidy.ploidy');
 test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -n 5');
 test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -g GT');
 test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -g GT -n 5');
-test_vcf_plugin($opts,in=>'view.GL',out=>'view.PL.vcf',cmd=>'+tag2tag',args=>'-- -r --gl-to-pl');
-test_vcf_plugin($opts,in=>'merge.a',out=>'fill-tags.out',cmd=>'+fill-tags');
+test_vcf_plugin($opts,in=>'view.GL',out=>'view.PL.vcf',cmd=>'+tag2tag --no-version',args=>'-- -r --gl-to-pl');
+test_vcf_plugin($opts,in=>'merge.a',out=>'fill-tags.out',cmd=>'+fill-tags --no-version',args=>'-- -t AN,AC,AC_Hom,AC_Het,AC_Hemi');
+test_vcf_plugin($opts,in=>'view',out=>'fill-tags.2.out',cmd=>'+fill-tags --no-version',args=>'-- -t AC,AN,AF,NS');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.vcf.out',do_bcf=>0,args=>'');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.bcf.out',do_bcf=>1,args=>'');
 test_vcf_concat($opts,in=>['concat.2.a','concat.2.b'],out=>'concat.2.vcf.out',do_bcf=>0,args=>'-a');
@@ -770,11 +771,11 @@ sub test_vcf_plugin
     if ( !exists($args{args}) ) { $args{args} = ''; }
     $args{args} =~ s/{PATH}/$$opts{path}/g;
     bgzip_tabix_vcf($opts,"$args{in}");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools $args{cmd} --no-version $$opts{tmp}/$args{in}.vcf.gz $args{args}");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools $args{cmd} $$opts{tmp}/$args{in}.vcf.gz $args{args}");
 
     cmd("$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz > $$opts{tmp}/$args{in}.bcf");
     cmd("$$opts{bin}/bcftools index -f $$opts{tmp}/$args{in}.bcf");
-    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools $args{cmd} --no-version $$opts{tmp}/$args{in}.bcf $args{args} | grep -v ^##bcftools_");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools $args{cmd} $$opts{tmp}/$args{in}.bcf $args{args} | grep -v ^##bcftools_");
 }
 sub test_vcf_concat
 {

From be92659d29e202b4d9edcb52406e9f12939470f4 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 12 Feb 2016 14:57:01 +0000
Subject: [PATCH 145/211] test plugins via travis too

* remove old LD_LIBRARY_PATH specification
* test on osx too
---
 .travis.yml | 23 +++++++++++++----------
 1 file changed, 13 insertions(+), 10 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 333cc7356..608ce7af7 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,20 +1,23 @@
 # Control file for continuous integration testing at http://travis-ci.org/
 
 language: c
-compiler:
-  - clang
-  - gcc
-
-env:
-  global:
-    - HTSDIR=./htslib
-    - LD_LIBRARY_PATH=$TRAVIS_BUILD_DIR/htslib:$LD_LIBRARY_PATH
 
 matrix:
   include:
+    - os: linux
+      compiler: clang
+    - os: linux
+      compiler: gcc
     # An unoptimised C99 build, for detecting non-static inline functions
-    - compiler: gcc
+    - os: linux
+      compiler: gcc
       env: CFLAGS="-std=gnu99 -O0"
+    - os: osx
+      compiler: clang
+
+env:
+  global:
+    - HTSDIR=./htslib
 
 before_script:
   # Clone samtools/htslib (or another repository, as specified by a Travis CI
@@ -22,4 +25,4 @@ before_script:
   # same name, if any, or otherwise the default branch.
   - .travis/clone ${HTSREPO:-git://github.com/samtools/htslib.git} $HTSDIR $TRAVIS_BRANCH
 
-script: make -e && make -e test
+script: make plugindir=$TRAVIS_BUILD_DIR/plugins -e && make -e test-plugins

From 681d80c20d078f953ff39140f7e519c94cb4fd1d Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 11 Feb 2016 14:44:32 +0000
Subject: [PATCH 146/211] peakfit build with GSLv2, resolves #378

---
 peakfit.c | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/peakfit.c b/peakfit.c
index 2bc849226..8094b5d52 100644
--- a/peakfit.c
+++ b/peakfit.c
@@ -26,6 +26,7 @@
 
 #include "peakfit.h"
 #include <stdio.h>
+#include <gsl/gsl_version.h>
 #include <gsl/gsl_vector.h>
 #include <gsl/gsl_multifit_nlin.h>
 #include <htslib/hts.h>
@@ -550,9 +551,14 @@ double peakfit_run(peakfit_t *pkf, int nvals, double *xvals, double *yvals)
             }
             if ( ret ) break;
 
+#if GSL_MAJOR_VERSION >= 2
+            int info;
+            test1 = gsl_multifit_fdfsolver_test(solver, 1e-8,1e-8, 0.0, &info);
+#else
             gsl_multifit_gradient(solver->J, solver->f, grad);
             test1 = gsl_multifit_test_gradient(grad, 1e-8);
             test2 = gsl_multifit_test_delta(solver->dx, solver->x, 1e-8, 1e-8);
+#endif
         }
         while ((test1==GSL_CONTINUE || test2==GSL_CONTINUE) && ++niter<niter_max);
         if ( pkf->verbose >1 )

From a121590a44efabe8e66e23b087632eae282fbb77 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 19 Feb 2016 15:19:53 +0000
Subject: [PATCH 147/211] plot-vcfstats: update expected headers [minor]

should have been updated after 6fed5ac7a68a2cd0bc2121b99bcfbb3eacbec3e5 and c121e22a189d179462a2e510e4ec705e83bacb47
---
 plot-vcfstats | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/plot-vcfstats b/plot-vcfstats
index 5989062f4..74a42ca6e 100755
--- a/plot-vcfstats
+++ b/plot-vcfstats
@@ -174,12 +174,12 @@ sub parse_params
             {
                 id=>'GCsS',
                 header=>'GCsS, Genotype concordance by sample (SNPs)',
-                exp=>"# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches"
+                exp=>"# GCsS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared"
             },
             {
                 id=>'GCiS',
                 header=>'GCiS, Genotype concordance by sample (indels)',
-                exp=>"# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches"
+                exp=>"# GCiS\t[2]id\t[3]sample\t[4]non-reference discordance rate\t[5]RR Hom matches\t[6]RA Het matches\t[7]AA Hom matches\t[8]RR Hom mismatches\t[9]RA Het mismatches\t[10]AA Hom mismatches\t[11]dosage r-squared"
             },
             {
                 id=>'PSC',
@@ -189,7 +189,7 @@ sub parse_params
             {
                 id=>'PSI',
                 header=>'PSI, Per-sample Indels',
-                exp=>"# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio"
+                exp=>"# PSI\t[2]id\t[3]sample\t[4]in-frame\t[5]out-frame\t[6]not applicable\t[7]out/(in+out) ratio\t[8]nHets\t[9]nAA"
             },
             {
                 id=>'DP',

From ef4e8a9d9cf8b30c00f50050df060a3d34e79536 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 19 Feb 2016 16:05:20 +0000
Subject: [PATCH 148/211] vcfannotate: fix typo [minor]

---
 vcfannotate.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/vcfannotate.c b/vcfannotate.c
index 8e9ba3a42..d5164f333 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -1764,8 +1764,8 @@ static void usage(args_t *args)
     fprintf(stderr, "   -c, --columns <list>           list of columns in the annotation file, e.g. CHROM,POS,REF,ALT,-,INFO/TAG. See man page for details\n");
     fprintf(stderr, "   -e, --exclude <expr>           exclude sites for which the expression is true (see man page for details)\n");
     fprintf(stderr, "   -h, --header-lines <file>      lines which should be appended to the VCF header\n");
-    fprintf(stderr, "   -I, --set-id [+]<format>       set ID column, see man pagee for details\n");
-    fprintf(stderr, "   -i, --include <expr>           select sites for which the expression is true (see man pagee for details)\n");
+    fprintf(stderr, "   -I, --set-id [+]<format>       set ID column, see man page for details\n");
+    fprintf(stderr, "   -i, --include <expr>           select sites for which the expression is true (see man page for details)\n");
     fprintf(stderr, "   -m, --mark-sites [+-]<tag>     add INFO/tag flag to sites which are (\"+\") or are not (\"-\") listed in the -a file\n");
     fprintf(stderr, "       --no-version               do not append version and command line to the header\n");
     fprintf(stderr, "   -o, --output <file>            write output to a file [standard output]\n");

From 9f5ee2163fed0617cc4160abfe7046aa02212fd3 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 19 Feb 2016 16:48:09 +0000
Subject: [PATCH 149/211] vcfcall: fix typo in error message [minor]

---
 vcfcall.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcfcall.c b/vcfcall.c
index d4a19d99e..e5bbf1167 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -386,7 +386,7 @@ static void init_data(args_t *args)
     if ( args->regions )
     {
         if ( bcf_sr_set_regions(args->aux.srs, args->regions, args->regions_is_file)<0 )
-            error("Failed to read the targets: %s\n", args->regions);
+            error("Failed to read the regions: %s\n", args->regions);
     }
 
     if ( !bcf_sr_add_reader(args->aux.srs, args->bcf_fname) ) error("Failed to open %s: %s\n", args->bcf_fname,bcf_sr_strerror(args->aux.srs->errnum));

From 2f4a2b232103bffe673c7eb7f9e2e0304fb55af6 Mon Sep 17 00:00:00 2001
From: dlaehnemann <david.laehnemann@hhu.de>
Date: Fri, 4 Dec 2015 14:37:58 +0100
Subject: [PATCH 150/211] new plugin: GTisec to count genotype intersections
 across all possible sample subsets in a vcf file

Commit messages, oldest first:

Basic compiling version of vcfGTcmp that does not do any comparing, yet.

Basic working version of GTcmp. Output is banker's sequence sorted per
sample, i.e. with increasing cardinality of sample subsets of the
current sample. No circos file printing included...

Basic working Circos config file printing. Not tested with circos, yet,
as karyotype and link files are still missing.

Basic version of all circos file printing is tested to work correctly.
Figure production using those files in circos is not yet tested.

Circos plotting file output thoroughly tested with circos and adjusted
to make sample sets easily distinguishable.

Implement counting of missing genotypes, including a switch to turn this behaviour on (off by default). This includes cleaning up of cmp_GT(), i.e. all printing previously done within this function is now in this tools main function and cmp_GT only does counting.

Ensure that karyotype band colors and subset ribbon colors can be searched-and-replaced separately in case of more than 9 samples and thus no automatic color assignment.

Minor cleanup of code adaptations from Corin Lawson's banker's sequence code.

(Hopefully) improve tool description line.

Circos printing functionality was moved to a separate command line tool
and this tool was renamed from GTcmp to gtisec for "genotype
intersections" of all possible subsets of samples. Output is now more
flexible, and all possible option combinations have been tested against
test/view.vcf with manually checked results in test/view.gtisec.* files.
Output options are:
* a basic version is in global banker's sequence order that is easily
parseable
* -m: counts of missing values can be included optionally
* -v: output can be made verbose, then including all the respective
sample names before each count
* -H: output can be put into a human-readable sample sort order (implies
verbose output).

Removed unnecessary functions carried over from original banker's
sequence code. Improved the tools description at the top of the file
comment, including reason for using banker's sequence. Added some
comments explaining the GT comparisons.

Checked for memory leaks using valgrind and removed one related to the
quick lookup table of the n choose k function choose(). This lookup
table is now part of the args_t struct, initialized in init_data and
freed by destroy data.

Added reference to tools using the output to the code file description
and the comments section of the printed output. Tested that output is
otherwise unchanged, using test/view.gtisec*.out files.

Address error of automatic Travis CI build number 3.

Change column order in verbose (-v) and human readable (-H) output, so
that the count comes in the first column (consistent with regular
output) and the samples list comes in the second column. Thanks to @pd3
for the suggestion. test/view.gtisec*.out files updated accordingly.

Changed subtool vcfgtisec into plugin GTisec, including all necessary building and test file changes.

Include test cases in test.pl and update test output to omit lines containing commit numbers.

Making tests pass.

[NEWS] GTisec: new plugin courtesy of @dlaehnemann to count genotype intersections
       across all possible sample subsets in a vcf file.
---
 plugins/GTisec.c         | 470 +++++++++++++++++++++++++++++++++++++++
 plugins/GTisec.mk        |   2 +
 test/test.pl             |   8 +
 test/view.GTisec.H.out   |  20 ++
 test/view.GTisec.Hm.out  |  25 +++
 test/view.GTisec.Hmv.out |  25 +++
 test/view.GTisec.Hv.out  |  20 ++
 test/view.GTisec.m.out   |  20 ++
 test/view.GTisec.mv.out  |  20 ++
 test/view.GTisec.out     |  15 ++
 test/view.GTisec.v.out   |  15 ++
 11 files changed, 640 insertions(+)
 create mode 100644 plugins/GTisec.c
 create mode 100644 plugins/GTisec.mk
 create mode 100644 test/view.GTisec.H.out
 create mode 100644 test/view.GTisec.Hm.out
 create mode 100644 test/view.GTisec.Hmv.out
 create mode 100644 test/view.GTisec.Hv.out
 create mode 100644 test/view.GTisec.m.out
 create mode 100644 test/view.GTisec.mv.out
 create mode 100644 test/view.GTisec.out
 create mode 100644 test/view.GTisec.v.out

diff --git a/plugins/GTisec.c b/plugins/GTisec.c
new file mode 100644
index 000000000..adfbdb972
--- /dev/null
+++ b/plugins/GTisec.c
@@ -0,0 +1,470 @@
+/*  plugins/GTisec.c -- collect genotype intersection counts of all possible
+                   subsets of the present samples and output in banker's
+                   sequence order (in this sequence, the number of contained
+                   samples increases monotonically, a property that is e.g.
+                   useful for programatically creating plotting files for the
+                   R package VennDiagram or the plotting tool circos from the
+                   counts, as in the command line tools bankers2VennDiagram and
+                   bankers2circos at htpps://github.com/dlaehnemann/bankers2)
+
+    Copyright (C) 2016 Computational Biology of Infection Research,
+                       Helmholtz Centre for Infection Research, Braunschweig,
+                       Germany
+
+    Author: David Laehnemann <david.laehnemann@helmholtz-hzi.de>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <unistd.h>
+#include <inttypes.h>
+
+#include <htslib/vcf.h>
+#include <htslib/synced_bcf_reader.h>
+#include <htslib/khash.h>
+KHASH_MAP_INIT_INT(gts2smps, uint32_t)
+
+#include "bcftools.h"
+
+/*!
+ * Flag definitions for args.flag
+ */
+#define MISSING        (1<<0)
+#define VERBOSE        (1<<1)
+#define SMPORDER       (1<<2)
+
+typedef struct _args_t
+{
+    bcf_srs_t *file;    /*! multi-sample VCF file */
+    bcf_hdr_t *hdr;     /*! VCF file header */
+    FILE *out;          /*! output file pointer */
+    int nsmp; /*! number of samples, can be determined from header but is needed in multiple contexts */
+    int nsmpp2; /*! 2^(nsmp) (is needed multiple times) */
+    int *gt_arr; /*! temporary array, to store GTs of current line/record */
+    int ngt_arr; /*! hold the number of current GT array entries */
+    uint32_t *bankers; /*! array to store banker's sequence for all possible sample subsets for
+                                programmatic indexing into smp_is for output printing, e.g. for three
+                                samples A, B and C this would be the following order:
+                                [   C,   B,   A,  CB,  CA,  BA, CBA ]
+                                [ 100, 010, 001, 110, 101, 011, 111 ]
+                                */
+    uint64_t *quick; /*! array to store n choose k lookup table of choose() function */
+    uint8_t flag; /*! several flags, for positions see above*/
+    uint64_t *missing_gts; /*! array to count missing genotypes of each sample */
+    uint64_t *smp_is; /*! array to track all possible intersections between
+                 samples, with each bit in the index integer belonging to one
+                 sample. E.g. for three samples A, B and C, count would be in
+                 the following order:
+                 [   A,   B,  AB,   C,  AC,  BC, ABC ]
+                 [ 001, 010, 011, 100, 101, 110, 111 ]
+                 */
+}
+args_t;
+
+static args_t args;
+uint32_t compute_bankers(unsigned long a);
+
+const char *about(void)
+{
+    return "Count genotype intersections across all possible sample subsets in a vcf file.\n";
+}
+
+
+const char *usage(void)
+{
+    return
+        "\n"
+        "About:   Count genotype intersections across all possible sample subsets in a vcf file.\n"
+        "Usage:   bcftools +GTisec <multisample.bcf/.vcf.gz> [General Options] -- [Plugin Options] \n"
+        "\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -m, --missing                   if set, include count of missing genotypes per sample in output\n"
+        "   -v, --verbose                   if set, annotate count rows with corresponding sample subset lists\n"
+        "   -H, --human-readable            if set, create human readable output; i.e. sort output by sample and\n"
+        "                                   print each subset's intersection count once for each sample contained\n"
+        "                                   in the subset; implies verbose output (-v)\n"
+        "\n"
+        "Example:\n"
+        "   bcftools +GTisec in.vcf -- -v # for verbose output\n"
+        "   bcftools +GTisec in.vcf -- -H # for human readable output\n"
+        "\n";
+}
+
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    memset(&args,0,sizeof(args_t));
+    args.flag = 0;
+
+    static struct option loptions[] =
+    {
+        {"help",            no_argument,      0,'h'},
+        {"missing",         no_argument,      0,'m'},
+        {"verbose",         no_argument,      0,'v'},
+        {"human-readable",  no_argument,      0,'H'},
+        {0,0,0,0}
+    };
+
+    char c;
+    while ((c = getopt_long(argc, argv, "?mvHh",loptions,NULL)) >= 0)
+    {
+        switch (c)
+        {
+            case 'm': args.flag |= MISSING; break;
+            case 'v': args.flag |= VERBOSE; break;
+            case 'H': args.flag |= ( SMPORDER | VERBOSE ); break;
+            case 'h': usage(); break;
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( optind != argc )  usage();  // too many files given
+
+
+    args.hdr = in;
+
+    if ( !bcf_hdr_nsamples(args.hdr) )
+    {
+        error("No samples in input file.\n");
+    }
+
+    args.nsmp = bcf_hdr_nsamples(args.hdr);
+    if ( args.nsmp > 32 ) error("Too many samples. A maximum of 32 is supported.\n");
+    args.nsmpp2 = pow( 2, args.nsmp);
+    args.bankers = (uint32_t*) calloc( args.nsmpp2, sizeof(uint32_t) );
+    args.quick = (uint64_t*) calloc((args.nsmp * (args.nsmp + 1)) / 4, sizeof(unsigned long));
+    if ( args.flag & MISSING ) args.missing_gts = (uint64_t*) calloc( args.nsmp, sizeof(uint64_t));
+    args.smp_is = (uint64_t*) calloc( args.nsmpp2, sizeof(uint64_t));
+    if ( bcf_hdr_id2int(args.hdr, BCF_DT_ID, "GT")<0 ) error("[E::%s] GT not present in the header\n", __func__);
+
+    args.gt_arr = NULL;
+    args.ngt_arr = 0;
+
+    args.out = stdout;
+
+    /*! Header printing */
+    FILE *fp = args.out;
+    fprintf(fp, "# This file was produced by bcftools +GTisec (%s+htslib-%s)\n", bcftools_version(), hts_version());
+    fprintf(fp, "# The command line was:\tbcftools +GTisec %s ", argv[0]);
+    int i;
+    for (i=1; i < argc; i++)
+    {
+        fprintf(fp, " %s", argv[i]);
+    }
+    fprintf(fp,"\n");
+    fprintf(fp,"# This file can be used as input to the subset plotting tools at:\n"
+               "#   https://github.com/dlaehnemann/bankers2\n");
+    fprintf(fp,"# Genotype intersections across samples:\n");
+    fprintf(fp,"@SMPS");
+    for (i = args.nsmp-1; i >= 0; i--)
+    {
+        fprintf(fp," %s", bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, i));
+    }
+    fprintf(fp,"\n");
+    if ( args.flag & MISSING )
+    {
+        if ( args.flag & SMPORDER )
+        {
+            fprintf(fp, "# The first line of each sample contains its count of missing genotypes, with a '-' appended\n"
+                        "#   to the sample name.\n");
+        }
+        else
+        {
+            fprintf(fp, "# The first %i lines contain the counts for missing values of each sample in the order provided\n"
+                        "#   in the SMPS-line above. Intersection counts only start afterwards.\n", args.nsmp);
+        }
+    }
+    if ( args.flag & SMPORDER )
+    {
+        fprintf(fp, "# Human readable output (-H) was requested. Subset intersection counts are therefore sorted by\n"
+                    "#   sample and repeated for each contained sample. For each sample, counts are in banker's \n"
+                    "#   sequence order regarding all other samples.\n");
+    }
+    else
+    {
+        fprintf(fp, "# Subset intersection counts are in global banker's sequence order.\n");
+        if ( args.nsmp > 2 )
+        {
+            fprintf(fp, "#   After exclusive sample counts in order of the SMPS-line, banker's sequence continues with:\n"
+                        "#   %s,%s   %s,%s   ...\n",
+                            bcf_hdr_int2id(in, BCF_DT_SAMPLE, args.nsmp-1 ),
+                            bcf_hdr_int2id(in, BCF_DT_SAMPLE, args.nsmp-2 ),
+                            bcf_hdr_int2id(in, BCF_DT_SAMPLE, args.nsmp-1 ),
+                            bcf_hdr_int2id(in, BCF_DT_SAMPLE, args.nsmp-3 )
+                            );
+        }
+    }
+    if (args.flag & VERBOSE )
+    {
+        fprintf(fp,"# [1] Number of shared non-ref genotypes \t[2] Samples sharing non-ref genotype (GT)\n");
+    }
+    else
+    {
+        fprintf(fp,"# [1] Number of shared non-ref genotypes\n");
+    }
+
+    /* Compute banker's sequence for following printing by sample and
+     * with increasing subset size.
+     */
+    uint32_t j;
+    for ( j = 0; j < args.nsmpp2; j++ )
+    {
+        args.bankers[j] = compute_bankers(j);
+    }
+
+    return 1;
+}
+
+
+/* ADAPTED CODE FROM CORIN LAWSON (START)
+ * https://github.com/au-phiware/bankers/blob/master/c/bankers.c
+ * who implemented ideas of Eric Burnett:
+ * http://www.thelowlyprogrammer.com/2010/04/indexing-and-enumerating-subsets-of.html
+ */
+
+/*
+ * Compute the binomial coefficient of `n choose k'.
+ * Use the fact that binom(n, k) = binom(n, n - k).
+ * Use a lookup table (triangle, actually) for speed.
+ * Otherwise it's dumb (heart) recursion.
+ * Added relative to Corin Lawson:
+ * * Passing in of sample number through pointer to args struct
+ * * Make quick lookup table external to keep it persistent with clean allocation
+ *   and freeing
+ */
+uint64_t choose(unsigned int n, unsigned int k) {
+    if (n == 0)
+        return 0;
+    if (n == k || k == 0)
+        return 1;
+    if (k > n / 2)
+        k = n - k;
+
+    unsigned int i = (n * (n - 1)) / 4 + k - 1;
+    if (args.quick[i] == 0)
+        args.quick[i] = choose(n - 1, k - 1) + choose(n - 1, k);
+
+    return args.quick[i];
+}
+
+/*
+ * Returns the Banker's number at the specified position, a.
+ * Derived from the recursive bit flip method.
+ * Added relative to Corin Lawson:
+ * * Uses same lookup table solution as choose function, just
+ *   maintained externally to persist across separate function calls.
+ * * Uses bitwise symmetry of banker's sequence to use bitwise inversion
+ *   instead of recursive bit flip for second half of sequence.
+ */
+uint32_t compute_bankers(unsigned long a)
+{
+    if (a == 0)
+        return 0;
+
+    if ( args.bankers[a] == 0 )
+    {
+        if ( a >= (args.nsmpp2 / 2) )
+            return args.bankers[a] = ( compute_bankers(args.nsmpp2 - (a+1)) ^ (args.nsmpp2 - 1) ); // use bitwise symmetry of bankers sequence
+        unsigned int c = 0;
+        uint32_t n = args.nsmp;
+        uint64_t e = a, binom;
+        binom = choose(n, c);
+        do {
+            e -= binom;
+        } while ((binom = choose(n, ++c)) <= e);
+
+        do {
+            if (e == 0 || (binom = choose(n - 1, c - 1)) > e)
+                c--, args.bankers[a] |= 1;
+            else
+                e -= binom;
+        } while (--n && c && ((args.bankers[a] <<= 1) || 1));
+        args.bankers[a] <<= n;
+    }
+
+    return args.bankers[a];
+}
+
+// ADAPTED CODE FROM CORIN LAWSON END
+
+
+/*
+ * GT field (genotype) comparison function.
+ */
+bcf1_t *process(bcf1_t *rec)
+{
+    uint64_t i;
+    bcf_unpack(rec, BCF_UN_FMT); // unpack the Format fields, including the GT field
+    int gte_smp = 0; // number GT array entries per sample (should be 2, one entry per allele)
+    if ( (gte_smp = bcf_get_genotypes(args.hdr, rec, &(args.gt_arr), &(args.ngt_arr) ) ) <= 0 )
+    {
+        error("GT not present at %s: %d\n", args.hdr->id[BCF_DT_CTG][rec->rid].key, rec->pos+1);
+    }
+
+    gte_smp /= args.nsmp; // divide total number of genotypes array entries (= args.ngt_arr) by number of samples
+    int ret;
+
+    // stick all genotypes in a hash as keys and store up to 32 samples in a corresponding flag as its value
+    khiter_t bucket;
+    khash_t(gts2smps) *gts = kh_init(gts2smps); // create hash
+    for ( i = 0; i < args.nsmp; i++ )
+    {
+        int *gt_ptr = args.gt_arr + gte_smp * i;
+
+        if (bcf_gt_is_missing(gt_ptr[0]) || ( gte_smp == 2 && bcf_gt_is_missing(gt_ptr[1]) ) )
+        {
+            if ( args.flag & MISSING ) args.missing_gts[i]++; // count missing genotypes, if requested
+            continue; // don't do anything else for missing genotypes, their "sharing" gives no info...
+        }
+
+        int a = bcf_gt_allele(gt_ptr[0]);
+        int b;
+        if ( gte_smp == 2 ) // two entries available per sample, padded with missing values for haploid genotypes
+        {
+            b = bcf_gt_allele(gt_ptr[1]);
+        }
+        else if (gte_smp == 1 ) // use missing value for second entry in hash key generation below, if only one is available
+        {
+            b = bcf_gt_allele(bcf_int32_vector_end);
+        }
+        else
+        {
+            error("gtisec does not support ploidy higher than 2.\n");
+        }
+
+        int idx = bcf_alleles2gt(a,b); // generate genotype specific hash key
+
+        bucket = kh_get(gts2smps, gts, idx); // get the genotype's hash bucket
+
+        if ( bucket == kh_end(gts) ) { // means that key does not exist
+            bucket = kh_put(gts2smps, gts, idx, &ret); // create bucket with genotype index as key and return its iterator
+            kh_val(gts, bucket) = 0; // initialize the bucket with all sample bits unset
+        }
+        kh_value(gts, bucket) |= (1<<i); // set the sample's bit to 1 in this genotype's bucket
+    }
+
+    // iterate over genotypes and for each genotype increment the appropriate smp_is entry
+    for ( bucket = kh_begin(gts); bucket != kh_end(gts); ++bucket ) // iterate over all genotypes at this position
+    {
+        if ( kh_exist(gts, bucket) ) // for existing genotype buckets
+        {
+            uint32_t s = kh_val(gts, bucket); // get the 32 bit flag
+            args.smp_is[s]++; // add to the corresponding subset
+        }
+    }
+    kh_destroy(gts2smps, gts); // destroy hash
+
+    return NULL;
+}
+
+void destroy(void)
+{
+    int32_t i;
+    int s;
+
+    FILE *fp = args.out;
+
+    /* Printing to File */
+    if ( args.flag & SMPORDER )
+    {
+        /* Iterate over samples, printing out all subsets including
+         * the current sample, with the current sample first. This
+         * includes multiple printouts of the same sample but makes
+         * output more readable and is also needed for circos files
+         * printing.
+         */
+        for ( s = args.nsmp-1; s >= 0; s--)
+        {
+            if ( args.flag & MISSING ) // if missing genotype counts are requested, print them to standard output
+            {
+                fprintf(fp, "%"PRIu64"\t%s-\n", args.missing_gts[s], bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, s));
+            }
+            for ( i = 1; i < args.nsmpp2; i++ )
+            {
+                if ( (args.bankers[i]>>s) & 1 )
+                {
+                    fprintf(fp, "%"PRIu64"\t", args.smp_is[ args.bankers[i] ]); // print out count of genotypes shared by samples in current banker's sequence position
+                    int j;
+                    /* Print sample list */
+                    fprintf(fp, "%s", bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, s)); // print current sample first
+                    for ( j = args.nsmp-1; j >= 0; j-- )
+                    {
+                        if ( (args.bankers[i] ^ (1<<s)) & (1<<j) ) // exclude current sample from printing again
+                        {
+                            fprintf(fp, ",%s", bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, j ) ); // print out sample list, starting with our current major sample
+                        }
+                    }
+                    fprintf(fp, "\n" );
+                }
+            }
+        }
+    }
+    else if ( args.flag & VERBOSE )
+    {
+        if ( args.flag & MISSING ) // if missing genotype counts are requested, print them to standard output
+        {
+            for ( s = args.nsmp-1; s >= 0; s--)
+            {
+                fprintf(fp, "%"PRIu64"\t%s-\n", args.missing_gts[s], bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, s));
+            }
+        }
+        for ( i = 1; i < args.nsmpp2; i++ )
+        {
+            fprintf(fp, "%"PRIu64"\t", args.smp_is[ args.bankers[i] ]); // print out count of genotypes shared by samples in current banker's sequence position
+            int j = 0;
+            for ( s = args.nsmp-1; s >= 0; s--)
+            {
+               if ( (args.bankers[i]>>s) & 1 )
+               {
+                   fprintf(fp, "%s%s", j ? "," : "", bcf_hdr_int2id(args.hdr, BCF_DT_SAMPLE, s) ); // samples in specified order
+                   j = 1;
+               }
+            }
+            fprintf(fp, "\n" );
+        }
+    }
+    else
+    {
+        if ( args.flag & MISSING ) // if missing genotype counts are requested, print them to standard output
+        {
+            for ( s = args.nsmp-1; s >= 0; s--)
+            {
+                fprintf(fp, "%"PRIu64"\n", args.missing_gts[s]);
+            }
+        }
+        for ( i = 1; i < args.nsmpp2; i++ )
+        {
+            fprintf(fp, "%"PRIu64"\n", args.smp_is[ args.bankers[i] ]); // print out count of genotypes shared by samples in current banker's sequence position
+        }
+    }
+    fclose(fp);
+
+    /* freeing up args */
+    free(args.gt_arr);
+    free(args.bankers);
+    free(args.quick);
+    if (args.flag & MISSING) free(args.missing_gts);
+    free(args.smp_is);
+}
diff --git a/plugins/GTisec.mk b/plugins/GTisec.mk
new file mode 100644
index 000000000..58d1cc739
--- /dev/null
+++ b/plugins/GTisec.mk
@@ -0,0 +1,2 @@
+plugins/GTisec.so: plugins/GTisec.c version.h version.c 
+	$(CC) $(PLUGIN_FLAGS) $(CFLAGS) $(EXTRA_CPPFLAGS) $(CPPFLAGS) $(LDFLAGS) -o $@ version.c $< $(LIBS)
diff --git a/test/test.pl b/test/test.pl
index 7a54de292..2c353753a 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -188,6 +188,14 @@
 test_vcf_plugin($opts,in=>'view.GL',out=>'view.PL.vcf',cmd=>'+tag2tag --no-version',args=>'-- -r --gl-to-pl');
 test_vcf_plugin($opts,in=>'merge.a',out=>'fill-tags.out',cmd=>'+fill-tags --no-version',args=>'-- -t AN,AC,AC_Hom,AC_Het,AC_Hemi');
 test_vcf_plugin($opts,in=>'view',out=>'fill-tags.2.out',cmd=>'+fill-tags --no-version',args=>'-- -t AC,AN,AF,NS');
+test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.out',cmd=>'+GTisec',args=>' | grep -v bcftools');
+test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.H.out',cmd=>'+GTisec',args=>'-- -H | grep -v bcftools');
+test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.Hm.out',cmd=>'+GTisec',args=>'-- -Hm | grep -v bcftools');
+test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.Hmv.out',cmd=>'+GTisec',args=>'-- -Hmv | grep -v bcftools');
+test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.Hv.out',cmd=>'+GTisec',args=>'-- -Hv | grep -v bcftools');
+test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.m.out',cmd=>'+GTisec',args=>'-- -m | grep -v bcftools');
+test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.mv.out',cmd=>'+GTisec',args=>'-- -mv | grep -v bcftools');
+test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.v.out',cmd=>'+GTisec',args=>'-- -v | grep -v bcftools');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.vcf.out',do_bcf=>0,args=>'');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.bcf.out',do_bcf=>1,args=>'');
 test_vcf_concat($opts,in=>['concat.2.a','concat.2.b'],out=>'concat.2.vcf.out',do_bcf=>0,args=>'-a');
diff --git a/test/view.GTisec.H.out b/test/view.GTisec.H.out
new file mode 100644
index 000000000..5cf831bb8
--- /dev/null
+++ b/test/view.GTisec.H.out
@@ -0,0 +1,20 @@
+# This file can be used as input to the subset plotting tools at:
+#   https://github.com/dlaehnemann/bankers2
+# Genotype intersections across samples:
+@SMPS NA00003 NA00002 NA00001
+# Human readable output (-H) was requested. Subset intersection counts are therefore sorted by
+#   sample and repeated for each contained sample. For each sample, counts are in banker's 
+#   sequence order regarding all other samples.
+# [1] Number of shared non-ref genotypes 	[2] Samples sharing non-ref genotype (GT)
+9	NA00003
+1	NA00003,NA00002
+0	NA00003,NA00001
+1	NA00003,NA00002,NA00001
+4	NA00002
+1	NA00002,NA00003
+8	NA00002,NA00001
+1	NA00002,NA00003,NA00001
+5	NA00001
+0	NA00001,NA00003
+8	NA00001,NA00002
+1	NA00001,NA00003,NA00002
diff --git a/test/view.GTisec.Hm.out b/test/view.GTisec.Hm.out
new file mode 100644
index 000000000..e70f86b2a
--- /dev/null
+++ b/test/view.GTisec.Hm.out
@@ -0,0 +1,25 @@
+# This file can be used as input to the subset plotting tools at:
+#   https://github.com/dlaehnemann/bankers2
+# Genotype intersections across samples:
+@SMPS NA00003 NA00002 NA00001
+# The first line of each sample contains its count of missing genotypes, with a '-' appended
+#   to the sample name.
+# Human readable output (-H) was requested. Subset intersection counts are therefore sorted by
+#   sample and repeated for each contained sample. For each sample, counts are in banker's 
+#   sequence order regarding all other samples.
+# [1] Number of shared non-ref genotypes 	[2] Samples sharing non-ref genotype (GT)
+4	NA00003-
+9	NA00003
+1	NA00003,NA00002
+0	NA00003,NA00001
+1	NA00003,NA00002,NA00001
+1	NA00002-
+4	NA00002
+1	NA00002,NA00003
+8	NA00002,NA00001
+1	NA00002,NA00003,NA00001
+1	NA00001-
+5	NA00001
+0	NA00001,NA00003
+8	NA00001,NA00002
+1	NA00001,NA00003,NA00002
diff --git a/test/view.GTisec.Hmv.out b/test/view.GTisec.Hmv.out
new file mode 100644
index 000000000..e70f86b2a
--- /dev/null
+++ b/test/view.GTisec.Hmv.out
@@ -0,0 +1,25 @@
+# This file can be used as input to the subset plotting tools at:
+#   https://github.com/dlaehnemann/bankers2
+# Genotype intersections across samples:
+@SMPS NA00003 NA00002 NA00001
+# The first line of each sample contains its count of missing genotypes, with a '-' appended
+#   to the sample name.
+# Human readable output (-H) was requested. Subset intersection counts are therefore sorted by
+#   sample and repeated for each contained sample. For each sample, counts are in banker's 
+#   sequence order regarding all other samples.
+# [1] Number of shared non-ref genotypes 	[2] Samples sharing non-ref genotype (GT)
+4	NA00003-
+9	NA00003
+1	NA00003,NA00002
+0	NA00003,NA00001
+1	NA00003,NA00002,NA00001
+1	NA00002-
+4	NA00002
+1	NA00002,NA00003
+8	NA00002,NA00001
+1	NA00002,NA00003,NA00001
+1	NA00001-
+5	NA00001
+0	NA00001,NA00003
+8	NA00001,NA00002
+1	NA00001,NA00003,NA00002
diff --git a/test/view.GTisec.Hv.out b/test/view.GTisec.Hv.out
new file mode 100644
index 000000000..5cf831bb8
--- /dev/null
+++ b/test/view.GTisec.Hv.out
@@ -0,0 +1,20 @@
+# This file can be used as input to the subset plotting tools at:
+#   https://github.com/dlaehnemann/bankers2
+# Genotype intersections across samples:
+@SMPS NA00003 NA00002 NA00001
+# Human readable output (-H) was requested. Subset intersection counts are therefore sorted by
+#   sample and repeated for each contained sample. For each sample, counts are in banker's 
+#   sequence order regarding all other samples.
+# [1] Number of shared non-ref genotypes 	[2] Samples sharing non-ref genotype (GT)
+9	NA00003
+1	NA00003,NA00002
+0	NA00003,NA00001
+1	NA00003,NA00002,NA00001
+4	NA00002
+1	NA00002,NA00003
+8	NA00002,NA00001
+1	NA00002,NA00003,NA00001
+5	NA00001
+0	NA00001,NA00003
+8	NA00001,NA00002
+1	NA00001,NA00003,NA00002
diff --git a/test/view.GTisec.m.out b/test/view.GTisec.m.out
new file mode 100644
index 000000000..8d217a5d2
--- /dev/null
+++ b/test/view.GTisec.m.out
@@ -0,0 +1,20 @@
+# This file can be used as input to the subset plotting tools at:
+#   https://github.com/dlaehnemann/bankers2
+# Genotype intersections across samples:
+@SMPS NA00003 NA00002 NA00001
+# The first 3 lines contain the counts for missing values of each sample in the order provided
+#   in the SMPS-line above. Intersection counts only start afterwards.
+# Subset intersection counts are in global banker's sequence order.
+#   After exclusive sample counts in order of the SMPS-line, banker's sequence continues with:
+#   NA00003,NA00002   NA00003,NA00001   ...
+# [1] Number of shared non-ref genotypes
+4
+1
+1
+9
+4
+5
+1
+0
+8
+1
diff --git a/test/view.GTisec.mv.out b/test/view.GTisec.mv.out
new file mode 100644
index 000000000..1772a3b78
--- /dev/null
+++ b/test/view.GTisec.mv.out
@@ -0,0 +1,20 @@
+# This file can be used as input to the subset plotting tools at:
+#   https://github.com/dlaehnemann/bankers2
+# Genotype intersections across samples:
+@SMPS NA00003 NA00002 NA00001
+# The first 3 lines contain the counts for missing values of each sample in the order provided
+#   in the SMPS-line above. Intersection counts only start afterwards.
+# Subset intersection counts are in global banker's sequence order.
+#   After exclusive sample counts in order of the SMPS-line, banker's sequence continues with:
+#   NA00003,NA00002   NA00003,NA00001   ...
+# [1] Number of shared non-ref genotypes 	[2] Samples sharing non-ref genotype (GT)
+4	NA00003-
+1	NA00002-
+1	NA00001-
+9	NA00003
+4	NA00002
+5	NA00001
+1	NA00003,NA00002
+0	NA00003,NA00001
+8	NA00002,NA00001
+1	NA00003,NA00002,NA00001
diff --git a/test/view.GTisec.out b/test/view.GTisec.out
new file mode 100644
index 000000000..2b2b0f6d7
--- /dev/null
+++ b/test/view.GTisec.out
@@ -0,0 +1,15 @@
+# This file can be used as input to the subset plotting tools at:
+#   https://github.com/dlaehnemann/bankers2
+# Genotype intersections across samples:
+@SMPS NA00003 NA00002 NA00001
+# Subset intersection counts are in global banker's sequence order.
+#   After exclusive sample counts in order of the SMPS-line, banker's sequence continues with:
+#   NA00003,NA00002   NA00003,NA00001   ...
+# [1] Number of shared non-ref genotypes
+9
+4
+5
+1
+0
+8
+1
diff --git a/test/view.GTisec.v.out b/test/view.GTisec.v.out
new file mode 100644
index 000000000..8ec3aa315
--- /dev/null
+++ b/test/view.GTisec.v.out
@@ -0,0 +1,15 @@
+# This file can be used as input to the subset plotting tools at:
+#   https://github.com/dlaehnemann/bankers2
+# Genotype intersections across samples:
+@SMPS NA00003 NA00002 NA00001
+# Subset intersection counts are in global banker's sequence order.
+#   After exclusive sample counts in order of the SMPS-line, banker's sequence continues with:
+#   NA00003,NA00002   NA00003,NA00001   ...
+# [1] Number of shared non-ref genotypes 	[2] Samples sharing non-ref genotype (GT)
+9	NA00003
+4	NA00002
+5	NA00001
+1	NA00003,NA00002
+0	NA00003,NA00001
+8	NA00002,NA00001
+1	NA00003,NA00002,NA00001

From 0bed387d08e558d278a3029b876c27f6ca870225 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 4 Mar 2016 11:06:44 +0000
Subject: [PATCH 151/211] docs: add some clarification for view filters. fix
 some typos. closes #357

---
 doc/bcftools.txt | 17 +++++++++++++----
 1 file changed, 13 insertions(+), 4 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 6b771dfe7..a37132efa 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -169,7 +169,7 @@ specific commands to see if they apply.
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     Output compressed BCF ('b'), uncompressed BCF ('u'), compressed VCF ('z'), uncompressed VCF ('v').
     Use the -Ou option when piping between bcftools subcommands to speed up
-    performance by removing unecessary compression/decompression and
+    performance by removing unnecessary compression/decompression and
     VCF<-->BCF conversion.
 
 *-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
@@ -607,7 +607,7 @@ demand. The original calling model can be invoked with the *-c* option.
     genotype calling maximizes likelihood of a particular combination of
     genotypes for father, mother and the child
     P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn).
-    By providing three values, the mutation rate Pn is set explictly for SNPs,
+    By providing three values, the mutation rate Pn is set explicitly for SNPs,
     deletions and insertions, respectively.  If two values are given, the first
     is interpreted as the mutation rate of SNPs and the second is used to
     calculate the mutation rate of indels according to their length as
@@ -1505,7 +1505,7 @@ file for help.
     see *<<common_options,Common Options>>*
 
 *-s, --sample* 'string'::
-    samply name
+    sample name
 
 *-t, --targets* 'LIST'::
     see *<<common_options,Common Options>>*
@@ -1674,7 +1674,7 @@ Transition probabilities:
 
 *--AF-tag* 'TAG'::
     use the specified INFO tag 'TAG' as an allele frequency estimate
-    instead of the defaul AC and AN tags. Sites which do not have 'TAG'
+    instead of the default AC and AN tags. Sites which do not have 'TAG'
     will be skipped.
     
 *--AF-file* 'FILE'::
@@ -1872,6 +1872,15 @@ Convert between VCF and BCF. Former *bcftools subset*.
 
 
 ==== Filter options:
+Note that filter options below dealing with counting the number of alleles
+will, for speed, first check for the values of AC and AN in the INFO column to 
+avoid parsing all the genotype (FORMAT/GT) fields in the VCF. This means
+that a filter like '--min-af 0.1' will be based `AC/AN' where AC and AN come
+from either INFO/AC and INFO/AN if available or FORMAT/GT if not. It will not
+filter on another field like INFO/AF. The '--include' and '--exclude' filter
+expressions should instead be used to explicitly filter based on fields in
+the INFO column, e.g. '--exclude AF<0.1'.
+
 *-c, --min-ac* 'INT'[':nref'|':alt1'|':minor'|':major'|:'nonmajor']::
     minimum allele count (INFO/AC) of sites to be printed.
     Specifying the type of allele is optional and can be set to 

From e38a10aea6dd60355d725740008377ab004b8556 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 4 Mar 2016 11:07:09 +0000
Subject: [PATCH 152/211] whitespace [minor]

---
 vcfconvert.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcfconvert.c b/vcfconvert.c
index 94e90e88f..1e60d30a9 100644
--- a/vcfconvert.c
+++ b/vcfconvert.c
@@ -1309,7 +1309,7 @@ static void usage(void)
     fprintf(stderr, "       --no-version               do not append version and command line to the header\n");
     fprintf(stderr, "   -o, --output <file>            output file name [stdout]\n");
     fprintf(stderr, "   -O, --output-type <b|u|z|v>    b: compressed BCF, u: uncompressed BCF, z: compressed VCF, v: uncompressed VCF [v]\n");
-    fprintf(stderr, "       --threads <int>         number of extra output compression threads [0]\n");
+    fprintf(stderr, "       --threads <int>            number of extra output compression threads [0]\n");
     fprintf(stderr, "\n");
     fprintf(stderr, "GEN/SAMPLE conversion (input/output from IMPUTE2):\n");
     fprintf(stderr, "   -G, --gensample2vcf <...>   <prefix>|<gen-file>,<sample-file>\n");

From bf38eac19fbaede4fe9c1f2c17c061747c665ab9 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 4 Mar 2016 16:06:53 +0000
Subject: [PATCH 153/211] norm: should not crash on deletions in telomere N
 regions which cannot be extended to the left

Fixes #385
---
 test/norm.fa           | 2 ++
 test/norm.fa.fai       | 1 +
 test/norm.telomere.out | 5 +++++
 test/norm.telomere.vcf | 4 ++++
 test/test.pl           | 1 +
 vcfnorm.c              | 6 ++++--
 6 files changed, 17 insertions(+), 2 deletions(-)
 create mode 100644 test/norm.telomere.out
 create mode 100644 test/norm.telomere.vcf

diff --git a/test/norm.fa b/test/norm.fa
index 53e6b163f..2eecd7f32 100644
--- a/test/norm.fa
+++ b/test/norm.fa
@@ -24,3 +24,5 @@ TCCCCTCTTGACCTCTCTCTATTTTTTTTTTTTTTTCTGAGATGGATTTTTGCTCTTGTT
 GTCTCAAAAAAAAAAAAAAAAAAAAGAAAAG
 >21
 TTTATTATTATTATTATTAAATTGAATTTATTTAGTGTACATACATTCATGTGTATTGTG
+>22
+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
diff --git a/test/norm.fa.fai b/test/norm.fa.fai
index 40b06b7c4..da3fb859e 100644
--- a/test/norm.fa.fai
+++ b/test/norm.fa.fai
@@ -5,3 +5,4 @@
 4	60	985	60	61
 5	31	1070	31	32
 21	60	1106	60	61
+22	30	1171	30	31
diff --git a/test/norm.telomere.out b/test/norm.telomere.out
new file mode 100644
index 000000000..59431fa90
--- /dev/null
+++ b/test/norm.telomere.out
@@ -0,0 +1,5 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=22,length=30>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+22	1	.	NN	N	.	.	.
diff --git a/test/norm.telomere.vcf b/test/norm.telomere.vcf
new file mode 100644
index 000000000..55ff94b3d
--- /dev/null
+++ b/test/norm.telomere.vcf
@@ -0,0 +1,4 @@
+##fileformat=VCFv4.2
+##contig=<ID=22,length=30>
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
+22	17	.	NN	N	.	.	.
diff --git a/test/test.pl b/test/test.pl
index 2c353753a..a897afdb3 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -103,6 +103,7 @@
 test_vcf_norm($opts,in=>'norm.merge.3',out=>'norm.merge.3.out',args=>'-m+');
 test_vcf_norm($opts,in=>'norm.merge',out=>'norm.merge.strict.out',args=>'-m+ -s');
 test_vcf_norm($opts,in=>'norm.setref',out=>'norm.setref.out',args=>'-Nc s',fai=>'norm');
+test_vcf_norm($opts,in=>'norm.telomere',out=>'norm.telomere.out',fai=>'norm');
 test_vcf_view($opts,in=>'view',out=>'view.1.out',args=>'-aUc1 -C1 -s NA00002 -v snps',reg=>'');
 test_vcf_view($opts,in=>'view',out=>'view.2.out',args=>'-f PASS -Xks NA00003',reg=>'-r20,Y');
 test_vcf_view($opts,in=>'view',out=>'view.3.out',args=>'-xs NA00003',reg=>'');
diff --git a/vcfnorm.c b/vcfnorm.c
index fdac00546..781833ceb 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -296,17 +296,19 @@ static int realign(args_t *args, bcf1_t *line)
         if ( i>0 && als[i].l==als[0].l && !strcasecmp(als[0].s,als[i].s) ) return ERR_DUP_ALLELE;
     }
 
-
     // trim from right
     int ori_pos = line->pos;
     while (1)
     {
         // is the rightmost base identical in all alleles?
+        int min_len = als[0].l;
         for (i=1; i<line->n_allele; i++)
         {
             if ( als[0].s[ als[0].l-1 ]!=als[i].s[ als[i].l-1 ] ) break;
+            if ( als[i].l < min_len ) min_len = als[i].l;
         }
         if ( i!=line->n_allele ) break; // there are differences, cannot be trimmed
+        if ( min_len<=1 && line->pos==0 ) break;
 
         int pad_from_left = 0;
         for (i=0; i<line->n_allele; i++) // trim all alleles
@@ -344,7 +346,7 @@ static int realign(args_t *args, bcf1_t *line)
             if ( als[0].s[ntrim_left]!=als[i].s[ntrim_left] ) break;
             if ( min_len > als[i].l - ntrim_left ) min_len = als[i].l - ntrim_left;
         }
-        if ( i!=line->n_allele || min_len==1 ) break; // there are differences, cannot be trimmed
+        if ( i!=line->n_allele || min_len<=1 ) break; // there are differences, cannot be trimmed
         ntrim_left++;
     }
     if ( ntrim_left )

From 2211509a59848f857182723b2fd82f61ee1c054a Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 14 Mar 2016 16:12:31 +0000
Subject: [PATCH 154/211] impute-info: do calculation with double; only convert
 to float on insert into VCF

---
 plugins/impute-info.c | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/plugins/impute-info.c b/plugins/impute-info.c
index c3c74ecea..ad5a0d155 100644
--- a/plugins/impute-info.c
+++ b/plugins/impute-info.c
@@ -1,6 +1,6 @@
 /*  plugins/impute-info.c -- adds info metrics to a VCF file.
 
-    Copyright (C) 2015 Genome Research Ltd.
+    Copyright (C) 2015-2016 Genome Research Ltd.
 
     Author: Shane McCarthy <sm15@sanger.ac.uk>
 
@@ -121,13 +121,13 @@ bcf1_t *process(bcf1_t *rec)
         return rec; // require biallelic diploid, return site unchanged
     }
 
-    float esum = 0, e2sum = 0, fsum = 0;
+    double esum = 0, e2sum = 0, fsum = 0;
     #define BRANCH(type_t,is_missing,is_vector_end) \
     { \
         type_t *ptr = (type_t*) buf; \
         for (i=0; i<rec->n_sample; i++) \
         { \
-            float vals[3] = {0,0,0}; \
+            double vals[3] = {0,0,0}; \
             for (j=0; j<nret; j++) \
             { \
                 if ( is_missing || is_vector_end ) break; \
@@ -147,8 +147,8 @@ bcf1_t *process(bcf1_t *rec)
     }
     #undef BRANCH
 
-    float theta = esum / (2 * (float)nval);
-    float info  = (theta>0 && theta<1) ? 1 - (fsum - e2sum) / (2 * (float)nval * theta * (1.0 - theta)) : 1;
+    double theta = esum / (2 * (double)nval);
+    float info  = (theta>0 && theta<1) ? (float)(1 - (fsum - e2sum) / (2 * (double)nval * theta * (1.0 - theta))) : 1;
 
     bcf_update_info_float(out_hdr, rec, "INFO", &info, 1);
     nrec++;

From afecb4e96c3abc188e7fc155e35720e01aa13a81 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Tue, 15 Mar 2016 16:15:48 +0000
Subject: [PATCH 155/211] getopt_long() returns int, not char

Much like fgetc() returning EOF, we need to store getopt_long()'s
result in an int so that we can reliably check the -1 return value.
Hat tip @daviesrob; fixes the usage errors part of #389.
---
 consensus.c          | 2 +-
 plugins/GTisec.c     | 2 +-
 plugins/color-chrs.c | 2 +-
 plugins/fill-tags.c  | 2 +-
 plugins/mendelian.c  | 2 +-
 plugins/tag2tag.c    | 2 +-
 plugins/vcf2sex.c    | 3 ++-
 polysomy.c           | 3 ++-
 8 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/consensus.c b/consensus.c
index 7a615fef0..051f3536c 100644
--- a/consensus.c
+++ b/consensus.c
@@ -623,7 +623,7 @@ int main_consensus(int argc, char *argv[])
         {"chain",1,0,'c'},
         {0,0,0,0}
     };
-    char c;
+    int c;
     while ((c = getopt_long(argc, argv, "h?s:1iH:f:o:m:c:",loptions,NULL)) >= 0) 
     {
         switch (c) 
diff --git a/plugins/GTisec.c b/plugins/GTisec.c
index adfbdb972..eaa0b1521 100644
--- a/plugins/GTisec.c
+++ b/plugins/GTisec.c
@@ -127,7 +127,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         {0,0,0,0}
     };
 
-    char c;
+    int c;
     while ((c = getopt_long(argc, argv, "?mvHh",loptions,NULL)) >= 0)
     {
         switch (c)
diff --git a/plugins/color-chrs.c b/plugins/color-chrs.c
index 6a9175e70..909065e5c 100644
--- a/plugins/color-chrs.c
+++ b/plugins/color-chrs.c
@@ -159,7 +159,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         {"unrelated",1,0,'u'},
         {0,0,0,0}
     };
-    char c;
+    int c;
     while ((c = getopt_long(argc, argv, "?ht:u:p:",loptions,NULL)) >= 0)
     {
         switch (c) 
diff --git a/plugins/fill-tags.c b/plugins/fill-tags.c
index 2fff25803..025ac32d5 100644
--- a/plugins/fill-tags.c
+++ b/plugins/fill-tags.c
@@ -117,7 +117,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         {"tags",1,0,'t'},
         {0,0,0,0}
     };
-    char c;
+    int c;
     while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0)
     {
         switch (c) 
diff --git a/plugins/mendelian.c b/plugins/mendelian.c
index 186e3e512..304a27a7d 100644
--- a/plugins/mendelian.c
+++ b/plugins/mendelian.c
@@ -100,7 +100,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         {"count",0,0,'c'},
         {0,0,0,0}
     };
-    char c;
+    int c;
     while ((c = getopt_long(argc, argv, "?ht:T:l:cd",loptions,NULL)) >= 0)
     {
         switch (c) 
diff --git a/plugins/tag2tag.c b/plugins/tag2tag.c
index ec8956582..6145a6237 100644
--- a/plugins/tag2tag.c
+++ b/plugins/tag2tag.c
@@ -83,7 +83,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         {"gl-to-pl",0,0,2},
         {0,0,0,0}
     };
-    char c;
+    int c;
     while ((c = getopt_long(argc, argv, "?hr",loptions,NULL)) >= 0)
     {
         switch (c) 
diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index ddba74c4d..9cb0ed5dc 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -389,7 +389,8 @@ int run(int argc, char **argv)
         {"background",1,0,'b'},
         {0,0,0,0}
     };
-    char c, *tmp, *ploidy_fname = NULL;
+    char *tmp, *ploidy_fname = NULL;
+    int c;
     while ((c = getopt_long(argc, argv, "p:n:g:m:vb:",loptions,NULL)) >= 0)
     {
         switch (c) {
diff --git a/polysomy.c b/polysomy.c
index c5a5394e1..93f41844c 100644
--- a/polysomy.c
+++ b/polysomy.c
@@ -675,7 +675,8 @@ int main_polysomy(int argc, char *argv[])
         {"regions-file",1,0,'R'},
         {0,0,0,0}
     };
-    char c, *tmp;
+    char *tmp;
+    int c;
     while ((c = getopt_long(argc, argv, "h?o:vt:T:r:R:s:f:p:c:im:b:n:S:",loptions,NULL)) >= 0)
     {
         switch (c)

From 3eb4e8ece828c00aa4ebb76dd24255aeab20708b Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Wed, 16 Mar 2016 11:08:00 +0000
Subject: [PATCH 156/211] Mark error() as HTS_NORETURN

...as it always calls exit().  Prevents a "'b' may be used uninitialised"
warning in plugins/GTisec.c.
---
 Makefile   | 2 +-
 bcftools.h | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/Makefile b/Makefile
index b84556523..b1c21440d 100644
--- a/Makefile
+++ b/Makefile
@@ -129,7 +129,7 @@ endif
 plugins: $(PLUGINS)
 
 
-bcftools_h = bcftools.h $(htslib_vcf_h)
+bcftools_h = bcftools.h $(htslib_hts_defs_h) $(htslib_vcf_h)
 call_h = call.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) vcmp.h
 convert_h = convert.h $(htslib_vcf_h)
 tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h)
diff --git a/bcftools.h b/bcftools.h
index 6f22272b9..d4e856da7 100644
--- a/bcftools.h
+++ b/bcftools.h
@@ -26,6 +26,7 @@ THE SOFTWARE.  */
 #define BCFTOOLS_H
 
 #include <stdarg.h>
+#include <htslib/hts_defs.h>
 #include <htslib/vcf.h>
 #include <math.h>
 
@@ -37,7 +38,7 @@ THE SOFTWARE.  */
 #define FT_STDIN (1<<3)
 
 char *bcftools_version(void);
-void error(const char *format, ...);
+void error(const char *format, ...) HTS_NORETURN;
 void bcf_hdr_append_version(bcf_hdr_t *hdr, int argc, char **argv, const char *cmd);
 const char *hts_bcf_wmode(int file_type);
 

From 4c933867d8d30f9d79186dfaca697653e77153a8 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Wed, 16 Mar 2016 11:20:15 +0000
Subject: [PATCH 157/211] Check return codes from bgzf_read() / bgzf_write()
 calls

---
 reheader.c  | 2 +-
 vcfconcat.c | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/reheader.c b/reheader.c
index 7248cbb4b..0466c16ca 100644
--- a/reheader.c
+++ b/reheader.c
@@ -243,7 +243,7 @@ static void reheader_vcf_gz(args_t *args)
 
     // Output the modified header
     BGZF *bgzf_out = bgzf_open(args->output_fname ? args->output_fname : "-","w");;
-    bgzf_write(bgzf_out, hdr.s, hdr.l);
+    if ( bgzf_write(bgzf_out, hdr.s, hdr.l) < 0 ) error("Can't write BGZF header (code %d)\n", bgzf_out->errcode);
     free(hdr.s);
 
     // Output all remainig data read with the header block
diff --git a/vcfconcat.c b/vcfconcat.c
index 32421378c..bd6a00a25 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -578,12 +578,12 @@ static void naive_concat(args_t *args)
             error("Failed to read %s: %s\n", args->fnames[i], strerror(errno));
 
         uint8_t magic[5];
-        if ( bgzf_read(fp, magic, 5)<0 ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
+        if ( bgzf_read(fp, magic, 5) != 5 ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
         if (strncmp((char*)magic, "BCF\2\2", 5) != 0) error("Invalid BCF magic string in %s\n", args->fnames[i]);
 
-        bgzf_read(fp, &tmp.l, 4);
+        if ( bgzf_read(fp, &tmp.l, 4) != 4 ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
         hts_expand(char,tmp.l,tmp.m,tmp.s);
-        bgzf_read(fp, tmp.s, tmp.l);
+        if ( bgzf_read(fp, tmp.s, tmp.l) != tmp.l ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
 
         // write only the first header
         if ( i==0 )

From 21994b91b382c778d13f882080a36c145cd20f7c Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 17 Mar 2016 07:37:00 +0000
Subject: [PATCH 158/211] GLs are log10 scaled, not ln scaled. Fixes #394

---
 plugins/tag2tag.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugins/tag2tag.c b/plugins/tag2tag.c
index 6145a6237..8178326eb 100644
--- a/plugins/tag2tag.c
+++ b/plugins/tag2tag.c
@@ -118,7 +118,7 @@ bcf1_t *process(bcf1_t *rec)
         for (i=0; i<n; i++)
         {
             if ( bcf_float_is_missing(farr[i]) || bcf_float_is_vector_end(farr[i]) ) continue;
-            farr[i] = farr[i] ? log(farr[i]) : -99;
+            farr[i] = farr[i] ? log10(farr[i]) : -99;
         }
         bcf_update_format_float(out_hdr,rec,"GL",farr,n);
         if ( drop_source_tag )

From 47e811cc2e4c212d69ef28ed2a57663acee663f3 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Thu, 31 Mar 2016 13:15:13 +0100
Subject: [PATCH 159/211] Fix docs grammar [minor]

Obsoletes the rest of debian/1.3-3:debian/patches/spelling.patch
---
 doc/bcftools.txt | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index a37132efa..379a0975a 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -266,7 +266,7 @@ specific commands to see if they apply.
 [[annotate]]
 === bcftools annotate '[OPTIONS]' 'FILE'
 
-This command allows to add or remove annotations.
+Add or remove annotations.
 
 *-a, --annotations* 'file'::
     Bgzip-compressed and tabix-indexed file with annotations. The file
@@ -1472,7 +1472,7 @@ const char *about(void);
 // Longer description used by 'bcftools +name -h'
 const char *usage(void);
 
-// Called once at startup, allows to initialize local variables.
+// Called once at startup, allows initialization of local variables.
 // Return 1 to suppress normal VCF/BCF header output, -1 on critical
 // errors, 0 otherwise.
 int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);

From c45b93d11608504db3bea296ff7868cd9e18651f Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 18 Apr 2016 14:19:33 +0100
Subject: [PATCH 160/211] docs: clarify use of BED files in --regions-file and
 --targets-file options

Closes #411
---
 doc/bcftools.txt | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 379a0975a..c91bb9c2b 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -179,11 +179,15 @@ specific commands to see if they apply.
 *-R, --regions-file* 'FILE'::
     Regions can be specified either on command line or in a VCF, BED, or
     tab-delimited file (the default).  The columns of the tab-delimited file
-    are: CHROM, POS, and,  optionally,  POS_TO,  where positions are 1-based
-    and inclusive.  Uncompressed files are stored in memory, while
-    bgzip-compressed and tabix-indexed region files are streamed.  Note that
-    sequence names must match exactly, "chr20" is not the same as "20".
-    Also note that chromosome ordering in 'FILE' will be respected,
+    are: CHROM, POS, and, optionally,  POS_TO,  where positions are 1-based
+    and inclusive. The columns of the tab-delimited BED file are also
+    CHROM, POS and POS_TO (trailing columns are ignored), but coordinates
+    are 0-based, half-open.  To indicate that a file be treated as BED rather
+    than the 1-based tab-delimited file, the file must have the ".bed" or
+    ".bed.gz" suffix (case-insensitive). Uncompressed files are stored in
+    memory, while bgzip-compressed and tabix-indexed region files are streamed.
+    Note that sequence names must match exactly, "chr20" is not the same as
+    "20".  Also note that chromosome ordering in 'FILE' will be respected,
     the VCF will be processed in the order in which chromosomes first appear
     in 'FILE'. However, within chromosomes, the VCF will always be
     processed in ascending genomic coordinate order no matter what order they

From ee9905297767ba1f5ab1c8b223e5b39ed39bfdef Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 18 Apr 2016 14:23:49 +0100
Subject: [PATCH 161/211] docs: update man and html docs

---
 doc/bcftools.1    |  96 +++++++++++++++++++++++++++++++++++++------
 doc/bcftools.html | 101 ++++++++++++++++++++++++++++++++++++++--------
 2 files changed, 168 insertions(+), 29 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index d2783d499..a85c9a1b1 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2015-12-15 14:02 GMT
+.\"      Date: 2016-04-18 14:18 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2015\-12\-15 14:02 GMT" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2016\-04\-18 14:18 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2015\-12\-15 14:02 GMT\fR and refers to bcftools git version \fB1\&.2\-191\-g6737c5c+\fR\&.
+This manual page was last updated \fB2016\-04\-18 14:18 BST\fR and refers to bcftools git version \fB1\&.3\-36\-g47e811c+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -393,6 +393,11 @@ Skip sites where FILTER column does not contain any of the strings listed in
 \fI\&.,PASS\fR\&.
 .RE
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+Do not append version and command line information to the output VCF header\&.
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 When output consists of a single stream, write it to
@@ -402,7 +407,7 @@ rather than to standard output, where it is written by default\&.
 .PP
 \fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
 .RS 4
-Output compressed BCF (\fIb\fR), uncompressed BCF (\fIu\fR), compressed VCF (\fIz\fR), uncompressed VCF (\fIv\fR)\&. Use the \-Ou option when piping between bcftools subcommands to speed up performance by removing unecessary compression/decompression and VCF←→BCF conversion\&.
+Output compressed BCF (\fIb\fR), uncompressed BCF (\fIu\fR), compressed VCF (\fIz\fR), uncompressed VCF (\fIv\fR)\&. Use the \-Ou option when piping between bcftools subcommands to speed up performance by removing unnecessary compression/decompression and VCF←→BCF conversion\&.
 .RE
 .PP
 \fB\-r, \-\-regions\fR \fIchr\fR|\fIchr:pos\fR|\fIchr:from\-to\fR|\fIchr:from\-\fR[,\&...]
@@ -416,7 +421,7 @@ cannot be used in combination with
 .PP
 \fB\-R, \-\-regions\-file\fR \fIFILE\fR
 .RS 4
-Regions can be specified either on command line or in a VCF, BED, or tab\-delimited file (the default)\&. The columns of the tab\-delimited file are: CHROM, POS, and, optionally, POS_TO, where positions are 1\-based and inclusive\&. Uncompressed files are stored in memory, while bgzip\-compressed and tabix\-indexed region files are streamed\&. Note that sequence names must match exactly, "chr20" is not the same as "20"\&. Also note that chromosome ordering in
+Regions can be specified either on command line or in a VCF, BED, or tab\-delimited file (the default)\&. The columns of the tab\-delimited file are: CHROM, POS, and, optionally, POS_TO, where positions are 1\-based and inclusive\&. The columns of the tab\-delimited BED file are also CHROM, POS and POS_TO (trailing columns are ignored), but coordinates are 0\-based, half\-open\&. To indicate that a file be treated as BED rather than the 1\-based tab\-delimited file, the file must have the "\&.bed" or "\&.bed\&.gz" suffix (case\-insensitive)\&. Uncompressed files are stored in memory, while bgzip\-compressed and tabix\-indexed region files are streamed\&. Note that sequence names must match exactly, "chr20" is not the same as "20"\&. Also note that chromosome ordering in
 \fIFILE\fR
 will be respected, the VCF will be processed in the order in which chromosomes first appear in
 \fIFILE\fR\&. However, within chromosomes, the VCF will always be processed in ascending genomic coordinate order no matter what order they appear in
@@ -546,7 +551,7 @@ or
 .RE
 .SS "bcftools annotate \fI[OPTIONS]\fR \fIFILE\fR"
 .sp
-This command allows to add or remove annotations\&.
+Add or remove annotations\&.
 .PP
 \fB\-a, \-\-annotations\fR \fIfile\fR
 .RS 4
@@ -637,6 +642,12 @@ annotate sites which are present ("+") or absent ("\-") in the
 file with a new INFO/TAG flag
 .RE
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -861,6 +872,12 @@ This command replaces the former \fBbcftools view\fR caller\&. Some of the origi
 \fBFile format options:\fR
 .RS 4
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -1041,7 +1058,7 @@ calling model (conflicts with
 likelihood of novel mutation for constrained
 \fB\-C\fR
 \fItrio\fR
-calling\&. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1\-Pn)\&. By providing three values, the mutation rate Pn is set explictly for SNPs, deletions and insertions, respectively\&. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=\fIfloat\fR*exp(\-a\-b*len), where a=22\&.8689, b=0\&.2994 for insertions and a=21\&.9313, b=0\&.2856 for deletions [pubmed:23975140]\&. If only one value is given, the same mutation rate Pn is used for SNPs and indels\&.
+calling\&. The trio genotype calling maximizes likelihood of a particular combination of genotypes for father, mother and the child P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1\-Pn)\&. By providing three values, the mutation rate Pn is set explicitly for SNPs, deletions and insertions, respectively\&. If two values are given, the first is interpreted as the mutation rate of SNPs and the second is used to calculate the mutation rate of indels according to their length as Pn=\fIfloat\fR*exp(\-a\-b*len), where a=22\&.8689, b=0\&.2994 for insertions and a=21\&.9313, b=0\&.2856 for deletions [pubmed:23975140]\&. If only one value is given, the same mutation rate Pn is used for SNPs and indels\&.
 .RE
 .PP
 \fB\-p, \-\-pval\-threshold\fR \fIfloat\fR
@@ -1076,7 +1093,7 @@ haploid output for males and skips females (requires PED file with
 .RE
 .SS "bcftools concat \fI[OPTIONS]\fR \fIFILE1\fR \fIFILE2\fR [\&...]"
 .sp
-Concatenate or combine VCF/BCF files\&. All source files must have the same sample columns appearing in the same order\&. Can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one\&. The input files must be sorted by chr and position\&. The files must be given in the correct order to produce sorted VCF on output unless the \fB\-a, \-\-allow\-overlaps\fR option is specified\&.
+Concatenate or combine VCF/BCF files\&. All source files must have the same sample columns appearing in the same order\&. Can be used, for example, to concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel VCF into one\&. The input files must be sorted by chr and position\&. The files must be given in the correct order to produce sorted VCF on output unless the \fB\-a, \-\-allow\-overlaps\fR option is specified\&. With the \-\-naive option, the files are concatenated without being recompressed, which is very fast but dangerous if the BCF headers differ\&.
 .PP
 \fB\-a, \-\-allow\-overlaps\fR
 .RS 4
@@ -1110,6 +1127,17 @@ Read the list of files from a file\&.
 Ligate phased VCFs by matching phase at overlapping haplotypes
 .RE
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-n, \-\-naive\fR
+.RS 4
+Concatenate BCF files without recompression\&. This is very fast but requires that all files have the same headers\&. This is because all tags and chromosome names in the BCF body rely on the implicit order of the contig and tag definitions in the header\&. Currently no sanity checks are in place and only works for compressed BCF files\&. Dangerous, use with caution\&.
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -1273,6 +1301,12 @@ see
 \fBVCF output options:\fR
 .RS 4
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -1593,6 +1627,12 @@ is true\&. For valid expressions see
 define behaviour at sites with existing FILTER annotations\&. The default mode replaces existing filters of failed sites with a new FILTER string while leaving sites which pass untouched when non\-empty and setting to "PASS" when the FILTER string is absent\&. The "+" mode appends new FILTER strings of failed sites instead of replacing them\&. The "x" mode resets filters of sites which pass to "PASS"\&. Modes "+" and "x" can both be set\&.
 .RE
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -1641,6 +1681,12 @@ see
 see
 \fBCommon Options\fR
 .RE
+.PP
+\fB\-\-threads\fR \fIINT\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
 .SS "bcftools gtcheck [\fIOPTIONS\fR] [\-g \fIgenotypes\&.vcf\&.gz\fR] \fIquery\&.vcf\&.gz\fR"
 .sp
 Checks sample identity or, without \fB\-g\fR, multi\-sample cross\-check is performed\&.
@@ -2066,6 +2112,12 @@ The option controls what types of multiallelic records can be created:
 .RE
 .\}
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -2142,6 +2194,12 @@ split multiallelic sites into biallelic records (\fI\-\fR) or join biallelic sit
 \fIany\fR\&.
 .RE
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-N, \-\-do\-not\-normalize\fR
 .RS 4
 the
@@ -2264,6 +2322,12 @@ see
 \fBVCF output options:\fR
 .RS 4
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-o, \-\-output\fR \fIFILE\fR
 .RS 4
 see
@@ -2512,7 +2576,7 @@ const char *about(void);
 // Longer description used by \*(Aqbcftools +name \-h\*(Aq
 const char *usage(void);
 
-// Called once at startup, allows to initialize local variables\&.
+// Called once at startup, allows initialization of local variables\&.
 // Return 1 to suppress normal VCF/BCF header output, \-1 on critical
 // errors, 0 otherwise\&.
 int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);
@@ -2558,7 +2622,7 @@ see
 .PP
 \fB\-s, \-\-sample\fR \fIstring\fR
 .RS 4
-samply name
+sample name
 .RE
 .PP
 \fB\-t, \-\-targets\fR \fILIST\fR
@@ -2781,7 +2845,7 @@ see
 .PP
 \fB\-s, \-\-samples\fR \fIFILE\fR
 .RS 4
-new sample names, one name per line, in the same order as they appear in the VCF file\&. Alternatively, only samples which need to be renamed can be listed as "old_name new_name\en" pairs separated by whitespaces, each on separate line\&.
+new sample names, one name per line, in the same order as they appear in the VCF file\&. Alternatively, only samples which need to be renamed can be listed as "old_name new_name\en" pairs separated by whitespaces, each on a separate line\&. If a sample name contains spaces, the spaces can be escaped using the backslash character, for example "Not\e a\e good\e sample\e name"\&.
 .RE
 .SS "bcftools roh [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR"
 .sp
@@ -2841,7 +2905,7 @@ in case allele frequency is not known, use the
 .RS 4
 use the specified INFO tag
 \fITAG\fR
-as an allele frequency estimate instead of the defaul AC and AN tags\&. Sites which do not have
+as an allele frequency estimate instead of the default AC and AN tags\&. Sites which do not have
 \fITAG\fR
 will be skipped\&.
 .RE
@@ -3098,6 +3162,12 @@ suppress the header in VCF output
 compression level\&. 0 stands for uncompressed, 1 for best speed and 9 for best compression\&.
 .RE
 .PP
+\fB\-\-no\-version\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
 \fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
 .RS 4
 see
@@ -3180,6 +3250,8 @@ see
 .ps +1
 \fBFilter options:\fR
 .RS 4
+.sp
+Note that filter options below dealing with counting the number of alleles will, for speed, first check for the values of AC and AN in the INFO column to avoid parsing all the genotype (FORMAT/GT) fields in the VCF\&. This means that a filter like \fI\-\-min\-af 0\&.1\fR will be based \(oqAC/AN\(cq where AC and AN come from either INFO/AC and INFO/AN if available or FORMAT/GT if not\&. It will not filter on another field like INFO/AF\&. The \fI\-\-include\fR and \fI\-\-exclude\fR filter expressions should instead be used to explicitly filter based on fields in the INFO column, e\&.g\&. \fI\-\-exclude AF<0\&.1\fR\&.
 .PP
 \fB\-c, \-\-min\-ac\fR \fIINT\fR[\fI:nref\fR|\fI:alt1\fR|\fI:minor\fR|\fI:major\fR|:\*(Aqnonmajor\*(Aq]
 .RS 4
diff --git a/doc/bcftools.html b/doc/bcftools.html
index 012d67017..d089aec16 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp1931920"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25197440"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
@@ -8,7 +8,7 @@
 work in most, but not all situations. In general, whenever multiple VCFs are
 read simultaneously, they must be indexed and therefore also compressed.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2015-12-15 14:02 GMT</strong></span> and refers to bcftools git version <span class="strong"><strong>1.2-191-g6737c5c+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2016-04-18 14:18 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.3-36-g47e811c+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -117,6 +117,10 @@
     in <span class="emphasis"><em>LIST</em></span>. For example, to include only sites which have no filters set,
     use <span class="strong"><strong>-f</strong></span> <span class="emphasis"><em>.,PASS</em></span>.
 </dd><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    Do not append version and command line information to the output VCF header.
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     When output consists of a single stream, write it to <span class="emphasis"><em>FILE</em></span> rather than
@@ -126,7 +130,7 @@
 </span></dt><dd>
     Output compressed BCF (<span class="emphasis"><em>b</em></span>), uncompressed BCF (<span class="emphasis"><em>u</em></span>), compressed VCF (<span class="emphasis"><em>z</em></span>), uncompressed VCF (<span class="emphasis"><em>v</em></span>).
     Use the -Ou option when piping between bcftools subcommands to speed up
-    performance by removing unecessary compression/decompression and
+    performance by removing unnecessary compression/decompression and
     VCF←→BCF conversion.
 </dd><dt><span class="term">
 <span class="strong"><strong>-r, --regions</strong></span> <span class="emphasis"><em>chr</em></span>|<span class="emphasis"><em>chr:pos</em></span>|<span class="emphasis"><em>chr:from-to</em></span>|<span class="emphasis"><em>chr:from-</em></span>[,…]
@@ -138,11 +142,15 @@
 </span></dt><dd>
     Regions can be specified either on command line or in a VCF, BED, or
     tab-delimited file (the default).  The columns of the tab-delimited file
-    are: CHROM, POS, and,  optionally,  POS_TO,  where positions are 1-based
-    and inclusive.  Uncompressed files are stored in memory, while
-    bgzip-compressed and tabix-indexed region files are streamed.  Note that
-    sequence names must match exactly, "chr20" is not the same as "20".
-    Also note that chromosome ordering in <span class="emphasis"><em>FILE</em></span> will be respected,
+    are: CHROM, POS, and, optionally,  POS_TO,  where positions are 1-based
+    and inclusive. The columns of the tab-delimited BED file are also
+    CHROM, POS and POS_TO (trailing columns are ignored), but coordinates
+    are 0-based, half-open.  To indicate that a file be treated as BED rather
+    than the 1-based tab-delimited file, the file must have the ".bed" or
+    ".bed.gz" suffix (case-insensitive). Uncompressed files are stored in
+    memory, while bgzip-compressed and tabix-indexed region files are streamed.
+    Note that sequence names must match exactly, "chr20" is not the same as
+    "20".  Also note that chromosome ordering in <span class="emphasis"><em>FILE</em></span> will be respected,
     the VCF will be processed in the order in which chromosomes first appear
     in <span class="emphasis"><em>FILE</em></span>. However, within chromosomes, the VCF will always be
     processed in ascending genomic coordinate order no matter what order they
@@ -217,7 +225,7 @@
 </span></dt><dd>
     Number of output compression threads to use in addition to main thread.
     Only used when <span class="emphasis"><em>--output-type</em></span> is <span class="emphasis"><em>b</em></span> or <span class="emphasis"><em>z</em></span>. Default: 0.
-</dd></dl></div></div><div class="refsect2" title="bcftools annotate [OPTIONS] FILE"><a id="annotate"></a><h3>bcftools annotate <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>This command allows to add or remove annotations.</p><div class="variablelist"><dl><dt><span class="term">
+</dd></dl></div></div><div class="refsect2" title="bcftools annotate [OPTIONS] FILE"><a id="annotate"></a><h3>bcftools annotate <span class="emphasis"><em>[OPTIONS]</em></span> <span class="emphasis"><em>FILE</em></span></h3><p>Add or remove annotations.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-a, --annotations</strong></span> <span class="emphasis"><em>file</em></span>
 </span></dt><dd>
     Bgzip-compressed and tabix-indexed file with annotations. The file
@@ -288,6 +296,10 @@
 </span></dt><dd>
     annotate sites which are present ("+") or absent ("-") in the <span class="strong"><strong>-a</strong></span> file with a new INFO/TAG flag
 </dd><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -450,6 +462,10 @@
 functionality has been temporarily lost in the process of transition under
 <a class="ulink" href="http://github.com/samtools/htslib" target="_top">htslib</a>, but will be added back on popular
 demand. The original calling model can be invoked with the <span class="strong"><strong>-c</strong></span> option.</p><div class="refsect3" title="File format options:"><a id="_file_format_options"></a><h4>File format options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -566,7 +582,7 @@
     genotype calling maximizes likelihood of a particular combination of
     genotypes for father, mother and the child
     P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn).
-    By providing three values, the mutation rate Pn is set explictly for SNPs,
+    By providing three values, the mutation rate Pn is set explicitly for SNPs,
     deletions and insertions, respectively.  If two values are given, the first
     is interpreted as the mutation rate of SNPs and the second is used to
     calculate the mutation rate of indels according to their length as
@@ -598,7 +614,9 @@
 concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel
 VCF into one. The input files must be sorted by chr and position. The files
 must be given in the correct order to produce sorted VCF on output unless
-the <span class="strong"><strong>-a, --allow-overlaps</strong></span> option is specified.</p><div class="variablelist"><dl><dt><span class="term">
+the <span class="strong"><strong>-a, --allow-overlaps</strong></span> option is specified. With the --naive option, the files
+are concatenated without being recompressed, which is very fast but dangerous
+if the BCF headers differ.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-a, --allow-overlaps</strong></span>
 </span></dt><dd>
     First coordinate of the next file can precede last record of the current file.
@@ -624,6 +642,18 @@
 </span></dt><dd>
     Ligate phased VCFs by matching phase at overlapping haplotypes
 </dd><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-n, --naive</strong></span>
+</span></dt><dd>
+    Concatenate BCF files without recompression. This is very fast but requires
+    that all files have the same headers. This is because all tags and
+    chromosome names in the BCF body rely on the implicit order of the contig
+    and tag definitions in the header. Currently no sanity checks
+    are in place and only works for compressed BCF files. Dangerous, use with caution.
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -714,6 +744,10 @@
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="VCF output options:"><a id="_vcf_output_options"></a><h4>VCF output options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -907,6 +941,10 @@
     strings of failed sites instead of replacing them. The "x" mode resets
     filters of sites which pass to "PASS". Modes "+" and "x" can both be set.
 </dd><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -937,6 +975,10 @@
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd><dt><span class="term">
 <span class="strong"><strong>-T, --targets-file</strong></span> <span class="emphasis"><em>file</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect2" title="bcftools gtcheck [OPTIONS] [-g genotypes.vcf.gz] query.vcf.gz"><a id="gtcheck"></a><h3>bcftools gtcheck [<span class="emphasis"><em>OPTIONS</em></span>] [<span class="strong"><strong>-g</strong></span> <span class="emphasis"><em>genotypes.vcf.gz</em></span>] <span class="emphasis"><em>query.vcf.gz</em></span></h3><p>Checks sample identity or, without <span class="strong"><strong>-g</strong></span>, multi-sample cross-check is performed.</p><div class="variablelist"><dl><dt><span class="term">
@@ -1165,6 +1207,10 @@
 -m both   ..  both SNP and indel records can be multiallelic
 -m all    ..  SNP records can be merged with indel records
 -m id     ..  merge by ID</pre><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1223,6 +1269,10 @@
     <span class="emphasis"><em>both</em></span>; if SNPs and indels should be merged into a single record, specify
     <span class="emphasis"><em>any</em></span>.
 </dd><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-N, --do-not-normalize</strong></span><a id="do_not_normalize"></a>
 </span></dt><dd>
     the <span class="emphasis"><em>-c s</em></span> option can be used to fix or set the REF allele from the
@@ -1292,6 +1342,10 @@
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
 </dd></dl></div></div><div class="refsect3" title="VCF output options:"><a id="_vcf_output_options_2"></a><h4>VCF output options:</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1400,7 +1454,7 @@
 // Longer description used by 'bcftools +name -h'
 const char *usage(void);
 
-// Called once at startup, allows to initialize local variables.
+// Called once at startup, allows initialization of local variables.
 // Return 1 to suppress normal VCF/BCF header output, -1 on critical
 // errors, 0 otherwise.
 int init(int argc, char **argv, bcf_hdr_t *in_hdr, bcf_hdr_t *out_hdr);
@@ -1427,7 +1481,7 @@
 </dd><dt><span class="term">
 <span class="strong"><strong>-s, --sample</strong></span> <span class="emphasis"><em>string</em></span>
 </span></dt><dd>
-    samply name
+    sample name
 </dd><dt><span class="term">
 <span class="strong"><strong>-t, --targets</strong></span> <span class="emphasis"><em>LIST</em></span>
 </span></dt><dd>
@@ -1561,8 +1615,10 @@
 </span></dt><dd>
     new sample names, one name per line, in the same order as they appear
     in the VCF file. Alternatively, only samples which need to be renamed
-    can be listed as "old_name new_name\n" pairs separated by
-    whitespaces, each on separate line.
+    can be listed as "old_name new_name\n" pairs separated by whitespaces,
+    each on a separate line. If a sample name contains spaces, the
+    spaces can be escaped using the backslash character, for example
+    "Not\ a\ good\ sample\ name".
 </dd></dl></div></div><div class="refsect2" title="bcftools roh [OPTIONS] file.vcf.gz"><a id="roh"></a><h3>bcftools roh [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>A program for detecting runs of homo/autozygosity. Only bi-allelic sites
 are considered.</p><div class="refsect3" title="The HMM model:"><a id="_the_hmm_model"></a><h4>The HMM model:</h4><pre class="screen">Notation:
   D  = Data, AZ = autozygosity, HW = Hardy-Weinberg (non-autozygosity),
@@ -1590,7 +1646,7 @@
 <span class="strong"><strong>--AF-tag</strong></span> <span class="emphasis"><em>TAG</em></span>
 </span></dt><dd>
     use the specified INFO tag <span class="emphasis"><em>TAG</em></span> as an allele frequency estimate
-    instead of the defaul AC and AN tags. Sites which do not have <span class="emphasis"><em>TAG</em></span>
+    instead of the default AC and AN tags. Sites which do not have <span class="emphasis"><em>TAG</em></span>
     will be skipped.
 </dd><dt><span class="term">
 <span class="strong"><strong>--AF-file</strong></span> <span class="emphasis"><em>FILE</em></span>
@@ -1759,6 +1815,10 @@
     compression level. 0 stands for uncompressed, 1 for best speed and 9 for
     best compression.
 </dd><dt><span class="term">
+<span class="strong"><strong>--no-version</strong></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
 <span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
@@ -1803,7 +1863,14 @@
 <span class="strong"><strong>-S, --samples-file</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
-</dd></dl></div></div><div class="refsect3" title="Filter options:"><a id="_filter_options"></a><h4>Filter options:</h4><div class="variablelist"><dl><dt><span class="term">
+</dd></dl></div></div><div class="refsect3" title="Filter options:"><a id="_filter_options"></a><h4>Filter options:</h4><p>Note that filter options below dealing with counting the number of alleles
+will, for speed, first check for the values of AC and AN in the INFO column to
+avoid parsing all the genotype (FORMAT/GT) fields in the VCF. This means
+that a filter like <span class="emphasis"><em>--min-af 0.1</em></span> will be based ‘AC/AN’ where AC and AN come
+from either INFO/AC and INFO/AN if available or FORMAT/GT if not. It will not
+filter on another field like INFO/AF. The <span class="emphasis"><em>--include</em></span> and <span class="emphasis"><em>--exclude</em></span> filter
+expressions should instead be used to explicitly filter based on fields in
+the INFO column, e.g. <span class="emphasis"><em>--exclude AF&lt;0.1</em></span>.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-c, --min-ac</strong></span> <span class="emphasis"><em>INT</em></span>[<span class="emphasis"><em>:nref</em></span>|<span class="emphasis"><em>:alt1</em></span>|<span class="emphasis"><em>:minor</em></span>|<span class="emphasis"><em>:major</em></span>|:'nonmajor']
 </span></dt><dd>
     minimum allele count (INFO/AC) of sites to be printed.

From 77e76e5c378f9b299a23f22fe66be345e1790341 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 29 Apr 2016 09:00:15 +0100
Subject: [PATCH 162/211] filter: fix bug with uninitialised key

Fixes #406
---
 filter.c          | 2 +-
 test/query.24.out | 3 +++
 test/test.pl      | 1 +
 3 files changed, 5 insertions(+), 1 deletion(-)
 create mode 100644 test/query.24.out

diff --git a/filter.c b/filter.c
index c56ae6d12..4ffaec34a 100644
--- a/filter.c
+++ b/filter.c
@@ -1511,7 +1511,7 @@ filter_t *filter_init(bcf_hdr_t *hdr, const char *str)
             // Look for j="." and k numeric type
             int j = i-1, k = i-2;
             if ( !out[j].is_str ) { k = i-1, j = i-2; }
-            if ( out[k].hdr_id>0 && out[j].is_str && !strcmp(".",out[j].key) )
+            if ( out[k].hdr_id>0 && out[j].is_str && out[j].key && !strcmp(".",out[j].key) )
             {
                 int type = bcf_hdr_id2type(filter->hdr,out[k].type,out[k].hdr_id);
                 if ( type==BCF_HT_INT ) { out[j].is_str = 0; out[j].is_missing = 1; bcf_float_set_missing(out[j].values[0]); }
diff --git a/test/query.24.out b/test/query.24.out
new file mode 100644
index 000000000..0fb1c83a4
--- /dev/null
+++ b/test/query.24.out
@@ -0,0 +1,3 @@
+3000003 .
+3000004 xxx
+3000005 ..
diff --git a/test/test.pl b/test/test.pl
index a897afdb3..e7d7416c3 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -94,6 +94,7 @@
 test_vcf_query($opts,in=>'missing',out=>'query.23.out',args=>q[-i'ISTR!="."' -f'%POS %ISTR\\n']);
 test_vcf_query($opts,in=>'missing',out=>'query.23.out',args=>q[-e'ISTR="."'  -f'%POS %ISTR\\n']);
 test_vcf_query($opts,in=>'missing',out=>'query.22.out',args=>q[-e'ISTR!="."' -f'%POS %ISTR\\n']);
+test_vcf_query($opts,in=>'missing',out=>'query.24.out',args=>q[-i'FILTER="q11"' -f'%POS %ISTR\\n']);
 test_vcf_norm($opts,in=>'norm',out=>'norm.out',fai=>'norm');
 test_vcf_norm($opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.split.2',out=>'norm.split.2.out',args=>'-m-');

From 679c6e68802481bc4865e0969eef3e773a52002a Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 23 Mar 2016 07:43:10 +0000
Subject: [PATCH 163/211] norm: informative error messages on fields with wrong
 Number=R,A values

Resolves #364
---
 vcfnorm.c | 27 ++++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/vcfnorm.c b/vcfnorm.c
index 781833ceb..d3b9fee42 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -390,18 +390,24 @@ static void split_info_numeric(args_t *args, bcf1_t *src, bcf_info_t *info, int
         int len = bcf_hdr_id2length(args->hdr,BCF_HL_INFO,info->key); \
         if ( len==BCF_VL_A ) \
         { \
-            assert( ret==src->n_allele-1); \
+            if ( ret!=src->n_allele-1 ) \
+                error("Error: wrong number of fields in INFO/%s at %s:%d, expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),src->pos+1,src->n_allele-1,ret); \
             bcf_update_info_##type(args->hdr,dst,tag,vals+ialt,1); \
         } \
         else if ( len==BCF_VL_R ) \
         { \
-            assert( ret==src->n_allele); \
+            if ( ret!=src->n_allele ) \
+                error("Error: wrong number of fields in INFO/%s at %s:%d, expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),src->pos+1,src->n_allele,ret); \
             if ( ialt!=0 ) vals[1] = vals[ialt+1]; \
             bcf_update_info_##type(args->hdr,dst,tag,vals,2); \
         } \
         else if ( len==BCF_VL_G ) \
         { \
-            assert( ret==src->n_allele*(src->n_allele+1)/2 ); \
+            if ( ret!=src->n_allele*(src->n_allele+1)/2 ) \
+                error("Error: wrong number of fields in INFO/%s at %s:%d, expected %d, found %d\n", \
+                        tag,bcf_seqname(args->hdr,src),src->pos+1,src->n_allele*(src->n_allele+1)/2,ret); \
             if ( ialt!=0 ) \
             { \
                 vals[1] = vals[bcf_alleles2gt(0,ialt+1)]; \
@@ -545,7 +551,9 @@ static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int
         } \
         if ( len==BCF_VL_A ) \
         { \
-            assert( nvals==(src->n_allele-1)*nsmpl); \
+            if ( nvals!=(src->n_allele-1)*nsmpl ) \
+                error("Error: wrong number of fields in FMT/%s at %s:%d, expected %d, found %d\n", \
+                    tag,bcf_seqname(args->hdr,src),src->pos+1,(src->n_allele-1)*nsmpl,nvals); \
             nvals /= nsmpl; \
             type_t *src_vals = vals, *dst_vals = vals; \
             for (i=0; i<nsmpl; i++) \
@@ -558,7 +566,9 @@ static void split_format_numeric(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int
         } \
         else if ( len==BCF_VL_R ) \
         { \
-            assert( nvals==src->n_allele*nsmpl); \
+            if ( nvals!=src->n_allele*nsmpl ) \
+                error("Error: wrong number of fields in FMT/%s at %s:%d, expected %d, found %d\n", \
+                    tag,bcf_seqname(args->hdr,src),src->pos+1,src->n_allele*nsmpl,nvals); \
             nvals /= nsmpl; \
             type_t *src_vals = vals, *dst_vals = vals; \
             for (i=0; i<nsmpl; i++) \
@@ -682,7 +692,10 @@ static void split_format_string(args_t *args, bcf1_t *src, bcf_fmt_t *fmt, int i
                 if ( *se==',' ) nfields++;
                 se++;
             }
-            assert( nfields==src->n_allele*(src->n_allele+1)/2 || nfields==src->n_allele );
+            if ( nfields!=src->n_allele*(src->n_allele+1)/2 && nfields!=src->n_allele )
+                error("Error: wrong number of fields in FMT/%s at %s:%d, expected %d or %d, found %d\n",
+                        tag,bcf_seqname(args->hdr,src),src->pos+1,src->n_allele*(src->n_allele+1)/2,src->n_allele,nfields);
+
             int len = 0;
             if ( nfields==src->n_allele )   // haploid
             {
@@ -994,7 +1007,7 @@ static void merge_format_genotype(args_t *args, bcf1_t **lines, int nlines, bcf_
                 else
                 {
                     int ial = bcf_gt_allele(gt2[k]);
-                    assert( ial<args->maps[i].nals );
+                    if ( ial>=args->maps[i].nals ) error("Error at %s:%d: incorrect allele index %d\n",bcf_seqname(args->hdr,lines[i]),lines[i]->pos+1,ial);
                     gt[k] = bcf_gt_unphased( args->maps[i].map[ial] ) | bcf_gt_is_phased(gt[k]);
                 }
             }

From 8eb3804ac9c133b0dbe5abea960fa6cd4eb0dda0 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 25 Mar 2016 13:02:52 +0000
Subject: [PATCH 164/211] concat: `--naive` option now works for both bcf and
 vcf.gz

---
 test/test.pl | 71 +++++++++++++++++++++++++++++++++++++++----
 vcfconcat.c  | 86 +++++++++++++++++++++++++++++++++++++++++++---------
 2 files changed, 136 insertions(+), 21 deletions(-)

diff --git a/test/test.pl b/test/test.pl
index e7d7416c3..dc1fcfa84 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -206,6 +206,7 @@
 test_vcf_concat($opts,in=>['concat.2.a','concat.2.b'],out=>'concat.4.bcf.out',do_bcf=>1,args=>'-aD');
 test_vcf_concat($opts,in=>['concat.3.a','concat.3.b','concat.3.0','concat.3.c','concat.3.d','concat.3.e','concat.3.f'],out=>'concat.3.vcf.out',do_bcf=>0,args=>'-l');
 test_vcf_concat($opts,in=>['concat.3.a','concat.3.b','concat.3.0','concat.3.c','concat.3.d','concat.3.e','concat.3.f'],out=>'concat.3.bcf.out',do_bcf=>1,args=>'-l');
+test_naive_concat($opts,name=>'naive_concat',max_hdr_lines=>10000,max_body_lines=>10000,nfiles=>10);
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.1.out',header=>'reheader.hdr');
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.2.out',samples=>'reheader.samples');
 test_vcf_reheader($opts,in=>'reheader',out=>'reheader.2.out',samples=>'reheader.samples2');
@@ -319,7 +320,7 @@ sub cmd
 sub test_cmd
 {
     my ($opts,%args) = @_;
-    if ( !exists($args{out}) )
+    if ( !exists($args{out}) && !exists($args{exp}) )
     {
         if ( !exists($args{in}) ) { error("FIXME: expected out or in key\n"); }
         $args{out} = "$args{in}.out";
@@ -348,13 +349,17 @@ sub test_cmd
         }
     }
     my $exp = '';
-    if ( open(my $fh,'<',"$$opts{path}/$args{out}") )
+    if ( exists($args{exp}) ) { $exp = $args{exp}; }
+    else
     {
-        my @exp = <$fh>;
-        $exp = join('',@exp);
-        close($fh);
+        if ( open(my $fh,'<',"$$opts{path}/$args{out}") )
+        {
+            my @exp = <$fh>;
+            $exp = join('',@exp);
+            close($fh);
+        }
+        elsif ( !$$opts{redo_outputs} ) { failed($opts,$test,"$$opts{path}/$args{out}: $!"); return; }
     }
-    elsif ( !$$opts{redo_outputs} ) { failed($opts,$test,"$$opts{path}/$args{out}: $!"); return; }
 
     if ( $exp ne $out )
     {
@@ -855,3 +860,57 @@ sub test_vcf_consensus_chain
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools consensus $$opts{tmp}/$args{in}.vcf.gz -f $$opts{path}/$args{fa} $args{args} $mask $chain > /dev/null 2>/dev/null; cat $$opts{tmp}/$args{chain}.new");
 }
 
+sub test_naive_concat
+{
+    my ($opts,%args) = @_;
+
+    my $seed = srand();
+    print STDERR "Random seed for test_naive_concat: $seed\n";
+
+    my @files = ();
+    my $exp   = '';
+    for (my $n=0; $n<$args{nfiles}; $n++)
+    {
+        my $nhdr = 1 + int(rand($args{max_hdr_lines}));
+        my $nbdy = int(rand($args{max_body_lines}));
+        my $file = "$$opts{tmp}/$args{name}.$n";
+        push @files,$file;
+
+        open(my $fh,'>',"$file.vcf") or error("$file.vcf: $!");
+        print $fh "##fileformat=VCFv4.0\n";
+        print $fh "##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Read Depth\">\n";
+        print $fh "##contig=<ID=1,length=62435964>\n";
+        for (my $i=0; $i<$nhdr; $i++)
+        {
+            my $x = rand;
+            print $fh "##INFO=<ID=XX$i,Number=1,Type=Integer,Description=\"Test Tag $x\">\n";
+        }
+        print $fh join("\t",'#CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO')."\n";
+
+        # let one of the files have no body
+        if ( $n!=3 )
+        {
+            for (my $i=1; $i<=$nbdy; $i++)
+            {
+                my $x = int(rand(1000));
+                my $line = join("\t",'1',$i,'.','A','C','.','.',"DP=$x")."\n";
+                print $fh  $line;
+                $exp .= $line;
+            }
+        }
+        close($fh) or error("close failed: $file.vcf");
+    }
+
+    for my $file (@files)
+    {
+        cmd("$$opts{bin}/bcftools view -Ob -o $file.bcf $file.vcf"); 
+        cmd("$$opts{bin}/bcftools view -Oz -o $file.vcf.gz $file.vcf"); 
+    }
+
+    my $bcfs = join('.bcf ',@files).'.bcf';
+    test_cmd($opts,exp=>$exp,cmd=>"$$opts{bin}/bcftools concat --naive $bcfs | $$opts{bin}/bcftools view -H");
+
+    my $vcfs = join('.vcf.gz ',@files).'.vcf.gz';
+    test_cmd($opts,exp=>$exp,cmd=>"$$opts{bin}/bcftools concat --naive $vcfs | $$opts{bin}/bcftools view -H");
+}
+
diff --git a/vcfconcat.c b/vcfconcat.c
index bd6a00a25..e5b1699ed 100644
--- a/vcfconcat.c
+++ b/vcfconcat.c
@@ -555,6 +555,50 @@ static void concat(args_t *args)
     }
 }
 
+int print_vcf_gz_header(BGZF *fp, BGZF *bgzf_out, int print_header, kstring_t *tmp)
+{
+    char *buffer = (char*) fp->uncompressed_block;
+
+    // Read the header and find the position of the data block
+    if ( buffer[0]!='#' ) error("Could not parse the header, expected '#', found '%c'\n", buffer[0]);
+
+    int nskip = 1;     // end of the header in the current uncompressed block
+    while (1)
+    {
+        if ( buffer[nskip]=='\n' )
+        {
+            nskip++;
+            if ( nskip>=fp->block_length )
+            {
+                kputsn(buffer,nskip,tmp);
+                if ( bgzf_read_block(fp) != 0 ) return -1;
+                if ( !fp->block_length ) break;
+                nskip = 0;
+            }
+            // The header has finished
+            if ( buffer[nskip]!='#' )
+            {
+                kputsn(buffer,nskip,tmp);
+                break;
+            }
+        }
+        nskip++;
+        if ( nskip>=fp->block_length )
+        {
+            kputsn(buffer,fp->block_length,tmp);
+            if ( bgzf_read_block(fp) != 0 ) return -1;
+            if ( !fp->block_length ) break;
+            nskip = 0;
+        }
+    }
+    if ( print_header )
+    {
+        if ( bgzf_write(bgzf_out,tmp->s,tmp->l) != tmp->l ) error("Failed to write %d bytes\n", tmp->l);
+        tmp->l = 0;
+    }
+    return nskip;
+}
+
 static void naive_concat(args_t *args)
 {
     // only compressed BCF atm
@@ -563,38 +607,50 @@ static void naive_concat(args_t *args)
     const size_t page_size = 32768;
     char *buf = (char*) malloc(page_size);
     kstring_t tmp = {0,0,0};
-    int i;
+    int i, file_types = 0;
     for (i=0; i<args->nfnames; i++)
     {
         htsFile *hts_fp = hts_open(args->fnames[i],"r");
         if ( !hts_fp ) error("Failed to open: %s\n", args->fnames[i]);
         htsFormat type = *hts_get_format(hts_fp);
 
-        if ( type.format==vcf ) error("The --naive option currently works only for compressed BCFs, sorry :-/\n");
-        if ( type.compression!=bgzf ) error("The --naive option currently works only for compressed BCFs, sorry :-/\n");
+        if ( type.compression!=bgzf )
+            error("The --naive option works only for compressed BCFs or VCFs, sorry :-/\n");
+        file_types |= type.format==vcf ? 1 : 2;
+        if ( file_types==3 )
+            error("The --naive option works only for compressed files of the same type, all BCFs or all VCFs :-/\n");
 
         BGZF *fp = hts_get_bgzfp(hts_fp);
         if ( !fp || bgzf_read_block(fp) != 0 || !fp->block_length )
             error("Failed to read %s: %s\n", args->fnames[i], strerror(errno));
 
-        uint8_t magic[5];
-        if ( bgzf_read(fp, magic, 5) != 5 ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
-        if (strncmp((char*)magic, "BCF\2\2", 5) != 0) error("Invalid BCF magic string in %s\n", args->fnames[i]);
+        int nskip;
+        if ( type.format==bcf )
+        {
+            uint8_t magic[5];
+            if ( bgzf_read(fp, magic, 5) != 5 ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
+            if (strncmp((char*)magic, "BCF\2\2", 5) != 0) error("Invalid BCF magic string in %s\n", args->fnames[i]);
 
-        if ( bgzf_read(fp, &tmp.l, 4) != 4 ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
-        hts_expand(char,tmp.l,tmp.m,tmp.s);
-        if ( bgzf_read(fp, tmp.s, tmp.l) != tmp.l ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
+            if ( bgzf_read(fp, &tmp.l, 4) != 4 ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
+            hts_expand(char,tmp.l,tmp.m,tmp.s);
+            if ( bgzf_read(fp, tmp.s, tmp.l) != tmp.l ) error("Failed to read the BCF header in %s\n", args->fnames[i]);
 
-        // write only the first header
-        if ( i==0 )
+            // write only the first header
+            if ( i==0 )
+            {
+                if ( bgzf_write(bgzf_out, "BCF\2\2", 5) !=5 ) error("Failed to write %d bytes to %s\n", 5,args->output_fname);
+                if ( bgzf_write(bgzf_out, &tmp.l, 4) !=4 ) error("Failed to write %d bytes to %s\n", 4,args->output_fname);
+                if ( bgzf_write(bgzf_out, tmp.s, tmp.l) != tmp.l) error("Failed to write %d bytes to %s\n", tmp.l,args->output_fname);
+            }
+            nskip = fp->block_offset;
+        }
+        else
         {
-            if ( bgzf_write(bgzf_out, "BCF\2\2", 5) !=5 ) error("Failed to write %d bytes to %s\n", 5,args->output_fname);
-            if ( bgzf_write(bgzf_out, &tmp.l, 4) !=4 ) error("Failed to write %d bytes to %s\n", 4,args->output_fname);
-            if ( bgzf_write(bgzf_out, tmp.s, tmp.l) != tmp.l) error("Failed to write %d bytes to %s\n", tmp.l,args->output_fname);
+            nskip = print_vcf_gz_header(fp, bgzf_out, i==0?1:0, &tmp);
+            if ( nskip==-1 ) error("Error reading %s\n", args->fnames[i]);
         }
 
         // Output all non-header data that were read together with the header block
-        int nskip = fp->block_offset;
         if ( fp->block_length - nskip > 0 )
         {
             if ( bgzf_write(bgzf_out, fp->uncompressed_block+nskip, fp->block_length-nskip)<0 ) error("Error: %d\n",fp->errcode);

From e3ef8dabc4450cd7adbaaafb86840ebbf109ab98 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 13 Apr 2016 13:12:12 +0100
Subject: [PATCH 165/211] reheader: allow multispace delimiters in `reheader
 -s` files

---
 reheader.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/reheader.c b/reheader.c
index 0466c16ca..69018cd5a 100644
--- a/reheader.c
+++ b/reheader.c
@@ -89,7 +89,7 @@ static int set_sample_pairs(char **samples, int nsamples, kstring_t *hdr, int id
             ptr++;
         }
         if ( !*ptr ) break;
-        ptr++;
+        while ( *ptr && isspace(*ptr) ) ptr++;
         while ( *ptr )
         {
             if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }

From 0c88e1ad361730f235bcb639a05dcb0f1170836d Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Tue, 2 Feb 2016 14:51:59 +0000
Subject: [PATCH 166/211] mcall: trim all `Number=R` tags

* remove QS before (unnecessary) trimming so that
  `mcall_trim_numberR()` works with `call-c`
---
 mcall.c | 95 ++++++++++++++++++++++++++++-----------------------------
 1 file changed, 47 insertions(+), 48 deletions(-)

diff --git a/mcall.c b/mcall.c
index 495f849a8..9ace3ed5b 100644
--- a/mcall.c
+++ b/mcall.c
@@ -1,6 +1,6 @@
 /*  mcall.c -- multiallelic and rare variant calling.
 
-    Copyright (C) 2012-2014 Genome Research Ltd.
+    Copyright (C) 2012-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -1184,75 +1184,73 @@ static void mcall_trim_PLs(call_t *call, bcf1_t *rec, int nals, int nout_als, in
 
 void mcall_trim_numberR(call_t *call, bcf1_t *rec, int nals, int nout_als, int out_als)
 {
-    int i, ret;
+    if ( nals==nout_als ) return;
 
-    // at the moment we have DPR,AD,ADF,ADR all Number=R,Type=Integer,
-    // so only dealing with these cases at the moment
+    int i,j, nret, size = sizeof(float);
+
+    void *tmp_ori = call->itmp, *tmp_new = call->PLs;  // reusing PLs storage which is not used at this point
+    int ntmp_ori = call->n_itmp, ntmp_new = call->mPLs;
+
+    // INFO fields
     for (i=0; i<rec->n_info; i++)
     {
         bcf_info_t *info = &rec->d.info[i];
         int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_INFO,info->key);
-        if ( vlen!=BCF_VL_R ) continue;
-        int type = bcf_hdr_id2type(call->hdr,BCF_HL_INFO,info->key);
-        if ( type!=BCF_HT_INT ) continue;
+        if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag
+
+        int type  = bcf_hdr_id2type(call->hdr,BCF_HL_INFO,info->key);
+        const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key);
+        nret = bcf_get_info_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type);
+        if ( nret<=0 ) continue;
 
-        ret = bcf_get_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), &call->itmp, &call->n_itmp);
-        if ( ret>0 )
+        if ( nout_als==1 )
+            bcf_update_info_int32(call->hdr, rec, key, tmp_ori, 1);     // has to be the REF, the order could not change
+        else
         {
-            assert( ret==nals );
-            if ( out_als==1 )
-                bcf_update_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), call->itmp, 1);
-            else
+            for (j=0; j<nals; j++)
             {
-                int j;
-                for (j=0; j<nals; j++)
-                {
-                    if ( call->als_map[j]==-1 ) continue;   // to be dropped
-                    call->PLs[ call->als_map[j] ] = call->itmp[j]; // reusing PLs storage which is not used at this point
-                }
-                bcf_update_info_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,info->key), call->PLs, nout_als);
+                int k = call->als_map[j];
+                if ( k==-1 ) continue;   // to be dropped
+                memcpy(tmp_new+size*k, tmp_ori+size*j, size);
             }
+            bcf_update_info_int32(call->hdr, rec, key, tmp_new, nout_als);
         }
     }
 
+    // FORMAT fields
     for (i=0; i<rec->n_fmt; i++)
     {
         bcf_fmt_t *fmt = &rec->d.fmt[i];
         int vlen = bcf_hdr_id2length(call->hdr,BCF_HL_FMT,fmt->id);
-        if ( vlen!=BCF_VL_R ) continue;
+        if ( vlen!=BCF_VL_R ) continue; // not a Number=R tag
+
         int type = bcf_hdr_id2type(call->hdr,BCF_HL_FMT,fmt->id);
-        if ( type!=BCF_HT_INT ) continue;
+        const char *key = bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id);
+        nret = bcf_get_format_values(call->hdr, rec, key, &tmp_ori, &ntmp_ori, type);
+        if (nret<=0) continue;
+        int nsmpl = bcf_hdr_nsamples(call->hdr);
 
-        ret = bcf_get_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), &call->itmp, &call->n_itmp);
-        if ( ret>0 )
-        {
-            int j, nsmpl = bcf_hdr_nsamples(call->hdr);
-            int ndp = ret / nsmpl;
-            assert( ndp==nals );
-            if ( out_als==1 )
-            {
-                for (j=0; j<nsmpl; j++)
-                    call->PLs[j] = call->itmp[j*ndp];
+        assert( nret==nals*nsmpl );
 
-                bcf_update_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), call->PLs, nsmpl);
-            }
-            else
+        for (j=0; j<nsmpl; j++)
+        {
+            void *ptr_src = tmp_ori + j*nals*size;
+            void *ptr_dst = tmp_new + j*nout_als*size;
+            int k;
+            for (k=0; k<nals; k++)
             {
-                int k;
-                for (j=0; j<nsmpl; j++)
-                {
-                    int32_t *dp_dst = call->PLs + j*nout_als;
-                    int32_t *dp_src = call->itmp + j*ndp;
-                    for (k=0; k<nals; k++)
-                    {
-                        if ( call->als_map[k]==-1 ) continue;   // to be dropped
-                        dp_dst[ call->als_map[k] ] = dp_src[k]; // reusing PLs storage which is not used at this point
-                    }
-                }
-                bcf_update_format_int32(call->hdr, rec, bcf_hdr_int2id(call->hdr,BCF_DT_ID,fmt->id), call->PLs, nsmpl*nout_als);
+                int l = call->als_map[k];
+                if ( l==-1 ) continue;   // to be dropped
+                memcpy(ptr_dst+size*l, ptr_src+size*k, size);
             }
         }
+        bcf_update_format_int32(call->hdr, rec, key, tmp_new, nout_als*nsmpl);
     }
+
+    call->PLs    = (int32_t*) tmp_new;
+    call->mPLs   = ntmp_new;
+    call->itmp   = (int32_t*) tmp_ori;
+    call->n_itmp = ntmp_ori;
 }
 
 
@@ -1423,6 +1421,8 @@ int mcall(call_t *call, bcf1_t *rec)
         if ( qsum_tot ) for (i=0; i<nals; i++) call->qsum[i] /= qsum_tot;
     #endif
 
+    bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0);      // remove QS tag
+
     // Find the best combination of alleles
     int out_als, nout;
     if ( nals > 8*sizeof(out_als) )
@@ -1530,7 +1530,6 @@ int mcall(call_t *call, bcf1_t *rec)
     }
 
     bcf_update_info_int32(call->hdr, rec, "I16", NULL, 0);     // remove I16 tag
-    bcf_update_info_int32(call->hdr, rec, "QS", NULL, 0);      // remove QS tag
 
     return nout;
 }

From 0a5e8f8b6936f5ff93b042eaff269e0e45b20311 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 25 Apr 2016 08:45:37 +0100
Subject: [PATCH 167/211] call: new `-F, --prior-freqs` option

---
 call.h           |  1 +
 doc/bcftools.txt | 20 ++++++++++++++++++++
 mcall.c          | 33 ++++++++++++++++++++++++++++++++-
 vcfcall.c        | 11 ++++++++++-
 4 files changed, 63 insertions(+), 2 deletions(-)

diff --git a/call.h b/call.h
index bbf0a52b4..9254bf67b 100644
--- a/call.h
+++ b/call.h
@@ -72,6 +72,7 @@ typedef struct
     double trio_Pm_SNPs, trio_Pm_del, trio_Pm_ins;      // P(mendelian) for trio calling, see mcall_call_trio_genotypes()
     int32_t *ugts, *cgts;   // unconstraind and constrained GTs
     uint32_t output_tags;
+    char *prior_AN, *prior_AC;  // reference panel AF tags (AF=AC/AN)
 
     // ccall only
     double indel_frac, min_perm_p, min_lrt;
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index c91bb9c2b..4d1b522a4 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -571,6 +571,26 @@ demand. The original calling model can be invoked with the *-c* option.
     GQ and GP fields are supported. For convenience, the fields can be given
     as lower case letters.
 
+*-F, --prior-freqs* 'AN','AC'::
+    take advantage of prior knowledge of population allele frequencies. The
+    workflow looks like this:
+----
+    # Extract AN,AC values from an existing VCF, such 1000Genomes
+    bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' 1000Genomes.bcf | bgzip -c > AFs.tab.gz
+
+    # If the tags AN,AC are not already present, use the +fill-AN-AC plugin
+    bcftools +fill-AN-AC 1000Genomes.bcf | bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' | bgzip -c > AFs.tab.gz
+    tabix -s1 -b2 -e2 AFs.tab.gz
+
+    # Create a VCF header description, here we name the tags REF_AN,REF_AC
+    cat AFs.hdr
+    ##INFO=<ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes">
+    ##INFO=<ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele">
+
+    # Now before calling, stream the raw mpileup output through `bcftools annotate` to add the frequencies
+    bcftools mpileup [...] -Ou | bcftools annotate -a AFs.tab.gz -h AFs.hdr -c CHROM,POS,REF,ALT,REF_AN,REF_AC -Ou | bcftools call -mv -F REF_AN,REF_AC [...]
+----
+
 *-g, --gvcf* 'INT'::
     output also gVCF blocks of homozygous REF calls. The parameter 'INT' is the
     minimum per-sample depth required to include a site in the non-variant
diff --git a/mcall.c b/mcall.c
index 9ace3ed5b..a9ffe1e8e 100644
--- a/mcall.c
+++ b/mcall.c
@@ -107,6 +107,16 @@ int calc_Pkij(int fals, int mals, int kals, int fpl, int mpl, int kpl)
 //
 static void mcall_init_trios(call_t *call)
 {
+    if ( call->prior_AN )
+    {
+        int id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AN);
+        if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AN);
+        if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) )  error("No such FORMAT tag \"%s\"\n", call->prior_AN);
+        id = bcf_hdr_id2int(call->hdr,BCF_DT_ID,call->prior_AC);
+        if ( id==-1 ) error("No such tag \"%s\"\n", call->prior_AC);
+        if ( !bcf_hdr_idinfo_exists(call->hdr,BCF_HL_FMT,id) )  error("No such FORMAT tag \"%s\"\n", call->prior_AC);
+    }
+
     // 23, 138, 478 possible diploid trio genotypes with 2, 3, 4 alleles
     call->ntrio[FTYPE_222][2] = 15; call->ntrio[FTYPE_222][3] = 78;  call->ntrio[FTYPE_222][4] = 250;
     call->ntrio[FTYPE_121][2] = 8;  call->ntrio[FTYPE_121][3] = 27;  call->ntrio[FTYPE_121][4] = 64;
@@ -1393,7 +1403,7 @@ int mcall(call_t *call, bcf1_t *rec)
     #if QS_FROM_PDG
         estimate_qsum(call, rec);
     #else
-        // Get sum of qualities
+        // Get sum of qualities, serves as an AF estimate, f_x = QS/N in Eq. 1 in call-m math notes.
         int nqs = bcf_get_info_float(call->hdr, rec, "QS", &call->qsum, &call->nqsum);
         if ( nqs<=0 ) error("The QS annotation not present at %s:%d\n", bcf_seqname(call->hdr,rec),rec->pos+1);
         if ( nqs < nals )
@@ -1404,6 +1414,27 @@ int mcall(call_t *call, bcf1_t *rec)
             hts_expand(float,nals,call->nqsum,call->qsum);
             for (i=nqs; i<nals; i++) call->qsum[i] = 0;
         }
+
+        // If available, take into account reference panel AFs
+        if ( call->prior_AN && bcf_get_info_int32(call->hdr, rec, call->prior_AN ,&call->ac, &call->nac)==1 )
+        {
+            int an = call->ac[0];
+            if ( bcf_get_info_int32(call->hdr, rec, call->prior_AC ,&call->ac, &call->nac)==nals-1 )
+            {
+                int ac0 = an;   // number of alleles in the reference population
+                for (i=0; i<nals-1; i++)
+                {
+                    if ( call->ac[i]==bcf_int32_vector_end ) break;
+                    if ( call->ac[i]==bcf_int32_missing ) continue;
+                    ac0 -= call->ac[i];
+                    call->qsum[i+1] += call->ac[i]*0.5;
+                }
+                if ( ac0<0 ) error("Incorrect %s,%s values at %s:%d\n", call->prior_AN,call->prior_AC,bcf_seqname(call->hdr,rec),rec->pos+1);
+                call->qsum[0] += ac0*0.5;
+                for (i=0; i<nals; i++) call->qsum[i] /= nsmpl + 0.5*an;
+            }
+        }
+
         float qsum_tot = 0;
         for (i=0; i<nals; i++) qsum_tot += call->qsum[i];
         if ( !call->qsum[0] )
diff --git a/vcfcall.c b/vcfcall.c
index e5bbf1167..767099216 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -618,6 +618,7 @@ static void usage(args_t *args)
     fprintf(stderr, "Input/output options:\n");
     fprintf(stderr, "   -A, --keep-alts                 keep all possible alternate alleles at variant sites\n");
     fprintf(stderr, "   -f, --format-fields <list>      output format fields: GQ,GP (lowercase allowed) []\n");
+    fprintf(stderr, "   -F, --prior-freqs <AN,AC>       use prior allele frequencies\n");
     fprintf(stderr, "   -g, --gvcf <int>,[...]          group non-variant sites into gVCF blocks by minimum per-sample DP\n");
     fprintf(stderr, "   -i, --insert-missed             output also sites missed by mpileup but present in -T\n");
     fprintf(stderr, "   -M, --keep-masked-ref           keep sites with masked reference allele (REF=N)\n");
@@ -667,6 +668,7 @@ int main_vcfcall(int argc, char *argv[])
     {
         {"help",no_argument,NULL,'h'},
         {"format-fields",required_argument,NULL,'f'},
+        {"prior-freqs",required_argument,NULL,'F'},
         {"gvcf",required_argument,NULL,'g'},
         {"output",required_argument,NULL,'o'},
         {"output-type",required_argument,NULL,'O'},
@@ -698,7 +700,7 @@ int main_vcfcall(int argc, char *argv[])
     };
 
     char *tmp = NULL;
-    while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:n:P:f:ig:XY", loptions, NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "h?o:O:r:R:s:S:t:T:ANMV:vcmp:C:n:P:f:ig:XYF:", loptions, NULL)) >= 0)
     {
         switch (c)
         {
@@ -713,6 +715,13 @@ int main_vcfcall(int argc, char *argv[])
             case 'c': args.flag |= CF_CCALL; break;          // the original EM based calling method
             case 'i': args.flag |= CF_INS_MISSED; break;
             case 'v': args.aux.flag |= CALL_VARONLY; break;
+            case 'F': 
+                args.aux.prior_AN = optarg;
+                args.aux.prior_AC = index(optarg,',');
+                if ( !args.aux.prior_AC ) error("Expected two tags with -F (e.g. AN,AC), got \"%s\"\n",optarg);
+                *args.aux.prior_AC = 0;
+                args.aux.prior_AC++;
+                break;
             case 'g': 
                 args.gvcf = gvcf_init(optarg);
                 if ( !args.gvcf ) error("Could not parse: --gvcf %s\n", optarg);

From 4b16ea3888807a33b0b459ed240aca22975e0fad Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 3 May 2016 09:58:37 +0100
Subject: [PATCH 168/211] docs: fix up alphabetic order of commands in docs
 cnv>call

---
 doc/bcftools.txt | 169 ++++++++++++++++++++++++-----------------------
 1 file changed, 85 insertions(+), 84 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 4d1b522a4..a54d6ff8b 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -412,90 +412,6 @@ Add or remove annotations.
     bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf
 ----
 
-[[cnv]]
-=== bcftools cnv '[OPTIONS]' 'FILE'
-
-Copy number variation caller, requires a VCF annotated with the Illumina's
-B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
-considers the following copy number states: CN 2 (normal), 1 (single-copy
-loss), 0 (complete loss), 3 (single-copy gain).
-
-
-==== General Options:
-
-*-c, --control-sample* 'string'::
-    optional control sample name. If given, pairwise calling is performed
-    and the *-P*  option can be used
-
-*-f, --AF-file* 'file'::
-    read allele frequencies from  a tab-delimited file with the columns CHR,POS,REF,ALT,AF
-
-*-o, --output-dir 'path'::
-    output directory 
-
-*-p, --plot-threshold 'float'::
-    call *matplotlib* to produce plots for chromosomes with quality at least 'float',
-    useful for visual inspection of the calls. With *-p 0*, plots for all chromosomes will be 
-    generated. If not given, a *matplotlib* script will be created but not called.
-
-*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
-    see *<<common_options,Common Options>>*
-
-*-R, --regions-file* 'file'::
-    see *<<common_options,Common Options>>*
-
-*-s, --query-sample* 'string'::
-    query samply name
-
-*-t, --targets* 'LIST'::
-    see *<<common_options,Common Options>>*
-
-*-T, --targets-file* 'FILE'::
-    see *<<common_options,Common Options>>*
-
-==== HMM Options:
-
-*-a, --aberrant* 'float'[,'float']::
-    fraction of aberrant cells in query and control. The hallmark of
-    duplications and contaminations is the BAF value of heterozygous markers
-    which is dependent on the fraction of aberrant cells. Sensitivity to
-    smaller fractions of cells can be increased by setting *-a* to a lower value. Note
-    however, that this comes at the cost of increased false discovery rate.
-
-*-b, --BAF-weight* 'float'::
-    relative contribution from BAF
-
-*d, --BAF-dev* 'float'[,'float']::
-    expected BAF deviation in query and control, i.e. the noise observed
-    in the data.
-
-*-e, --err-prob* 'float'::
-    uniform error probability
-
-*-l, --LRR-weight* 'float'::
-    relative contribution from LRR. With noisy data, this option can have big effect
-    on the number of calls produced. In truly random noise (such as in simulated data),
-    the value should be set high (1.0), but in the presence of systematic noise
-    when LRR are not informative, lower values result in cleaner calls (0.2).
-
-*-L, --LRR-smooth-win* 'int'::
-    reduce LRR noise by applying moving average given this window size
-
-*-O, --optimize* 'float'::
-    iteratively estimate the fraction of aberrant cells, down to the given fraction.
-    Lowering this value from the default 1.0 to say, 0.3, can help discover more
-    events but also increases noise
-
-*-P, --same-prob* 'float'::
-    the prior probability of the query and the control sample being the same.
-    Setting to 0 calls both independently, setting to 1 forces the same copy
-    number state in both.
-
-*-x, --xy-prob* 'float'::
-    the HMM probability of transition to another copy number state. Increasing this
-    values leads to smaller and more frequent calls.
-
-
 
 
 [[call]]
@@ -655,6 +571,91 @@ demand. The original calling model can be invoked with the *-c* option.
     haploid output for males and skips females (requires PED file with *-s*)
 
 
+[[cnv]]
+=== bcftools cnv '[OPTIONS]' 'FILE'
+
+Copy number variation caller, requires a VCF annotated with the Illumina's
+B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
+considers the following copy number states: CN 2 (normal), 1 (single-copy
+loss), 0 (complete loss), 3 (single-copy gain).
+
+
+==== General Options:
+
+*-c, --control-sample* 'string'::
+    optional control sample name. If given, pairwise calling is performed
+    and the *-P*  option can be used
+
+*-f, --AF-file* 'file'::
+    read allele frequencies from  a tab-delimited file with the columns CHR,POS,REF,ALT,AF
+
+*-o, --output-dir 'path'::
+    output directory 
+
+*-p, --plot-threshold 'float'::
+    call *matplotlib* to produce plots for chromosomes with quality at least 'float',
+    useful for visual inspection of the calls. With *-p 0*, plots for all chromosomes will be 
+    generated. If not given, a *matplotlib* script will be created but not called.
+
+*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
+    see *<<common_options,Common Options>>*
+
+*-R, --regions-file* 'file'::
+    see *<<common_options,Common Options>>*
+
+*-s, --query-sample* 'string'::
+    query samply name
+
+*-t, --targets* 'LIST'::
+    see *<<common_options,Common Options>>*
+
+*-T, --targets-file* 'FILE'::
+    see *<<common_options,Common Options>>*
+
+==== HMM Options:
+
+*-a, --aberrant* 'float'[,'float']::
+    fraction of aberrant cells in query and control. The hallmark of
+    duplications and contaminations is the BAF value of heterozygous markers
+    which is dependent on the fraction of aberrant cells. Sensitivity to
+    smaller fractions of cells can be increased by setting *-a* to a lower value. Note
+    however, that this comes at the cost of increased false discovery rate.
+
+*-b, --BAF-weight* 'float'::
+    relative contribution from BAF
+
+*d, --BAF-dev* 'float'[,'float']::
+    expected BAF deviation in query and control, i.e. the noise observed
+    in the data.
+
+*-e, --err-prob* 'float'::
+    uniform error probability
+
+*-l, --LRR-weight* 'float'::
+    relative contribution from LRR. With noisy data, this option can have big effect
+    on the number of calls produced. In truly random noise (such as in simulated data),
+    the value should be set high (1.0), but in the presence of systematic noise
+    when LRR are not informative, lower values result in cleaner calls (0.2).
+
+*-L, --LRR-smooth-win* 'int'::
+    reduce LRR noise by applying moving average given this window size
+
+*-O, --optimize* 'float'::
+    iteratively estimate the fraction of aberrant cells, down to the given fraction.
+    Lowering this value from the default 1.0 to say, 0.3, can help discover more
+    events but also increases noise
+
+*-P, --same-prob* 'float'::
+    the prior probability of the query and the control sample being the same.
+    Setting to 0 calls both independently, setting to 1 forces the same copy
+    number state in both.
+
+*-x, --xy-prob* 'float'::
+    the HMM probability of transition to another copy number state. Increasing this
+    values leads to smaller and more frequent calls.
+
+
+
 [[concat]]
 === bcftools concat '[OPTIONS]' 'FILE1' 'FILE2' [...]
 

From e8b7c5bd91aeae0f59bf18fa5458d668f9ad14d4 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Wed, 11 May 2016 11:09:17 +0100
Subject: [PATCH 169/211] Use bcf_hdr_format() rather than deprecated
 bcf_hdr_fmt_text()

Uses new HTSlib function added in samtools/htslib@f581de8b6714cf69416ce6f9d4d4f050996699b8.
---
 reheader.c | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/reheader.c b/reheader.c
index 69018cd5a..429bf7efd 100644
--- a/reheader.c
+++ b/reheader.c
@@ -371,9 +371,7 @@ static void reheader_bcf(args_t *args, int is_compressed)
     htsFile *fp = args->fp;
     bcf_hdr_t *hdr = bcf_hdr_read(fp); if ( !hdr ) error("Failed to read the header: %s\n", args->fname);
     kstring_t htxt = {0,0,0};
-    int hlen;
-    htxt.s = bcf_hdr_fmt_text(hdr, 1, &hlen);
-    htxt.l = hlen;
+    bcf_hdr_format(hdr, 1, &htxt);
 
     int i, nsamples = 0;
     char **samples = NULL;

From f7f36d9f086a7c7fb7d66bd84221c22e60917d2b Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Thu, 12 May 2016 11:03:35 +0100
Subject: [PATCH 170/211] Avoid angle brackets around option arguments

Use emphasis or bold instead.  Avoids accidentally turning -m <-|+>
into left-arrow|plus.
---
 doc/bcftools.txt | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index c91bb9c2b..d72685e06 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1070,7 +1070,7 @@ Checks sample identity or, without *-g*, multi-sample cross-check is performed.
 
 
 [[index]]
-=== bcftools index ['OPTIONS']  '<in.bcf>|<in.vcf.gz>'
+=== bcftools index ['OPTIONS']  'in.bcf'|'in.vcf.gz'
 Creates index for bgzip compressed VCF/BCF files for random access. CSI
 (coordinate-sorted index) is created by default. The CSI format
 supports indexing of chromosomes up to length 2&#94;31. TBI (tabix index)
@@ -1289,9 +1289,9 @@ the *<<fasta_ref,--fasta-ref>>* option is supplied.
     and normalization, however, see also the *<<do_not_normalize,--do-not-normalize>>*
     option below.
 
-*-m, --multiallelics* <-|+>['snps'|'indels'|'both'|'any']::
-    split multiallelic sites into biallelic records ('-') or join
-    biallelic sites into multiallelic records ('+'). An optional type string
+*-m, --multiallelics* *-*|*+*['snps'|'indels'|'both'|'any']::
+    split multiallelic sites into biallelic records (*-*) or join
+    biallelic sites into multiallelic records (*+*). An optional type string
     can follow which controls variant types which should be split or merged
     together: If only SNP records should be split or merged, specify 'snps'; if
     both SNPs and indels should be merged separately into two records, specify

From b9e0105eb21432ea098b53e09e53a4eec9dd9244 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 15 Feb 2016 22:15:44 +0000
Subject: [PATCH 171/211] annotate: add `-m` support for VCF, not just
 tab-delimited annot files

---
 vcfannotate.c | 19 +++++++++++++------
 1 file changed, 13 insertions(+), 6 deletions(-)

diff --git a/vcfannotate.c b/vcfannotate.c
index d5164f333..6426f2789 100644
--- a/vcfannotate.c
+++ b/vcfannotate.c
@@ -1552,7 +1552,6 @@ static void init_data(args_t *args)
     if ( args->mark_sites )
     {
         if ( !args->targets_fname ) error("The -a option not given\n");
-        if ( args->tgts_is_vcf ) error("Apologies, this has not been implemented yet: -a is a VCF\n");  // very easy to add..
         bcf_hdr_printf(args->hdr_out,"##INFO=<ID=%s,Number=0,Type=Flag,Description=\"Sites %slisted in %s\">",
             args->mark_sites,args->mark_sites_logic==MARK_LISTED?"":"not ",args->mark_sites);
     }
@@ -1731,12 +1730,20 @@ static void annotate(args_t *args, bcf1_t *line)
                 bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,i<args->nalines?0:1);
         }
     }
-    else if ( args->files->nreaders == 2 && bcf_sr_has_line(args->files,1) )
+    else if ( args->files->nreaders == 2 )
     {
-        bcf1_t *aline = bcf_sr_get_line(args->files,1);
-        for (j=0; j<args->ncols; j++)
-            if ( args->cols[j].setter(args,line,&args->cols[j],aline) )
-                error("fixme: Could not set %s at %s:%d\n", args->cols[j].hdr_key,bcf_seqname(args->hdr,line),line->pos+1);
+        if ( bcf_sr_has_line(args->files,1) )
+        {
+            bcf1_t *aline = bcf_sr_get_line(args->files,1);
+            for (j=0; j<args->ncols; j++)
+                if ( args->cols[j].setter(args,line,&args->cols[j],aline) )
+                    error("fixme: Could not set %s at %s:%d\n", args->cols[j].hdr_key,bcf_seqname(args->hdr,line),line->pos+1);
+
+            if ( args->mark_sites )
+                bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL,args->mark_sites_logic==MARK_LISTED ? 1 : 0);
+        }
+        else if ( args->mark_sites )
+            bcf_update_info_flag(args->hdr_out,line,args->mark_sites,NULL, args->mark_sites_logic==MARK_UNLISTED ? 1 : 0);
     }
     if ( args->set_ids )
     {

From ee8148d31f97c39c77fd7d5b4a4e1d5ca8408031 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Tue, 17 May 2016 13:08:06 +0100
Subject: [PATCH 172/211] Refactorings and warning preventions [minor]

Avoid "may be used uninitialised" warning by telling the compiler
that C_UNRL and C_TRIO are the only possibilities.  Fix "break" typo.
Use strchr() to clarify string parsing.  Clarify that printf("\n")
statements terminate their printf loops.
---
 plugins/color-chrs.c |  1 +
 plugins/mendelian.c  | 11 +++++++----
 plugins/vcf2sex.c    |  3 ++-
 test/test-rbuf.c     |  6 ++++--
 vcfmerge.c           |  8 +++++---
 5 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/plugins/color-chrs.c b/plugins/color-chrs.c
index 909065e5c..993ff4b6a 100644
--- a/plugins/color-chrs.c
+++ b/plugins/color-chrs.c
@@ -456,6 +456,7 @@ void flush_viterbi(args_t *args)
         s3 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->ifather);
         s2 = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,args->ichild);
     }
+    else abort();
 
     if ( !args->fp )
     {
diff --git a/plugins/mendelian.c b/plugins/mendelian.c
index 304a27a7d..b3c8bb884 100644
--- a/plugins/mendelian.c
+++ b/plugins/mendelian.c
@@ -26,6 +26,7 @@
 
 #include <stdio.h>
 #include <stdlib.h>
+#include <string.h>
 #include <getopt.h>
 #include <math.h>
 #include <htslib/hts.h>
@@ -145,18 +146,20 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         args.trios = (trio_t*) calloc(n,sizeof(trio_t));
         for (i=0; i<n; i++)
         {
-            char *ss = list[i], *se = list[i];
-            while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s: %s\n",trio_file, ss);
+            char *ss = list[i], *se;
+            se = strchr(ss, ',');
+            if ( !se ) error("Could not parse %s: %s\n",trio_file, ss);
             *se = 0;
             args.trios[i].imother = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
             if ( args.trios[i].imother<0 ) error("No such sample: \"%s\"\n", ss);
             ss = ++se; 
-            while ( *se && *se!=',' ) se++; if ( *se!=',' ) error("Could not parse %s\n",trio_file);
+            se = strchr(ss, ',');
+            if ( !se ) error("Could not parse %s\n",trio_file);
             *se = 0;
             args.trios[i].ifather = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
             if ( args.trios[i].ifather<0 ) error("No such sample: \"%s\"\n", ss);
             ss = ++se; 
-            while ( *se ) se++; if ( ss==se ) error("Could not parse %s\n",trio_file);
+            if ( *ss=='\0' ) error("Could not parse %s\n",trio_file);
             args.trios[i].ichild = bcf_hdr_id2int(args.hdr, BCF_DT_SAMPLE, ss);
             if ( args.trios[i].ichild<0 ) error("No such sample: \"%s\"\n", ss);
             free(list[i]);
diff --git a/plugins/vcf2sex.c b/plugins/vcf2sex.c
index 9cb0ed5dc..0df6d6a1f 100644
--- a/plugins/vcf2sex.c
+++ b/plugins/vcf2sex.c
@@ -412,7 +412,8 @@ int run(int argc, char **argv)
             case 'p': ploidy_fname = optarg; break; 
             case 'n': 
                 args->nsites = strtol(optarg,&tmp,10); 
-                if (*tmp) error("Unexpected argument to --nsites: %s\n", optarg); break; 
+                if (*tmp) error("Unexpected argument to --nsites: %s\n", optarg);
+                break;
             case 'h':
             case '?':
             default: error("%s", usage()); break;
diff --git a/test/test-rbuf.c b/test/test-rbuf.c
index bc8ebe92b..5c0480fde 100644
--- a/test/test-rbuf.c
+++ b/test/test-rbuf.c
@@ -29,8 +29,10 @@ DEALINGS IN THE SOFTWARE.  */
 void debug_print(rbuf_t *rbuf, int *dat)
 {
     int i;
-    for (i=-1; rbuf_next(rbuf, &i); ) printf(" %2d", i); printf("\n");
-    for (i=-1; rbuf_next(rbuf, &i); ) printf(" %2d", dat[i]); printf("\n");
+    for (i=-1; rbuf_next(rbuf, &i); ) printf(" %2d", i);
+    printf("\n");
+    for (i=-1; rbuf_next(rbuf, &i); ) printf(" %2d", dat[i]);
+    printf("\n");
 }
 
 int main(int argc, char **argv)
diff --git a/vcfmerge.c b/vcfmerge.c
index 02fac6bcc..3f5db9ece 100644
--- a/vcfmerge.c
+++ b/vcfmerge.c
@@ -274,7 +274,7 @@ static void info_rules_init(args_t *args)
         rule->type = bcf_hdr_id2type(args->out_hdr,BCF_HL_INFO,id);
         if ( rule->type!=BCF_HT_INT && rule->type!=BCF_HT_REAL && rule->type!=BCF_HT_STR ) error("The type is not supported: \"%s\"\n", rule->hdr_tag);
 
-        while ( *ss ) ss++; ss++;
+        ss = strchr(ss, '\0'); ss++;
         if ( !*ss ) error("Could not parse INFO rules, missing logic of \"%s\"\n", rule->hdr_tag);
 
         int is_join = 0;
@@ -300,7 +300,8 @@ static void info_rules_init(args_t *args)
                 error("Only fixed-length vectors are supported with -i %s:%s\n", ss, rule->hdr_tag);
         }
 
-        while ( *ss ) ss++; ss++; n++;
+        ss = strchr(ss, '\0'); ss++;
+        n++;
     }
     free(str.s);
     free(tmp);
@@ -1658,7 +1659,8 @@ void debug_maux(args_t *args, int pos, int var_type)
         fprintf(stderr,"\n");
     }
     fprintf(stderr," counts: ");
-    for (j=0; j<maux->nals; j++) fprintf(stderr,"%s   %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]); fprintf(stderr,"\n");
+    for (j=0; j<maux->nals; j++) fprintf(stderr,"%s   %dx %s", j==0?"":",",maux->cnt[j], maux->als[j]);
+    fprintf(stderr,"\n");
     for (j=0; j<files->nreaders; j++)
     {
         bcf_sr_t *reader = &files->readers[j];

From 170198d1e6d9072c639c7fb30f95995563e856d8 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Tue, 24 May 2016 14:23:57 +0100
Subject: [PATCH 173/211] Fix test_cmd(exp=>"expected") when test fails

If you use test_cmd(...,exp=>,...) then you must also use out=> with
a suitable output filename.  Normally the output file does not exist;
but if the test fails, both {out} and {out}.new will be created.
---
 test/test.pl | 27 +++++++++++++++------------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/test/test.pl b/test/test.pl
index dc1fcfa84..da493fd86 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -320,7 +320,7 @@ sub cmd
 sub test_cmd
 {
     my ($opts,%args) = @_;
-    if ( !exists($args{out}) && !exists($args{exp}) )
+    if ( !exists($args{out}) )
     {
         if ( !exists($args{in}) ) { error("FIXME: expected out or in key\n"); }
         $args{out} = "$args{in}.out";
@@ -350,23 +350,20 @@ sub test_cmd
     }
     my $exp = '';
     if ( exists($args{exp}) ) { $exp = $args{exp}; }
-    else
+    elsif ( open(my $fh,'<',"$$opts{path}/$args{out}") )
     {
-        if ( open(my $fh,'<',"$$opts{path}/$args{out}") )
-        {
-            my @exp = <$fh>;
-            $exp = join('',@exp);
-            close($fh);
-        }
-        elsif ( !$$opts{redo_outputs} ) { failed($opts,$test,"$$opts{path}/$args{out}: $!"); return; }
+        my @exp = <$fh>;
+        $exp = join('',@exp);
+        close($fh);
     }
+    elsif ( !$$opts{redo_outputs} ) { failed($opts,$test,"$$opts{path}/$args{out}: $!"); return; }
 
     if ( $exp ne $out )
     {
         open(my $fh,'>',"$$opts{path}/$args{out}.new") or error("$$opts{path}/$args{out}.new");
         print $fh $out;
         close($fh);
-        if ( !-e "$$opts{path}/$args{out}" )
+        if ( !-e "$$opts{path}/$args{out}" && !exists($args{exp}) )
         {
             rename("$$opts{path}/$args{out}.new","$$opts{path}/$args{out}") or error("rename $$opts{path}/$args{out}.new $$opts{path}/$args{out}: $!");
             print "\tthe file with expected output does not exist, creating new one:\n";
@@ -374,6 +371,12 @@ sub test_cmd
         }
         else
         {
+            if ( exists($args{exp}) )
+            {
+                open(my $fh,'>',"$$opts{path}/$args{out}") or error("$$opts{path}/$args{out}");
+                print $fh $exp;
+                close($fh);
+            }
             failed($opts,$test,"The outputs differ:\n\t\t$$opts{path}/$args{out}\n\t\t$$opts{path}/$args{out}.new");
         }
         return;
@@ -908,9 +911,9 @@ sub test_naive_concat
     }
 
     my $bcfs = join('.bcf ',@files).'.bcf';
-    test_cmd($opts,exp=>$exp,cmd=>"$$opts{bin}/bcftools concat --naive $bcfs | $$opts{bin}/bcftools view -H");
+    test_cmd($opts,exp=>$exp,out=>"concat.naive.bcf.out",cmd=>"$$opts{bin}/bcftools concat --naive $bcfs | $$opts{bin}/bcftools view -H");
 
     my $vcfs = join('.vcf.gz ',@files).'.vcf.gz';
-    test_cmd($opts,exp=>$exp,cmd=>"$$opts{bin}/bcftools concat --naive $vcfs | $$opts{bin}/bcftools view -H");
+    test_cmd($opts,exp=>$exp,out=>"concat.naive.vcf.out",cmd=>"$$opts{bin}/bcftools concat --naive $vcfs | $$opts{bin}/bcftools view -H");
 }
 

From 16414e6f772f65285c425e3cbd2fdb908550f727 Mon Sep 17 00:00:00 2001
From: John Marshall <jm18@sanger.ac.uk>
Date: Fri, 27 May 2016 14:26:49 +0100
Subject: [PATCH 174/211] Avoid segfault when QUAL < 0

QUAL is Phred-scaled so by definition is >= 0.0.  If we get invalid
input with a negative QUAL, clip it into the bin with 0, similarly to
the clipping beyond m_qual.  Hat tip Peter Johansson on samtools-help.
---
 vcfstats.c | 10 ++++++++--
 1 file changed, 8 insertions(+), 2 deletions(-)

diff --git a/vcfstats.c b/vcfstats.c
index 1032bf87b..45b28b7ae 100644
--- a/vcfstats.c
+++ b/vcfstats.c
@@ -187,6 +187,12 @@ static inline int idist_i2bin(idist_t *d, int i)
     return i-1+d->min;
 }
 
+static inline int clip_nonnegative(float x, int limit)
+{
+    if (x >= limit || isnan(x)) return limit - 1;
+    else if (x <= 0.0) return 0;
+    else return (int) x;
+}
 
 #define IC_DBG 0
 #if IC_DBG
@@ -621,7 +627,7 @@ static void do_indel_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
     bcf1_t *line = reader->buffer[0];
 
     #if QUAL_STATS
-        int iqual = line->qual >= args->m_qual || isnan(line->qual) ? args->m_qual - 1 : line->qual;
+        int iqual = clip_nonnegative(line->qual, args->m_qual);
         stats->qual_indels[iqual]++;
     #endif
 
@@ -756,7 +762,7 @@ static void do_snp_stats(args_t *args, stats_t *stats, bcf_sr_t *reader)
     if ( ref<0 ) return;
 
     #if QUAL_STATS
-        int iqual = line->qual >= args->m_qual || isnan(line->qual) ? args->m_qual - 1 : line->qual;
+        int iqual = clip_nonnegative(line->qual, args->m_qual);
         stats->qual_snps[iqual]++;
     #endif
 

From df3ca41b95a454462598919f5123ebbbfcb7ed6b Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 6 May 2016 20:15:05 +0100
Subject: [PATCH 175/211] consensus: handle variants which overlap region
 boundaries

Fixes #400
---
 consensus.c | 33 +++++++++++++++++++++++++++++----
 1 file changed, 29 insertions(+), 4 deletions(-)

diff --git a/consensus.c b/consensus.c
index 051f3536c..79b4a5f91 100644
--- a/consensus.c
+++ b/consensus.c
@@ -409,12 +409,27 @@ static void apply_variant(args_t *args, bcf1_t *rec)
         rec->d.allele[1][0] = gt2iupac(ial,jal);
     }
 
+    int len_diff = 0, alen = 0;
     int idx = rec->pos - args->fa_ori_pos + args->fa_mod_off;
-    if ( idx<0 || idx>=args->fa_buf.l ) 
+    if ( idx<0 )
+    {
+        fprintf(stderr,"Warning: ignoring overlapping variant starting at %s:%d\n", bcf_seqname(args->hdr,rec),rec->pos+1);
+        return;
+    }
+    if ( rec->rlen > args->fa_buf.l - idx )
+    {
+        rec->rlen = args->fa_buf.l - idx;
+        alen = strlen(rec->d.allele[ialt]);
+        if ( alen > rec->rlen )
+        {
+            rec->d.allele[ialt][rec->rlen] = 0;
+            fprintf(stderr,"Warning: trimming variant starting at %s:%d\n", bcf_seqname(args->hdr,rec),rec->pos+1);
+        }
+    }
+    if ( idx>=args->fa_buf.l ) 
         error("FIXME: %s:%d .. idx=%d, ori_pos=%d, len=%d, off=%d\n",bcf_seqname(args->hdr,rec),rec->pos+1,idx,args->fa_ori_pos,args->fa_buf.l,args->fa_mod_off);
 
     // sanity check the reference base
-    int len_diff = 0, alen = 0;
     if ( rec->d.allele[ialt][0]=='<' )
     {
         if ( strcasecmp(rec->d.allele[ialt], "<DEL>") )
@@ -519,7 +534,7 @@ static void consensus(args_t *args)
     {
         if ( str.s[0]=='>' )
         {
-            // new sequence encountered, apply all chached variants
+            // new sequence encountered, apply all cached variants
             while ( args->vcf_rbuf.n )
             {
                 if (args->chain) {
@@ -576,7 +591,17 @@ static void consensus(args_t *args)
         }
         if ( !rec_ptr ) flush_fa_buffer(args, 60);
     }
-    if (args->chain) {
+    bcf1_t **rec_ptr = NULL;
+    while ( args->rid>=0 && (rec_ptr = next_vcf_line(args)) )
+    {
+        bcf1_t *rec = *rec_ptr;
+        if ( rec->rid!=args->rid ) break;
+        if ( args->fa_end_pos && rec->pos > args->fa_end_pos ) break;
+        if ( args->fa_ori_pos + args->fa_buf.l - args->fa_mod_off <= rec->pos ) break;
+        apply_variant(args, rec);
+    }
+    if (args->chain)
+    {
         print_chain(args);
         destroy_chain(args);
     }

From 25d042b833987d32e5de1fc3a109d357c4d0f738 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 20 Jun 2016 07:44:39 +0100
Subject: [PATCH 176/211] norm: strict checking of non-ACGTN bases in `norm
 -cwx`

Fixes #439
---
 vcfnorm.c | 35 +++++++++++++++++++++++++++++------
 1 file changed, 29 insertions(+), 6 deletions(-)

diff --git a/vcfnorm.c b/vcfnorm.c
index d3b9fee42..daac7532e 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -87,10 +87,21 @@ static inline int replace_iupac_codes(char *seq, int nseq)
     for (i=0; i<nseq; i++)
     {
         char c = toupper(seq[i]);
-        if ( c!='A' && c!='C' && c!='G' && c!='T' ) { seq[i] = 'N'; n++; }
+        if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) { seq[i] = 'N'; n++; }
     }
     return n;
 }
+static inline int has_non_acgtn(char *seq, int nseq)
+{
+    char *end = nseq ? seq + nseq : seq + UINT32_MAX;   // arbitrary large number
+    while ( *seq && seq<end )
+    {
+        char c = toupper(*seq);
+        if ( c!='A' && c!='C' && c!='G' && c!='T' && c!='N' ) return 1;
+        seq++;
+    }
+    return 0;
+}
 
 static void fix_ref(args_t *args, bcf1_t *line)
 {
@@ -261,13 +272,17 @@ static int realign(args_t *args, bcf1_t *line)
     int i, nref, reflen = strlen(line->d.allele[0]);
     char *ref = faidx_fetch_seq(args->fai, (char*)args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos, line->pos+reflen-1, &nref);
     if ( !ref ) error("faidx_fetch_seq failed at %s:%d\n", args->hdr->id[BCF_DT_CTG][line->rid].key, line->pos+1);
-    replace_iupac_codes(ref,nref);
+    replace_iupac_codes(ref,nref);  // any non-ACGT character in fasta ref is replaced with N
 
-    // does REF contain non-standard bases?
-    if ( replace_iupac_codes(line->d.allele[0],reflen) )
+    // does VCF REF contain non-standard bases?
+    if ( has_non_acgtn(line->d.allele[0],reflen) )
     {
-        args->nchanged++;
-        bcf_update_alleles(args->hdr,line,(const char**)line->d.allele,line->n_allele);
+        if ( args->check_ref==CHECK_REF_EXIT )
+            error("Non-ACGTN reference allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[0]);
+        if ( args->check_ref & CHECK_REF_WARN )
+            fprintf(stderr,"NON_ACGTN_REF\t%s\t%d\t%s\n", bcf_seqname(args->hdr,line),line->pos+1,line->d.allele[0]);
+        free(ref);
+        return ERR_REF_MISMATCH;
     }
     if ( strcasecmp(ref,line->d.allele[0]) )
     {
@@ -289,6 +304,14 @@ static int realign(args_t *args, bcf1_t *line)
     for (i=0; i<line->n_allele; i++)
     {
         if ( line->d.allele[i][0]=='<' ) return ERR_SYMBOLIC;  // symbolic allele
+        if ( has_non_acgtn(line->d.allele[i],0) )
+        {
+            if ( args->check_ref==CHECK_REF_EXIT )
+                error("Non-ACGTN alternate allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[i]);
+            if ( args->check_ref & CHECK_REF_WARN )
+                fprintf(stderr,"NON_ACGTN_ALT\t%s\t%d\t%s\n", bcf_seqname(args->hdr,line),line->pos+1,line->d.allele[i]);
+            return ERR_REF_MISMATCH;
+        }
 
         als[i].l = 0;
         kputs(line->d.allele[i], &als[i]);

From d083c5b39bd4effaa38fb23575fa762dd1f7561f Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 20 May 2016 19:34:36 +0100
Subject: [PATCH 177/211] roh: fix nonfunctional --AF-dflt option

also clarify a comment line in the code
---
 vcfroh.c | 47 +++++++++++++++++++++++------------------------
 1 file changed, 23 insertions(+), 24 deletions(-)

diff --git a/vcfroh.c b/vcfroh.c
index 95605592f..ead7adc14 100644
--- a/vcfroh.c
+++ b/vcfroh.c
@@ -502,7 +502,7 @@ int parse_line(args_t *args, bcf1_t *line, double *alt_freq, double *pdg)
     args->nitmp = 0;
 
     // Set allele frequency
-    int ret;
+    int ret = 0;
     if ( args->af_tag )
     {
         // Use an INFO tag provided by the user
@@ -517,36 +517,35 @@ int parse_line(args_t *args, bcf1_t *line, double *alt_freq, double *pdg)
         // Read AF from a file
         ret = read_AF(args->files->targets, line, alt_freq);
     }
+    else if ( args->dflt_AF > 0 )
+    {
+        *alt_freq = args->dflt_AF;
+    }
+    else if ( args->estimate_AF )
+    {
+        // Estimate AF from GTs of all samples or samples listed in a file
+        ret = estimate_AF(args, line, alt_freq);    // reads GTs into args->itmp
+    }
     else
     {
-        // Use GTs or AC/AN: GTs when AC/AN not present or when GTs explicitly requested by --estimate-AF
-        ret = -1;
-        if ( !args->estimate_AF )
+        // Use AC/AN
+        int AC = -1, AN = 0;
+        ret = bcf_get_info_int32(args->hdr, line, "AN", &args->itmp, &args->mitmp);
+        if ( ret==1 )
         {
-            int AC = -1, AN = 0;
-            ret = bcf_get_info_int32(args->hdr, line, "AN", &args->itmp, &args->mitmp);
-            if ( ret==1 )
-            {
-                AN = args->itmp[0];
-                ret = bcf_get_info_int32(args->hdr, line, "AC", &args->itmp, &args->mitmp);
-                if ( ret>0 )
-                    AC = args->itmp[0];
-            }
-            if ( AN<=0 || AC<0 ) 
-                ret = -1;
-            else 
-                *alt_freq = (double) AC/AN;
+            AN = args->itmp[0];
+            ret = bcf_get_info_int32(args->hdr, line, "AC", &args->itmp, &args->mitmp);
+            if ( ret>0 )
+                AC = args->itmp[0];
         }
-        if ( ret==-1 )
-            ret = estimate_AF(args, line, alt_freq);    // reads GTs into args->itmp
+        if ( AN<=0 || AC<0 ) 
+            ret = -1;
+        else 
+            *alt_freq = (double) AC/AN;
     }
 
     if ( ret<0 ) return ret;
-    if ( *alt_freq==0.0 )
-    {
-        if ( args->dflt_AF==0 ) return -1;       // we skip sites with AF=0
-        *alt_freq = args->dflt_AF;
-    }
+    if ( *alt_freq==0.0 ) return -1;
 
     // Set P(D|G)
     if ( args->fake_PLs )

From 2035ddd696b83455210be5cae2d2c775c4aca2aa Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 13 Jun 2016 13:34:22 +0100
Subject: [PATCH 178/211] call: re-enable numeric ploidy definitions via
 `--samples-file`

Fixes #436
---
 test/mpileup.2.samples |  3 +++
 test/mpileup.X.2.out   | 40 +++++++++++++++++++++++++++++++++++++++
 test/mpileup.c.X.2.out | 43 ++++++++++++++++++++++++++++++++++++++++++
 test/test.pl           |  2 ++
 vcfcall.c              |  6 +++---
 5 files changed, 91 insertions(+), 3 deletions(-)
 create mode 100644 test/mpileup.2.samples
 create mode 100644 test/mpileup.X.2.out
 create mode 100644 test/mpileup.c.X.2.out

diff --git a/test/mpileup.2.samples b/test/mpileup.2.samples
new file mode 100644
index 000000000..07b1eae64
--- /dev/null
+++ b/test/mpileup.2.samples
@@ -0,0 +1,3 @@
+HG00100	2
+HG00101	1
+HG00102	2
diff --git a/test/mpileup.X.2.out b/test/mpileup.X.2.out
new file mode 100644
index 000000000..1c63822dc
--- /dev/null
+++ b/test/mpileup.X.2.out
@@ -0,0 +1,40 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=ICB,Number=1,Type=Float,Description="Inbreeding Coefficient Binomial test (bigger is better)">
+##INFO=<ID=HOB,Number=1,Type=Float,Description="Bias in the number of HOMs number (smaller is better)">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	302	.	T	TA	481	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=49	GT:PL:DP:DV	0/1:167,0,96:11:6	1:157,9:7:6	1/1:201,21,0:7:7
+X	828	.	T	C	321	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,4,8,11;MQ=60	GT:PL:DP:DV	0/1:211,0,35:12:10	1:116,91:9:5	1/1:120,12,0:4:4
+X	834	.	G	A	308	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=2,3,7,10;MQ=60	GT:PL:DP:DV	0/1:185,0,46:11:9	1:128,59:8:5	1/1:89,9,0:3:3
+X	1665	.	T	C	3.10525	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=7,11,1,1;MQ=55	GT:PL:DP:DV	0/0:0,21,185:7:0	0:0,222:9:0	0/1:35,0,51:4:2
+X	1869	.	A	T	119	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=6,9,5,4;MQ=58	GT:PL:DP:DV	0/1:115,0,224:18:7	0:16,104:5:1	1/1:42,3,0:1:1
+X	2041	.	G	A	424	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=6,5,12,7;MQ=58	GT:PL:DP:DV	0/1:229,0,212:21:11	1:32,24:2:1	1/1:223,21,0:7:7
+X	2220	.	G	A	257	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=6,2,1,11;MQ=58	GT:PL:DP:DV	0/1:139,0,130:12:6	1:69,46:4:2	1/1:131,12,0:4:4
+X	2564	.	A	G	178	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=1,4,4,5;MQ=60	GT:PL:DP:DV	0/1:88,0,78:6:3	1:57,56:4:2	1/1:124,12,0:4:4
+X	3104	.	C	T	24.1975	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;ICB=0.235294;HOB=0.18;AC=1;AN=5;DP4=8,15,2,0;MQ=58	GT:PL:DP:DV	0/0:0,48,255:16:0	0:0,144:4:0	0/1:59,0,93:5:2
+X	3587	.	G	A	332	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;ICB=0.461538;HOB=0.02;AC=3;AN=5;DP4=4,7,10,6;MQ=60	GT:PL:DP:DV	0/1:161,0,184:14:7	0:22,118:5:1	1/1:212,24,0:8:8
+X	3936	.	A	G	412	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;ICB=0.235294;HOB=0.18;AC=4;AN=5;DP4=5,6,6,17;MQ=56	GT:PL:DP:DV	0/1:233,0,206:20:11	1:77,58:6:4	1/1:196,24,0:8:8
diff --git a/test/mpileup.c.X.2.out b/test/mpileup.c.X.2.out
new file mode 100644
index 000000000..25022d9bc
--- /dev/null
+++ b/test/mpileup.c.X.2.out
@@ -0,0 +1,43 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##samtoolsVersion=1.1-19-g6b249e2+htslib-1.1-74-g845c515
+##samtoolsCommand=samtools mpileup -uvDV -b xxx//mpileup.bam.list -f xxx//mpileup.ref.fa.gz
+##reference=file://xxx//mpileup.ref.fa.gz
+##contig=<ID=X,length=81195210>
+##ALT=<ID=X,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AF2,Number=1,Type=Float,Description="Max-likelihood estimate of the first and second group ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+X	302	.	T	TA	999	.	INDEL;IDV=7;IMF=1;DP=25;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0;AF1=0.685575;AC1=4;DP4=2,4,8,11;MQ=51;FQ=61.4911;PV4=1,1,1,1	GT:PL:DP:DV	0/1:167,0,96:11:6	0:157,0,9:7:6	1/1:201,21,0:7:7
+X	828	.	T	C	999	.	DP=25;VDB=0.842082;SGB=-4.20907;RPB=0.950652;MQB=1;MQSB=1;BQB=0.929717;MQ0F=0;AF1=0.656389;AC1=4;DP4=2,4,8,11;MQ=60;FQ=89.3748;PV4=1,1,1,0.32233	GT:PL:DP:DV	0/1:211,0,35:12:10	0:116,91:9:5	1/1:120,12,0:4:4
+X	834	.	G	A	999	.	DP=25;VDB=0.788006;SGB=-4.01214;RPB=0.999233;MQB=1;MQSB=1;BQB=0.821668;MQ0F=0;AF1=0.646503;AC1=4;DP4=2,3,7,10;MQ=60;FQ=68.6952;PV4=1,1,1,0.228905	GT:PL:DP:DV	0/1:185,0,46:11:9	0:128,59:8:5	1/1:89,9,0:3:3
+X	1665	.	T	C	3.14059	.	DP=20;VDB=0.1;SGB=0.346553;RPB=0.222222;MQB=0.611111;MQSB=0.988166;BQB=0.944444;MQ0F=0;AF1=0.167199;AC1=1;DP4=7,11,1,1;MQ=56;FQ=3.56819;PV4=1,0.239991,0.0798553,0.27333	GT:PL:DP:DV	0/0:0,21,185:7:0	0:0,222:9:0	0/1:35,0,51:4:2
+X	1869	.	A	T	134.348	.	DP=24;VDB=0.928022;SGB=-11.9537;RPB=0.984127;MQB=0.96464;MQSB=0.931547;BQB=0.359155;MQ0F=0;AF1=0.598209;AC1=4;DP4=6,9,5,4;MQ=59;FQ=138.299;PV4=0.675175,0.0234896,1,0.324361	GT:PL:DP:DV	0/1:115,0,224:18:7	0:16,104:5:1	1/1:42,3,0:1:1
+X	2041	.	G	A	999	.	DP=31;VDB=0.816435;SGB=-4.18892;RPB=0.88473;MQB=0.972375;MQSB=0.968257;BQB=0.311275;MQ0F=0;AF1=0.665982;AC1=4;DP4=6,5,12,7;MQ=59;FQ=999;PV4=0.71163,1,0.228209,0.143795	GT:PL:DP:DV	0/1:229,0,212:21:11	0:32,24:2:1	1/1:223,21,0:7:7
+X	2220	.	G	A	999	.	DP=21;VDB=0.532753;SGB=-3.51597;RPB=0.964198;MQB=0.898397;MQSB=0.875769;BQB=0.0354359;MQ0F=0;AF1=0.656341;AC1=4;DP4=6,2,1,11;MQ=59;FQ=139.373;PV4=0.00443756,1,1,1	GT:PL:DP:DV	0/1:139,0,130:12:6	0:69,46:4:2	1/1:131,12,0:4:4
+X	2564	.	A	G	227.769	.	DP=15;VDB=0.690812;SGB=-3.20711;RPB=0.197899;MQB=1;MQSB=1;BQB=0.965069;MQ0F=0;AF1=0.656337;AC1=4;DP4=1,4,4,5;MQ=60;FQ=97.3723;PV4=0.58042,1,1,1	GT:PL:DP:DV	0/1:88,0,78:6:3	0:57,56:4:2	1/1:124,12,0:4:4
+X	3104	.	C	T	24.364	.	DP=25;VDB=0.8;SGB=0.346553;RPB=0.717391;MQB=0.956522;MQSB=0.962269;BQB=0.978261;MQ0F=0;AF1=0.170892;AC1=1;DP4=8,15,2,0;MQ=59;FQ=25.179;PV4=0.15,1,1,1	GT:PL:DP:DV	0/0:0,48,255:16:0	0:0,144:4:0	0/1:59,0,93:5:2
+X	3587	.	G	A	353.302	.	DP=29;VDB=0.902044;SGB=-3.91326;RPB=0.800999;MQB=1;MQSB=1;BQB=0.156944;MQ0F=0;AF1=0.665739;AC1=4;DP4=4,7,10,6;MQ=60;FQ=358.057;PV4=0.25186,0.0986321,1,1	GT:PL:DP:DV	0/1:161,0,184:14:7	0:22,118:5:1	1/1:212,24,0:8:8
+X	3936	.	A	G	999	.	DP=37;VDB=0.0574114;SGB=-4.60123;RPB=0.741697;MQB=0.812605;MQSB=0.143788;BQB=0.883831;MQ0F=0;AF1=0.666004;AC1=4;DP4=5,6,6,17;MQ=57;FQ=999;PV4=0.434446,0.125787,1,1	GT:PL:DP:DV	0/1:233,0,206:20:11	0:77,58:6:4	1/1:196,24,0:8:8
diff --git a/test/test.pl b/test/test.pl
index c1bcdfd67..bb4323cd8 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -145,11 +145,13 @@
 test_vcf_call($opts,in=>'mpileup',out=>'mpileup.2.out',args=>'-mg0');
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
 test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
+test_vcf_call($opts,in=>'mpileup.X',out=>'mpileup.X.2.out',args=>'-mv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.2.samples');
 test_vcf_call_cAls($opts,in=>'mpileup',out=>'mpileup.cAls.out',tab=>'mpileup');
 test_vcf_call($opts,in=>'mpileup.c',out=>'mpileup.c.1.out',args=>'-cv');
 # test_vcf_call($opts,in=>'mpileup.c',out=>'mpileup.c.2.out',args=>'-cg0');
 test_vcf_call($opts,in=>'mpileup.c.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.samples');
 test_vcf_call($opts,in=>'mpileup.c.X',out=>'mpileup.c.X.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.ped');
+test_vcf_call($opts,in=>'mpileup.c.X',out=>'mpileup.c.X.2.out',args=>'-cv --ploidy-file {PATH}/mpileup.ploidy -S {PATH}/mpileup.2.samples');
 test_vcf_filter($opts,in=>'filter.1',out=>'filter.1.out',args=>'-mx -g2 -G2');
 test_vcf_filter($opts,in=>'filter.2',out=>'filter.2.out',args=>q[-e'QUAL==59.2 || (INDEL=0 & (FMT/GQ=25 | FMT/DP=10))' -sModified -S.]);
 test_vcf_filter($opts,in=>'filter.3',out=>'filter.3.out',args=>q[-e'DP=19'],fmt=>'%POS\\t%FILTER\\t%DP[\\t%GT]\\n');
diff --git a/vcfcall.c b/vcfcall.c
index cc4aff29d..f29002098 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -411,7 +411,7 @@ static void init_data(args_t *args)
         {
             args->nsamples = bcf_hdr_nsamples(args->aux.hdr);
             args->sample2sex = (int*) malloc(sizeof(int)*args->nsamples);
-            for (i=0; i<args->nsamples; i++) args->sample2sex[i] = 0;
+            for (i=0; i<args->nsamples; i++) args->sample2sex[i] = 2;
         }
     }
     if ( args->nsamples )
@@ -779,8 +779,8 @@ int main_vcfcall(int argc, char *argv[])
 
     if ( !ploidy_fname && !ploidy )
     {
-        fprintf(stderr,"Note: Neither --ploidy nor --ploidy-file given, assuming all sites are diploid\n");
-        args.ploidy = ploidy_init_string("",2);
+        if ( !args.samples_is_file ) fprintf(stderr,"Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid\n");
+        args.ploidy = ploidy_init_string("* * * 0 0\n* * * 1 1\n* * * 2 2\n",2);
     }
 
     if ( !args.ploidy ) error("Could not initialize ploidy\n");

From be8b378d2a187d3942e9148190a58ba919c44b83 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Mon, 2 May 2016 12:29:06 +0100
Subject: [PATCH 179/211] cnv: add params estimated by -O to the summary cnv
 output

---
 vcfcnv.c | 46 ++++++++++++++++++++++++++++++++++++----------
 1 file changed, 36 insertions(+), 10 deletions(-)

diff --git a/vcfcnv.c b/vcfcnv.c
index e4b9372c9..ffe71c42c 100644
--- a/vcfcnv.c
+++ b/vcfcnv.c
@@ -266,17 +266,15 @@ static void init_data(args_t *args)
     hmm_init_states(args->hmm, args->iprobs);
 
     args->summary_fh = stdout;
-    if ( args->output_dir )
+    init_sample_files(&args->query_sample, args->output_dir);
+    if ( args->control_sample.name )
     {
-        init_sample_files(&args->query_sample, args->output_dir);
-        if ( args->control_sample.name )
-        {
-            init_sample_files(&args->control_sample, args->output_dir);
-            args->summary_fh = open_file(&args->summary_fname,"w","%s/summary.tab",args->output_dir);
-        }
-        else
-            args->summary_fh = NULL;    // one sample only, no two-file summary
+        init_sample_files(&args->control_sample, args->output_dir);
+        args->summary_fh = open_file(&args->summary_fname,"w","%s/summary.tab",args->output_dir);
     }
+    else
+        args->summary_fh = NULL;    // one sample only, no two-file summary
+        
 
     int i;
     FILE *fh = args->summary_fh ? args->summary_fh : args->query_sample.summary_fh;
@@ -295,6 +293,19 @@ static void init_data(args_t *args)
                 "# RG, Regions\t[2]Chromosome\t[3]Start\t[4]End\t[5]Copy number:%s\t[6]Quality\t[7]nSites\t[8]nHETs\n",
                 args->query_sample.name
                );
+    if ( args->optimize_frac )
+    {
+        fprintf(args->query_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n");
+        if ( args->control_sample.name )
+        {
+            fprintf(args->control_sample.summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t[5]Cell fraction\t[6]BAF deviation\n");
+            fprintf(args->summary_fh, "# CF, cell fraction estimate\t[2]Chromosome\t[3]Start\t[4]End\t"
+                "[5]Cell fraction:%s\t[6]Cell fraction:%s\t[7]BAF deviation:%s\t[8]BAF deviation:%s\n",
+                args->query_sample.name,args->control_sample.name,
+                args->query_sample.name,args->control_sample.name
+                );
+        }
+    }
 }
 
 char *msprintf(const char *fmt, ...);
@@ -556,6 +567,7 @@ static void destroy_data(args_t *args)
     free(args->sites);
     free(args->eprob);
     free(args->tprob);
+    free(args->iprobs);
     free(args->summary_fname);
     free(args->nonref_afs);
     free(args->query_sample.baf);
@@ -960,6 +972,20 @@ static void cnv_flush_viterbi(args_t *args)
         if ( args->control_sample.name )
             fprintf(stderr,"\t.. %f %f", args->control_sample.cell_frac,args->control_sample.baf_dev2);
         fprintf(stderr,"\n");
+
+        fprintf(args->query_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n",
+            bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+            args->query_sample.cell_frac,sqrt(args->query_sample.baf_dev2));
+        if ( args->control_sample.name )
+        {
+            fprintf(args->control_sample.summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%f\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+                    args->control_sample.cell_frac,sqrt(args->control_sample.baf_dev2));
+            fprintf(args->summary_fh,"CF\t%s\t%d\t%d\t%.2f\t%.2f\t%f\t%f\n",
+                    bcf_hdr_id2name(args->hdr,args->prev_rid),args->sites[0]+1,args->sites[args->nsites-1]+1,
+                    args->query_sample.cell_frac, args->control_sample.cell_frac,
+                    sqrt(args->query_sample.baf_dev2), sqrt(args->control_sample.baf_dev2));
+        }
     }
     set_emission_probs(args);
 
@@ -1351,7 +1377,7 @@ int main_vcfcnv(int argc, char *argv[])
     else fname = argv[optind];
     if ( !fname ) usage(args);
 
-    if ( args->plot_th<=100 && !args->output_dir ) error("Expected -o option with -p\n");
+    if ( !args->output_dir ) error("Expected -o option\n");
     if ( args->regions_list )
     {
         if ( bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )

From 101061cd738c816ed203c0f56d622d4f78e046a5 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 21 Jun 2016 11:06:14 +0100
Subject: [PATCH 180/211] call: add some extra info to the ploidy help message
 [minor]

---
 vcfcall.c | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/vcfcall.c b/vcfcall.c
index f29002098..b6f3b4d67 100644
--- a/vcfcall.c
+++ b/vcfcall.c
@@ -146,7 +146,7 @@ static ploidy_predef_t ploidy_predefs[] =
           "*  * *     F 2\n"
     },
     { .alias  = "GRCh38",
-      .about  = "Human Genome reference assembly GRCh38 / hg38, plain chromosome naming (1,2,3,..)",
+      .about  = "Human Genome reference assembly GRCh38 / hg38",
       .ploidy =
           "X 1 9999 M 1\n"
           "X 2781480 155701381 M 1\n"
@@ -569,7 +569,10 @@ ploidy_t *init_ploidy(char *alias)
 
     if ( !pld->alias )
     {
-        fprintf(stderr,"Predefined ploidies:\n");
+        fprintf(stderr,"\nPRE-DEFINED PLOIDY FILES\n\n");
+        fprintf(stderr," * Columns are: CHROM,FROM,TO,SEX,PLOIDY\n");
+        fprintf(stderr," * Coordinates are 1-based inclusive.\n");
+        fprintf(stderr," * A '*' means any value not otherwise defined.\n\n");
         pld = ploidy_predefs;
         while ( pld->alias )
         {

From e29f2f538daec0cccc2ca9c3924da8d4876f4cf1 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 3 Jun 2016 10:22:06 +0100
Subject: [PATCH 181/211] plugin: decrease verbosity of plugin -l, old output
 via -lv and -lvv

---
 vcfplugin.c | 33 +++++++++++++++++++--------------
 1 file changed, 19 insertions(+), 14 deletions(-)

diff --git a/vcfplugin.c b/vcfplugin.c
index 87a773f50..5afdb69cd 100644
--- a/vcfplugin.c
+++ b/vcfplugin.c
@@ -1,6 +1,6 @@
 /*  vcfplugin.c -- plugin modules for operating on VCF/BCF files.
 
-    Copyright (C) 2013-2015 Genome Research Ltd.
+    Copyright (C) 2013-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -47,7 +47,7 @@ typedef struct _plugin_t plugin_t;
  *   Plugin API:
  *   ----------
  *   const char *about(void)
- *      - short description used by 'bcftools plugin -l'
+ *      - short description used by 'bcftools plugin -lv'
  *
  *   const char *usage(void)
  *      - longer description used by 'bcftools +name -h'
@@ -170,11 +170,11 @@ static void add_plugin_paths(args_t *args, const char *path)
                 args->plugin_paths = (char**) realloc(args->plugin_paths,sizeof(char*)*(args->nplugin_paths+1));
                 args->plugin_paths[args->nplugin_paths] = dir;
                 args->nplugin_paths++;
-                if ( args->verbose ) fprintf(stderr, "plugin directory %s .. ok\n", dir);
+                if ( args->verbose > 1 ) fprintf(stderr, "plugin directory %s .. ok\n", dir);
             }
             else
             {
-                if ( args->verbose ) fprintf(stderr, "plugin directory %s .. %s\n", dir, strerror(errno));
+                if ( args->verbose > 1 ) fprintf(stderr, "plugin directory %s .. %s\n", dir, strerror(errno));
                 free(dir);
             }
 
@@ -210,7 +210,7 @@ static void *dlopen_plugin(args_t *args, const char *fname)
         {
             tmp = msprintf("%s/%s.so", args->plugin_paths[i],fname);
             handle = dlopen(tmp, RTLD_NOW); // valgrind complains about unfreed memory, not our problem though
-            if ( args->verbose )
+            if ( args->verbose > 1 )
             {
                 if ( !handle ) fprintf(stderr,"%s:\n\tdlopen   .. %s\n", tmp,dlerror());
                 else fprintf(stderr,"%s:\n\tdlopen   .. ok\n", tmp);
@@ -221,7 +221,7 @@ static void *dlopen_plugin(args_t *args, const char *fname)
     }
 
     handle = dlopen(fname, RTLD_NOW);
-    if ( args->verbose )
+    if ( args->verbose > 1 )
     {
         if ( !handle ) fprintf(stderr,"%s:\n\tdlopen   .. %s\n", fname,dlerror());
         else fprintf(stderr,"%s:\n\tdlopen   .. ok\n", fname);
@@ -266,19 +266,19 @@ static int load_plugin(args_t *args, const char *fname, int exit_on_error, plugi
     if ( ret )
         plugin->init = NULL;
     else
-        if ( args->verbose ) fprintf(stderr,"\tinit     .. ok\n");
+        if ( args->verbose > 1 ) fprintf(stderr,"\tinit     .. ok\n");
 
     plugin->run = (dl_run_f) dlsym(plugin->handle, "run");
     ret = dlerror();
     if ( ret )
         plugin->run = NULL;
     else
-        if ( args->verbose ) fprintf(stderr,"\trun      .. ok\n");
+        if ( args->verbose > 1 ) fprintf(stderr,"\trun      .. ok\n");
 
     if ( !plugin->init && !plugin->run )
     {
         if ( exit_on_error ) error("Could not initialize %s, neither run or init found \n", plugin->name);
-        else if ( args->verbose ) fprintf(stderr,"\tinit/run .. not found\n");
+        else if ( args->verbose > 1 ) fprintf(stderr,"\tinit/run .. not found\n");
         return -1;
     }
 
@@ -287,7 +287,7 @@ static int load_plugin(args_t *args, const char *fname, int exit_on_error, plugi
     if ( ret )
     {
         if ( exit_on_error ) error("Could not initialize %s, version string not found\n", plugin->name);
-        else if ( args->verbose ) fprintf(stderr,"\tversion  .. not found\n");
+        else if ( args->verbose > 1 ) fprintf(stderr,"\tversion  .. not found\n");
         return -1;
     }
 
@@ -392,8 +392,13 @@ static int list_plugins(args_t *args)
         qsort(plugins, nplugins, sizeof(plugins[0]), cmp_plugin_name);
 
         for (i=0; i<nplugins; i++)
-            printf("\n-- %s --\n%s", plugins[i].name, plugins[i].about());
-        printf("\n");
+        {
+            if ( args->verbose )
+                printf("\n-- %s --\n%s", plugins[i].name, plugins[i].about());
+            else
+                printf("%s\n", plugins[i].name);
+        }
+        if ( args->verbose ) printf("\n");
     }
     else
         print_plugin_usage_hint();
@@ -460,7 +465,7 @@ static void usage(args_t *args)
     fprintf(stderr, "Plugin options:\n");
     fprintf(stderr, "   -h, --help                  list plugin's options\n");
     fprintf(stderr, "   -l, --list-plugins          list available plugins. See BCFTOOLS_PLUGINS environment variable and man page for details\n");
-    fprintf(stderr, "   -v, --verbose               print debugging information on plugin failure\n");
+    fprintf(stderr, "   -v, --verbose               print verbose information, -vv increases verbosity\n");
     fprintf(stderr, "   -V, --version               print version string and exit\n");
     fprintf(stderr, "\n");
     exit(1);
@@ -518,7 +523,7 @@ int main_plugin(int argc, char *argv[])
     {
         switch (c) {
             case 'V': version_only = 1; break;
-            case 'v': args->verbose = 1; break;
+            case 'v': args->verbose++; break;
             case 'o': args->output_fname = optarg; break;
             case 'O':
                 switch (optarg[0]) {

From 4bf6c480e12fbc5f00ebcce6ee88deace07e6075 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 31 Mar 2016 09:08:25 +0100
Subject: [PATCH 182/211] tag2tag: new `--gp-to-gt` option

---
 plugins/tag2tag.c | 68 ++++++++++++++++++++++++++++++++++++++++++-----
 1 file changed, 62 insertions(+), 6 deletions(-)

diff --git a/plugins/tag2tag.c b/plugins/tag2tag.c
index 8178326eb..f56e00eb1 100644
--- a/plugins/tag2tag.c
+++ b/plugins/tag2tag.c
@@ -1,6 +1,6 @@
-/*  plugins/tag2tag.c -- Convert between similar tags, such as GL and GP.
+/*  plugins/tag2tag.c -- convert between similar tags
 
-    Copyright (C) 2014 Genome Research Ltd.
+    Copyright (C) 2014-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -33,12 +33,13 @@ DEALINGS IN THE SOFTWARE.  */
 
 #define GP_TO_GL 1
 #define GL_TO_PL 2
+#define GP_TO_GT 3
 
 static int mode = 0, drop_source_tag = 0;
 static bcf_hdr_t *in_hdr, *out_hdr;
 static float *farr = NULL;
 static int32_t *iarr = NULL;
-static int mfarr = 0;
+static int mfarr = 0, miarr = 0;
 
 const char *about(void)
 {
@@ -55,8 +56,8 @@ const char *usage(void)
         "   run \"bcftools plugin\" for a list of common options\n"
         "\n"
         "Plugin options:\n"
-//todo        "       --gl-to-gp    convert FORMAT/GL to FORMAT/GP\n" 
         "       --gp-to-gl    convert FORMAT/GP to FORMAT/GL\n"
+        "       --gp-to-gt    convert FORMAT/GP to FORMAT/GT by taking argmax of GP\n"
         "       --gl-to-pl    convert FORMAT/GL to FORMAT/PL\n"
         "   -r, --replace     drop the source tag\n"
         "\n"
@@ -81,6 +82,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         {"replace",0,0,'r'},
         {"gp-to-gl",0,0,1},
         {"gl-to-pl",0,0,2},
+        {"gp-to-gt",0,0,3},
         {0,0,0,0}
     };
     int c;
@@ -90,6 +92,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         {
             case  1 : mode = GP_TO_GL; break;
             case  2 : mode = GL_TO_PL; break;
+            case  3 : mode = GP_TO_GT; break;
             case 'r': drop_source_tag = 1; break;
             case 'h':
             case '?':
@@ -105,6 +108,8 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GL,Number=G,Type=Float,Description=\"Genotype Likelihoods\">");
     else if ( mode==GL_TO_PL )
         init_header(out_hdr,drop_source_tag?"GL":NULL,BCF_HL_FMT,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred scaled genotype likelihoods\">");
+    else if ( mode==GP_TO_GT )
+        init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
 
     return 0;
 }
@@ -131,8 +136,7 @@ bcf1_t *process(bcf1_t *rec)
             fprintf(stderr, "Could not read tag: GL\n");
             exit(1);
         }
-            
-        
+
         // create extra space to store converted data
         iarr = (int32_t*) malloc(n * sizeof(int32_t));
         if(!iarr) n = -4;
@@ -150,6 +154,58 @@ bcf1_t *process(bcf1_t *rec)
         if ( drop_source_tag )
             bcf_update_format_float(out_hdr,rec,"GL",NULL,0);
     }
+    else if ( mode==GP_TO_GT )
+    {
+        int nals  = rec->n_allele;
+        int nsmpl = bcf_hdr_nsamples(in_hdr);
+        hts_expand(int32_t,nsmpl*2,miarr,iarr);
+
+        n = bcf_get_format_float(in_hdr,rec,"GP",&farr,&mfarr);
+        n /= nsmpl;
+        for (i=0; i<nsmpl; i++)
+        {
+            float *ptr = farr + i*n;
+            if ( bcf_float_is_missing(ptr[0]) )
+            {
+                iarr[2*i] = iarr[2*i+1] = bcf_gt_missing;
+                continue;
+            }
+
+            int j, jmax = 0;
+            for (j=1; j<n; j++)
+            {
+                if ( bcf_float_is_missing(ptr[j]) || bcf_float_is_vector_end(ptr[j]) ) break;
+                if ( ptr[j] > ptr[jmax] ) jmax = j;
+            }
+
+            // haploid genotype
+            if ( j==nals )
+            {
+                iarr[2*i]   = bcf_gt_unphased(jmax);
+                iarr[2*i+1] = bcf_int32_vector_end;
+                continue;
+            }
+
+            if ( j!=nals*(nals+1)/2 )
+                error("Wrong number of GP values for diploid genotype at %s:%d, expected %d, found %d\n",
+                    bcf_seqname(in_hdr,rec),rec->pos+1, nals*(nals+1)/2,j);
+
+            // most common case: RR
+            if ( jmax==0 )
+            {
+                iarr[2*i] = iarr[2*i+1] = bcf_gt_unphased(0);
+                continue;
+            }
+
+            int a,b;
+            bcf_gt2alleles(jmax,&a,&b);
+            iarr[2*i]   = bcf_gt_unphased(a);
+            iarr[2*i+1] = bcf_gt_unphased(b);
+        }
+        bcf_update_genotypes(out_hdr,rec,iarr,nsmpl*2);
+        if ( drop_source_tag )
+            bcf_update_format_float(out_hdr,rec,"GP",NULL,0);
+    }
     return rec;
 }
 

From 206c4ee33f6a16e730b51c85c1ce53b63a36bd63 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 28 Jun 2016 10:20:30 +0100
Subject: [PATCH 183/211] tag2tag: add hard-call `--threshold` option; add
 `--gp-to-gt` test

---
 plugins/tag2tag.c | 41 ++++++++++++++++++++++++++---------------
 test/test.pl      |  1 +
 test/view.GP.vcf  | 42 ++++++++++++++++++++++++++++++++++++++++++
 test/view.GT.vcf  | 42 ++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 111 insertions(+), 15 deletions(-)
 create mode 100644 test/view.GP.vcf
 create mode 100644 test/view.GT.vcf

diff --git a/plugins/tag2tag.c b/plugins/tag2tag.c
index f56e00eb1..0dc877a16 100644
--- a/plugins/tag2tag.c
+++ b/plugins/tag2tag.c
@@ -37,29 +37,30 @@ DEALINGS IN THE SOFTWARE.  */
 
 static int mode = 0, drop_source_tag = 0;
 static bcf_hdr_t *in_hdr, *out_hdr;
-static float *farr = NULL;
+static float *farr = NULL, thresh = 0.1;
 static int32_t *iarr = NULL;
 static int mfarr = 0, miarr = 0;
 
 const char *about(void)
 {
-    return "Convert between similar tags, such as GL and GP.\n";
+    return "Convert between similar tags, such as GL, PL and GP.\n";
 }
 
 const char *usage(void)
 {
     return 
         "\n"
-        "About: Convert between similar tags, such as GL and GP.\n"
+        "About: Convert between similar tags, such as GL, PL and GP.\n"
         "Usage: bcftools +tag2tag [General Options] -- [Plugin Options]\n"
         "Options:\n"
         "   run \"bcftools plugin\" for a list of common options\n"
         "\n"
         "Plugin options:\n"
-        "       --gp-to-gl    convert FORMAT/GP to FORMAT/GL\n"
-        "       --gp-to-gt    convert FORMAT/GP to FORMAT/GT by taking argmax of GP\n"
-        "       --gl-to-pl    convert FORMAT/GL to FORMAT/PL\n"
-        "   -r, --replace     drop the source tag\n"
+        "       --gp-to-gl           convert FORMAT/GP to FORMAT/GL\n"
+        "       --gp-to-gt           convert FORMAT/GP to FORMAT/GT by taking argmax of GP\n"
+        "       --gl-to-pl           convert FORMAT/GL to FORMAT/PL\n"
+        "   -r, --replace            drop the source tag\n"
+        "   -t, --threshold <float>  threshold for GP to GT hard-call [0.1]\n"
         "\n"
         "Example:\n"
         "   bcftools +tag2tag in.vcf -- -r --gp-to-gl\n"
@@ -79,14 +80,15 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
 {
     static struct option loptions[] =
     {
-        {"replace",0,0,'r'},
-        {"gp-to-gl",0,0,1},
-        {"gl-to-pl",0,0,2},
-        {"gp-to-gt",0,0,3},
-        {0,0,0,0}
+        {"replace",no_argument,NULL,'r'},
+        {"gp-to-gl",no_argument,NULL,1},
+        {"gl-to-pl",no_argument,NULL,2},
+        {"gp-to-gt",no_argument,NULL,3},
+        {"threshold",required_argument,NULL,'t'},
+        {NULL,0,NULL,0}
     };
     int c;
-    while ((c = getopt_long(argc, argv, "?hr",loptions,NULL)) >= 0)
+    while ((c = getopt_long(argc, argv, "?hrt:",loptions,NULL)) >= 0)
     {
         switch (c) 
         {
@@ -94,6 +96,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
             case  2 : mode = GL_TO_PL; break;
             case  3 : mode = GP_TO_GT; break;
             case 'r': drop_source_tag = 1; break;
+            case 't': thresh = atof(optarg); break;
             case 'h':
             case '?':
             default: error("%s", usage()); break;
@@ -108,8 +111,10 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
         init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GL,Number=G,Type=Float,Description=\"Genotype Likelihoods\">");
     else if ( mode==GL_TO_PL )
         init_header(out_hdr,drop_source_tag?"GL":NULL,BCF_HL_FMT,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"Phred scaled genotype likelihoods\">");
-    else if ( mode==GP_TO_GT )
+    else if ( mode==GP_TO_GT ) {
+        if (thresh<0||thresh>1) error("--threshold must be in the range [0,1]: %f\n", thresh);
         init_header(out_hdr,drop_source_tag?"GP":NULL,BCF_HL_FMT,"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">");
+    }
 
     return 0;
 }
@@ -181,7 +186,7 @@ bcf1_t *process(bcf1_t *rec)
             // haploid genotype
             if ( j==nals )
             {
-                iarr[2*i]   = bcf_gt_unphased(jmax);
+                iarr[2*i]   = ptr[jmax] < 1-thresh ? bcf_gt_missing : bcf_gt_unphased(jmax);
                 iarr[2*i+1] = bcf_int32_vector_end;
                 continue;
             }
@@ -190,6 +195,12 @@ bcf1_t *process(bcf1_t *rec)
                 error("Wrong number of GP values for diploid genotype at %s:%d, expected %d, found %d\n",
                     bcf_seqname(in_hdr,rec),rec->pos+1, nals*(nals+1)/2,j);
 
+            if (ptr[jmax] < 1-thresh)
+            {
+                iarr[2*i] = iarr[2*i+1] = bcf_gt_missing;
+                continue;
+            }
+
             // most common case: RR
             if ( jmax==0 )
             {
diff --git a/test/test.pl b/test/test.pl
index bb4323cd8..c1bf1211f 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -190,6 +190,7 @@
 test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -g GT');
 test_vcf_plugin($opts,in=>'vcf2sex',out=>'vcf2sex.out',cmd=>'+vcf2sex',args=>'-- -g GT -n 5');
 test_vcf_plugin($opts,in=>'view.GL',out=>'view.PL.vcf',cmd=>'+tag2tag --no-version',args=>'-- -r --gl-to-pl');
+test_vcf_plugin($opts,in=>'view.GP',out=>'view.GT.vcf',cmd=>'+tag2tag --no-version',args=>'-- -r --gp-to-gt -t 0.2');
 test_vcf_plugin($opts,in=>'merge.a',out=>'fill-tags.out',cmd=>'+fill-tags --no-version',args=>'-- -t AN,AC,AC_Hom,AC_Het,AC_Hemi');
 test_vcf_plugin($opts,in=>'view',out=>'fill-tags.2.out',cmd=>'+fill-tags --no-version',args=>'-- -t AC,AN,AF,NS');
 test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.out',cmd=>'+GTisec',args=>' | grep -v bcftools');
diff --git a/test/view.GP.vcf b/test/view.GP.vcf
new file mode 100644
index 000000000..cf5beed2d
--- /dev/null
+++ b/test/view.GP.vcf
@@ -0,0 +1,42 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=22,length=51304566>
+##contig=<ID=Y,length=59373566>
+##FORMAT=<ID=GP,Number=G,Type=Float,Description="Phred-scaled genotype posterior probabilities">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12890	NA12891	NA12892
+22	16050159	.	C	T	68	.	.	GP	0.962,0.038,0	0,1,0	1,0,0
+22	16050252	.	A	T	85	.	.	GP	0.934,0.059,0.007	0,1,0	1,0,0
+22	16051249	.	T	C	32.1761	.	.	GP	0,1,0	1,0,0	1,0,0
+22	16051347	.	G	C	283	.	.	GP	0,0.443,0.557	0,1,0	1,0,0
+22	16051453	.	A	C	3.42882	.	.	GP	0.001,0.999,0	1,0,0	1,0,0
+22	16051497	.	A	G	362	.	.	GP	0,0.008,0.992	0,1,0	1,0,0
+22	16051968	.	C	A	136	.	.	GP	0.972,0.024,0.003	0,1,0	1,0,0
+22	16052167	.	AAAACAAACAAACAAACAAACAAACAAACAAAC	AAAACAAACAAACAAACAAACAAACAAACAAACAAACAAAC	217	.	.	GP	0.333,0.333,0.333	0,0,1	1,0,0
+22	16052169	.	AACAAACA	AACAAACAGACAAACA	241	.	.	GP	0.003,0.995,0.002	0,1,0	1,0,0
+22	16052180	.	AAAC	AAACCAACTAAC	221	.	.	GP	0.909,0.091,0	0,1,0	1,0,0
+22	16052239	.	A	G	172	.	.	GP	0.984,0.016,0	0,1,0	1,0,0
+22	16052513	.	G	C	153	.	.	GP	1,0,0	0,1,0	1,0,0
+22	16052618	.	G	A	124	.	.	GP	0.997,0.003,0	0,1,0	1,0,0
+22	16053659	.	A	C	352	.	.	GP	0,0.002,0.998	0,0,1	1,0,0
+22	16053791	.	C	A	287	.	.	GP	0,1,0	0,1,0	1,0,0
+22	16054454	.	C	T	14.2772	.	.	GP	0,0.76,0.24	1,0,0	1,0,0
+22	16054667	.	C	G	179	.	.	GP	0.998,0.002,0	0,1,0	1,0,0
+22	16054740	.	A	G	126	.	.	GP	0.994,0.006,0	0,1,0	1,0,0
+22	16055942	.	C	T	385	.	.	GP	0,0.008,0.992	0,0,1	1,0,0
+22	16056126	.	G	A	263	.	.	GP	0,0.969,0.031	0,1,0	1,0,0
+22	16056854	.	G	GA	17.3105	.	.	GP	0.996,0.004,0	0,1,0	1,0,0
+22	16057248	.	G	A	167	.	.	GP	0.988,0.012,0	0,1,0	1,0,0
+22	16057320	.	G	A	20.0168	.	.	GP	0,0.998,0.002	1,0,0	1,0,0
+22	16057417	.	C	T	16.3704	.	.	GP	0,1,0	1,0,0	1,0,0
+22	16058070	.	A	G	452	.	.	GP	0,0,1	0,0,1	0,0,1
+22	16058415	.	A	G	212	.	.	GP	0.997,0.003,0	0,0,1	1,0,0
+22	16058463	.	C	T	136	.	.	GP	0,0.666,0.334	1,0,0	1,0,0
+22	16058758	.	C	A	107	.	.	GP	0,0.166,0.834	1,0,0	1,0,0
+22	16058766	.	G	A	15.517	.	.	GP	0.999,0.001,0	0,0.201,0.799	1,0,0
+22	16058852	.	A	T	198	.	.	GP	0,0.112,0.888	0,0,1	1,0,0
+22	16058883	.	A	G	129	.	.	GP	0,0.334,0.666	0,0,1	1,0,0
+22	16059081	.	A	G	212	.	.	GP	0.984,0.016,0	0,0,1	1,0,0
+22	16059734	.	C	T	114	.	.	GP	0,0.038,0.962	1,0,0	1,0,0
+22	16059753	.	A	T	212	.	.	GP	0.998,0.002,0	0,0,1	1,0,0
+Y	16059973	.	C	A	195	.	.	GP	0.975,0.025	1,0	0,1
+Y	16060178	.	G	A	187	.	.	GP	0.969,0.031	0,1	0.5,0.5
diff --git a/test/view.GT.vcf b/test/view.GT.vcf
new file mode 100644
index 000000000..2cf172559
--- /dev/null
+++ b/test/view.GT.vcf
@@ -0,0 +1,42 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=22,length=51304566>
+##contig=<ID=Y,length=59373566>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12890	NA12891	NA12892
+22	16050159	.	C	T	68	.	.	GT	0/0	0/1	0/0
+22	16050252	.	A	T	85	.	.	GT	0/0	0/1	0/0
+22	16051249	.	T	C	32.1761	.	.	GT	0/1	0/0	0/0
+22	16051347	.	G	C	283	.	.	GT	./.	0/1	0/0
+22	16051453	.	A	C	3.42882	.	.	GT	0/1	0/0	0/0
+22	16051497	.	A	G	362	.	.	GT	1/1	0/1	0/0
+22	16051968	.	C	A	136	.	.	GT	0/0	0/1	0/0
+22	16052167	.	AAAACAAACAAACAAACAAACAAACAAACAAAC	AAAACAAACAAACAAACAAACAAACAAACAAACAAACAAAC	217	.	.	GT	./.	1/1	0/0
+22	16052169	.	AACAAACA	AACAAACAGACAAACA	241	.	.	GT	0/1	0/1	0/0
+22	16052180	.	AAAC	AAACCAACTAAC	221	.	.	GT	0/0	0/1	0/0
+22	16052239	.	A	G	172	.	.	GT	0/0	0/1	0/0
+22	16052513	.	G	C	153	.	.	GT	0/0	0/1	0/0
+22	16052618	.	G	A	124	.	.	GT	0/0	0/1	0/0
+22	16053659	.	A	C	352	.	.	GT	1/1	1/1	0/0
+22	16053791	.	C	A	287	.	.	GT	0/1	0/1	0/0
+22	16054454	.	C	T	14.2772	.	.	GT	./.	0/0	0/0
+22	16054667	.	C	G	179	.	.	GT	0/0	0/1	0/0
+22	16054740	.	A	G	126	.	.	GT	0/0	0/1	0/0
+22	16055942	.	C	T	385	.	.	GT	1/1	1/1	0/0
+22	16056126	.	G	A	263	.	.	GT	0/1	0/1	0/0
+22	16056854	.	G	GA	17.3105	.	.	GT	0/0	0/1	0/0
+22	16057248	.	G	A	167	.	.	GT	0/0	0/1	0/0
+22	16057320	.	G	A	20.0168	.	.	GT	0/1	0/0	0/0
+22	16057417	.	C	T	16.3704	.	.	GT	0/1	0/0	0/0
+22	16058070	.	A	G	452	.	.	GT	1/1	1/1	1/1
+22	16058415	.	A	G	212	.	.	GT	0/0	1/1	0/0
+22	16058463	.	C	T	136	.	.	GT	./.	0/0	0/0
+22	16058758	.	C	A	107	.	.	GT	1/1	0/0	0/0
+22	16058766	.	G	A	15.517	.	.	GT	0/0	./.	0/0
+22	16058852	.	A	T	198	.	.	GT	1/1	1/1	0/0
+22	16058883	.	A	G	129	.	.	GT	./.	1/1	0/0
+22	16059081	.	A	G	212	.	.	GT	0/0	1/1	0/0
+22	16059734	.	C	T	114	.	.	GT	1/1	0/0	0/0
+22	16059753	.	A	T	212	.	.	GT	0/0	1/1	0/0
+Y	16059973	.	C	A	195	.	.	GT	0	0	1
+Y	16060178	.	G	A	187	.	.	GT	0	1	.

From 3c7df1dd22ad42f9dfe0e4afc83e690db5019918 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Wed, 3 Feb 2016 15:10:18 +0000
Subject: [PATCH 184/211] plugin: new trio-switch-rate plugin

---
 plugins/trio-switch-rate.c | 264 +++++++++++++++++++++++++++++++++++++
 1 file changed, 264 insertions(+)
 create mode 100644 plugins/trio-switch-rate.c

diff --git a/plugins/trio-switch-rate.c b/plugins/trio-switch-rate.c
new file mode 100644
index 000000000..254d8c1fd
--- /dev/null
+++ b/plugins/trio-switch-rate.c
@@ -0,0 +1,264 @@
+/* The MIT License
+
+   Copyright (c) 2016 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <htslib/kstring.h>
+#include <htslib/kseq.h>
+#include <htslib/khash_str2int.h>
+#include "bcftools.h"
+
+typedef struct
+{
+    int father, mother, child;      // VCF sample index
+    int prev, ipop;
+    uint32_t err, nswitch, ntest;
+}
+trio_t;
+
+typedef struct
+{
+    char *name;
+    uint32_t err, nswitch, ntest, ntrio;
+    float pswitch;
+}
+pop_t;
+
+typedef struct
+{
+    int argc;
+    char **argv;
+    bcf_hdr_t *hdr;
+    trio_t *trio;
+    int ntrio, mtrio;
+    int32_t *gt_arr;
+    int npop;
+    pop_t *pop;
+    int mgt_arr, prev_rid;
+}
+args_t;
+
+args_t args;
+
+const char *about(void)
+{
+    return "Calculate phase switch rate in trio samples, children samples must have phased GTs.\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Calculate phase switch rate in trio children.\n"
+        "Usage: bcftools +trio-swich-rate [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -p, --ped <file>        \n"
+        "\n"
+        "Example:\n"
+        "   bcftools +trio-switch-rate file.bcf -- -p file.ped\n"
+        "\n";
+}
+
+void parse_ped(args_t *args, char *fname)
+{
+    htsFile *fp = hts_open(fname, "r");
+    if ( !fp ) error("Could not read: %s\n", fname);
+
+    kstring_t str = {0,0,0};
+    if ( hts_getline(fp, KS_SEP_LINE, &str) <= 0 ) error("Empty file: %s\n", fname);
+
+    void *pop2i = khash_str2int_init();
+
+    int moff = 0, *off = NULL;
+    while ( hts_getline(fp, KS_SEP_LINE, &str)>=0 )
+    {
+        // BB03    HG01884 HG01885 HG01956 2   0   ACB child   0   0   0   0
+        int ncols = ksplit_core(str.s,'\t',&moff,&off);
+        if ( ncols<4 ) error("Could not parse the ped file: %s\n", str.s);
+
+        int father = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[2]]);
+        if ( father<0 ) continue;
+        int mother = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[3]]);
+        if ( mother<0 ) continue;
+        int child = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[1]]);
+        if ( child<0 ) continue;
+
+        args->ntrio++;
+        hts_expand0(trio_t,args->ntrio,args->mtrio,args->trio);
+        trio_t *trio = &args->trio[args->ntrio-1];
+        trio->father = father;
+        trio->mother = mother;
+        trio->child  = child;
+
+        char *pop_name = &str.s[off[6]];
+        if ( !khash_str2int_has_key(pop2i,pop_name) )
+        {
+            pop_name = strdup(&str.s[off[6]]);
+            khash_str2int_set(pop2i,pop_name,args->npop);
+            args->npop++;
+            args->pop = (pop_t*) realloc(args->pop,args->npop*sizeof(*args->pop));
+            memset(args->pop+args->npop-1,0,sizeof(*args->pop));
+            args->pop[args->npop-1].name = pop_name;
+        }
+        khash_str2int_get(pop2i,pop_name,&trio->ipop);
+        args->pop[trio->ipop].ntrio++;
+    }
+
+    khash_str2int_destroy(pop2i);
+    free(str.s);
+    free(off);
+    hts_close(fp);
+}
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    memset(&args,0,sizeof(args_t));
+    args.argc   = argc; args.argv = argv;
+    args.prev_rid = -1;
+    args.hdr = in;
+    char *ped_fname = NULL;
+    static struct option loptions[] =
+    {
+        {"ped",1,0,'p'},
+        {0,0,0,0}
+    };
+    int c;
+    while ((c = getopt_long(argc, argv, "?hp:",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 'p': ped_fname = optarg; break;
+            case 'h':
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( !ped_fname ) error("Expected the -p option\n");
+    parse_ped(&args, ped_fname);
+    return 1;
+}
+
+typedef struct
+{
+    int a, b, phased;
+}
+gt_t;
+
+inline int parse_genotype(gt_t *gt, int32_t *ptr)
+{
+    if ( ptr[0]==bcf_gt_missing ) return 0;
+    if ( ptr[1]==bcf_gt_missing ) return 0;
+    if ( ptr[1]==bcf_int32_vector_end ) return 0;
+    gt->phased = bcf_gt_is_phased(ptr[1]) ? 1 : 0;
+    gt->a = bcf_gt_allele(ptr[0]); if ( gt->a > 1 ) return 0;  // consider only the first two alleles at biallelic sites
+    gt->b = bcf_gt_allele(ptr[1]); if ( gt->b > 1 ) return 0;
+    return 1;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    int ngt = bcf_get_genotypes(args.hdr, rec, &args.gt_arr, &args.mgt_arr);
+    if ( ngt<0 ) return NULL;
+    ngt /= bcf_hdr_nsamples(args.hdr);
+    if ( ngt!=2 ) return NULL;
+
+    int i;
+    if ( rec->rid!=args.prev_rid )
+    {
+        args.prev_rid = rec->rid;
+        for (i=0; i<args.ntrio; i++) args.trio[i].prev = 0;
+    }
+
+    gt_t child, father, mother;
+    for (i=0; i<args.ntrio; i++)
+    {
+        trio_t *trio = &args.trio[i];
+
+        if ( !parse_genotype(&child, args.gt_arr + ngt*trio->child) ) continue;
+        if ( !child.phased ) continue;
+        if ( child.a+child.b != 1 ) continue;       // child is not a het
+
+        if ( !parse_genotype(&father, args.gt_arr + ngt*trio->father) ) continue;
+        if ( !parse_genotype(&mother, args.gt_arr + ngt*trio->mother) ) continue;
+        if ( father.a+father.b == 1 && mother.a+mother.b == 1 ) continue;     // both parents are hets
+        if ( father.a+father.b == mother.a+mother.b ) { trio->err++; continue; }    // mendelian error
+
+        int test_phase = 0; 
+        if ( father.a==father.b ) test_phase = 1 + (child.a==father.a);
+        else if ( mother.a==mother.b ) test_phase = 1 + (child.b==mother.a);
+        if ( trio->prev > 0 )
+        {
+            if ( trio->prev!=test_phase ) trio->nswitch++;
+        }
+        trio->ntest++;
+        trio->prev = test_phase;
+    }
+    return NULL;
+}
+
+void destroy(void)
+{
+    int i;
+    printf("# This file was produced by: bcftools +trio-switch-rate(%s+htslib-%s)\n", bcftools_version(),hts_version());
+    printf("# The command line was:\tbcftools +%s", args.argv[0]);
+    for (i=1; i<args.argc; i++) printf(" %s",args.argv[i]);
+    printf("\n#\n");
+    printf("# TRIO\t[2]Father\t[3]Mother\t[4]Child\t[5]nTested\t[6]nMendelian Errors\t[7]nSwitch\t[8]nSwitch (%%)\n");
+    printf("# POP\t[2]Name\t[3]\t[4]Number of trios\t[5]avgTested\t[6]avgMendelian Errors\t[7]avgSwitch\t[8]avgSwitch (%%)\n");
+    for (i=0; i<args.ntrio; i++)
+    {
+        trio_t *trio = &args.trio[i];
+        printf("TRIO\t%s\t%s\t%s\t%d\t%d\t%d\t%.2f\n",
+            bcf_hdr_int2id(args.hdr,BCF_DT_SAMPLE,trio->father),
+            bcf_hdr_int2id(args.hdr,BCF_DT_SAMPLE,trio->mother),
+            bcf_hdr_int2id(args.hdr,BCF_DT_SAMPLE,trio->child),
+            trio->ntest, trio->err, trio->nswitch, trio->nswitch*100./trio->ntest
+        );
+        pop_t *pop = &args.pop[trio->ipop];
+        pop->err     += trio->err;
+        pop->nswitch += trio->nswitch;
+        pop->ntest   += trio->ntest;
+        pop->pswitch += trio->nswitch*100./trio->ntest;
+    }
+    for (i=0; i<args.npop; i++)
+    {
+        pop_t *pop = &args.pop[i];
+        printf("POP\t%s\t%d\t%.0f\t%.0f\t%.0f\t%.2f\n", pop->name,pop->ntrio,
+            (float)pop->ntest/pop->ntrio,(float)pop->err/pop->ntrio,(float)pop->nswitch/pop->ntrio,
+            pop->pswitch/pop->ntrio);
+    }
+    for (i=0; i<args.npop; i++) free(args.pop[i].name);
+    free(args.pop);
+    free(args.trio);
+    free(args.gt_arr);
+}

From a0107db87aa2201a4b00a6b46370d94424e7f79c Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 27 Jun 2016 13:31:22 +0100
Subject: [PATCH 185/211] trio-switch-rate: add test and clean a few edge cases

* added a test
* do not ignore the first line of the PED file. Standard PED files
  do not have a header line
* prevent segfault when population column is not provided - this
  is an optional column
* fix divide by zero case
* PED files can be space or tab delimited
* declare inline `parse_genotype` function to avoid undefined symbol error when compiling with `-std=gnu99`
---
 plugins/trio-switch-rate.c | 57 ++++++++++++++++++++++----------------
 test/test.pl               |  1 +
 test/trio.out              |  7 +++++
 test/trio.ped              |  6 ++++
 test/trio.vcf              | 16 +++++++++++
 5 files changed, 63 insertions(+), 24 deletions(-)
 create mode 100644 test/trio.out
 create mode 100644 test/trio.ped
 create mode 100644 test/trio.vcf

diff --git a/plugins/trio-switch-rate.c b/plugins/trio-switch-rate.c
index 254d8c1fd..34f840dd1 100644
--- a/plugins/trio-switch-rate.c
+++ b/plugins/trio-switch-rate.c
@@ -82,7 +82,8 @@ const char *usage(void)
         "   run \"bcftools plugin\" for a list of common options\n"
         "\n"
         "Plugin options:\n"
-        "   -p, --ped <file>        \n"
+        "   -p, --ped <file>        PED file with optional 7th column to group\n"
+        "                           results by population\n"
         "\n"
         "Example:\n"
         "   bcftools +trio-switch-rate file.bcf -- -p file.ped\n"
@@ -100,10 +101,11 @@ void parse_ped(args_t *args, char *fname)
     void *pop2i = khash_str2int_init();
 
     int moff = 0, *off = NULL;
-    while ( hts_getline(fp, KS_SEP_LINE, &str)>=0 )
+    do
     {
+        // familyID    sampleID paternalID maternalID sex   phenotype   population relationship   siblings   secondOrder   thirdOrder   children    comment
         // BB03    HG01884 HG01885 HG01956 2   0   ACB child   0   0   0   0
-        int ncols = ksplit_core(str.s,'\t',&moff,&off);
+        int ncols = ksplit_core(str.s,0,&moff,&off);
         if ( ncols<4 ) error("Could not parse the ped file: %s\n", str.s);
 
         int father = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[2]]);
@@ -120,19 +122,21 @@ void parse_ped(args_t *args, char *fname)
         trio->mother = mother;
         trio->child  = child;
 
-        char *pop_name = &str.s[off[6]];
-        if ( !khash_str2int_has_key(pop2i,pop_name) )
-        {
-            pop_name = strdup(&str.s[off[6]]);
-            khash_str2int_set(pop2i,pop_name,args->npop);
-            args->npop++;
-            args->pop = (pop_t*) realloc(args->pop,args->npop*sizeof(*args->pop));
-            memset(args->pop+args->npop-1,0,sizeof(*args->pop));
-            args->pop[args->npop-1].name = pop_name;
+        if (ncols>6) {
+            char *pop_name = &str.s[off[6]];
+            if ( !khash_str2int_has_key(pop2i,pop_name) )
+            {
+                pop_name = strdup(&str.s[off[6]]);
+                khash_str2int_set(pop2i,pop_name,args->npop);
+                args->npop++;
+                args->pop = (pop_t*) realloc(args->pop,args->npop*sizeof(*args->pop));
+                memset(args->pop+args->npop-1,0,sizeof(*args->pop));
+                args->pop[args->npop-1].name = pop_name;
+            }
+            khash_str2int_get(pop2i,pop_name,&trio->ipop);
+            args->pop[trio->ipop].ntrio++;
         }
-        khash_str2int_get(pop2i,pop_name,&trio->ipop);
-        args->pop[trio->ipop].ntrio++;
-    }
+    } while ( hts_getline(fp, KS_SEP_LINE, &str)>=0 );
 
     khash_str2int_destroy(pop2i);
     free(str.s);
@@ -149,7 +153,7 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
     char *ped_fname = NULL;
     static struct option loptions[] =
     {
-        {"ped",1,0,'p'},
+        {"ped",required_argument,NULL,'p'},
         {0,0,0,0}
     };
     int c;
@@ -174,6 +178,8 @@ typedef struct
 }
 gt_t;
 
+int parse_genotype(gt_t *gt, int32_t *ptr);
+
 inline int parse_genotype(gt_t *gt, int32_t *ptr)
 {
     if ( ptr[0]==bcf_gt_missing ) return 0;
@@ -230,11 +236,10 @@ void destroy(void)
 {
     int i;
     printf("# This file was produced by: bcftools +trio-switch-rate(%s+htslib-%s)\n", bcftools_version(),hts_version());
-    printf("# The command line was:\tbcftools +%s", args.argv[0]);
+    printf("# The command line was:\tbcftools +trio-switch-rate %s", args.argv[0]);
     for (i=1; i<args.argc; i++) printf(" %s",args.argv[i]);
     printf("\n#\n");
     printf("# TRIO\t[2]Father\t[3]Mother\t[4]Child\t[5]nTested\t[6]nMendelian Errors\t[7]nSwitch\t[8]nSwitch (%%)\n");
-    printf("# POP\t[2]Name\t[3]\t[4]Number of trios\t[5]avgTested\t[6]avgMendelian Errors\t[7]avgSwitch\t[8]avgSwitch (%%)\n");
     for (i=0; i<args.ntrio; i++)
     {
         trio_t *trio = &args.trio[i];
@@ -242,14 +247,18 @@ void destroy(void)
             bcf_hdr_int2id(args.hdr,BCF_DT_SAMPLE,trio->father),
             bcf_hdr_int2id(args.hdr,BCF_DT_SAMPLE,trio->mother),
             bcf_hdr_int2id(args.hdr,BCF_DT_SAMPLE,trio->child),
-            trio->ntest, trio->err, trio->nswitch, trio->nswitch*100./trio->ntest
+            trio->ntest, trio->err, trio->nswitch, trio->ntest ? trio->nswitch*100./trio->ntest : 0
         );
-        pop_t *pop = &args.pop[trio->ipop];
-        pop->err     += trio->err;
-        pop->nswitch += trio->nswitch;
-        pop->ntest   += trio->ntest;
-        pop->pswitch += trio->nswitch*100./trio->ntest;
+        if (args.npop) {
+            pop_t *pop = &args.pop[trio->ipop];
+            pop->err     += trio->err;
+            pop->nswitch += trio->nswitch;
+            pop->ntest   += trio->ntest;
+            pop->pswitch += trio->ntest ? trio->nswitch*100./trio->ntest : 0;
+        }
     }
+    printf("# POP\tpopulation or other grouping defined by an optional 7-th column of the PED file\n");
+    printf("# POP\t[2]Name\t[3]Number of trios\t[4]avgTested\t[5]avgMendelian Errors\t[6]avgSwitch\t[7]avgSwitch (%%)\n");
     for (i=0; i<args.npop; i++)
     {
         pop_t *pop = &args.pop[i];
diff --git a/test/test.pl b/test/test.pl
index c1bf1211f..992451ef4 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -201,6 +201,7 @@
 test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.m.out',cmd=>'+GTisec',args=>'-- -m | grep -v bcftools');
 test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.mv.out',cmd=>'+GTisec',args=>'-- -mv | grep -v bcftools');
 test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.v.out',cmd=>'+GTisec',args=>'-- -v | grep -v bcftools');
+test_vcf_plugin($opts,in=>'trio',out=>'trio.out',cmd=>'+trio-switch-rate',args=>'-- -p {PATH}/trio.ped | grep -v bcftools');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.vcf.out',do_bcf=>0,args=>'');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.bcf.out',do_bcf=>1,args=>'');
 test_vcf_concat($opts,in=>['concat.2.a','concat.2.b'],out=>'concat.2.vcf.out',do_bcf=>0,args=>'-a');
diff --git a/test/trio.out b/test/trio.out
new file mode 100644
index 000000000..6c9f4a673
--- /dev/null
+++ b/test/trio.out
@@ -0,0 +1,7 @@
+#
+# TRIO	[2]Father	[3]Mother	[4]Child	[5]nTested	[6]nMendelian Errors	[7]nSwitch	[8]nSwitch (%)
+TRIO	HG00101	HG00102	HG00100	5	4	0	0.00
+TRIO	HG00201	HG00202	HG00200	11	0	2	18.18
+# POP	population or other grouping defined by an optional 7-th column of the PED file
+# POP	[2]Name	[3]Number of trios	[4]avgTested	[5]avgMendelian Errors	[6]avgSwitch	[7]avgSwitch (%)
+POP	CEU	2	8	2	1	9.09
diff --git a/test/trio.ped b/test/trio.ped
new file mode 100644
index 000000000..22fa04951
--- /dev/null
+++ b/test/trio.ped
@@ -0,0 +1,6 @@
+HG00100 HG00100 HG00101 HG00102 2 0 CEU
+HG00101 HG00101 0 0 1 0 CEU
+HG00102 HG00102 0 0 2 0 CEU
+HG00200 HG00200 HG00201 HG00202 2 0 CEU
+HG00201 HG00201 0 0 1 0 CEU
+HG00202 HG00202 0 0 2 0 CEU
diff --git a/test/trio.vcf b/test/trio.vcf
new file mode 100644
index 000000000..a9f36c0c4
--- /dev/null
+++ b/test/trio.vcf
@@ -0,0 +1,16 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=20,length=81195210>
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102	HG00200	HG00201	HG00202
+20	302	.	T	TA	999	.	.	GT	0|1	1|0	1|1	0|1	1|0	1|1
+20	828	.	T	C	999	.	.	GT	0|1	1|1	1|1	0|1	1|0	1|1
+20	834	.	G	A	999	.	.	GT	0|1	0|1	1|1	1|0	1|0	1|1
+20	1665	.	T	C	999	.	.	GT	1|0	0|1	0|1	0|1	1|0	1|1
+20	1869	.	A	T	999	.	.	GT	0|1	0|0	1|1	0|1	1|0	1|1
+20	2041	.	G	A	999	.	.	GT	0|1	1|1	1|1	0|1	1|0	1|1
+20	2220	.	G	A	999	.	.	GT	0|1	1|0	1|1	0|1	1|0	1|1
+20	2564	.	A	G	999	.	.	GT	0|1	1|1	1|1	0|1	1|0	1|1
+20	3104	.	C	T	999	.	.	GT	0|0	0|0	0|1	0|1	1|0	1|1
+20	3587	.	G	A	999	.	.	GT	0|1	0|1	1|1	0|1	1|0	1|1
+20	3936	.	A	G	999	.	.	GT	0|1	1|1	1|1	0|1	1|0	1|1

From c78a6f50bbb7c5dde953d7896dbde5f82b45a27f Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 17 Mar 2016 15:26:35 +0000
Subject: [PATCH 186/211] plugin: new plugin to detect sites with statistically
 significant differences in FMT/AD

---
 plugins/ad-bias.c | 206 ++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 206 insertions(+)
 create mode 100644 plugins/ad-bias.c

diff --git a/plugins/ad-bias.c b/plugins/ad-bias.c
new file mode 100644
index 000000000..6dcac7c96
--- /dev/null
+++ b/plugins/ad-bias.c
@@ -0,0 +1,206 @@
+/* The MIT License
+
+   Copyright (c) 2016 Genome Research Ltd.
+
+   Author: Petr Danecek <pd3@sanger.ac.uk>
+   
+   Permission is hereby granted, free of charge, to any person obtaining a copy
+   of this software and associated documentation files (the "Software"), to deal
+   in the Software without restriction, including without limitation the rights
+   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+   copies of the Software, and to permit persons to whom the Software is
+   furnished to do so, subject to the following conditions:
+   
+   The above copyright notice and this permission notice shall be included in
+   all copies or substantial portions of the Software.
+   
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+   THE SOFTWARE.
+
+ */
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <getopt.h>
+#include <math.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+#include <htslib/kstring.h>
+#include <htslib/kseq.h>
+#include <htslib/kfunc.h>
+#include <inttypes.h>
+#include "bcftools.h"
+#include "convert.h"
+
+typedef struct
+{
+    int smpl,ctrl;      // VCF sample index
+    const char *smpl_name, *ctrl_name;
+}
+pair_t;
+
+typedef struct
+{
+    bcf_hdr_t *hdr;
+    pair_t *pair;
+    int npair, mpair;
+    int32_t *ad_arr;
+    int mad_arr;
+    double th;
+    convert_t *convert;
+    kstring_t str;
+    uint64_t nsite,ncmp;
+}
+args_t;
+
+args_t args;
+
+const char *about(void)
+{
+    return "Find positions with wildly varying ALT allele frequency (Fisher test on FMT/AD).\n";
+}
+
+const char *usage(void)
+{
+    return 
+        "\n"
+        "About: Find positions with wildly varying ALT allele frequency (Fisher test on FMT/AD).\n"
+        "Usage: bcftools +ad-bias [General Options] -- [Plugin Options]\n"
+        "Options:\n"
+        "   run \"bcftools plugin\" for a list of common options\n"
+        "\n"
+        "Plugin options:\n"
+        "   -f, --format <string>       Optional tags to append to output (`bcftools query` style of format)\n"
+        "   -s, --samples <file>        List of sample pairs, one tab-delimited pair per line\n"
+        "   -t, --threshold <float>     Output only hits with p-value smaller than <float> [1e-3]\n"
+        "\n"
+        "Example:\n"
+        "   bcftools +ad-bias file.bcf -- -t 1e-3 -s samples.txt\n"
+        "\n";
+}
+
+void parse_samples(args_t *args, char *fname)
+{
+    htsFile *fp = hts_open(fname, "r");
+    if ( !fp ) error("Could not read: %s\n", fname);
+
+    kstring_t str = {0,0,0};
+    if ( hts_getline(fp, KS_SEP_LINE, &str) <= 0 ) error("Empty file: %s\n", fname);
+
+    int moff = 0, *off = NULL;
+    while ( hts_getline(fp, KS_SEP_LINE, &str)>=0 )
+    {
+        // HPSI0513i-veqz_6    HPSI0513pf-veqz
+        int ncols = ksplit_core(str.s,'\t',&moff,&off);
+        if ( ncols<2 ) error("Could not parse the sample file: %s\n", str.s);
+
+        int smpl = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[0]]);
+        if ( smpl<0 ) continue;
+        int ctrl = bcf_hdr_id2int(args->hdr,BCF_DT_SAMPLE,&str.s[off[1]]);
+        if ( ctrl<0 ) continue;
+
+        args->npair++;
+        hts_expand0(pair_t,args->npair,args->mpair,args->pair);
+        pair_t *pair = &args->pair[args->npair-1];
+        pair->ctrl = ctrl;
+        pair->smpl = smpl;
+        pair->smpl_name = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,pair->smpl);
+        pair->ctrl_name = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,pair->ctrl);
+    }
+
+    free(str.s);
+    free(off);
+    hts_close(fp);
+}
+
+int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
+{
+    memset(&args,0,sizeof(args_t));
+    args.hdr = in;
+    args.th  = 1e-3;
+    char *fname = NULL, *format = NULL;
+    static struct option loptions[] =
+    {
+        {"format",1,0,'f'},
+        {"samples",1,0,'s'},
+        {"threshold",1,0,'t'},
+        {0,0,0,0}
+    };
+    int c;
+    char *tmp;
+    while ((c = getopt_long(argc, argv, "?hs:t:f:",loptions,NULL)) >= 0)
+    {
+        switch (c) 
+        {
+            case 't':
+                args.th = strtod(optarg,&tmp);
+                if ( *tmp ) error("Could not parse: -t %s\n", optarg);
+                break;
+            case 's': fname = optarg; break;
+            case 'f': format = optarg; break;
+            case 'h':
+            case '?':
+            default: error("%s", usage()); break;
+        }
+    }
+    if ( !fname ) error("Expected the -s option\n");
+    parse_samples(&args, fname);
+    if ( format ) args.convert = convert_init(args.hdr, NULL, 0, format);
+    printf("# [1]FT, Fisher Test\t[2]Sample\t[3]Control\t[4]Chrom\t[5]Pos\t[6]smpl.nREF\t[7]smpl.nALT\t[8]ctrl.nREF\t[9]ctrl.nALT\t[10]P-value");
+    if ( format ) printf("\t[11-]User data: %s", format);
+    printf("\n");
+    printf("# [1]SN, Summary Numbers\t[2]Number of Pairs\t[3]Number of Sites\t[4]Number of comparisons\t[5]P-value output threshold\n");
+    return 1;
+}
+
+bcf1_t *process(bcf1_t *rec)
+{
+    int nad = bcf_get_format_int32(args.hdr, rec, "AD", &args.ad_arr, &args.mad_arr);
+    if ( nad<0 ) return NULL;
+    nad /= bcf_hdr_nsamples(args.hdr);
+    
+    if ( args.convert ) convert_line(args.convert, rec, &args.str);
+    args.nsite++;
+
+    int i;
+    for (i=0; i<args.npair; i++)
+    {
+        pair_t *pair = &args.pair[i];
+        int32_t *aptr = args.ad_arr + nad*pair->smpl;
+        int32_t *bptr = args.ad_arr + nad*pair->ctrl;
+
+        if ( aptr[0]==bcf_int32_missing ) continue;
+        if ( bptr[0]==bcf_int32_missing ) continue;
+
+        args.ncmp++;
+
+        int n11 = aptr[0], n12 = aptr[1];
+        int n21 = bptr[0], n22 = bptr[1];
+        double left, right, two;
+        double fisher = kt_fisher_exact(n11,n12,n21,n22, &left,&right,&two);
+        if ( fisher >= args.th ) continue;
+
+        printf("FT\t%s\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%e",
+            pair->smpl_name,pair->ctrl_name,
+            bcf_hdr_id2name(args.hdr,rec->rid), rec->pos+1,
+            n11,n12,n21,n22, fisher
+            );
+        if ( args.convert ) printf("\t%s", args.str.s);
+        printf("\n");
+    }
+    return NULL;
+}
+
+void destroy(void)
+{
+    printf("SN\t%d\t%"PRId64"\t%"PRId64"\t%e\n",args.npair,args.nsite,args.ncmp,args.th);
+    if ( args.convert) convert_destroy(args.convert);
+    free(args.str.s);
+    free(args.pair);
+    free(args.ad_arr);
+}

From dd118898d198836d3cd54f97d891cdf7c8195624 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 28 Jun 2016 09:00:17 +0100
Subject: [PATCH 187/211] ad-bias: do not skip first line of samples file;
 added test

---
 plugins/ad-bias.c    | 22 +++++++++++++---------
 test/ad-bias.out     | 25 +++++++++++++++++++++++++
 test/ad-bias.samples |  2 ++
 test/ad-bias.vcf     | 42 ++++++++++++++++++++++++++++++++++++++++++
 test/test.pl         |  1 +
 5 files changed, 83 insertions(+), 9 deletions(-)
 create mode 100644 test/ad-bias.out
 create mode 100644 test/ad-bias.samples
 create mode 100644 test/ad-bias.vcf

diff --git a/plugins/ad-bias.c b/plugins/ad-bias.c
index 6dcac7c96..f0a993701 100644
--- a/plugins/ad-bias.c
+++ b/plugins/ad-bias.c
@@ -93,7 +93,7 @@ void parse_samples(args_t *args, char *fname)
     if ( hts_getline(fp, KS_SEP_LINE, &str) <= 0 ) error("Empty file: %s\n", fname);
 
     int moff = 0, *off = NULL;
-    while ( hts_getline(fp, KS_SEP_LINE, &str)>=0 )
+    do
     {
         // HPSI0513i-veqz_6    HPSI0513pf-veqz
         int ncols = ksplit_core(str.s,'\t',&moff,&off);
@@ -111,7 +111,7 @@ void parse_samples(args_t *args, char *fname)
         pair->smpl = smpl;
         pair->smpl_name = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,pair->smpl);
         pair->ctrl_name = bcf_hdr_int2id(args->hdr,BCF_DT_SAMPLE,pair->ctrl);
-    }
+    } while ( hts_getline(fp, KS_SEP_LINE, &str)>=0 );
 
     free(str.s);
     free(off);
@@ -126,10 +126,10 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
     char *fname = NULL, *format = NULL;
     static struct option loptions[] =
     {
-        {"format",1,0,'f'},
-        {"samples",1,0,'s'},
-        {"threshold",1,0,'t'},
-        {0,0,0,0}
+        {"format",required_argument,NULL,'f'},
+        {"samples",required_argument,NULL,'s'},
+        {"threshold",required_argument,NULL,'t'},
+        {NULL,0,NULL,0}
     };
     int c;
     char *tmp;
@@ -151,10 +151,13 @@ int init(int argc, char **argv, bcf_hdr_t *in, bcf_hdr_t *out)
     if ( !fname ) error("Expected the -s option\n");
     parse_samples(&args, fname);
     if ( format ) args.convert = convert_init(args.hdr, NULL, 0, format);
-    printf("# [1]FT, Fisher Test\t[2]Sample\t[3]Control\t[4]Chrom\t[5]Pos\t[6]smpl.nREF\t[7]smpl.nALT\t[8]ctrl.nREF\t[9]ctrl.nALT\t[10]P-value");
+    printf("# This file was produced by: bcftools +ad-bias(%s+htslib-%s)\n", bcftools_version(),hts_version());
+    printf("# The command line was:\tbcftools +ad-bias %s", argv[0]);
+    for (c=1; c<argc; c++) printf(" %s",argv[c]);
+    printf("\n#\n");
+    printf("# FT, Fisher Test\t[2]Sample\t[3]Control\t[4]Chrom\t[5]Pos\t[6]smpl.nREF\t[7]smpl.nALT\t[8]ctrl.nREF\t[9]ctrl.nALT\t[10]P-value");
     if ( format ) printf("\t[11-]User data: %s", format);
     printf("\n");
-    printf("# [1]SN, Summary Numbers\t[2]Number of Pairs\t[3]Number of Sites\t[4]Number of comparisons\t[5]P-value output threshold\n");
     return 1;
 }
 
@@ -198,8 +201,9 @@ bcf1_t *process(bcf1_t *rec)
 
 void destroy(void)
 {
+    printf("# SN, Summary Numbers\t[2]Number of Pairs\t[3]Number of Sites\t[4]Number of comparisons\t[5]P-value output threshold\n");
     printf("SN\t%d\t%"PRId64"\t%"PRId64"\t%e\n",args.npair,args.nsite,args.ncmp,args.th);
-    if ( args.convert) convert_destroy(args.convert);
+    if (args.convert) convert_destroy(args.convert);
     free(args.str.s);
     free(args.pair);
     free(args.ad_arr);
diff --git a/test/ad-bias.out b/test/ad-bias.out
new file mode 100644
index 000000000..09939cbc0
--- /dev/null
+++ b/test/ad-bias.out
@@ -0,0 +1,25 @@
+#
+# FT, Fisher Test	[2]Sample	[3]Control	[4]Chrom	[5]Pos	[6]smpl.nREF	[7]smpl.nALT	[8]ctrl.nREF	[9]ctrl.nALT	[10]P-value
+FT	NA12890	NA12892	22	16051249	4	3	55	0	9.254363e-04
+FT	NA12890	NA12892	22	16051347	2	4	43	0	7.079613e-05
+FT	NA12890	NA12891	22	16051453	5	4	39	0	6.475486e-04
+FT	NA12890	NA12892	22	16051453	5	4	47	0	3.430532e-04
+FT	NA12890	NA12892	22	16051497	0	8	44	0	1.328836e-09
+FT	NA12890	NA12892	22	16053659	0	9	30	0	4.718870e-09
+FT	NA12890	NA12892	22	16053791	4	4	32	0	7.659481e-04
+FT	NA12890	NA12892	22	16055942	0	7	31	0	7.923770e-08
+FT	NA12890	NA12892	22	16056126	2	6	27	0	1.725030e-05
+FT	NA12890	NA12891	22	16058415	9	0	0	37	9.076747e-10
+FT	NA12890	NA12891	22	16058463	1	8	40	0	1.995662e-08
+FT	NA12890	NA12892	22	16058463	1	8	45	0	8.649972e-09
+FT	NA12890	NA12891	22	16058758	2	8	19	0	1.048427e-05
+FT	NA12890	NA12892	22	16058758	2	8	34	0	2.539036e-07
+FT	NA12890	NA12891	22	16058766	11	0	0	4	7.326007e-04
+FT	NA12890	NA12892	22	16058852	0	3	36	0	1.094212e-04
+FT	NA12890	NA12891	22	16059081	6	0	0	35	2.224007e-07
+FT	NA12890	NA12891	22	16059734	1	9	23	0	2.592884e-07
+FT	NA12890	NA12892	22	16059734	1	9	31	0	2.854341e-08
+FT	NA12890	NA12891	22	16059753	9	0	0	19	1.447828e-07
+FT	NA12890	NA12891	22	16060178	5	0	1	20	9.121313e-05
+# SN, Summary Numbers	[2]Number of Pairs	[3]Number of Sites	[4]Number of comparisons	[5]P-value output threshold
+SN	2	36	72	1.000000e-03
diff --git a/test/ad-bias.samples b/test/ad-bias.samples
new file mode 100644
index 000000000..426bad068
--- /dev/null
+++ b/test/ad-bias.samples
@@ -0,0 +1,2 @@
+NA12890	NA12891
+NA12890	NA12892
diff --git a/test/ad-bias.vcf b/test/ad-bias.vcf
new file mode 100644
index 000000000..e14231b42
--- /dev/null
+++ b/test/ad-bias.vcf
@@ -0,0 +1,42 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=22,length=51304566>
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA12890	NA12891	NA12892
+22	16050159	.	C	T	68	.	.	GT:AD	0/0:4,0	0/1:6,8	0/0:26,0
+22	16050252	.	A	T	85	.	.	GT:AD	0/0:3,0	0/1:13,13	0/0:40,0
+22	16051249	.	T	C	32.1761	.	.	GT:AD	0/1:4,3	0/0:41,0	0/0:55,0
+22	16051347	.	G	C	283	.	.	GT:AD	1/1:2,4	0/1:20,20	0/0:43,0
+22	16051453	.	A	C	3.42882	.	.	GT:AD	0/1:5,4	0/0:39,0	0/0:47,0
+22	16051497	.	A	G	362	.	.	GT:AD	1/1:0,8	0/1:14,20	0/0:44,0
+22	16051968	.	C	A	136	.	.	GT:AD	0/0:4,0	0/1:11,11	0/0:13,0
+22	16052167	.	AAAACAAACAAACAAACAAACAAACAAACAAAC	AAAACAAACAAACAAACAAACAAACAAACAAACAAACAAAC	217	.	.	GT:AD	./.:0,0	1/1:0,27	0/0:46,0
+22	16052169	.	AACAAACA	AACAAACAGACAAACA	241	.	.	GT:AD	0/1:1,1	0/1:7,29	0/0:54,0
+22	16052180	.	AAAC	AAACCAACTAAC	221	.	.	GT:AD	0/0:2,0	0/1:16,15	0/0:55,0
+22	16052239	.	A	G	172	.	.	GT:AD	0/0:5,0	0/1:12,17	0/0:44,0
+22	16052513	.	G	C	153	.	.	GT:AD	0/0:11,0	0/1:25,16	0/0:38,0
+22	16052618	.	G	A	124	.	.	GT:AD	0/0:7,0	0/1:29,12	0/0:41,0
+22	16053659	.	A	C	352	.	.	GT:AD	1/1:0,9	1/1:0,21	0/0:30,0
+22	16053791	.	C	A	287	.	.	GT:AD	0/1:4,4	0/1:13,16	0/0:32,0
+22	16054454	.	C	T	14.2772	.	.	GT:AD	0/1:2,2	0/0:34,0	0/0:31,0
+22	16054667	.	C	G	179	.	.	GT:AD	0/0:8,0	0/1:12,15	0/0:27,0
+22	16054740	.	A	G	126	.	.	GT:AD	0/0:6,0	0/1:11,16	0/0:26,0
+22	16055942	.	C	T	385	.	.	GT:AD	1/1:0,7	1/1:0,22	0/0:31,0
+22	16056126	.	G	A	263	.	.	GT:AD	0/1:2,6	0/1:12,16	0/0:27,0
+22	16056854	.	G	GA	17.3105	.	.	GT:AD	0/0:7,0	0/1:11,15	0/0:35,0
+22	16057248	.	G	A	167	.	.	GT:AD	0/0:5,0	0/1:15,14	0/0:32,0
+22	16057320	.	G	A	20.0168	.	.	GT:AD	0/1:2,2	0/0:25,0	0/0:36,0
+22	16057417	.	C	T	16.3704	.	.	GT:AD	0/1:2,2	0/0:36,0	0/0:25,0
+22	16058070	.	A	G	452	.	.	GT:AD	1/1:0,4	1/1:0,21	1/1:0,22
+22	16058415	.	A	G	212	.	.	GT:AD	0/0:9,0	1/1:0,37	0/0:35,2
+22	16058463	.	C	T	136	.	.	GT:AD	0/1:1,8	0/0:40,0	0/0:45,0
+22	16058758	.	C	A	107	.	.	GT:AD	1/1:2,8	0/0:19,0	0/0:34,0
+22	16058766	.	G	A	15.517	.	.	GT:AD	0/0:11,0	1/1:0,4	0/0:32,0
+22	16058852	.	A	T	198	.	.	GT:AD	1/1:0,3	1/1:0,19	0/0:36,0
+22	16058883	.	A	G	129	.	.	GT:AD	1/1:0,1	1/1:0,18	0/0:36,0
+22	16059081	.	A	G	212	.	.	GT:AD	0/0:6,0	1/1:0,35	0/0:35,0
+22	16059734	.	C	T	114	.	.	GT:AD	1/1:1,9	0/0:23,0	0/0:31,0
+22	16059753	.	A	T	212	.	.	GT:AD	0/0:9,0	1/1:0,19	0/0:28,0
+22	16059973	.	C	A	195	.	.	GT:AD	0/0:4,0	0/0:21,0	0/1:21,18
+22	16060178	.	G	A	187	.	.	GT:AD	0/0:5,0	1/1:1,20	0/0:36,0
diff --git a/test/test.pl b/test/test.pl
index 992451ef4..a91bd3fa9 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -202,6 +202,7 @@
 test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.mv.out',cmd=>'+GTisec',args=>'-- -mv | grep -v bcftools');
 test_vcf_plugin($opts,in=>'view',out=>'view.GTisec.v.out',cmd=>'+GTisec',args=>'-- -v | grep -v bcftools');
 test_vcf_plugin($opts,in=>'trio',out=>'trio.out',cmd=>'+trio-switch-rate',args=>'-- -p {PATH}/trio.ped | grep -v bcftools');
+test_vcf_plugin($opts,in=>'ad-bias',out=>'ad-bias.out',cmd=>'+ad-bias',args=>'-- -s {PATH}/ad-bias.samples | grep -v bcftools');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.vcf.out',do_bcf=>0,args=>'');
 test_vcf_concat($opts,in=>['concat.1.a','concat.1.b'],out=>'concat.1.bcf.out',do_bcf=>1,args=>'');
 test_vcf_concat($opts,in=>['concat.2.a','concat.2.b'],out=>'concat.2.vcf.out',do_bcf=>0,args=>'-a');

From e43ca8c70bbc78a4ef29be723c60a2ec7a029436 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 1 Jul 2016 09:47:56 +0100
Subject: [PATCH 188/211] norm: avoid regression when ALT is a spanning
 deletion `*`

* add tests for #452 and #439

Resolves #452
---
 test/norm.out |  1 +
 test/norm.vcf |  2 ++
 test/test.pl  |  2 +-
 vcfnorm.c     | 10 ++++++----
 4 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/test/norm.out b/test/norm.out
index e6796d1e1..002acdb6c 100644
--- a/test/norm.out
+++ b/test/norm.out
@@ -53,5 +53,6 @@
 20	275	.	A	C,G	999	PASS	INDEL;AN=2;AC=0,2	GT:PL:DP:FGF:FGI:FGS:FSTR	2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD	2:0,0,0:0:1e+06,2e+06,3e+06:1111,2222,3333:A,BB,CCC:WORD
 3	10	.	GTGGAC	GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
 3	17	.	CA	C	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+4	25	.	T	TT,*	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
 4	36	.	TC	C,TT,TTC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
 5	21	.	A	AAG	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
diff --git a/test/norm.vcf b/test/norm.vcf
index d000655cc..d7d784167 100644
--- a/test/norm.vcf
+++ b/test/norm.vcf
@@ -54,4 +54,6 @@
 3	10	.	GTGGAC	GTGGACACAC,GTGGACAC,GTGGACACACAC,GTGG,GTGGACACACACAC,ATGGACACACAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
 3	15	.	CACA	CAC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
 4	21	.	ATTTTTTTTTTTTTTTC	ATTTTTTTTTTTTTTC,ATTTTTTTTTTTTTTTT,ATTTTTTTTTTTTTTTTC	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+4	25	.	T	TT,*	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
+4	37	.	C	I	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
 5	22	.	A	AGA	999	PASS	INDEL;AN=0	GT:DP	./.:0	./.:0
diff --git a/test/test.pl b/test/test.pl
index a91bd3fa9..981cc0b56 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -95,7 +95,7 @@
 test_vcf_query($opts,in=>'missing',out=>'query.23.out',args=>q[-e'ISTR="."'  -f'%POS %ISTR\\n']);
 test_vcf_query($opts,in=>'missing',out=>'query.22.out',args=>q[-e'ISTR!="."' -f'%POS %ISTR\\n']);
 test_vcf_query($opts,in=>'missing',out=>'query.24.out',args=>q[-i'FILTER="q11"' -f'%POS %ISTR\\n']);
-test_vcf_norm($opts,in=>'norm',out=>'norm.out',fai=>'norm');
+test_vcf_norm($opts,in=>'norm',out=>'norm.out',fai=>'norm',args=>'-cx');
 test_vcf_norm($opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.split.2',out=>'norm.split.2.out',args=>'-m-');
 test_vcf_norm($opts,in=>'norm.split',fai=>'norm',out=>'norm.split.and.norm.out',args=>'-m-');
diff --git a/vcfnorm.c b/vcfnorm.c
index daac7532e..8fe10a8fa 100644
--- a/vcfnorm.c
+++ b/vcfnorm.c
@@ -259,10 +259,11 @@ static void fix_dup_alt(args_t *args, bcf1_t *line)
     if ( changed ) bcf_update_genotypes(args->hdr,line,gts,ngts);
 }
 
-#define ERR_DUP_ALLELE      -2
-#define ERR_REF_MISMATCH    -1
-#define ERR_OK              0
-#define ERR_SYMBOLIC        1
+#define ERR_DUP_ALLELE       -2
+#define ERR_REF_MISMATCH     -1
+#define ERR_OK                0
+#define ERR_SYMBOLIC          1
+#define ERR_SPANNING_DELETION 2
 
 static int realign(args_t *args, bcf1_t *line)
 {
@@ -304,6 +305,7 @@ static int realign(args_t *args, bcf1_t *line)
     for (i=0; i<line->n_allele; i++)
     {
         if ( line->d.allele[i][0]=='<' ) return ERR_SYMBOLIC;  // symbolic allele
+        if ( line->d.allele[i][0]=='*' ) return ERR_SPANNING_DELETION;  // spanning deletion
         if ( has_non_acgtn(line->d.allele[i],0) )
         {
             if ( args->check_ref==CHECK_REF_EXIT )

From fe43a831e432676da977827e5883d3f139372960 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 25 Apr 2016 12:43:29 +0100
Subject: [PATCH 189/211] copy over mpileup files from samtools

Not functional yet. Just copying over the files.

* bam_plcmd.c for the mpileup command
* bam2bcf.[ch] bam2bcf_indel.c for the VCF/BCF creation
* sample.[ch] for RG:SM handling
---
 bam2bcf.c       |  843 ++++++++++++++++++++++++++++++++++++++
 bam2bcf.h       |  139 +++++++
 bam2bcf_indel.c |  533 ++++++++++++++++++++++++
 bam_plcmd.c     | 1027 +++++++++++++++++++++++++++++++++++++++++++++++
 sample.c        |  134 +++++++
 sample.h        |   41 ++
 6 files changed, 2717 insertions(+)
 create mode 100644 bam2bcf.c
 create mode 100644 bam2bcf.h
 create mode 100644 bam2bcf_indel.c
 create mode 100644 bam_plcmd.c
 create mode 100644 sample.c
 create mode 100644 sample.h

diff --git a/bam2bcf.c b/bam2bcf.c
new file mode 100644
index 000000000..a824d5ac0
--- /dev/null
+++ b/bam2bcf.c
@@ -0,0 +1,843 @@
+/*  bam2bcf.c -- variant calling.
+
+    Copyright (C) 2010-2012 Broad Institute.
+    Copyright (C) 2012-2014 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <math.h>
+#include <stdint.h>
+#include <assert.h>
+#include <float.h>
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/kstring.h>
+#include <htslib/kfunc.h>
+#include "bam2bcf.h"
+
+extern  void ks_introsort_uint32_t(size_t n, uint32_t a[]);
+
+#define CALL_DEFTHETA 0.83
+#define DEF_MAPQ 20
+
+#define CAP_DIST 25
+
+bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
+{
+    bcf_callaux_t *bca;
+    if (theta <= 0.) theta = CALL_DEFTHETA;
+    bca = calloc(1, sizeof(bcf_callaux_t));
+    bca->capQ = 60;
+    bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
+    bca->min_baseQ = min_baseQ;
+    bca->e = errmod_init(1. - theta);
+    bca->min_frac = 0.002;
+    bca->min_support = 1;
+    bca->per_sample_flt = 0;
+    bca->npos = 100;
+    bca->ref_pos = malloc(bca->npos*sizeof(int));
+    bca->alt_pos = malloc(bca->npos*sizeof(int));
+    bca->nqual = 60;
+    bca->ref_mq  = malloc(bca->nqual*sizeof(int));
+    bca->alt_mq  = malloc(bca->nqual*sizeof(int));
+    bca->ref_bq  = malloc(bca->nqual*sizeof(int));
+    bca->alt_bq  = malloc(bca->nqual*sizeof(int));
+    bca->fwd_mqs = malloc(bca->nqual*sizeof(int));
+    bca->rev_mqs = malloc(bca->nqual*sizeof(int));
+    return bca;
+}
+
+void bcf_call_destroy(bcf_callaux_t *bca)
+{
+    if (bca == 0) return;
+    errmod_destroy(bca->e);
+    if (bca->npos) { free(bca->ref_pos); free(bca->alt_pos); bca->npos = 0; }
+    free(bca->ref_mq); free(bca->alt_mq); free(bca->ref_bq); free(bca->alt_bq);
+    free(bca->fwd_mqs); free(bca->rev_mqs);
+    bca->nqual = 0;
+    free(bca->bases); free(bca->inscns); free(bca);
+}
+
+// position in the sequence with respect to the aligned part of the read
+static int get_position(const bam_pileup1_t *p, int *len)
+{
+    int icig, n_tot_bases = 0, iread = 0, edist = p->qpos + 1;
+    for (icig=0; icig<p->b->core.n_cigar; icig++)
+    {
+        int cig  = bam_get_cigar(p->b)[icig] & BAM_CIGAR_MASK;
+        int ncig = bam_get_cigar(p->b)[icig] >> BAM_CIGAR_SHIFT;
+        if ( cig==BAM_CMATCH || cig==BAM_CEQUAL || cig==BAM_CDIFF )
+        {
+            n_tot_bases += ncig;
+            iread += ncig;
+            continue;
+        }
+        if ( cig==BAM_CINS )
+        {
+            n_tot_bases += ncig;
+            iread += ncig;
+            continue;
+        }
+        if ( cig==BAM_CSOFT_CLIP )
+        {
+            iread += ncig;
+            if ( iread<=p->qpos ) edist -= ncig;
+            continue;
+        }
+        if ( cig==BAM_CDEL ) continue;
+        if ( cig==BAM_CHARD_CLIP ) continue;
+        if ( cig==BAM_CPAD ) continue;
+        if ( cig==BAM_CREF_SKIP ) continue;
+        fprintf(stderr,"todo: cigar %d\n", cig);
+        assert(0);
+    }
+    *len = n_tot_bases;
+    return edist;
+}
+
+void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call)
+{
+    memset(bca->ref_pos,0,sizeof(int)*bca->npos);
+    memset(bca->alt_pos,0,sizeof(int)*bca->npos);
+    memset(bca->ref_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->alt_mq,0,sizeof(int)*bca->nqual);
+    memset(bca->ref_bq,0,sizeof(int)*bca->nqual);
+    memset(bca->alt_bq,0,sizeof(int)*bca->nqual);
+    memset(bca->fwd_mqs,0,sizeof(int)*bca->nqual);
+    memset(bca->rev_mqs,0,sizeof(int)*bca->nqual);
+    if ( call->ADF ) memset(call->ADF,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES);
+    if ( call->ADR ) memset(call->ADR,0,sizeof(int32_t)*(call->n+1)*B2B_MAX_ALLELES);
+}
+
+/*
+    Notes:
+    - Called from bam_plcmd.c by mpileup. Amongst other things, sets the bcf_callret1_t.qsum frequencies
+        which are carried over via bcf_call_combine and bcf_call2bcf to the output BCF as the QS annotation.
+        Later it's used for multiallelic calling by bcftools -m
+    - ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel.
+ */
+/*
+ * This function is called once for each sample.
+ * _n is number of pilesups pl contributing reads to this sample
+ * pl is pointer to array of _n pileups (one pileup per read)
+ * ref_base is the 4-bit representation of the reference base. It is negative if we are looking at an indel.
+ * bca is the settings to perform calls across all samples
+ * r is the returned value of the call
+ */
+int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r)
+{
+    int i, n, ref4, is_indel, ori_depth = 0;
+
+    // clean from previous run
+    r->ori_depth = 0;
+    r->mq0 = 0;
+    memset(r->qsum,0,sizeof(float)*4);
+    memset(r->anno,0,sizeof(double)*16);
+    memset(r->p,0,sizeof(float)*25);
+
+    if (ref_base >= 0) {
+        ref4 = seq_nt16_int[ref_base];
+        is_indel = 0;
+    } else ref4 = 4, is_indel = 1;
+    if (_n == 0) return -1;
+    // enlarge the bases array if necessary
+    if (bca->max_bases < _n) {
+        bca->max_bases = _n;
+        kroundup32(bca->max_bases);
+        bca->bases = (uint16_t*)realloc(bca->bases, 2 * bca->max_bases);
+    }
+    // fill the bases array
+    for (i = n = 0; i < _n; ++i) {
+        const bam_pileup1_t *p = pl + i;
+        int q, b, mapQ, baseQ, is_diff, min_dist, seqQ;
+        // set base
+        if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue;
+        ++ori_depth;
+        mapQ  = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+        if ( !mapQ ) r->mq0++;
+        baseQ = q = is_indel? p->aux&0xff : (int)bam_get_qual(p->b)[p->qpos]; // base/indel quality
+        seqQ = is_indel? (p->aux>>8&0xff) : 99;
+        if (q < bca->min_baseQ) continue;
+        if (q > seqQ) q = seqQ;
+        mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
+        if (q > mapQ) q = mapQ;
+        if (q > 63) q = 63;
+        if (q < 4) q = 4;       // MQ=0 reads count as BQ=4
+        if (!is_indel) {
+            b = bam_seqi(bam_get_seq(p->b), p->qpos); // base
+            b = seq_nt16_int[b? b : ref_base]; // b is the 2-bit base
+            is_diff = (ref4 < 4 && b == ref4)? 0 : 1;
+        } else {
+            b = p->aux>>16&0x3f;
+            is_diff = (b != 0);
+        }
+        bca->bases[n++] = q<<5 | (int)bam_is_rev(p->b)<<4 | b;
+        // collect annotations
+        if (b < 4)
+        {
+            r->qsum[b] += q;
+            if ( r->ADF )
+            {
+                if ( bam_is_rev(p->b) )
+                    r->ADR[b]++;
+                else
+                    r->ADF[b]++;
+            }
+        }
+        ++r->anno[0<<2|is_diff<<1|bam_is_rev(p->b)];
+        min_dist = p->b->core.l_qseq - 1 - p->qpos;
+        if (min_dist > p->qpos) min_dist = p->qpos;
+        if (min_dist > CAP_DIST) min_dist = CAP_DIST;
+        r->anno[1<<2|is_diff<<1|0] += baseQ;
+        r->anno[1<<2|is_diff<<1|1] += baseQ * baseQ;
+        r->anno[2<<2|is_diff<<1|0] += mapQ;
+        r->anno[2<<2|is_diff<<1|1] += mapQ * mapQ;
+        r->anno[3<<2|is_diff<<1|0] += min_dist;
+        r->anno[3<<2|is_diff<<1|1] += min_dist * min_dist;
+
+        // collect for bias tests
+        if ( baseQ > 59 ) baseQ = 59;
+        if ( mapQ > 59 ) mapQ = 59;
+        int len, pos = get_position(p, &len);
+        int epos = (double)pos/(len+1) * bca->npos;
+        int ibq  = baseQ/60. * bca->nqual;
+        int imq  = mapQ/60. * bca->nqual;
+        if ( bam_is_rev(p->b) ) bca->rev_mqs[imq]++;
+        else bca->fwd_mqs[imq]++;
+        if ( bam_seqi(bam_get_seq(p->b),p->qpos) == ref_base )
+        {
+            bca->ref_pos[epos]++;
+            bca->ref_bq[ibq]++;
+            bca->ref_mq[imq]++;
+        }
+        else
+        {
+            bca->alt_pos[epos]++;
+            bca->alt_bq[ibq]++;
+            bca->alt_mq[imq]++;
+        }
+    }
+    r->ori_depth = ori_depth;
+    // glfgen
+    errmod_cal(bca->e, n, 5, bca->bases, r->p); // calculate PL of each genotype
+    return n;
+}
+
+
+/*
+ *  calc_vdb() - returns value between zero (most biased) and one (no bias)
+ *               on success, or HUGE_VAL when VDB cannot be calculated because
+ *               of insufficient depth (<2x)
+ *
+ *  Variant Distance Bias tests if the variant bases are positioned within the
+ *  reads with sufficient randomness. Unlike other tests, it looks only at
+ *  variant reads and therefore gives different kind of information than Read
+ *  Position Bias for instance. VDB was developed for detecting artefacts in
+ *  RNA-seq calls where reads from spliced transcripts span splice site
+ *  boundaries.  The current implementation differs somewhat from the original
+ *  version described in supplementary material of PMID:22524474, but the idea
+ *  remains the same. (Here the random variable tested is the average distance
+ *  from the averaged position, not the average pairwise distance.)
+ *
+ *  For coverage of 2x, the calculation is exact but is approximated for the
+ *  rest. The result is most accurate between 4-200x. For 3x or >200x, the
+ *  reported values are slightly more favourable than those of a true random
+ *  distribution.
+ */
+double calc_vdb(int *pos, int npos)
+{
+    // Note well: the parameters were obtained by fitting to simulated data of
+    // 100bp reads. This assumes rescaling to 100bp in bcf_call_glfgen().
+    const int readlen = 100;
+    assert( npos==readlen );
+
+    #define nparam 15
+    const float param[nparam][3] = { {3,0.079,18}, {4,0.09,19.8}, {5,0.1,20.5}, {6,0.11,21.5},
+        {7,0.125,21.6}, {8,0.135,22}, {9,0.14,22.2}, {10,0.153,22.3}, {15,0.19,22.8},
+        {20,0.22,23.2}, {30,0.26,23.4}, {40,0.29,23.5}, {50,0.35,23.65}, {100,0.5,23.7},
+        {200,0.7,23.7} };
+
+    int i, dp = 0;
+    float mean_pos = 0, mean_diff = 0;
+    for (i=0; i<npos; i++)
+    {
+        if ( !pos[i] ) continue;
+        dp += pos[i];
+        mean_pos += pos[i]*i;
+    }
+    if ( dp<2 ) return HUGE_VAL;     // one or zero reads can be placed anywhere
+
+    mean_pos /= dp;
+    for (i=0; i<npos; i++)
+    {
+        if ( !pos[i] ) continue;
+        mean_diff += pos[i] * fabs(i - mean_pos);
+    }
+    mean_diff /= dp;
+
+    int ipos = mean_diff;   // tuned for float-to-int implicit conversion
+    if ( dp==2 )
+        return (2*readlen-2*(ipos+1)-1)*(ipos+1)/(readlen-1)/(readlen*0.5);
+
+    if ( dp>=200 )
+        i = nparam; // shortcut for big depths
+    else
+    {
+        for (i=0; i<nparam; i++)
+            if ( param[i][0]>=dp ) break;
+    }
+    float pshift, pscale;
+    if ( i==nparam )
+    {
+        // the depth is too high, go with 200x
+        pscale = param[nparam-1][1];
+        pshift = param[nparam-1][2];
+    }
+    else if ( i>0 && param[i][0]!=dp )
+    {
+        // linear interpolation of parameters
+        pscale = (param[i-1][1] + param[i][1])*0.5;
+        pshift = (param[i-1][2] + param[i][2])*0.5;
+    }
+    else
+    {
+        pscale = param[i][1];
+        pshift = param[i][2];
+    }
+    return 0.5*kf_erfc(-(mean_diff-pshift)*pscale);
+}
+
+double calc_chisq_bias(int *a, int *b, int n)
+{
+    int na = 0, nb = 0, i, ndf = n;
+    for (i=0; i<n; i++) na += a[i];
+    for (i=0; i<n; i++) nb += b[i];
+    if ( !na || !nb ) return HUGE_VAL;
+
+    double chisq = 0;
+    for (i=0; i<n; i++)
+    {
+        if ( !a[i] && !b[i] ) ndf--;
+        else
+        {
+            double tmp = a[i] - b[i];
+            chisq += tmp*tmp/(a[i]+b[i]);
+        }
+    }
+    /*
+        kf_gammq: incomplete gamma function Q(a,x) = 1 - P(a,x) = Gamma(a,x)/Gamma(a)
+        1 if the distributions are identical, 0 if very different
+    */
+    double prob = kf_gammaq(0.5*ndf, 0.5*chisq);
+    return prob;
+}
+
+double mann_whitney_1947(int n, int m, int U)
+{
+    if (U<0) return 0;
+    if (n==0||m==0) return U==0 ? 1 : 0;
+    return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U);
+}
+
+double mann_whitney_1947_cdf(int n, int m, int U)
+{
+    int i;
+    double sum = 0;
+    for (i=0; i<=U; i++)
+        sum += mann_whitney_1947(n,m,i);
+    return sum;
+}
+
+double calc_mwu_bias_cdf(int *a, int *b, int n)
+{
+    int na = 0, nb = 0, i;
+    double U = 0, ties = 0;
+    for (i=0; i<n; i++)
+    {
+        na += a[i];
+        U  += a[i] * (nb + b[i]*0.5);
+        nb += b[i];
+        if ( a[i] && b[i] )
+        {
+            double tie = a[i] + b[i];
+            ties += (tie*tie-1)*tie;
+        }
+    }
+    if ( !na || !nb ) return HUGE_VAL;
+
+    // Always work with the smaller U
+    double U_min = ((double)na * nb) - U;
+    if ( U < U_min ) U_min = U;
+
+    if ( na==1 ) return 2.0 * (floor(U_min)+1) / (nb+1);
+    if ( nb==1 ) return 2.0 * (floor(U_min)+1) / (na+1);
+
+    // Normal approximation, very good for na>=8 && nb>=8 and reasonable if na<8 or nb<8
+    if ( na>=8 || nb>=8 )
+    {
+        double mean = ((double)na*nb)*0.5;
+        // Correction for ties:
+        //      double N = na+nb;
+        //      double var2 = (N*N-1)*N-ties;
+        //      if ( var2==0 ) return 1.0;
+        //      var2 *= ((double)na*nb)/N/(N-1)/12.0;
+        // No correction for ties:
+        double var2 = ((double)na*nb)*(na+nb+1)/12.0;
+        double z = (U_min - mean)/sqrt(2*var2);   // z is N(0,1)
+        return 2.0 - kf_erfc(z);  // which is 1 + erf(z)
+    }
+
+    // Exact calculation
+    double pval = 2*mann_whitney_1947_cdf(na,nb,U_min);
+    return pval>1 ? 1 : pval;
+}
+
+double calc_mwu_bias(int *a, int *b, int n)
+{
+    int na = 0, nb = 0, i;
+    double U = 0, ties = 0;
+    for (i=0; i<n; i++)
+    {
+        na += a[i];
+        U  += a[i] * (nb + b[i]*0.5);
+        nb += b[i];
+        if ( a[i] && b[i] )
+        {
+            double tie = a[i] + b[i];
+            ties += (tie*tie-1)*tie;
+        }
+    }
+    if ( !na || !nb ) return HUGE_VAL;
+    if ( na==1 || nb==1 ) return 1.0;       // Flat probability, all U values are equally likely
+
+    double mean = ((double)na*nb)*0.5;
+    if ( na==2 || nb==2 )
+    {
+        // Linear approximation
+        return U>mean ? (2.0*mean-U)/mean : U/mean;
+    }
+    // Correction for ties:
+    //      double N = na+nb;
+    //      double var2 = (N*N-1)*N-ties;
+    //      if ( var2==0 ) return 1.0;
+    //      var2 *= ((double)na*nb)/N/(N-1)/12.0;
+    // No correction for ties:
+    double var2 = ((double)na*nb)*(na+nb+1)/12.0;
+    if ( na>=8 || nb>=8 )
+    {
+        // Normal approximation, very good for na>=8 && nb>=8 and reasonable if na<8 or nb<8
+        return exp(-0.5*(U-mean)*(U-mean)/var2);
+    }
+
+    // Exact calculation
+    return mann_whitney_1947(na,nb,U) * sqrt(2*M_PI*var2);
+}
+
+static inline double logsumexp2(double a, double b)
+{
+    if ( a>b )
+        return log(1 + exp(b-a)) + a;
+    else
+        return log(1 + exp(a-b)) + b;
+}
+
+void calc_SegBias(const bcf_callret1_t *bcr, bcf_call_t *call)
+{
+    call->seg_bias = HUGE_VAL;
+    if ( !bcr ) return;
+
+    int nr = call->anno[2] + call->anno[3]; // number of observed non-reference reads
+    if ( !nr ) return;
+
+    int avg_dp = (call->anno[0] + call->anno[1] + nr) / call->n;    // average depth
+    double M   = floor((double)nr / avg_dp + 0.5);   // an approximate number of variants samples in the population
+    if ( M>call->n ) M = call->n;       // clamp M at the number of samples
+    else if ( M==0 ) M = 1;
+    double f = M / 2. / call->n;        // allele frequency
+    double p = (double) nr / call->n;   // number of variant reads per sample expected if variant not real (poisson)
+    double q = (double) nr / M;         // number of variant reads per sample expected if variant is real (poisson)
+    double sum = 0;
+    const double log2 = log(2.0);
+
+    // fprintf(stderr,"M=%.1f  p=%e q=%e f=%f  dp=%d\n",M,p,q,f,avg_dp);
+    int i;
+    for (i=0; i<call->n; i++)
+    {
+        int oi = bcr[i].anno[2] + bcr[i].anno[3];       // observed number of non-ref reads
+        double tmp;
+        if ( oi )
+        {
+            // tmp = log(f) + oi*log(q/p) - q + log(2*(1-f) + f*pow(2,oi)*exp(-q)) + p; // this can under/overflow
+            tmp = logsumexp2(log(2*(1-f)), log(f) + oi*log2 - q);
+            tmp += log(f) + oi*log(q/p) - q + p;
+        }
+        else
+            tmp = log(2*f*(1-f)*exp(-q) + f*f*exp(-2*q) + (1-f)*(1-f)) + p;
+        sum += tmp;
+        // fprintf(stderr,"oi=%d %e\n", oi,tmp);
+    }
+    call->seg_bias = sum;
+}
+
+/**
+ *  bcf_call_combine() - sets the PL array and VDB, RPB annotations, finds the top two alleles
+ *  @n:         number of samples
+ *  @calls:     each sample's calls
+ *  @bca:       auxiliary data structure for holding temporary values
+ *  @ref_base:  the reference base
+ *  @call:      filled with the annotations
+ *
+ *  Combines calls across the various samples being studied
+ *  1. For each allele at each base across all samples the quality is summed so
+ *     you end up with a set of quality sums for each allele present 2. The quality
+ *     sums are sorted.
+ *  3. Using the sorted quality sums we now create the allele ordering array
+ *     A\subN. This is done by doing the following:
+ *     a) If the reference allele is known it always comes first, otherwise N
+ *        comes first.
+ *     b) Then the rest of the alleles are output in descending order of quality
+ *        sum (which we already know the qsum array was sorted).  Any allelles with
+ *        qsum 0 will be excluded.
+ *  4. Using the allele ordering array we create the genotype ordering array.
+ *     In the worst case with an unknown reference this will be:  A0/A0 A1/A0 A1/A1
+ *     A2/A0 A2/A1 A2/A2 A3/A0 A3/A1 A3/A2 A3/A3 A4/A0 A4/A1 A4/A2 A4/A3 A4/A4
+ *  5. The genotype ordering array is then used to extract data from the error
+ *     model 5*5 matrix and is used to produce a Phread likelihood array for each
+ *     sample.
+ */
+int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call)
+{
+    int ref4, i, j;
+    float qsum[5] = {0,0,0,0,0};
+    if (ref_base >= 0) {
+        call->ori_ref = ref4 = seq_nt16_int[ref_base];
+        if (ref4 > 4) ref4 = 4;
+    } else call->ori_ref = -1, ref4 = 0;
+
+    // calculate qsum, this is done by summing normalized qsum across all samples,
+    // to account for differences in coverage
+    for (i = 0; i < n; ++i)
+    {
+        float sum = 0;
+        for (j = 0; j < 4; ++j) sum += calls[i].qsum[j];
+        if ( sum )
+            for (j = 0; j < 4; j++) qsum[j] += calls[i].qsum[j] / sum;
+    }
+
+    // sort qsum in ascending order (insertion sort)
+    float *ptr[5], *tmp;
+    for (i=0; i<5; i++) ptr[i] = &qsum[i];
+    for (i=1; i<4; i++)
+        for (j=i; j>0 && *ptr[j] < *ptr[j-1]; j--)
+            tmp = ptr[j], ptr[j] = ptr[j-1], ptr[j-1] = tmp;
+
+    // Set the reference allele and alternative allele(s)
+    for (i=0; i<5; i++) call->a[i] = -1;
+    for (i=0; i<5; i++) call->qsum[i] = 0;
+    call->unseen = -1;
+    call->a[0] = ref4;
+    for (i=3, j=1; i>=0; i--)   // i: alleles sorted by QS; j, a[j]: output allele ordering
+    {
+        int ipos = ptr[i] - qsum;   // position in sorted qsum array
+        if ( ipos==ref4 )
+            call->qsum[0] = qsum[ipos];    // REF's qsum
+        else
+        {
+            if ( !qsum[ipos] ) break;       // qsum is 0, this and consequent alleles are not seen in the pileup
+            call->qsum[j] = qsum[ipos];
+            call->a[j++]  = ipos;
+        }
+    }
+    if (ref_base >= 0)
+    {
+        // for SNPs, find the "unseen" base
+        if (((ref4 < 4 && j < 4) || (ref4 == 4 && j < 5)) && i >= 0)
+            call->unseen = j, call->a[j++] = ptr[i] - qsum;
+        call->n_alleles = j;
+    }
+    else
+    {
+        call->n_alleles = j;
+        if (call->n_alleles == 1) return -1; // no reliable supporting read. stop doing anything
+    }
+    /*
+     * Set the phread likelihood array (call->PL) This array is 15 entries long
+     * for each sample because that is size of an upper or lower triangle of a
+     * worst case 5x5 matrix of possible genotypes. This worst case matrix will
+     * occur when all 4 possible alleles are present and the reference allele
+     * is unknown.  The sides of the matrix will correspond to the reference
+     * allele (if known) followed by the alleles present in descending order of
+     * quality sum
+     */
+    {
+        int x, g[15], z;
+        double sum_min = 0.;
+        x = call->n_alleles * (call->n_alleles + 1) / 2;
+        // get the possible genotypes
+        // this is done by creating an ordered list of locations g for call (allele a, allele b) in the genotype likelihood matrix
+        for (i = z = 0; i < call->n_alleles; ++i) {
+            for (j = 0; j <= i; ++j) {
+                g[z++] = call->a[j] * 5 + call->a[i];
+            }
+        }
+        // for each sample calculate the PL
+        for (i = 0; i < n; ++i)
+        {
+            int32_t *PL = call->PL + x * i;
+            const bcf_callret1_t *r = calls + i;
+            float min = FLT_MAX;
+            for (j = 0; j < x; ++j) {
+                if (min > r->p[g[j]]) min = r->p[g[j]];
+            }
+            sum_min += min;
+            for (j = 0; j < x; ++j) {
+                int y;
+                y = (int)(r->p[g[j]] - min + .499);
+                if (y > 255) y = 255;
+                PL[j] = y;
+            }
+        }
+        if ( call->DP4 )
+        {
+            for (i=0; i<n; i++)
+            {
+                call->DP4[4*i]   = calls[i].anno[0];
+                call->DP4[4*i+1] = calls[i].anno[1];
+                call->DP4[4*i+2] = calls[i].anno[2];
+                call->DP4[4*i+3] = calls[i].anno[3];
+            }
+        }
+        if ( call->ADF )
+        {
+            assert( call->n_alleles<=B2B_MAX_ALLELES );   // this is always true for SNPs and so far for indels as well
+
+            // reorder ADR,ADF to match the allele ordering at this site
+            int32_t tmp[B2B_MAX_ALLELES];
+            int32_t *adr = call->ADR + B2B_MAX_ALLELES, *adr_out = call->ADR + B2B_MAX_ALLELES;
+            int32_t *adf = call->ADF + B2B_MAX_ALLELES, *adf_out = call->ADF + B2B_MAX_ALLELES;
+            int32_t *adr_tot = call->ADR;   // the first bin stores total counts per site
+            int32_t *adf_tot = call->ADF;
+            for (i=0; i<n; i++)
+            {
+                for (j=0; j<call->n_alleles; j++)
+                {
+                    tmp[j] = adr[ call->a[j] ];
+                    adr_tot[j] += tmp[j];
+                }
+                for (j=0; j<call->n_alleles; j++) adr_out[j] = tmp[j];
+                for (j=0; j<call->n_alleles; j++)
+                {
+                    tmp[j] = adf[ call->a[j] ];
+                    adf_tot[j] += tmp[j];
+                }
+                for (j=0; j<call->n_alleles; j++) adf_out[j] = tmp[j];
+                adf_out += call->n_alleles;
+                adr_out += call->n_alleles;
+                adr += B2B_MAX_ALLELES;
+                adf += B2B_MAX_ALLELES;
+            }
+        }
+
+//      if (ref_base < 0) fprintf(stderr, "%d,%d,%f,%d\n", call->n_alleles, x, sum_min, call->unseen);
+        call->shift = (int)(sum_min + .499);
+    }
+    // combine annotations
+    memset(call->anno, 0, 16 * sizeof(double));
+    call->ori_depth = 0;
+    call->depth     = 0;
+    call->mq0       = 0;
+    for (i = 0; i < n; ++i) {
+        call->depth += calls[i].anno[0] + calls[i].anno[1] + calls[i].anno[2] + calls[i].anno[3];
+        call->ori_depth += calls[i].ori_depth;
+        call->mq0 += calls[i].mq0;
+        for (j = 0; j < 16; ++j) call->anno[j] += calls[i].anno[j];
+    }
+
+    calc_SegBias(calls, call);
+
+    // calc_chisq_bias("XPOS", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_pos, bca->alt_pos, bca->npos);
+    // calc_chisq_bias("XMQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_mq, bca->alt_mq, bca->nqual);
+    // calc_chisq_bias("XBQ", call->bcf_hdr->id[BCF_DT_CTG][call->tid].key, call->pos, bca->ref_bq, bca->alt_bq, bca->nqual);
+
+    call->mwu_pos = calc_mwu_bias(bca->ref_pos, bca->alt_pos, bca->npos);
+    call->mwu_mq  = calc_mwu_bias(bca->ref_mq,  bca->alt_mq,  bca->nqual);
+    call->mwu_bq  = calc_mwu_bias(bca->ref_bq,  bca->alt_bq,  bca->nqual);
+    call->mwu_mqs = calc_mwu_bias(bca->fwd_mqs, bca->rev_mqs, bca->nqual);
+
+#if CDF_MWU_TESTS
+    call->mwu_pos_cdf = calc_mwu_bias_cdf(bca->ref_pos, bca->alt_pos, bca->npos);
+    call->mwu_mq_cdf  = calc_mwu_bias_cdf(bca->ref_mq,  bca->alt_mq,  bca->nqual);
+    call->mwu_bq_cdf  = calc_mwu_bias_cdf(bca->ref_bq,  bca->alt_bq,  bca->nqual);
+    call->mwu_mqs_cdf = calc_mwu_bias_cdf(bca->fwd_mqs, bca->rev_mqs, bca->nqual);
+#endif
+
+    call->vdb = calc_vdb(bca->alt_pos, bca->npos);
+
+    return 0;
+}
+
+int bcf_call2bcf(bcf_call_t *bc, bcf1_t *rec, bcf_callret1_t *bcr, int fmt_flag, const bcf_callaux_t *bca, const char *ref)
+{
+    extern double kt_fisher_exact(int n11, int n12, int n21, int n22, double *_left, double *_right, double *two);
+    int i, j, nals = 1;
+
+    bcf_hdr_t *hdr = bc->bcf_hdr;
+    rec->rid  = bc->tid;
+    rec->pos  = bc->pos;
+    rec->qual = 0;
+
+    bc->tmp.l = 0;
+    if (bc->ori_ref < 0)    // indel
+    {
+        // REF
+        kputc(ref[bc->pos], &bc->tmp);
+        for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp);
+
+        // ALT
+        for (i=1; i<4; i++)
+        {
+            if (bc->a[i] < 0) break;
+            kputc(',', &bc->tmp); kputc(ref[bc->pos], &bc->tmp);
+
+            if (bca->indel_types[bc->a[i]] < 0) { // deletion
+                for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
+                    kputc(ref[bc->pos+1+j], &bc->tmp);
+            } else { // insertion; cannot be a reference unless a bug
+                char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
+                for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
+                    kputc("ACGTN"[(int)inscns[j]], &bc->tmp);
+                for (j = 0; j < bca->indelreg; ++j) kputc(ref[bc->pos+1+j], &bc->tmp);
+            }
+            nals++;
+        }
+    }
+    else    // SNP
+    {
+        kputc("ACGTN"[bc->ori_ref], &bc->tmp);
+        for (i=1; i<5; i++)
+        {
+            if (bc->a[i] < 0) break;
+            kputc(',', &bc->tmp);
+            if ( bc->unseen==i ) kputs("<*>", &bc->tmp);
+            else kputc("ACGT"[bc->a[i]], &bc->tmp);
+            nals++;
+        }
+    }
+    bcf_update_alleles_str(hdr, rec, bc->tmp.s);
+
+    bc->tmp.l = 0;
+
+    // INFO
+    if (bc->ori_ref < 0)
+    {
+        bcf_update_info_flag(hdr, rec, "INDEL", NULL, 1);
+        bcf_update_info_int32(hdr, rec, "IDV", &bca->max_support, 1);
+        bcf_update_info_float(hdr, rec, "IMF", &bca->max_frac, 1);
+    }
+    bcf_update_info_int32(hdr, rec, "DP", &bc->ori_depth, 1);
+    if ( fmt_flag&B2B_INFO_ADF )
+        bcf_update_info_int32(hdr, rec, "ADF", bc->ADF, rec->n_allele);
+    if ( fmt_flag&B2B_INFO_ADR )
+        bcf_update_info_int32(hdr, rec, "ADR", bc->ADR, rec->n_allele);
+    if ( fmt_flag&(B2B_INFO_AD|B2B_INFO_DPR) )
+    {
+        for (i=0; i<rec->n_allele; i++) bc->ADF[i] += bc->ADR[i];
+        if ( fmt_flag&B2B_INFO_AD )
+            bcf_update_info_int32(hdr, rec, "AD", bc->ADF, rec->n_allele);
+        if ( fmt_flag&B2B_INFO_DPR )
+            bcf_update_info_int32(hdr, rec, "DPR", bc->ADF, rec->n_allele);
+    }
+
+    float tmpf[16];
+    for (i=0; i<16; i++) tmpf[i] = bc->anno[i];
+    bcf_update_info_float(hdr, rec, "I16", tmpf, 16);
+    bcf_update_info_float(hdr, rec, "QS", bc->qsum, nals);
+
+    if ( bc->vdb != HUGE_VAL )      bcf_update_info_float(hdr, rec, "VDB", &bc->vdb, 1);
+    if ( bc->seg_bias != HUGE_VAL ) bcf_update_info_float(hdr, rec, "SGB", &bc->seg_bias, 1);
+    if ( bc->mwu_pos != HUGE_VAL )  bcf_update_info_float(hdr, rec, "RPB", &bc->mwu_pos, 1);
+    if ( bc->mwu_mq != HUGE_VAL )   bcf_update_info_float(hdr, rec, "MQB", &bc->mwu_mq, 1);
+    if ( bc->mwu_mqs != HUGE_VAL )  bcf_update_info_float(hdr, rec, "MQSB", &bc->mwu_mqs, 1);
+    if ( bc->mwu_bq != HUGE_VAL )   bcf_update_info_float(hdr, rec, "BQB", &bc->mwu_bq, 1);
+#if CDF_MWU_TESTS
+    if ( bc->mwu_pos_cdf != HUGE_VAL )  bcf_update_info_float(hdr, rec, "RPB2", &bc->mwu_pos_cdf, 1);
+    if ( bc->mwu_mq_cdf != HUGE_VAL )   bcf_update_info_float(hdr, rec, "MQB2", &bc->mwu_mq_cdf, 1);
+    if ( bc->mwu_mqs_cdf != HUGE_VAL )  bcf_update_info_float(hdr, rec, "MQSB2", &bc->mwu_mqs_cdf, 1);
+    if ( bc->mwu_bq_cdf != HUGE_VAL )   bcf_update_info_float(hdr, rec, "BQB2", &bc->mwu_bq_cdf, 1);
+#endif
+    tmpf[0] = bc->ori_depth ? (float)bc->mq0/bc->ori_depth : 0;
+    bcf_update_info_float(hdr, rec, "MQ0F", tmpf, 1);
+
+    // FORMAT
+    rec->n_sample = bc->n;
+    bcf_update_format_int32(hdr, rec, "PL", bc->PL, nals*(nals+1)/2 * rec->n_sample);
+    if ( fmt_flag&B2B_FMT_DP )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+            ptr[i] = bc->DP4[4*i] + bc->DP4[4*i+1] + bc->DP4[4*i+2] + bc->DP4[4*i+3];
+        bcf_update_format_int32(hdr, rec, "DP", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_DV )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+            ptr[i] = bc->DP4[4*i+2] + bc->DP4[4*i+3];
+        bcf_update_format_int32(hdr, rec, "DV", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_SP )
+    {
+        int32_t *ptr = (int32_t*) bc->fmt_arr;
+        for (i=0; i<bc->n; i++)
+        {
+            int fwd_ref = bc->DP4[4*i], rev_ref =  bc->DP4[4*i+1], fwd_alt = bc->DP4[4*i+2], rev_alt = bc->DP4[4*i+3];
+            if ( fwd_ref+rev_ref<2 || fwd_alt+rev_alt<2 || fwd_ref+fwd_alt<2 || rev_ref+rev_alt<2 )
+                ptr[i] = 0;
+            else
+            {
+                double left, right, two;
+                kt_fisher_exact(fwd_ref, rev_ref, fwd_alt, rev_alt, &left, &right, &two);
+                int32_t x = (int)(-4.343 * log(two) + .499);
+                if (x > 255) x = 255;
+                ptr[i] = x;
+            }
+        }
+        bcf_update_format_int32(hdr, rec, "SP", bc->fmt_arr, rec->n_sample);
+    }
+    if ( fmt_flag&B2B_FMT_DP4 )
+        bcf_update_format_int32(hdr, rec, "DP4", bc->DP4, rec->n_sample*4);
+    if ( fmt_flag&B2B_FMT_ADF )
+        bcf_update_format_int32(hdr, rec, "ADF", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    if ( fmt_flag&B2B_FMT_ADR )
+        bcf_update_format_int32(hdr, rec, "ADR", bc->ADR+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    if ( fmt_flag&(B2B_FMT_AD|B2B_FMT_DPR) )
+    {
+        for (i=0; i<rec->n_sample*rec->n_allele; i++) bc->ADF[B2B_MAX_ALLELES+i] += bc->ADR[B2B_MAX_ALLELES+i];
+        if ( fmt_flag&B2B_FMT_AD )
+            bcf_update_format_int32(hdr, rec, "AD", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+        if ( fmt_flag&B2B_FMT_DPR )
+            bcf_update_format_int32(hdr, rec, "DPR", bc->ADF+B2B_MAX_ALLELES, rec->n_sample*rec->n_allele);
+    }
+
+    return 0;
+}
diff --git a/bam2bcf.h b/bam2bcf.h
new file mode 100644
index 000000000..54e5faaaa
--- /dev/null
+++ b/bam2bcf.h
@@ -0,0 +1,139 @@
+/*  bam2bcf.h -- variant calling.
+
+    Copyright (C) 2010-2012 Broad Institute.
+    Copyright (C) 2012-2014 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM2BCF_H
+#define BAM2BCF_H
+
+#include <stdint.h>
+#include <htslib/hts.h>
+#include <htslib/vcf.h>
+
+/**
+ *  A simplified version of Mann-Whitney U-test is calculated
+ *  by default (no CDF) because it is faster and seems to work
+ *  better in machine learning filtering. When enabled by setting
+ *  CDF_MWU_TESTS, additional annotations will appear on mpileup's
+ *  output (RPB2 in addition to RPB, etc.).
+ */
+#ifndef CDF_MWU_TESTS
+#define CDF_MWU_TESTS 0
+#endif
+
+#define B2B_INDEL_NULL 10000
+
+#define B2B_FMT_DP      (1<<0)
+#define B2B_FMT_SP      (1<<1)
+#define B2B_FMT_DV      (1<<2)
+#define B2B_FMT_DP4     (1<<3)
+#define B2B_FMT_DPR     (1<<4)
+#define B2B_INFO_DPR    (1<<5)
+#define B2B_FMT_AD      (1<<6)
+#define B2B_FMT_ADF     (1<<7)
+#define B2B_FMT_ADR     (1<<8)
+#define B2B_INFO_AD     (1<<9)
+#define B2B_INFO_ADF    (1<<10)
+#define B2B_INFO_ADR    (1<<11)
+
+#define B2B_MAX_ALLELES 5
+
+typedef struct __bcf_callaux_t {
+    int capQ, min_baseQ;
+    int openQ, extQ, tandemQ; // for indels
+    uint32_t min_support, max_support; // for collecting indel candidates
+    double min_frac; // for collecting indel candidates
+    float max_frac; // for collecting indel candidates
+    int per_sample_flt; // indel filtering strategy
+    int *ref_pos, *alt_pos, npos, *ref_mq, *alt_mq, *ref_bq, *alt_bq, *fwd_mqs, *rev_mqs, nqual; // for bias tests
+    // for internal uses
+    int max_bases;
+    int indel_types[4];     // indel lengths
+    int maxins, indelreg;
+    int read_len;
+    char *inscns;
+    uint16_t *bases;        // 5bit: unused, 6:quality, 1:is_rev, 4:2-bit base or indel allele (index to bcf_callaux_t.indel_types)
+    errmod_t *e;
+    void *rghash;
+} bcf_callaux_t;
+
+typedef struct {
+    uint32_t ori_depth;
+    unsigned int mq0;
+    int32_t *ADF, *ADR;
+    float qsum[4];
+    // The fields are:
+    //      depth fwd   .. ref (0) and non-ref (2)
+    //      depth rev   .. ref (1) and non-ref (3)
+    //      baseQ       .. ref (4) and non-ref (6)
+    //      baseQ^2     .. ref (5) and non-ref (7)
+    //      mapQ        .. ref (8) and non-ref (10)
+    //      mapQ^2      .. ref (9) and non-ref (11)
+    //      minDist     .. ref (12) and non-ref (14)
+    //      minDist^2   .. ref (13) and non-ref (15)
+    // Note that this probably needs a more thorough fix: int types in
+    // bcf_call_t do overflow with high-coverage data, such as exomes, and
+    // BCFv2 supports only floats which may not suffice.
+    double anno[16];
+    float p[25];        // phred-scaled likelihood of each genotype
+} bcf_callret1_t;
+
+typedef struct {
+    int tid, pos;
+    bcf_hdr_t *bcf_hdr;
+    int a[5]; // alleles: ref, alt, alt2, alt3
+    float qsum[5];  // for the QS tag
+    int n, n_alleles, shift, ori_ref, unseen;
+    int n_supp; // number of supporting non-reference reads
+    double anno[16];
+    unsigned int depth, ori_depth, mq0;
+    int32_t *PL, *DP4, *ADR, *ADF;
+    uint8_t *fmt_arr;
+    float vdb; // variant distance bias
+    float mwu_pos, mwu_mq, mwu_bq, mwu_mqs;
+#if CDF_MWU_TESTS
+    float mwu_pos_cdf, mwu_mq_cdf, mwu_bq_cdf, mwu_mqs_cdf;
+#endif
+    float seg_bias;
+    kstring_t tmp;
+} bcf_call_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+    bcf_callaux_t *bcf_call_init(double theta, int min_baseQ);
+    void bcf_call_destroy(bcf_callaux_t *bca);
+    int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t *bca, bcf_callret1_t *r);
+    int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
+    int bcf_call2bcf(bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
+                     const bcf_callaux_t *bca, const char *ref);
+    int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
+                          const void *rghash);
+    void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
new file mode 100644
index 000000000..2b42b09d7
--- /dev/null
+++ b/bam2bcf_indel.c
@@ -0,0 +1,533 @@
+/*  bam2bcf_indel.c -- indel caller.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2012-2014 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <assert.h>
+#include <ctype.h>
+#include <string.h>
+#include "htslib/hts.h"
+#include "htslib/sam.h"
+#include "bam2bcf.h"
+#include "htslib/khash.h"
+KHASH_SET_INIT_STR(rg)
+
+#include "htslib/ksort.h"
+KSORT_INIT_GENERIC(uint32_t)
+
+#define MINUS_CONST 0x10000000
+#define INDEL_WINDOW_SIZE 50
+
+void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
+{
+    const char *s, *p, *q, *r, *t;
+    khash_t(rg) *hash;
+    if (list == 0 || hdtext == 0) return _hash;
+    if (_hash == 0) _hash = kh_init(rg);
+    hash = (khash_t(rg)*)_hash;
+    if ((s = strstr(hdtext, "@RG\t")) == 0) return hash;
+    do {
+        t = strstr(s + 4, "@RG\t"); // the next @RG
+        if ((p = strstr(s, "\tID:")) != 0) p += 4;
+        if ((q = strstr(s, "\tPL:")) != 0) q += 4;
+        if (p && q && (t == 0 || (p < t && q < t))) { // ID and PL are both present
+            int lp, lq;
+            char *x;
+            for (r = p; *r && *r != '\t' && *r != '\n'; ++r) { }
+            lp = r - p;
+            for (r = q; *r && *r != '\t' && *r != '\n'; ++r) { }
+            lq = r - q;
+            x = calloc((lp > lq? lp : lq) + 1, 1);
+            for (r = q; *r && *r != '\t' && *r != '\n'; ++r) x[r-q] = *r;
+            if (strstr(list, x)) { // insert ID to the hash table
+                khint_t k;
+                int ret;
+                for (r = p; *r && *r != '\t' && *r != '\n'; ++r) x[r-p] = *r;
+                x[r-p] = 0;
+                k = kh_get(rg, hash, x);
+                if (k == kh_end(hash)) k = kh_put(rg, hash, x, &ret);
+                else free(x);
+            } else free(x);
+        }
+        s = t;
+    } while (s);
+    return hash;
+}
+
+void bcf_call_del_rghash(void *_hash)
+{
+    khint_t k;
+    khash_t(rg) *hash = (khash_t(rg)*)_hash;
+    if (hash == 0) return;
+    for (k = kh_begin(hash); k < kh_end(hash); ++k)
+        if (kh_exist(hash, k))
+            free((char*)kh_key(hash, k));
+    kh_destroy(rg, hash);
+}
+
+static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
+{
+    int k, x = c->pos, y = 0, last_y = 0;
+    *_tpos = c->pos;
+    for (k = 0; k < c->n_cigar; ++k) {
+        int op = cigar[k] & BAM_CIGAR_MASK;
+        int l = cigar[k] >> BAM_CIGAR_SHIFT;
+        if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+            if (c->pos > tpos) return y;
+            if (x + l > tpos) {
+                *_tpos = tpos;
+                return y + (tpos - x);
+            }
+            x += l; y += l;
+            last_y = y;
+        } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+        else if (op == BAM_CDEL || op == BAM_CREF_SKIP) {
+            if (x + l > tpos) {
+                *_tpos = is_left? x : x + l;
+                return y;
+            }
+            x += l;
+        }
+    }
+    *_tpos = x;
+    return last_y;
+}
+// FIXME: check if the inserted sequence is consistent with the homopolymer run
+// l is the relative gap length and l_run is the length of the homopolymer on the reference
+static inline int est_seqQ(const bcf_callaux_t *bca, int l, int l_run)
+{
+    int q, qh;
+    q = bca->openQ + bca->extQ * (abs(l) - 1);
+    qh = l_run >= 3? (int)(bca->tandemQ * (double)abs(l) / l_run + .499) : 1000;
+    return q < qh? q : qh;
+}
+
+static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
+{
+    int i, j, max = 0, max_i = pos, score = 0;
+    l = abs(l);
+    for (i = pos + 1, j = 0; ref[i]; ++i, ++j) {
+        if (ins4) score += (toupper(ref[i]) != "ACGTN"[(int)ins4[j%l]])? -10 : 1;
+        else score += (toupper(ref[i]) != toupper(ref[pos+1+j%l]))? -10 : 1;
+        if (score < 0) break;
+        if (max < score) max = score, max_i = i;
+    }
+    return max_i - pos;
+}
+
+/*
+    notes:
+        - n .. number of samples
+        - the routine sets bam_pileup1_t.aux of each read as follows:
+            - 6: unused
+            - 6: the call; index to bcf_callaux_t.indel_types   .. (aux>>16)&0x3f
+            - 8: estimated sequence quality                     .. (aux>>8)&0xff
+            - 8: indel quality                                  .. aux&0xff
+ */
+int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
+                      const void *rghash)
+{
+    int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
+    int N, K, l_run, ref_type, n_alt;
+    char *inscns = 0, *ref2, *query, **ref_sample;
+    khash_t(rg) *hash = (khash_t(rg)*)rghash;
+    if (ref == 0 || bca == 0) return -1;
+    // mark filtered reads
+    if (rghash) {
+        N = 0;
+        for (s = N = 0; s < n; ++s) {
+            for (i = 0; i < n_plp[s]; ++i) {
+                bam_pileup1_t *p = plp[s] + i;
+                const uint8_t *rg = bam_aux_get(p->b, "RG");
+                p->aux = 1; // filtered by default
+                if (rg) {
+                    khint_t k = kh_get(rg, hash, (const char*)(rg + 1));
+                    if (k != kh_end(hash)) p->aux = 0, ++N; // not filtered
+                }
+            }
+        }
+        if (N == 0) return -1; // no reads left
+    }
+    // determine if there is a gap
+    for (s = N = 0; s < n; ++s) {
+        for (i = 0; i < n_plp[s]; ++i)
+            if (plp[s][i].indel != 0) break;
+        if (i < n_plp[s]) break;
+    }
+    if (s == n) return -1; // there is no indel at this position.
+    for (s = N = 0; s < n; ++s) N += n_plp[s]; // N is the total number of reads
+    { // find out how many types of indels are present
+        bca->max_support = bca->max_frac = 0;
+        int m, n_alt = 0, n_tot = 0, indel_support_ok = 0;
+        uint32_t *aux;
+        aux = calloc(N + 1, 4);
+        m = max_rd_len = 0;
+        aux[m++] = MINUS_CONST; // zero indel is always a type
+        for (s = 0; s < n; ++s) {
+            int na = 0, nt = 0;
+            for (i = 0; i < n_plp[s]; ++i) {
+                const bam_pileup1_t *p = plp[s] + i;
+                if (rghash == 0 || p->aux == 0) {
+                    ++nt;
+                    if (p->indel != 0) {
+                        ++na;
+                        aux[m++] = MINUS_CONST + p->indel;
+                    }
+                }
+                j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b));
+                if (j > max_rd_len) max_rd_len = j;
+            }
+            double frac = (double)na/nt;
+            if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac )
+                indel_support_ok = 1;
+            if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac;
+            n_alt += na;
+            n_tot += nt;
+        }
+        // To prevent long stretches of N's to be mistaken for indels (sometimes thousands of bases),
+        //  check the number of N's in the sequence and skip places where half or more reference bases are Ns.
+        int nN=0; for (i=pos; i-pos<max_rd_len && ref[i]; i++) if ( ref[i]=='N' ) nN++;
+        if ( nN*2>(i-pos) ) { free(aux); return -1; }
+
+        ks_introsort(uint32_t, m, aux);
+        // squeeze out identical types
+        for (i = 1, n_types = 1; i < m; ++i)
+            if (aux[i] != aux[i-1]) ++n_types;
+        // Taking totals makes it hard to call rare indels
+        if ( !bca->per_sample_flt )
+            indel_support_ok = ( (double)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1;
+        if ( n_types == 1 || !indel_support_ok ) { // then skip
+            free(aux); return -1;
+        }
+        if (n_types >= 64) {
+            free(aux);
+            // TODO revisit how/whether to control printing this warning
+            if (hts_verbose >= 2)
+                fprintf(stderr, "[%s] excessive INDEL alleles at position %d. Skip the position.\n", __func__, pos + 1);
+            return -1;
+        }
+        types = (int*)calloc(n_types, sizeof(int));
+        t = 0;
+        types[t++] = aux[0] - MINUS_CONST;
+        for (i = 1; i < m; ++i)
+            if (aux[i] != aux[i-1])
+                types[t++] = aux[i] - MINUS_CONST;
+        free(aux);
+        for (t = 0; t < n_types; ++t)
+            if (types[t] == 0) break;
+        ref_type = t; // the index of the reference type (0)
+    }
+    { // calculate left and right boundary
+        left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
+        right = pos + INDEL_WINDOW_SIZE;
+        if (types[0] < 0) right -= types[0];
+        // in case the alignments stand out the reference
+        for (i = pos; i < right; ++i)
+            if (ref[i] == 0) break;
+        right = i;
+    }
+    /* The following block fixes a long-existing flaw in the INDEL
+     * calling model: the interference of nearby SNPs. However, it also
+     * reduces the power because sometimes, substitutions caused by
+     * indels are not distinguishable from true mutations. Multiple
+     * sequence realignment helps to increase the power.
+     *
+     * Masks mismatches present in at least 70% of the reads with 'N'.
+     */
+    { // construct per-sample consensus
+        int L = right - left + 1, max_i, max2_i;
+        uint32_t *cns, max, max2;
+        char *ref0, *r;
+        ref_sample = calloc(n, sizeof(char*));
+        cns = calloc(L, 4);
+        ref0 = calloc(L, 1);
+        for (i = 0; i < right - left; ++i)
+            ref0[i] = seq_nt16_table[(int)ref[i+left]];
+        for (s = 0; s < n; ++s) {
+            r = ref_sample[s] = calloc(L, 1);
+            memset(cns, 0, sizeof(int) * L);
+            // collect ref and non-ref counts
+            for (i = 0; i < n_plp[s]; ++i) {
+                bam_pileup1_t *p = plp[s] + i;
+                bam1_t *b = p->b;
+                uint32_t *cigar = bam_get_cigar(b);
+                uint8_t *seq = bam_get_seq(b);
+                int x = b->core.pos, y = 0;
+                for (k = 0; k < b->core.n_cigar; ++k) {
+                    int op = cigar[k]&0xf;
+                    int j, l = cigar[k]>>4;
+                    if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
+                        for (j = 0; j < l; ++j)
+                            if (x + j >= left && x + j < right)
+                                cns[x+j-left] += (bam_seqi(seq, y+j) == ref0[x+j-left])? 1 : 0x10000;
+                        x += l; y += l;
+                    } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
+                    else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+                }
+            }
+            // determine the consensus
+            for (i = 0; i < right - left; ++i) r[i] = ref0[i];
+            max = max2 = 0; max_i = max2_i = -1;
+            for (i = 0; i < right - left; ++i) {
+                if (cns[i]>>16 >= max>>16) max2 = max, max2_i = max_i, max = cns[i], max_i = i;
+                else if (cns[i]>>16 >= max2>>16) max2 = cns[i], max2_i = i;
+            }
+            if ((double)(max&0xffff) / ((max&0xffff) + (max>>16)) >= 0.7) max_i = -1;
+            if ((double)(max2&0xffff) / ((max2&0xffff) + (max2>>16)) >= 0.7) max2_i = -1;
+            if (max_i >= 0) r[max_i] = 15;
+            if (max2_i >= 0) r[max2_i] = 15;
+            //for (i = 0; i < right - left; ++i) fputc("=ACMGRSVTWYHKDBN"[(int)r[i]], stderr); fputc('\n', stderr);
+        }
+        free(ref0); free(cns);
+    }
+    { // the length of the homopolymer run around the current position
+        int c = seq_nt16_table[(int)ref[pos + 1]];
+        if (c == 15) l_run = 1;
+        else {
+            for (i = pos + 2; ref[i]; ++i)
+                if (seq_nt16_table[(int)ref[i]] != c) break;
+            l_run = i;
+            for (i = pos; i >= 0; --i)
+                if (seq_nt16_table[(int)ref[i]] != c) break;
+            l_run -= i + 1;
+        }
+    }
+    // construct the consensus sequence
+    max_ins = types[n_types - 1];   // max_ins is at least 0
+    if (max_ins > 0) {
+        int *inscns_aux = calloc(5 * n_types * max_ins, sizeof(int));
+        // count the number of occurrences of each base at each position for each type of insertion
+        for (t = 0; t < n_types; ++t) {
+            if (types[t] > 0) {
+                for (s = 0; s < n; ++s) {
+                    for (i = 0; i < n_plp[s]; ++i) {
+                        bam_pileup1_t *p = plp[s] + i;
+                        if (p->indel == types[t]) {
+                            uint8_t *seq = bam_get_seq(p->b);
+                            for (k = 1; k <= p->indel; ++k) {
+                                int c = seq_nt16_int[bam_seqi(seq, p->qpos + k)];
+                                assert(c<5);
+                                ++inscns_aux[(t*max_ins+(k-1))*5 + c];
+                            }
+                        }
+                    }
+                }
+            }
+        }
+        // use the majority rule to construct the consensus
+        inscns = calloc(n_types * max_ins, 1);
+        for (t = 0; t < n_types; ++t) {
+            for (j = 0; j < types[t]; ++j) {
+                int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
+                for (k = 0; k < 5; ++k)
+                    if (ia[k] > max)
+                        max = ia[k], max_k = k;
+                inscns[t*max_ins + j] = max? max_k : 4;
+                if ( max_k==4 ) { types[t] = 0; break; } // discard insertions which contain N's
+            }
+        }
+        free(inscns_aux);
+    }
+    // compute the likelihood given each type of indel for each read
+    max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
+    ref2  = calloc(max_ref2, 1);
+    query = calloc(right - left + max_rd_len + max_ins + 2, 1);
+    score1 = calloc(N * n_types, sizeof(int));
+    score2 = calloc(N * n_types, sizeof(int));
+    bca->indelreg = 0;
+    for (t = 0; t < n_types; ++t) {
+        int l, ir;
+        probaln_par_t apf1 = { 1e-4, 1e-2, 10 }, apf2 = { 1e-6, 1e-3, 10 };
+        apf1.bw = apf2.bw = abs(types[t]) + 3;
+        // compute indelreg
+        if (types[t] == 0) ir = 0;
+        else if (types[t] > 0) ir = est_indelreg(pos, ref, types[t], &inscns[t*max_ins]);
+        else ir = est_indelreg(pos, ref, -types[t], 0);
+        if (ir > bca->indelreg) bca->indelreg = ir;
+//      fprintf(stderr, "%d, %d, %d\n", pos, types[t], ir);
+        // realignment
+        for (s = K = 0; s < n; ++s) {
+            // write ref2
+            for (k = 0, j = left; j <= pos; ++j)
+                ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]];
+            if (types[t] <= 0) j += -types[t];
+            else for (l = 0; l < types[t]; ++l)
+                     ref2[k++] = inscns[t*max_ins + l];
+            for (; j < right && ref[j]; ++j)
+                ref2[k++] = seq_nt16_int[(int)ref_sample[s][j-left]];
+            for (; k < max_ref2; ++k) ref2[k] = 4;
+            if (j < right) right = j;
+            // align each read to ref2
+            for (i = 0; i < n_plp[s]; ++i, ++K) {
+                bam_pileup1_t *p = plp[s] + i;
+                int qbeg, qend, tbeg, tend, sc, kk;
+                uint8_t *seq = bam_get_seq(p->b);
+                uint32_t *cigar = bam_get_cigar(p->b);
+                if (p->b->core.flag&4) continue; // unmapped reads
+                // FIXME: the following loop should be better moved outside; nonetheless, realignment should be much slower anyway.
+                for (kk = 0; kk < p->b->core.n_cigar; ++kk)
+                    if ((cigar[kk]&BAM_CIGAR_MASK) == BAM_CREF_SKIP) break;
+                if (kk < p->b->core.n_cigar) continue;
+                // FIXME: the following skips soft clips, but using them may be more sensitive.
+                // determine the start and end of sequences for alignment
+                qbeg = tpos2qpos(&p->b->core, bam_get_cigar(p->b), left,  0, &tbeg);
+                qend = tpos2qpos(&p->b->core, bam_get_cigar(p->b), right, 1, &tend);
+                if (types[t] < 0) {
+                    int l = -types[t];
+                    tbeg = tbeg - l > left?  tbeg - l : left;
+                }
+                // write the query sequence
+                for (l = qbeg; l < qend; ++l)
+                    query[l - qbeg] = seq_nt16_int[bam_seqi(seq, l)];
+                { // do realignment; this is the bottleneck
+                    const uint8_t *qual = bam_get_qual(p->b), *bq;
+                    uint8_t *qq;
+                    qq = calloc(qend - qbeg, 1);
+                    bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
+                    if (bq) ++bq; // skip type
+                    for (l = qbeg; l < qend; ++l) {
+                        qq[l - qbeg] = bq? qual[l] + (bq[l] - 64) : qual[l];
+                        if (qq[l - qbeg] > 30) qq[l - qbeg] = 30;
+                        if (qq[l - qbeg] < 7) qq[l - qbeg] = 7;
+                    }
+                    sc = probaln_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+                                        (uint8_t*)query, qend - qbeg, qq, &apf1, 0, 0);
+                    l = (int)(100. * sc / (qend - qbeg) + .499); // used for adjusting indelQ below
+                    if (l > 255) l = 255;
+                    score1[K*n_types + t] = score2[K*n_types + t] = sc<<8 | l;
+                    if (sc > 5) {
+                        sc = probaln_glocal((uint8_t*)ref2 + tbeg - left, tend - tbeg + abs(types[t]),
+                                            (uint8_t*)query, qend - qbeg, qq, &apf2, 0, 0);
+                        l = (int)(100. * sc / (qend - qbeg) + .499);
+                        if (l > 255) l = 255;
+                        score2[K*n_types + t] = sc<<8 | l;
+                    }
+                    free(qq);
+                }
+/*
+                for (l = 0; l < tend - tbeg + abs(types[t]); ++l)
+                    fputc("ACGTN"[(int)ref2[tbeg-left+l]], stderr);
+                fputc('\n', stderr);
+                for (l = 0; l < qend - qbeg; ++l) fputc("ACGTN"[(int)query[l]], stderr);
+                fputc('\n', stderr);
+                fprintf(stderr, "pos=%d type=%d read=%d:%d name=%s qbeg=%d tbeg=%d score=%d\n", pos, types[t], s, i, bam1_qname(p->b), qbeg, tbeg, sc);
+*/
+            }
+        }
+    }
+    free(ref2); free(query);
+    { // compute indelQ
+        int *sc, tmp, *sumq;
+        sc   = alloca(n_types * sizeof(int));
+        sumq = alloca(n_types * sizeof(int));
+        memset(sumq, 0, sizeof(int) * n_types);
+        for (s = K = 0; s < n; ++s) {
+            for (i = 0; i < n_plp[s]; ++i, ++K) {
+                bam_pileup1_t *p = plp[s] + i;
+                int *sct = &score1[K*n_types], indelQ1, indelQ2, seqQ, indelQ;
+                for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
+                for (t = 1; t < n_types; ++t) // insertion sort
+                    for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
+                        tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+                /* errmod_cal() assumes that if the call is wrong, the
+                 * likelihoods of other events are equal. This is about
+                 * right for substitutions, but is not desired for
+                 * indels. To reuse errmod_cal(), I have to make
+                 * compromise for multi-allelic indels.
+                 */
+                if ((sc[0]&0x3f) == ref_type) {
+                    indelQ1 = (sc[1]>>14) - (sc[0]>>14);
+                    seqQ = est_seqQ(bca, types[sc[1]&0x3f], l_run);
+                } else {
+                    for (t = 0; t < n_types; ++t) // look for the reference type
+                        if ((sc[t]&0x3f) == ref_type) break;
+                    indelQ1 = (sc[t]>>14) - (sc[0]>>14);
+                    seqQ = est_seqQ(bca, types[sc[0]&0x3f], l_run);
+                }
+                tmp = sc[0]>>6 & 0xff;
+                indelQ1 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ1 + .499); // reduce indelQ
+                sct = &score2[K*n_types];
+                for (t = 0; t < n_types; ++t) sc[t] = sct[t]<<6 | t;
+                for (t = 1; t < n_types; ++t) // insertion sort
+                    for (j = t; j > 0 && sc[j] < sc[j-1]; --j)
+                        tmp = sc[j], sc[j] = sc[j-1], sc[j-1] = tmp;
+                if ((sc[0]&0x3f) == ref_type) {
+                    indelQ2 = (sc[1]>>14) - (sc[0]>>14);
+                } else {
+                    for (t = 0; t < n_types; ++t) // look for the reference type
+                        if ((sc[t]&0x3f) == ref_type) break;
+                    indelQ2 = (sc[t]>>14) - (sc[0]>>14);
+                }
+                tmp = sc[0]>>6 & 0xff;
+                indelQ2 = tmp > 111? 0 : (int)((1. - tmp/111.) * indelQ2 + .499);
+                // pick the smaller between indelQ1 and indelQ2
+                indelQ = indelQ1 < indelQ2? indelQ1 : indelQ2;
+                if (indelQ > 255) indelQ = 255;
+                if (seqQ > 255) seqQ = 255;
+                p->aux = (sc[0]&0x3f)<<16 | seqQ<<8 | indelQ; // use 22 bits in total
+                sumq[sc[0]&0x3f] += indelQ < seqQ? indelQ : seqQ;
+//              fprintf(stderr, "pos=%d read=%d:%d name=%s call=%d indelQ=%d seqQ=%d\n", pos, s, i, bam1_qname(p->b), types[sc[0]&0x3f], indelQ, seqQ);
+            }
+        }
+        // determine bca->indel_types[] and bca->inscns
+        bca->maxins = max_ins;
+        bca->inscns = realloc(bca->inscns, bca->maxins * 4);
+        for (t = 0; t < n_types; ++t)
+            sumq[t] = sumq[t]<<6 | t;
+        for (t = 1; t < n_types; ++t) // insertion sort
+            for (j = t; j > 0 && sumq[j] > sumq[j-1]; --j)
+                tmp = sumq[j], sumq[j] = sumq[j-1], sumq[j-1] = tmp;
+        for (t = 0; t < n_types; ++t) // look for the reference type
+            if ((sumq[t]&0x3f) == ref_type) break;
+        if (t) { // then move the reference type to the first
+            tmp = sumq[t];
+            for (; t > 0; --t) sumq[t] = sumq[t-1];
+            sumq[0] = tmp;
+        }
+        for (t = 0; t < 4; ++t) bca->indel_types[t] = B2B_INDEL_NULL;
+        for (t = 0; t < 4 && t < n_types; ++t) {
+            bca->indel_types[t] = types[sumq[t]&0x3f];
+            memcpy(&bca->inscns[t * bca->maxins], &inscns[(sumq[t]&0x3f) * max_ins], bca->maxins);
+        }
+        // update p->aux
+        for (s = n_alt = 0; s < n; ++s) {
+            for (i = 0; i < n_plp[s]; ++i) {
+                bam_pileup1_t *p = plp[s] + i;
+                int x = types[p->aux>>16&0x3f];
+                for (j = 0; j < 4; ++j)
+                    if (x == bca->indel_types[j]) break;
+                p->aux = j<<16 | (j == 4? 0 : (p->aux&0xffff));
+                if ((p->aux>>16&0x3f) > 0) ++n_alt;
+                //fprintf(stderr, "X pos=%d read=%d:%d name=%s call=%d type=%d seqQ=%d indelQ=%d\n", pos, s, i, bam1_qname(p->b), (p->aux>>16)&0x3f, bca->indel_types[(p->aux>>16)&0x3f], (p->aux>>8)&0xff, p->aux&0xff);
+            }
+        }
+    }
+    free(score1); free(score2);
+    // free
+    for (i = 0; i < n; ++i) free(ref_sample[i]);
+    free(ref_sample);
+    free(types); free(inscns);
+    return n_alt > 0? 0 : -1;
+}
diff --git a/bam_plcmd.c b/bam_plcmd.c
new file mode 100644
index 000000000..ddd2f0043
--- /dev/null
+++ b/bam_plcmd.c
@@ -0,0 +1,1027 @@
+/*  bam_plcmd.c -- mpileup subcommand.
+
+    Copyright (C) 2008-2015 Genome Research Ltd.
+    Portions copyright (C) 2009-2012 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <ctype.h>
+#include <string.h>
+#include <limits.h>
+#include <errno.h>
+#include <sys/stat.h>
+#include <getopt.h>
+#include <htslib/sam.h>
+#include <htslib/faidx.h>
+#include <htslib/kstring.h>
+#include <htslib/khash_str2int.h>
+#include "sam_header.h"
+#include "samtools.h"
+#include "sam_opts.h"
+
+static inline int printw(int c, FILE *fp)
+{
+    char buf[16];
+    int l, x;
+    if (c == 0) return fputc('0', fp);
+    for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
+    if (c < 0) buf[l++] = '-';
+    buf[l] = 0;
+    for (x = 0; x < l/2; ++x) {
+        int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
+    }
+    fputs(buf, fp);
+    return 0;
+}
+
+static inline void pileup_seq(FILE *fp, const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
+{
+    int j;
+    if (p->is_head) {
+        putc('^', fp);
+        putc(p->b->core.qual > 93? 126 : p->b->core.qual + 33, fp);
+    }
+    if (!p->is_del) {
+        int c = p->qpos < p->b->core.l_qseq
+            ? seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)]
+            : 'N';
+        if (ref) {
+            int rb = pos < ref_len? ref[pos] : 'N';
+            if (c == '=' || seq_nt16_table[c] == seq_nt16_table[rb]) c = bam_is_rev(p->b)? ',' : '.';
+            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
+        } else {
+            if (c == '=') c = bam_is_rev(p->b)? ',' : '.';
+            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
+        }
+        putc(c, fp);
+    } else putc(p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : '*', fp);
+    if (p->indel > 0) {
+        putc('+', fp); printw(p->indel, fp);
+        for (j = 1; j <= p->indel; ++j) {
+            int c = seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos + j)];
+            putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
+        }
+    } else if (p->indel < 0) {
+        printw(p->indel, fp);
+        for (j = 1; j <= -p->indel; ++j) {
+            int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
+            putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
+        }
+    }
+    if (p->is_tail) putc('$', fp);
+}
+
+#include <assert.h>
+#include "bam2bcf.h"
+#include "sample.h"
+
+#define MPLP_BCF        1
+#define MPLP_VCF        (1<<1)
+#define MPLP_NO_COMP    (1<<2)
+#define MPLP_NO_ORPHAN  (1<<3)
+#define MPLP_REALN      (1<<4)
+#define MPLP_NO_INDEL   (1<<5)
+#define MPLP_REDO_BAQ   (1<<6)
+#define MPLP_ILLUMINA13 (1<<7)
+#define MPLP_IGNORE_RG  (1<<8)
+#define MPLP_PRINT_POS  (1<<9)
+#define MPLP_PRINT_MAPQ (1<<10)
+#define MPLP_PER_SAMPLE (1<<11)
+#define MPLP_SMART_OVERLAPS (1<<12)
+
+void *bed_read(const char *fn);
+void bed_destroy(void *_h);
+int bed_overlap(const void *_h, const char *chr, int beg, int end);
+
+typedef struct {
+    int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
+    int rflag_require, rflag_filter;
+    int openQ, extQ, tandemQ, min_support; // for indels
+    double min_frac; // for indels
+    char *reg, *pl_list, *fai_fname, *output_fname;
+    faidx_t *fai;
+    void *bed, *rghash;
+    int argc;
+    char **argv;
+    sam_global_args ga;
+} mplp_conf_t;
+
+typedef struct {
+    char *ref[2];
+    int ref_id[2];
+    int ref_len[2];
+} mplp_ref_t;
+
+#define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
+
+typedef struct {
+    samFile *fp;
+    hts_itr_t *iter;
+    bam_hdr_t *h;
+    mplp_ref_t *ref;
+    const mplp_conf_t *conf;
+} mplp_aux_t;
+
+typedef struct {
+    int n;
+    int *n_plp, *m_plp;
+    bam_pileup1_t **plp;
+} mplp_pileup_t;
+
+static int mplp_get_ref(mplp_aux_t *ma, int tid,  char **ref, int *ref_len) {
+    mplp_ref_t *r = ma->ref;
+
+    //printf("get ref %d {%d/%p, %d/%p}\n", tid, r->ref_id[0], r->ref[0], r->ref_id[1], r->ref[1]);
+
+    if (!r || !ma->conf->fai) {
+        *ref = NULL;
+        return 0;
+    }
+
+    // Do we need to reference count this so multiple mplp_aux_t can
+    // track which references are in use?
+    // For now we just cache the last two. Sufficient?
+    if (tid == r->ref_id[0]) {
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+    if (tid == r->ref_id[1]) {
+        // Last, swap over
+        int tmp;
+        tmp = r->ref_id[0];  r->ref_id[0]  = r->ref_id[1];  r->ref_id[1]  = tmp;
+        tmp = r->ref_len[0]; r->ref_len[0] = r->ref_len[1]; r->ref_len[1] = tmp;
+
+        char *tc;
+        tc = r->ref[0]; r->ref[0] = r->ref[1]; r->ref[1] = tc;
+        *ref = r->ref[0];
+        *ref_len = r->ref_len[0];
+        return 1;
+    }
+
+    // New, so migrate to old and load new
+    free(r->ref[1]);
+    r->ref[1]     = r->ref[0];
+    r->ref_id[1]  = r->ref_id[0];
+    r->ref_len[1] = r->ref_len[0];
+
+    r->ref_id[0] = tid;
+    r->ref[0] = faidx_fetch_seq(ma->conf->fai,
+                                ma->h->target_name[r->ref_id[0]],
+                                0,
+                                INT_MAX,
+                                &r->ref_len[0]);
+
+    if (!r->ref[0]) {
+        r->ref[0] = NULL;
+        r->ref_id[0] = -1;
+        r->ref_len[0] = 0;
+        *ref = NULL;
+        return 0;
+    }
+
+    *ref = r->ref[0];
+    *ref_len = r->ref_len[0];
+    return 1;
+}
+
+static int mplp_func(void *data, bam1_t *b)
+{
+    char *ref;
+    mplp_aux_t *ma = (mplp_aux_t*)data;
+    int ret, skip = 0, ref_len;
+    do {
+        int has_ref;
+        ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
+        if (ret < 0) break;
+        // The 'B' cigar operation is not part of the specification, considering as obsolete.
+        //  bam_remove_B(b);
+        if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
+            skip = 1;
+            continue;
+        }
+        if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
+        if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
+        if (ma->conf->bed) { // test overlap
+            skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_endpos(b));
+            if (skip) continue;
+        }
+        if (ma->conf->rghash) { // exclude read groups
+            uint8_t *rg = bam_aux_get(b, "RG");
+            skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0);
+            if (skip) continue;
+        }
+        if (ma->conf->flag & MPLP_ILLUMINA13) {
+            int i;
+            uint8_t *qual = bam_get_qual(b);
+            for (i = 0; i < b->core.l_qseq; ++i)
+                qual[i] = qual[i] > 31? qual[i] - 31 : 0;
+        }
+
+        if (ma->conf->fai && b->core.tid >= 0) {
+            has_ref = mplp_get_ref(ma, b->core.tid, &ref, &ref_len);
+            if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
+                fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n",
+                        __func__, b->core.pos, ref_len, b->core.tid);
+                skip = 1;
+                continue;
+            }
+        } else {
+            has_ref = 0;
+        }
+
+        skip = 0;
+        if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
+        if (has_ref && ma->conf->capQ_thres > 10) {
+            int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
+            if (q < 0) skip = 1;
+            else if (b->core.qual > q) b->core.qual = q;
+        }
+        if (b->core.qual < ma->conf->min_mq) skip = 1;
+        else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1;
+    } while (skip);
+    return ret;
+}
+
+static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
+                       int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
+{
+    int i, j;
+    memset(m->n_plp, 0, m->n * sizeof(int));
+    for (i = 0; i < n; ++i) {
+        for (j = 0; j < n_plp[i]; ++j) {
+            const bam_pileup1_t *p = plp[i] + j;
+            uint8_t *q;
+            int id = -1;
+            q = ignore_rg? NULL : bam_aux_get(p->b, "RG");
+            if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
+            if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
+            if (id < 0 || id >= m->n) {
+                assert(q); // otherwise a bug
+                fprintf(stderr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
+                exit(EXIT_FAILURE);
+            }
+            if (m->n_plp[id] == m->m_plp[id]) {
+                m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
+                m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
+            }
+            m->plp[id][m->n_plp[id]++] = *p;
+        }
+    }
+}
+
+/*
+ * Performs pileup
+ * @param conf configuration for this pileup
+ * @param n number of files specified in fn
+ * @param fn filenames
+ */
+static int mpileup(mplp_conf_t *conf, int n, char **fn)
+{
+    extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
+    extern void bcf_call_del_rghash(void *rghash);
+    mplp_aux_t **data;
+    int i, tid, pos, *n_plp, beg0 = 0, end0 = INT_MAX, ref_len, max_depth, max_indel_depth;
+    const bam_pileup1_t **plp;
+    mplp_ref_t mp_ref = MPLP_REF_INIT;
+    bam_mplp_t iter;
+    bam_hdr_t *h = NULL; /* header of first file in input list */
+    char *ref;
+    void *rghash = NULL;
+    FILE *pileup_fp = NULL;
+
+    bcf_callaux_t *bca = NULL;
+    bcf_callret1_t *bcr = NULL;
+    bcf_call_t bc;
+    htsFile *bcf_fp = NULL;
+    bcf_hdr_t *bcf_hdr = NULL;
+
+    bam_sample_t *sm = NULL;
+    kstring_t buf;
+    mplp_pileup_t gplp;
+
+    memset(&gplp, 0, sizeof(mplp_pileup_t));
+    memset(&buf, 0, sizeof(kstring_t));
+    memset(&bc, 0, sizeof(bcf_call_t));
+    data = calloc(n, sizeof(mplp_aux_t*));
+    plp = calloc(n, sizeof(bam_pileup1_t*));
+    n_plp = calloc(n, sizeof(int));
+    sm = bam_smpl_init();
+
+    if (n == 0) {
+        fprintf(stderr,"[%s] no input file/data given\n", __func__);
+        exit(EXIT_FAILURE);
+    }
+
+    // read the header of each file in the list and initialize data
+    for (i = 0; i < n; ++i) {
+        bam_hdr_t *h_tmp;
+        data[i] = calloc(1, sizeof(mplp_aux_t));
+        data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in);
+        if ( !data[i]->fp )
+        {
+            fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
+            exit(EXIT_FAILURE);
+        }
+        if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
+            fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
+            exit(EXIT_FAILURE);
+        }
+        if (conf->fai_fname && hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) {
+            fprintf(stderr, "[%s] failed to process %s: %s\n",
+                    __func__, conf->fai_fname, strerror(errno));
+            exit(EXIT_FAILURE);
+        }
+        data[i]->conf = conf;
+        data[i]->ref = &mp_ref;
+        h_tmp = sam_hdr_read(data[i]->fp);
+        if ( !h_tmp ) {
+            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+            exit(EXIT_FAILURE);
+        }
+        bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
+        // Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
+        rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
+        if (conf->reg) {
+            hts_idx_t *idx = sam_index_load(data[i]->fp, fn[i]);
+            if (idx == NULL) {
+                fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
+                exit(EXIT_FAILURE);
+            }
+            if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) {
+                fprintf(stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]);
+                exit(EXIT_FAILURE);
+            }
+            if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end;
+            hts_idx_destroy(idx);
+        }
+        else
+            data[i]->iter = NULL;
+
+        if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file
+        else {
+            // FIXME: check consistency between h and h_tmp
+            bam_hdr_destroy(h_tmp);
+
+            // we store only the first file's header; it's (alleged to be)
+            // compatible with the i-th file's target_name lookup needs
+            data[i]->h = h;
+        }
+    }
+    // allocate data storage proportionate to number of samples being studied sm->n
+    gplp.n = sm->n;
+    gplp.n_plp = calloc(sm->n, sizeof(int));
+    gplp.m_plp = calloc(sm->n, sizeof(int));
+    gplp.plp = calloc(sm->n, sizeof(bam_pileup1_t*));
+
+    fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
+    // write the VCF header
+    if (conf->flag & MPLP_BCF)
+    {
+        const char *mode;
+        if ( conf->flag & MPLP_VCF )
+            mode = (conf->flag&MPLP_NO_COMP)? "wu" : "wz";   // uncompressed VCF or compressed VCF
+        else
+            mode = (conf->flag&MPLP_NO_COMP)? "wub" : "wb";  // uncompressed BCF or compressed BCF
+
+        bcf_fp = bcf_open(conf->output_fname? conf->output_fname : "-", mode);
+        if (bcf_fp == NULL) {
+            fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
+            exit(EXIT_FAILURE);
+        }
+
+        // BCF header creation
+        bcf_hdr = bcf_hdr_init("w");
+        kstring_t str = {0,0,NULL};
+
+        ksprintf(&str, "##samtoolsVersion=%s+htslib-%s\n",samtools_version(),hts_version());
+        bcf_hdr_append(bcf_hdr, str.s);
+
+        str.l = 0;
+        ksprintf(&str, "##samtoolsCommand=samtools mpileup");
+        for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
+        kputc('\n', &str);
+        bcf_hdr_append(bcf_hdr, str.s);
+
+        if (conf->fai_fname)
+        {
+            str.l = 0;
+            ksprintf(&str, "##reference=file://%s\n", conf->fai_fname);
+            bcf_hdr_append(bcf_hdr, str.s);
+        }
+
+        // Translate BAM @SQ tags to BCF ##contig tags
+        // todo: use/write new BAM header manipulation routines, fill also UR, M5
+        for (i=0; i<h->n_targets; i++)
+        {
+            str.l = 0;
+            ksprintf(&str, "##contig=<ID=%s,length=%d>", h->target_name[i], h->target_len[i]);
+            bcf_hdr_append(bcf_hdr, str.s);
+        }
+        free(str.s);
+        bcf_hdr_append(bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
+#if CDF_MWU_TESTS
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
+#endif
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
+        if ( conf->fmt_flag&B2B_FMT_DP )
+            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
+        if ( conf->fmt_flag&B2B_FMT_DV )
+            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
+        if ( conf->fmt_flag&B2B_FMT_DPR )
+            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+        if ( conf->fmt_flag&B2B_INFO_DPR )
+            bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+        if ( conf->fmt_flag&B2B_FMT_DP4 )
+            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
+        if ( conf->fmt_flag&B2B_FMT_SP )
+            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
+        if ( conf->fmt_flag&B2B_FMT_AD )
+            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
+        if ( conf->fmt_flag&B2B_FMT_ADF )
+            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
+        if ( conf->fmt_flag&B2B_FMT_ADR )
+            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
+        if ( conf->fmt_flag&B2B_INFO_AD )
+            bcf_hdr_append(bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
+        if ( conf->fmt_flag&B2B_INFO_ADF )
+            bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
+        if ( conf->fmt_flag&B2B_INFO_ADR )
+            bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
+
+        for (i=0; i<sm->n; i++)
+            bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
+        bcf_hdr_add_sample(bcf_hdr, NULL);
+        bcf_hdr_write(bcf_fp, bcf_hdr);
+        // End of BCF header creation
+
+        // Initialise the calling algorithm
+        bca = bcf_call_init(-1., conf->min_baseQ);
+        bcr = calloc(sm->n, sizeof(bcf_callret1_t));
+        bca->rghash = rghash;
+        bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
+        bca->min_frac = conf->min_frac;
+        bca->min_support = conf->min_support;
+        bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
+
+        bc.bcf_hdr = bcf_hdr;
+        bc.n = sm->n;
+        bc.PL = malloc(15 * sm->n * sizeof(*bc.PL));
+        if (conf->fmt_flag)
+        {
+            assert( sizeof(float)==sizeof(int32_t) );
+            bc.DP4 = malloc(sm->n * sizeof(int32_t) * 4);
+            bc.fmt_arr = malloc(sm->n * sizeof(float)); // all fmt_flag fields
+            if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
+            {
+                // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
+                bc.ADR = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+                bc.ADF = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+                for (i=0; i<sm->n; i++)
+                {
+                    bcr[i].ADR = bc.ADR + (i+1)*B2B_MAX_ALLELES;
+                    bcr[i].ADF = bc.ADF + (i+1)*B2B_MAX_ALLELES;
+                }
+            }
+        }
+    }
+    else {
+        pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout;
+
+        if (pileup_fp == NULL) {
+            fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno));
+            exit(EXIT_FAILURE);
+        }
+    }
+
+    // init pileup
+    iter = bam_mplp_init(n, mplp_func, (void**)data);
+    if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter);
+    max_depth = conf->max_depth;
+    if (max_depth * sm->n > 1<<20)
+        fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
+    if (max_depth * sm->n < 8000) {
+        max_depth = 8000 / sm->n;
+        fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
+    }
+    max_indel_depth = conf->max_indel_depth * sm->n;
+    bam_mplp_set_maxcnt(iter, max_depth);
+    bcf1_t *bcf_rec = bcf_init1();
+    int ret;
+    // begin pileup
+    while ( (ret=bam_mplp_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
+        if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
+        if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
+        mplp_get_ref(data[0], tid, &ref, &ref_len);
+        //printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
+        if (conf->flag & MPLP_BCF) {
+            int total_depth, _ref0, ref16;
+            for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
+            group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
+            _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+            ref16 = seq_nt16_table[_ref0];
+            bcf_callaux_clean(bca, &bc);
+            for (i = 0; i < gplp.n; ++i)
+                bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
+            bc.tid = tid; bc.pos = pos;
+            bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
+            bcf_clear1(bcf_rec);
+            bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
+            bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
+            // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
+            if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0)
+            {
+                bcf_callaux_clean(bca, &bc);
+                for (i = 0; i < gplp.n; ++i)
+                    bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
+                if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
+                    bcf_clear1(bcf_rec);
+                    bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
+                    bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
+                }
+            }
+        } else {
+            fprintf(pileup_fp, "%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
+            for (i = 0; i < n; ++i) {
+                int j, cnt;
+                for (j = cnt = 0; j < n_plp[i]; ++j) {
+                    const bam_pileup1_t *p = plp[i] + j;
+                    int c = p->qpos < p->b->core.l_qseq
+                             ? bam_get_qual(p->b)[p->qpos]
+                             : 0;
+                    if (c >= conf->min_baseQ) ++cnt;
+                }
+                fprintf(pileup_fp, "\t%d\t", cnt);
+                if (n_plp[i] == 0) {
+                    fputs("*\t*", pileup_fp);
+                    if (conf->flag & MPLP_PRINT_MAPQ) fputs("\t*", pileup_fp);
+                    if (conf->flag & MPLP_PRINT_POS) fputs("\t*", pileup_fp);
+                } else {
+                    for (j = 0; j < n_plp[i]; ++j) {
+                        const bam_pileup1_t *p = plp[i] + j;
+                        int c = p->qpos < p->b->core.l_qseq
+                            ? bam_get_qual(p->b)[p->qpos]
+                            : 0;
+                        if (c >= conf->min_baseQ)
+                            pileup_seq(pileup_fp, plp[i] + j, pos, ref_len, ref);
+                    }
+                    putc('\t', pileup_fp);
+                    for (j = 0; j < n_plp[i]; ++j) {
+                        const bam_pileup1_t *p = plp[i] + j;
+                        int c = p->qpos < p->b->core.l_qseq
+                            ? bam_get_qual(p->b)[p->qpos]
+                            : 0;
+                        if (c >= conf->min_baseQ) {
+                            c = c + 33 < 126? c + 33 : 126;
+                            putc(c, pileup_fp);
+                        }
+                    }
+                    if (conf->flag & MPLP_PRINT_MAPQ) {
+                        putc('\t', pileup_fp);
+                        for (j = 0; j < n_plp[i]; ++j) {
+                            const bam_pileup1_t *p = plp[i] + j;
+                            int c = bam_get_qual(p->b)[p->qpos];
+                            if ( c < conf->min_baseQ ) continue;
+                            c = plp[i][j].b->core.qual + 33;
+                            if (c > 126) c = 126;
+                            putc(c, pileup_fp);
+                        }
+                    }
+                    if (conf->flag & MPLP_PRINT_POS) {
+                        putc('\t', pileup_fp);
+                        int last = 0;
+                        for (j = 0; j < n_plp[i]; ++j) {
+                            const bam_pileup1_t *p = plp[i] + j;
+                            int c = bam_get_qual(p->b)[p->qpos];
+                            if ( c < conf->min_baseQ ) continue;
+
+                            if (last++) putc(',', pileup_fp);
+                            fprintf(pileup_fp, "%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
+                        }
+                    }
+                }
+            }
+            putc('\n', pileup_fp);
+        }
+    }
+
+    // clean up
+    free(bc.tmp.s);
+    bcf_destroy1(bcf_rec);
+    if (bcf_fp)
+    {
+        hts_close(bcf_fp);
+        bcf_hdr_destroy(bcf_hdr);
+        bcf_call_destroy(bca);
+        free(bc.PL);
+        free(bc.DP4);
+        free(bc.ADR);
+        free(bc.ADF);
+        free(bc.fmt_arr);
+        free(bcr);
+    }
+    if (pileup_fp && conf->output_fname) fclose(pileup_fp);
+    bam_smpl_destroy(sm); free(buf.s);
+    for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
+    free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
+    bcf_call_del_rghash(rghash);
+    bam_mplp_destroy(iter);
+    bam_hdr_destroy(h);
+    for (i = 0; i < n; ++i) {
+        sam_close(data[i]->fp);
+        if (data[i]->iter) hts_itr_destroy(data[i]->iter);
+        free(data[i]);
+    }
+    free(data); free(plp); free(n_plp);
+    free(mp_ref.ref[0]);
+    free(mp_ref.ref[1]);
+    return ret;
+}
+
+#define MAX_PATH_LEN 1024
+int read_file_list(const char *file_list,int *n,char **argv[])
+{
+    char buf[MAX_PATH_LEN];
+    int len, nfiles = 0;
+    char **files = NULL;
+    struct stat sb;
+
+    *n = 0;
+    *argv = NULL;
+
+    FILE *fh = fopen(file_list,"r");
+    if ( !fh )
+    {
+        fprintf(stderr,"%s: %s\n", file_list,strerror(errno));
+        return 1;
+    }
+
+    files = calloc(nfiles,sizeof(char*));
+    nfiles = 0;
+    while ( fgets(buf,MAX_PATH_LEN,fh) )
+    {
+        // allow empty lines and trailing spaces
+        len = strlen(buf);
+        while ( len>0 && isspace(buf[len-1]) ) len--;
+        if ( !len ) continue;
+
+        // check sanity of the file list
+        buf[len] = 0;
+        if (stat(buf, &sb) != 0)
+        {
+            // no such file, check if it is safe to print its name
+            int i, safe_to_print = 1;
+            for (i=0; i<len; i++)
+                if (!isprint(buf[i])) { safe_to_print = 0; break; }
+            if ( safe_to_print )
+                fprintf(stderr,"The file list \"%s\" appears broken, could not locate: %s\n", file_list,buf);
+            else
+                fprintf(stderr,"Does the file \"%s\" really contain a list of files and do all exist?\n", file_list);
+            return 1;
+        }
+
+        nfiles++;
+        files = realloc(files,nfiles*sizeof(char*));
+        files[nfiles-1] = strdup(buf);
+    }
+    fclose(fh);
+    if ( !nfiles )
+    {
+        fprintf(stderr,"No files read from %s\n", file_list);
+        return 1;
+    }
+    *argv = files;
+    *n    = nfiles;
+    return 0;
+}
+#undef MAX_PATH_LEN
+
+int parse_format_flag(const char *str)
+{
+    int i, flag = 0, n_tags;
+    char **tags = hts_readlist(str, 0, &n_tags);
+    for(i=0; i<n_tags; i++)
+    {
+        if ( !strcasecmp(tags[i],"DP") ) flag |= B2B_FMT_DP;
+        else if ( !strcasecmp(tags[i],"DV") ) { flag |= B2B_FMT_DV; fprintf(stderr, "[warning] tag DV functional, but deprecated. Please switch to `AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"SP") ) flag |= B2B_FMT_SP;
+        else if ( !strcasecmp(tags[i],"DP4") ) { flag |= B2B_FMT_DP4; fprintf(stderr, "[warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"DPR") ) { flag |= B2B_FMT_DPR; fprintf(stderr, "[warning] tag DPR functional, but deprecated. Please switch to `AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"INFO/DPR") ) { flag |= B2B_INFO_DPR; fprintf(stderr, "[warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"AD") ) flag |= B2B_FMT_AD;
+        else if ( !strcasecmp(tags[i],"ADF") ) flag |= B2B_FMT_ADF;
+        else if ( !strcasecmp(tags[i],"ADR") ) flag |= B2B_FMT_ADR;
+        else if ( !strcasecmp(tags[i],"INFO/AD") ) flag |= B2B_INFO_AD;
+        else if ( !strcasecmp(tags[i],"INFO/ADF") ) flag |= B2B_INFO_ADF;
+        else if ( !strcasecmp(tags[i],"INFO/ADR") ) flag |= B2B_INFO_ADR;
+        else
+        {
+            fprintf(stderr,"Could not parse tag \"%s\" in \"%s\"\n", tags[i], str);
+            exit(EXIT_FAILURE);
+        }
+        free(tags[i]);
+    }
+    if (n_tags) free(tags);
+    return flag;
+}
+
+static void print_usage(FILE *fp, const mplp_conf_t *mplp)
+{
+    char *tmp_require = bam_flag2str(mplp->rflag_require);
+    char *tmp_filter  = bam_flag2str(mplp->rflag_filter);
+
+    // Display usage information, formatted for the standard 80 columns.
+    // (The unusual string formatting here aids the readability of this
+    // source code in 80 columns, to the extent that's possible.)
+
+    fprintf(fp,
+"\n"
+"Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n"
+"\n"
+"Input options:\n"
+"  -6, --illumina1.3+      quality is in the Illumina-1.3+ encoding\n"
+"  -A, --count-orphans     do not discard anomalous read pairs\n"
+"  -b, --bam-list FILE     list of input BAM filenames, one per line\n"
+"  -B, --no-BAQ            disable BAQ (per-Base Alignment Quality)\n"
+"  -C, --adjust-MQ INT     adjust mapping quality; recommended:50, disable:0 [0]\n"
+"  -d, --max-depth INT     max per-file depth; avoids excessive memory usage [%d]\n", mplp->max_depth);
+    fprintf(fp,
+"  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs\n"
+"  -f, --fasta-ref FILE    faidx indexed reference sequence file\n"
+"  -G, --exclude-RG FILE   exclude read groups listed in FILE\n"
+"  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)\n"
+"  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
+    fprintf(fp,
+"  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
+    fprintf(fp,
+"  -r, --region REG        region in which pileup is generated\n"
+"  -R, --ignore-RG         ignore RG tags (one BAM = one sample)\n"
+"  --rf, --incl-flags STR|INT  required flags: skip reads with mask bits unset [%s]\n", tmp_require);
+    fprintf(fp,
+"  --ff, --excl-flags STR|INT  filter flags: skip reads with mask bits set\n"
+"                                            [%s]\n", tmp_filter);
+    fprintf(fp,
+"  -x, --ignore-overlaps   disable read-pair overlap detection\n"
+"\n"
+"Output options:\n"
+"  -o, --output FILE       write output to FILE [standard output]\n"
+"  -g, --BCF               generate genotype likelihoods in BCF format\n"
+"  -v, --VCF               generate genotype likelihoods in VCF format\n"
+"\n"
+"Output options for mpileup format (without -g/-v):\n"
+"  -O, --output-BP         output base positions on reads\n"
+"  -s, --output-MQ         output mapping quality\n"
+"\n"
+"Output options for genotype likelihoods (when -g/-v is used):\n"
+"  -t, --output-tags LIST  optional tags to output:\n"
+"               DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR []\n"
+"  -u, --uncompressed      generate uncompressed VCF/BCF output\n"
+"\n"
+"SNP/INDEL genotype likelihoods options (effective with -g/-v):\n"
+"  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
+    fprintf(fp,
+"  -F, --gap-frac FLOAT    minimum fraction of gapped reads [%g]\n", mplp->min_frac);
+    fprintf(fp,
+"  -h, --tandem-qual INT   coefficient for homopolymer errors [%d]\n", mplp->tandemQ);
+    fprintf(fp,
+"  -I, --skip-indels       do not perform indel calling\n"
+"  -L, --max-idepth INT    maximum per-file depth for INDEL calling [%d]\n", mplp->max_indel_depth);
+    fprintf(fp,
+"  -m, --min-ireads INT    minimum number gapped reads for indel candidates [%d]\n", mplp->min_support);
+    fprintf(fp,
+"  -o, --open-prob INT     Phred-scaled gap open seq error probability [%d]\n", mplp->openQ);
+    fprintf(fp,
+"  -p, --per-sample-mF     apply -m and -F per-sample for increased sensitivity\n"
+"  -P, --platforms STR     comma separated list of platforms for indels [all]\n");
+    sam_global_opt_help(fp, "-.--.");
+    fprintf(fp,
+"\n"
+"Notes: Assuming diploid individuals.\n");
+
+    free(tmp_require);
+    free(tmp_filter);
+}
+
+int bam_mpileup(int argc, char *argv[])
+{
+    int c;
+    const char *file_list = NULL;
+    char **fn = NULL;
+    int nfiles = 0, use_orphan = 0;
+    mplp_conf_t mplp;
+    memset(&mplp, 0, sizeof(mplp_conf_t));
+    mplp.min_baseQ = 13;
+    mplp.capQ_thres = 0;
+    mplp.max_depth = 250; mplp.max_indel_depth = 250;
+    mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
+    mplp.min_frac = 0.002; mplp.min_support = 1;
+    mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_SMART_OVERLAPS;
+    mplp.argc = argc; mplp.argv = argv;
+    mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
+    mplp.output_fname = NULL;
+    sam_global_args_init(&mplp.ga);
+
+    static const struct option lopts[] =
+    {
+        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0),
+        {"rf", required_argument, NULL, 1},   // require flag
+        {"ff", required_argument, NULL, 2},   // filter flag
+        {"incl-flags", required_argument, NULL, 1},
+        {"excl-flags", required_argument, NULL, 2},
+        {"output", required_argument, NULL, 3},
+        {"open-prob", required_argument, NULL, 4},
+        {"illumina1.3+", no_argument, NULL, '6'},
+        {"count-orphans", no_argument, NULL, 'A'},
+        {"bam-list", required_argument, NULL, 'b'},
+        {"no-BAQ", no_argument, NULL, 'B'},
+        {"no-baq", no_argument, NULL, 'B'},
+        {"adjust-MQ", required_argument, NULL, 'C'},
+        {"adjust-mq", required_argument, NULL, 'C'},
+        {"max-depth", required_argument, NULL, 'd'},
+        {"redo-BAQ", no_argument, NULL, 'E'},
+        {"redo-baq", no_argument, NULL, 'E'},
+        {"fasta-ref", required_argument, NULL, 'f'},
+        {"exclude-RG", required_argument, NULL, 'G'},
+        {"exclude-rg", required_argument, NULL, 'G'},
+        {"positions", required_argument, NULL, 'l'},
+        {"region", required_argument, NULL, 'r'},
+        {"ignore-RG", no_argument, NULL, 'R'},
+        {"ignore-rg", no_argument, NULL, 'R'},
+        {"min-MQ", required_argument, NULL, 'q'},
+        {"min-mq", required_argument, NULL, 'q'},
+        {"min-BQ", required_argument, NULL, 'Q'},
+        {"min-bq", required_argument, NULL, 'Q'},
+        {"ignore-overlaps", no_argument, NULL, 'x'},
+        {"BCF", no_argument, NULL, 'g'},
+        {"bcf", no_argument, NULL, 'g'},
+        {"VCF", no_argument, NULL, 'v'},
+        {"vcf", no_argument, NULL, 'v'},
+        {"output-BP", no_argument, NULL, 'O'},
+        {"output-bp", no_argument, NULL, 'O'},
+        {"output-MQ", no_argument, NULL, 's'},
+        {"output-mq", no_argument, NULL, 's'},
+        {"output-tags", required_argument, NULL, 't'},
+        {"uncompressed", no_argument, NULL, 'u'},
+        {"ext-prob", required_argument, NULL, 'e'},
+        {"gap-frac", required_argument, NULL, 'F'},
+        {"tandem-qual", required_argument, NULL, 'h'},
+        {"skip-indels", no_argument, NULL, 'I'},
+        {"max-idepth", required_argument, NULL, 'L'},
+        {"min-ireads ", required_argument, NULL, 'm'},
+        {"per-sample-mF", no_argument, NULL, 'p'},
+        {"per-sample-mf", no_argument, NULL, 'p'},
+        {"platforms", required_argument, NULL, 'P'},
+        {NULL, 0, NULL, 0}
+    };
+    while ((c = getopt_long(argc, argv, "Agf:r:l:q:Q:uRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsVvxt:",lopts,NULL)) >= 0) {
+        switch (c) {
+        case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
+        case  1 :
+            mplp.rflag_require = bam_str2flag(optarg);
+            if ( mplp.rflag_require<0 ) { fprintf(stderr,"Could not parse --rf %s\n", optarg); return 1; }
+            break;
+        case  2 :
+            mplp.rflag_filter = bam_str2flag(optarg);
+            if ( mplp.rflag_filter<0 ) { fprintf(stderr,"Could not parse --ff %s\n", optarg); return 1; }
+            break;
+        case  3 : mplp.output_fname = optarg; break;
+        case  4 : mplp.openQ = atoi(optarg); break;
+        case 'f':
+            mplp.fai = fai_load(optarg);
+            if (mplp.fai == NULL) return 1;
+            mplp.fai_fname = optarg;
+            break;
+        case 'd': mplp.max_depth = atoi(optarg); break;
+        case 'r': mplp.reg = strdup(optarg); break;
+        case 'l':
+                  // In the original version the whole BAM was streamed which is inefficient
+                  //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
+                  //  best strategy, that is streaming or jumping.
+                  mplp.bed = bed_read(optarg);
+                  if (!mplp.bed) { print_error_errno("mpileup", "Could not read file \"%s\"", optarg); return 1; }
+                  break;
+        case 'P': mplp.pl_list = strdup(optarg); break;
+        case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
+        case 'g': mplp.flag |= MPLP_BCF; break;
+        case 'v': mplp.flag |= MPLP_BCF | MPLP_VCF; break;
+        case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_BCF; break;
+        case 'B': mplp.flag &= ~MPLP_REALN; break;
+        case 'D': mplp.fmt_flag |= B2B_FMT_DP; fprintf(stderr, "[warning] samtools mpileup option `-D` is functional, but deprecated. Please switch to `-t DP` in future.\n"); break;
+        case 'S': mplp.fmt_flag |= B2B_FMT_SP; fprintf(stderr, "[warning] samtools mpileup option `-S` is functional, but deprecated. Please switch to `-t SP` in future.\n"); break;
+        case 'V': mplp.fmt_flag |= B2B_FMT_DV; fprintf(stderr, "[warning] samtools mpileup option `-V` is functional, but deprecated. Please switch to `-t DV` in future.\n"); break;
+        case 'I': mplp.flag |= MPLP_NO_INDEL; break;
+        case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
+        case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+        case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
+        case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
+        case 'O': mplp.flag |= MPLP_PRINT_POS; break;
+        case 'C': mplp.capQ_thres = atoi(optarg); break;
+        case 'q': mplp.min_mq = atoi(optarg); break;
+        case 'Q': mplp.min_baseQ = atoi(optarg); break;
+        case 'b': file_list = optarg; break;
+        case 'o': {
+                char *end;
+                long value = strtol(optarg, &end, 10);
+                // Distinguish between -o INT and -o FILE (a bit of a hack!)
+                if (*end == '\0') mplp.openQ = value;
+                else mplp.output_fname = optarg;
+            }
+            break;
+        case 'e': mplp.extQ = atoi(optarg); break;
+        case 'h': mplp.tandemQ = atoi(optarg); break;
+        case 'A': use_orphan = 1; break;
+        case 'F': mplp.min_frac = atof(optarg); break;
+        case 'm': mplp.min_support = atoi(optarg); break;
+        case 'L': mplp.max_indel_depth = atoi(optarg); break;
+        case 'G': {
+                FILE *fp_rg;
+                char buf[1024];
+                mplp.rghash = khash_str2int_init();
+                if ((fp_rg = fopen(optarg, "r")) == NULL)
+                    fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
+                while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
+                    khash_str2int_inc(mplp.rghash, strdup(buf));
+                fclose(fp_rg);
+            }
+            break;
+        case 't': mplp.fmt_flag |= parse_format_flag(optarg); break;
+        default:
+            if (parse_sam_global_opt(c, optarg, lopts, &mplp.ga) == 0) break;
+            /* else fall-through */
+        case '?':
+            print_usage(stderr, &mplp);
+            return 1;
+        }
+    }
+    if (!mplp.fai && mplp.ga.reference) {
+        mplp.fai_fname = mplp.ga.reference;
+        mplp.fai = fai_load(mplp.fai_fname);
+        if (mplp.fai == NULL) return 1;
+    }
+
+    if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
+    {
+        fprintf(stderr,"Error: The -B option cannot be combined with -E\n");
+        return 1;
+    }
+    if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
+    if (argc == 1)
+    {
+        print_usage(stderr, &mplp);
+        return 1;
+    }
+    int ret;
+    if (file_list) {
+        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+        ret = mpileup(&mplp,nfiles,fn);
+        for (c=0; c<nfiles; c++) free(fn[c]);
+        free(fn);
+    }
+    else
+        ret = mpileup(&mplp, argc - optind, argv + optind);
+    if (mplp.rghash) khash_str2int_destroy_free(mplp.rghash);
+    free(mplp.reg); free(mplp.pl_list);
+    if (mplp.fai) fai_destroy(mplp.fai);
+    if (mplp.bed) bed_destroy(mplp.bed);
+    return ret;
+}
diff --git a/sample.c b/sample.c
new file mode 100644
index 000000000..4cc89ce9b
--- /dev/null
+++ b/sample.c
@@ -0,0 +1,134 @@
+/*  sample.c -- group data by sample.
+
+    Copyright (C) 2010, 2011 Broad Institute.
+    Copyright (C) 2013 Genome Research Ltd.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#include <config.h>
+
+#include <stdlib.h>
+#include <string.h>
+#include "sample.h"
+#include "htslib/khash.h"
+KHASH_MAP_INIT_STR(sm, int)
+
+bam_sample_t *bam_smpl_init(void)
+{
+    bam_sample_t *s;
+    s = calloc(1, sizeof(bam_sample_t));
+    s->rg2smid = kh_init(sm);
+    s->sm2id = kh_init(sm);
+    return s;
+}
+
+void bam_smpl_destroy(bam_sample_t *sm)
+{
+    int i;
+    khint_t k;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    if (sm == 0) return;
+    for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
+    free(sm->smpl);
+    for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
+        if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
+    kh_destroy(sm, sm->rg2smid);
+    kh_destroy(sm, sm->sm2id);
+    free(sm);
+}
+
+static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
+{
+    khint_t k_rg, k_sm;
+    int ret;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    k_rg = kh_get(sm, rg2smid, key);
+    if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
+    k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
+    k_sm = kh_get(sm, sm2id, val);
+    if (k_sm == kh_end(sm2id)) { // absent
+        if (sm->n == sm->m) {
+            sm->m = sm->m? sm->m<<1 : 1;
+            sm->smpl = realloc(sm->smpl, sizeof(char*) * sm->m);
+        }
+        sm->smpl[sm->n] = strdup(val);
+        k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
+        kh_val(sm2id, k_sm) = sm->n++;
+    }
+    kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
+}
+
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
+{
+    const char *p = txt, *q, *r;
+    kstring_t buf, first_sm;
+    int n = 0;
+    khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
+    if (txt == 0) {
+        add_pair(sm, sm2id, fn, fn);
+        return 0;
+    }
+    memset(&buf, 0, sizeof(kstring_t));
+    memset(&first_sm, 0, sizeof(kstring_t));
+    while ((q = strstr(p, "@RG")) != 0) {
+        p = q + 3;
+        r = q = 0;
+        if ((q = strstr(p, "\tID:")) != 0) q += 4;
+        if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+        if (r && q) {
+            char *u, *v;
+            int oq, or;
+            for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+            for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+            oq = *u; or = *v; *u = *v = '\0';
+            buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
+            add_pair(sm, sm2id, buf.s, r);
+            if ( !first_sm.s )
+                kputs(r,&first_sm);
+            *u = oq; *v = or;
+        } else break;
+        p = q > r? q : r;
+        ++n;
+    }
+    if (n == 0) add_pair(sm, sm2id, fn, fn);
+    // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
+    //  use the tag instead.
+    else if ( n==1 && first_sm.s )
+        add_pair(sm,sm2id,fn,first_sm.s);
+    if ( first_sm.s )
+        free(first_sm.s);
+
+//  add_pair(sm, sm2id, fn, fn);
+    free(buf.s);
+    return 0;
+}
+
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
+{
+    khint_t k;
+    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+    if (rg) {
+        str->l = 0;
+        kputs(fn, str); kputc('/', str); kputs(rg, str);
+        k = kh_get(sm, rg2smid, str->s);
+    } else k = kh_get(sm, rg2smid, fn);
+    return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
+}
diff --git a/sample.h b/sample.h
new file mode 100644
index 000000000..8e8efa5b7
--- /dev/null
+++ b/sample.h
@@ -0,0 +1,41 @@
+/*  sample.h -- group data by sample.
+
+    Copyright (C) 2010 Broad Institute.
+
+    Author: Heng Li <lh3@sanger.ac.uk>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.  */
+
+#ifndef BAM_SAMPLE_H
+#define BAM_SAMPLE_H
+
+#include "htslib/kstring.h"
+
+typedef struct {
+    int n, m;
+    char **smpl;
+    void *rg2smid, *sm2id;
+} bam_sample_t;
+
+bam_sample_t *bam_smpl_init(void);
+int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt);
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str);
+void bam_smpl_destroy(bam_sample_t *sm);
+
+#endif

From e46a2cf8101d81a0327a30ef1440e2c2f265e747 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 25 Apr 2016 13:08:17 +0100
Subject: [PATCH 190/211] rename bam_plcmd.c -> mpileup.c

---
 bam_plcmd.c => mpileup.c | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)
 rename bam_plcmd.c => mpileup.c (99%)

diff --git a/bam_plcmd.c b/mpileup.c
similarity index 99%
rename from bam_plcmd.c
rename to mpileup.c
index ddd2f0043..1d47728b4 100644
--- a/bam_plcmd.c
+++ b/mpileup.c
@@ -1,4 +1,4 @@
-/*  bam_plcmd.c -- mpileup subcommand.
+/*  mpileup.c -- mpileup subcommand. Previously bam_plcmd.c from samtools
 
     Copyright (C) 2008-2015 Genome Research Ltd.
     Portions copyright (C) 2009-2012 Broad Institute.

From edc2bc644a62dc4b443e6545b134f0b0d1486469 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 25 Apr 2016 18:45:24 +0100
Subject: [PATCH 191/211] add mpileup command to bcftools

minimal changes to files copied from samtools in order to compile
in bcftools.

* use regidx from htslib rather than bedidx from samtools
* remove sam_opts calls as sam_opts.h not copied from samtools

Todo:

* copy over relevant functionality from sam_opts.h
* remove text based mpileup output
* update options and defaults
* bring over `---gvcf` and other changes from @pd3 fork
---
 Makefile        |  5 +++
 bam2bcf.c       | 20 ++++++------
 bam2bcf_indel.c | 34 ++++++++++----------
 main.c          |  5 +++
 mpileup.c       | 85 +++++++++++++++++++------------------------------
 sample.c        | 14 ++++----
 6 files changed, 75 insertions(+), 88 deletions(-)

diff --git a/Makefile b/Makefile
index 7dec9dd07..64f564fe6 100644
--- a/Makefile
+++ b/Makefile
@@ -46,6 +46,7 @@ OBJS     = main.o vcfindex.o tabix.o \
            vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o \
            vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
            vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
+           mpileup.o bam2bcf.o bam2bcf_indel.o sample.o \
            ccall.o em.o prob1.o kmin.o # the original samtools calling
 
 EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
@@ -138,6 +139,9 @@ ploidy_h = ploidy.h $(htslib_regidx_h)
 prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
 roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h)
 cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
+bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
+sam_h = sam.h $(htslib_sam_h) $(bam_h)
+sample_h = sample.h $(htslib_kstring_h)
 
 main.o: main.c $(htslib_hts_h) version.h $(bcftools_h)
 vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
@@ -173,6 +177,7 @@ ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)
 polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h
 peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
 consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h
+mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(bcftools_h) $(bam2bcf_h) $(sample_h)
 version.o: version.h version.c
 
 test/test-rbuf.o: test/test-rbuf.c rbuf.h
diff --git a/bam2bcf.c b/bam2bcf.c
index a824d5ac0..8bb799ebd 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -23,8 +23,6 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.  */
 
-#include <config.h>
-
 #include <math.h>
 #include <stdint.h>
 #include <assert.h>
@@ -46,7 +44,7 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
 {
     bcf_callaux_t *bca;
     if (theta <= 0.) theta = CALL_DEFTHETA;
-    bca = calloc(1, sizeof(bcf_callaux_t));
+    bca = (bcf_callaux_t*) calloc(1, sizeof(bcf_callaux_t));
     bca->capQ = 60;
     bca->openQ = 40; bca->extQ = 20; bca->tandemQ = 100;
     bca->min_baseQ = min_baseQ;
@@ -55,15 +53,15 @@ bcf_callaux_t *bcf_call_init(double theta, int min_baseQ)
     bca->min_support = 1;
     bca->per_sample_flt = 0;
     bca->npos = 100;
-    bca->ref_pos = malloc(bca->npos*sizeof(int));
-    bca->alt_pos = malloc(bca->npos*sizeof(int));
+    bca->ref_pos = (int*) malloc(bca->npos*sizeof(int));
+    bca->alt_pos = (int*) malloc(bca->npos*sizeof(int));
     bca->nqual = 60;
-    bca->ref_mq  = malloc(bca->nqual*sizeof(int));
-    bca->alt_mq  = malloc(bca->nqual*sizeof(int));
-    bca->ref_bq  = malloc(bca->nqual*sizeof(int));
-    bca->alt_bq  = malloc(bca->nqual*sizeof(int));
-    bca->fwd_mqs = malloc(bca->nqual*sizeof(int));
-    bca->rev_mqs = malloc(bca->nqual*sizeof(int));
+    bca->ref_mq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->alt_mq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->ref_bq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->alt_bq  = (int*) malloc(bca->nqual*sizeof(int));
+    bca->fwd_mqs = (int*) malloc(bca->nqual*sizeof(int));
+    bca->rev_mqs = (int*) malloc(bca->nqual*sizeof(int));
     return bca;
 }
 
diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 2b42b09d7..95cc5b076 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -23,8 +23,6 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.  */
 
-#include <config.h>
-
 #include <assert.h>
 #include <ctype.h>
 #include <string.h>
@@ -59,7 +57,7 @@ void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
             lp = r - p;
             for (r = q; *r && *r != '\t' && *r != '\n'; ++r) { }
             lq = r - q;
-            x = calloc((lp > lq? lp : lq) + 1, 1);
+            x = (char*) calloc((lp > lq? lp : lq) + 1, 1);
             for (r = q; *r && *r != '\t' && *r != '\n'; ++r) x[r-q] = *r;
             if (strstr(list, x)) { // insert ID to the hash table
                 khint_t k;
@@ -182,7 +180,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
         bca->max_support = bca->max_frac = 0;
         int m, n_alt = 0, n_tot = 0, indel_support_ok = 0;
         uint32_t *aux;
-        aux = calloc(N + 1, 4);
+        aux = (uint32_t*) calloc(N + 1, 4);
         m = max_rd_len = 0;
         aux[m++] = MINUS_CONST; // zero indel is always a type
         for (s = 0; s < n; ++s) {
@@ -260,13 +258,13 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
         int L = right - left + 1, max_i, max2_i;
         uint32_t *cns, max, max2;
         char *ref0, *r;
-        ref_sample = calloc(n, sizeof(char*));
-        cns = calloc(L, 4);
-        ref0 = calloc(L, 1);
+        ref_sample = (char**) calloc(n, sizeof(char*));
+        cns = (uint32_t*) calloc(L, 4);
+        ref0 = (char*) calloc(L, 1);
         for (i = 0; i < right - left; ++i)
             ref0[i] = seq_nt16_table[(int)ref[i+left]];
         for (s = 0; s < n; ++s) {
-            r = ref_sample[s] = calloc(L, 1);
+            r = ref_sample[s] = (char*) calloc(L, 1);
             memset(cns, 0, sizeof(int) * L);
             // collect ref and non-ref counts
             for (i = 0; i < n_plp[s]; ++i) {
@@ -317,7 +315,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
     // construct the consensus sequence
     max_ins = types[n_types - 1];   // max_ins is at least 0
     if (max_ins > 0) {
-        int *inscns_aux = calloc(5 * n_types * max_ins, sizeof(int));
+        int *inscns_aux = (int*) calloc(5 * n_types * max_ins, sizeof(int));
         // count the number of occurrences of each base at each position for each type of insertion
         for (t = 0; t < n_types; ++t) {
             if (types[t] > 0) {
@@ -337,7 +335,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
             }
         }
         // use the majority rule to construct the consensus
-        inscns = calloc(n_types * max_ins, 1);
+        inscns = (char*) calloc(n_types * max_ins, 1);
         for (t = 0; t < n_types; ++t) {
             for (j = 0; j < types[t]; ++j) {
                 int max = 0, max_k = -1, *ia = &inscns_aux[(t*max_ins+j)*5];
@@ -352,10 +350,10 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
     }
     // compute the likelihood given each type of indel for each read
     max_ref2 = right - left + 2 + 2 * (max_ins > -types[0]? max_ins : -types[0]);
-    ref2  = calloc(max_ref2, 1);
-    query = calloc(right - left + max_rd_len + max_ins + 2, 1);
-    score1 = calloc(N * n_types, sizeof(int));
-    score2 = calloc(N * n_types, sizeof(int));
+    ref2  = (char*) calloc(max_ref2, 1);
+    query = (char*) calloc(right - left + max_rd_len + max_ins + 2, 1);
+    score1 = (int*) calloc(N * n_types, sizeof(int));
+    score2 = (int*) calloc(N * n_types, sizeof(int));
     bca->indelreg = 0;
     for (t = 0; t < n_types; ++t) {
         int l, ir;
@@ -404,7 +402,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
                 { // do realignment; this is the bottleneck
                     const uint8_t *qual = bam_get_qual(p->b), *bq;
                     uint8_t *qq;
-                    qq = calloc(qend - qbeg, 1);
+                    qq = (uint8_t*) calloc(qend - qbeg, 1);
                     bq = (uint8_t*)bam_aux_get(p->b, "ZQ");
                     if (bq) ++bq; // skip type
                     for (l = qbeg; l < qend; ++l) {
@@ -440,8 +438,8 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
     free(ref2); free(query);
     { // compute indelQ
         int *sc, tmp, *sumq;
-        sc   = alloca(n_types * sizeof(int));
-        sumq = alloca(n_types * sizeof(int));
+        sc   = (int*) alloca(n_types * sizeof(int));
+        sumq = (int*) alloca(n_types * sizeof(int));
         memset(sumq, 0, sizeof(int) * n_types);
         for (s = K = 0; s < n; ++s) {
             for (i = 0; i < n_plp[s]; ++i, ++K) {
@@ -493,7 +491,7 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
         }
         // determine bca->indel_types[] and bca->inscns
         bca->maxins = max_ins;
-        bca->inscns = realloc(bca->inscns, bca->maxins * 4);
+        bca->inscns = (char*) realloc(bca->inscns, bca->maxins * 4);
         for (t = 0; t < n_types; ++t)
             sumq[t] = sumq[t]<<6 | t;
         for (t = 1; t < n_types; ++t) // insertion sort
diff --git a/main.c b/main.c
index 1892c1de5..2639d991b 100644
--- a/main.c
+++ b/main.c
@@ -54,6 +54,7 @@ int main_polysomy(int argc, char *argv[]);
 #endif
 int main_plugin(int argc, char *argv[]);
 int main_consensus(int argc, char *argv[]);
+int bam_mpileup(int argc, char *argv[]);
 
 typedef struct
 {
@@ -148,6 +149,10 @@ static cmd_t cmds[] =
       .alias = "gtcheck",
       .help  = "check sample concordance, detect sample swaps and contamination"
     },
+    { .func  = bam_mpileup,
+        .alias = "mpileup",
+        .help  = "multi-way pileup producing genotype likelihoods"
+    },
 #if USE_GPL
     { .func  = main_polysomy,
       .alias = "polysomy",
diff --git a/mpileup.c b/mpileup.c
index 1d47728b4..8bcca34ce 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -1,6 +1,6 @@
 /*  mpileup.c -- mpileup subcommand. Previously bam_plcmd.c from samtools
 
-    Copyright (C) 2008-2015 Genome Research Ltd.
+    Copyright (C) 2008-2016 Genome Research Ltd.
     Portions copyright (C) 2009-2012 Broad Institute.
 
     Author: Heng Li <lh3@sanger.ac.uk>
@@ -23,8 +23,6 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.  */
 
-#include <config.h>
-
 #include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
@@ -39,9 +37,8 @@ DEALINGS IN THE SOFTWARE.  */
 #include <htslib/faidx.h>
 #include <htslib/kstring.h>
 #include <htslib/khash_str2int.h>
-#include "sam_header.h"
-#include "samtools.h"
-#include "sam_opts.h"
+#include <htslib/regidx.h>
+#include "bcftools.h"
 
 static inline int printw(int c, FILE *fp)
 {
@@ -113,10 +110,6 @@ static inline void pileup_seq(FILE *fp, const bam_pileup1_t *p, int pos, int ref
 #define MPLP_PER_SAMPLE (1<<11)
 #define MPLP_SMART_OVERLAPS (1<<12)
 
-void *bed_read(const char *fn);
-void bed_destroy(void *_h);
-int bed_overlap(const void *_h, const char *chr, int beg, int end);
-
 typedef struct {
     int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
     int rflag_require, rflag_filter;
@@ -124,10 +117,10 @@ typedef struct {
     double min_frac; // for indels
     char *reg, *pl_list, *fai_fname, *output_fname;
     faidx_t *fai;
-    void *bed, *rghash;
+    void *rghash;
+    regidx_t *bed;
     int argc;
     char **argv;
-    sam_global_args ga;
 } mplp_conf_t;
 
 typedef struct {
@@ -227,7 +220,7 @@ static int mplp_func(void *data, bam1_t *b)
         if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
         if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
         if (ma->conf->bed) { // test overlap
-            skip = !bed_overlap(ma->conf->bed, ma->h->target_name[b->core.tid], b->core.pos, bam_endpos(b));
+            skip = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],b->core.pos, bam_endpos(b)-1, NULL) ? 0 : 1;
             if (skip) continue;
         }
         if (ma->conf->rghash) { // exclude read groups
@@ -287,7 +280,7 @@ static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
             }
             if (m->n_plp[id] == m->m_plp[id]) {
                 m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
-                m->plp[id] = realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
+                m->plp[id] = (bam_pileup1_t*) realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
             }
             m->plp[id][m->n_plp[id]++] = *p;
         }
@@ -327,9 +320,9 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
     memset(&gplp, 0, sizeof(mplp_pileup_t));
     memset(&buf, 0, sizeof(kstring_t));
     memset(&bc, 0, sizeof(bcf_call_t));
-    data = calloc(n, sizeof(mplp_aux_t*));
-    plp = calloc(n, sizeof(bam_pileup1_t*));
-    n_plp = calloc(n, sizeof(int));
+    data = (mplp_aux_t**) calloc(n, sizeof(mplp_aux_t*));
+    plp = (const bam_pileup1_t**) calloc(n, sizeof(bam_pileup1_t*));
+    n_plp = (int*) calloc(n, sizeof(int));
     sm = bam_smpl_init();
 
     if (n == 0) {
@@ -340,8 +333,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
     // read the header of each file in the list and initialize data
     for (i = 0; i < n; ++i) {
         bam_hdr_t *h_tmp;
-        data[i] = calloc(1, sizeof(mplp_aux_t));
-        data[i]->fp = sam_open_format(fn[i], "rb", &conf->ga.in);
+        data[i] = (mplp_aux_t*) calloc(1, sizeof(mplp_aux_t));
+        data[i]->fp = sam_open(fn[i], "rb");
         if ( !data[i]->fp )
         {
             fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
@@ -394,9 +387,9 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
     }
     // allocate data storage proportionate to number of samples being studied sm->n
     gplp.n = sm->n;
-    gplp.n_plp = calloc(sm->n, sizeof(int));
-    gplp.m_plp = calloc(sm->n, sizeof(int));
-    gplp.plp = calloc(sm->n, sizeof(bam_pileup1_t*));
+    gplp.n_plp = (int*) calloc(sm->n, sizeof(int));
+    gplp.m_plp = (int*) calloc(sm->n, sizeof(int));
+    gplp.plp = (bam_pileup1_t**) calloc(sm->n, sizeof(bam_pileup1_t*));
 
     fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
     // write the VCF header
@@ -418,11 +411,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         bcf_hdr = bcf_hdr_init("w");
         kstring_t str = {0,0,NULL};
 
-        ksprintf(&str, "##samtoolsVersion=%s+htslib-%s\n",samtools_version(),hts_version());
+        ksprintf(&str, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
         bcf_hdr_append(bcf_hdr, str.s);
 
         str.l = 0;
-        ksprintf(&str, "##samtoolsCommand=samtools mpileup");
+        ksprintf(&str, "##bcftoolsCommand=mpileup");
         for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
         kputc('\n', &str);
         bcf_hdr_append(bcf_hdr, str.s);
@@ -497,7 +490,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 
         // Initialise the calling algorithm
         bca = bcf_call_init(-1., conf->min_baseQ);
-        bcr = calloc(sm->n, sizeof(bcf_callret1_t));
+        bcr = (bcf_callret1_t*) calloc(sm->n, sizeof(bcf_callret1_t));
         bca->rghash = rghash;
         bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
         bca->min_frac = conf->min_frac;
@@ -506,12 +499,12 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 
         bc.bcf_hdr = bcf_hdr;
         bc.n = sm->n;
-        bc.PL = malloc(15 * sm->n * sizeof(*bc.PL));
+        bc.PL = (int32_t*) malloc(15 * sm->n * sizeof(*bc.PL));
         if (conf->fmt_flag)
         {
             assert( sizeof(float)==sizeof(int32_t) );
-            bc.DP4 = malloc(sm->n * sizeof(int32_t) * 4);
-            bc.fmt_arr = malloc(sm->n * sizeof(float)); // all fmt_flag fields
+            bc.DP4 = (int32_t*) malloc(sm->n * sizeof(int32_t) * 4);
+            bc.fmt_arr = (uint8_t*) malloc(sm->n * sizeof(float)); // all fmt_flag fields
             if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
             {
                 // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
@@ -551,7 +544,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
     // begin pileup
     while ( (ret=bam_mplp_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
         if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
-        if (conf->bed && tid >= 0 && !bed_overlap(conf->bed, h->target_name[tid], pos, pos+1)) continue;
+        if (conf->bed && tid >= 0 && !regidx_overlap(conf->bed, h->target_name[tid], pos, pos, NULL)) continue;
         mplp_get_ref(data[0], tid, &ref, &ref_len);
         //printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
         if (conf->flag & MPLP_BCF) {
@@ -696,7 +689,7 @@ int read_file_list(const char *file_list,int *n,char **argv[])
         return 1;
     }
 
-    files = calloc(nfiles,sizeof(char*));
+    files = (char**) calloc(nfiles,sizeof(char*));
     nfiles = 0;
     while ( fgets(buf,MAX_PATH_LEN,fh) )
     {
@@ -721,7 +714,7 @@ int read_file_list(const char *file_list,int *n,char **argv[])
         }
 
         nfiles++;
-        files = realloc(files,nfiles*sizeof(char*));
+        files = (char**) realloc(files,nfiles*sizeof(char*));
         files[nfiles-1] = strdup(buf);
     }
     fclose(fh);
@@ -776,7 +769,7 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 
     fprintf(fp,
 "\n"
-"Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n"
+"Usage: bcftools mpileup [options] in1.bam [in2.bam [...]]\n"
 "\n"
 "Input options:\n"
 "  -6, --illumina1.3+      quality is in the Illumina-1.3+ encoding\n"
@@ -832,9 +825,7 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "  -o, --open-prob INT     Phred-scaled gap open seq error probability [%d]\n", mplp->openQ);
     fprintf(fp,
 "  -p, --per-sample-mF     apply -m and -F per-sample for increased sensitivity\n"
-"  -P, --platforms STR     comma separated list of platforms for indels [all]\n");
-    sam_global_opt_help(fp, "-.--.");
-    fprintf(fp,
+"  -P, --platforms STR     comma separated list of platforms for indels [all]\n"
 "\n"
 "Notes: Assuming diploid individuals.\n");
 
@@ -859,11 +850,9 @@ int bam_mpileup(int argc, char *argv[])
     mplp.argc = argc; mplp.argv = argv;
     mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
     mplp.output_fname = NULL;
-    sam_global_args_init(&mplp.ga);
 
     static const struct option lopts[] =
     {
-        SAM_OPT_GLOBAL_OPTIONS('-', 0, '-', '-', 0),
         {"rf", required_argument, NULL, 1},   // require flag
         {"ff", required_argument, NULL, 2},   // filter flag
         {"incl-flags", required_argument, NULL, 1},
@@ -937,8 +926,8 @@ int bam_mpileup(int argc, char *argv[])
                   // In the original version the whole BAM was streamed which is inefficient
                   //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
                   //  best strategy, that is streaming or jumping.
-                  mplp.bed = bed_read(optarg);
-                  if (!mplp.bed) { print_error_errno("mpileup", "Could not read file \"%s\"", optarg); return 1; }
+                  mplp.bed = regidx_init(optarg,NULL,NULL,0,NULL);
+                  if (!mplp.bed) { fprintf(stderr, "bcftools mpileup: Could not read file \"%s\"", optarg); return 1; }
                   break;
         case 'P': mplp.pl_list = strdup(optarg); break;
         case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
@@ -946,9 +935,9 @@ int bam_mpileup(int argc, char *argv[])
         case 'v': mplp.flag |= MPLP_BCF | MPLP_VCF; break;
         case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_BCF; break;
         case 'B': mplp.flag &= ~MPLP_REALN; break;
-        case 'D': mplp.fmt_flag |= B2B_FMT_DP; fprintf(stderr, "[warning] samtools mpileup option `-D` is functional, but deprecated. Please switch to `-t DP` in future.\n"); break;
-        case 'S': mplp.fmt_flag |= B2B_FMT_SP; fprintf(stderr, "[warning] samtools mpileup option `-S` is functional, but deprecated. Please switch to `-t SP` in future.\n"); break;
-        case 'V': mplp.fmt_flag |= B2B_FMT_DV; fprintf(stderr, "[warning] samtools mpileup option `-V` is functional, but deprecated. Please switch to `-t DV` in future.\n"); break;
+        case 'D': mplp.fmt_flag |= B2B_FMT_DP; fprintf(stderr, "[warning] bcftools mpileup option `-D` is functional, but deprecated. Please switch to `-t DP` in future.\n"); break;
+        case 'S': mplp.fmt_flag |= B2B_FMT_SP; fprintf(stderr, "[warning] bcftools mpileup option `-S` is functional, but deprecated. Please switch to `-t SP` in future.\n"); break;
+        case 'V': mplp.fmt_flag |= B2B_FMT_DV; fprintf(stderr, "[warning] bcftools mpileup option `-V` is functional, but deprecated. Please switch to `-t DV` in future.\n"); break;
         case 'I': mplp.flag |= MPLP_NO_INDEL; break;
         case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
         case '6': mplp.flag |= MPLP_ILLUMINA13; break;
@@ -986,18 +975,10 @@ int bam_mpileup(int argc, char *argv[])
             break;
         case 't': mplp.fmt_flag |= parse_format_flag(optarg); break;
         default:
-            if (parse_sam_global_opt(c, optarg, lopts, &mplp.ga) == 0) break;
-            /* else fall-through */
-        case '?':
-            print_usage(stderr, &mplp);
+            fprintf(stderr,"Invalid option: '%c'\n", c);
             return 1;
         }
     }
-    if (!mplp.fai && mplp.ga.reference) {
-        mplp.fai_fname = mplp.ga.reference;
-        mplp.fai = fai_load(mplp.fai_fname);
-        if (mplp.fai == NULL) return 1;
-    }
 
     if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
     {
@@ -1022,6 +1003,6 @@ int bam_mpileup(int argc, char *argv[])
     if (mplp.rghash) khash_str2int_destroy_free(mplp.rghash);
     free(mplp.reg); free(mplp.pl_list);
     if (mplp.fai) fai_destroy(mplp.fai);
-    if (mplp.bed) bed_destroy(mplp.bed);
+    if (mplp.bed) regidx_destroy(mplp.bed);
     return ret;
 }
diff --git a/sample.c b/sample.c
index 4cc89ce9b..e48cf3a39 100644
--- a/sample.c
+++ b/sample.c
@@ -34,7 +34,7 @@ KHASH_MAP_INIT_STR(sm, int)
 bam_sample_t *bam_smpl_init(void)
 {
     bam_sample_t *s;
-    s = calloc(1, sizeof(bam_sample_t));
+    s = (bam_sample_t*) calloc(1, sizeof(bam_sample_t));
     s->rg2smid = kh_init(sm);
     s->sm2id = kh_init(sm);
     return s;
@@ -50,8 +50,8 @@ void bam_smpl_destroy(bam_sample_t *sm)
     free(sm->smpl);
     for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
         if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
-    kh_destroy(sm, sm->rg2smid);
-    kh_destroy(sm, sm->sm2id);
+    kh_destroy(sm, (khash_t(sm)*) sm->rg2smid);
+    kh_destroy(sm, (khash_t(sm)*) sm->sm2id);
     free(sm);
 }
 
@@ -67,7 +67,7 @@ static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, cons
     if (k_sm == kh_end(sm2id)) { // absent
         if (sm->n == sm->m) {
             sm->m = sm->m? sm->m<<1 : 1;
-            sm->smpl = realloc(sm->smpl, sizeof(char*) * sm->m);
+            sm->smpl = (char**) realloc(sm->smpl, sizeof(char*) * sm->m);
         }
         sm->smpl[sm->n] = strdup(val);
         k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
@@ -95,15 +95,15 @@ int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
         if ((r = strstr(p, "\tSM:")) != 0) r += 4;
         if (r && q) {
             char *u, *v;
-            int oq, or;
+            int ioq, ior;
             for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
             for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
-            oq = *u; or = *v; *u = *v = '\0';
+            ioq = *u; ior = *v; *u = *v = '\0';
             buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
             add_pair(sm, sm2id, buf.s, r);
             if ( !first_sm.s )
                 kputs(r,&first_sm);
-            *u = oq; *v = or;
+            *u = ioq; *v = ior;
         } else break;
         p = q > r? q : r;
         ++n;

From b5c2093d822a1b47a862e710c0570c7008d7d840 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 26 Apr 2016 12:31:08 +0100
Subject: [PATCH 192/211] remove mpileup text output

* deprecate `-g -v -u` options (still functional, but with warning)
* exit with message to use `samtools mpileup` if `-s/--output-MQ` used
* `-O` option was `--output-BP` and is not `--output-type` for consistency
  with other bcftools commands. If `[buzv]` not given as an option
  will warn

These catches for old text output options are probably not necessary
as users may not expect text output from `bcftools mpileup`.
---
 mpileup.c | 416 ++++++++++++++++++++----------------------------------
 1 file changed, 156 insertions(+), 260 deletions(-)

diff --git a/mpileup.c b/mpileup.c
index 8bcca34ce..4e0883fc0 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -55,43 +55,6 @@ static inline int printw(int c, FILE *fp)
     return 0;
 }
 
-static inline void pileup_seq(FILE *fp, const bam_pileup1_t *p, int pos, int ref_len, const char *ref)
-{
-    int j;
-    if (p->is_head) {
-        putc('^', fp);
-        putc(p->b->core.qual > 93? 126 : p->b->core.qual + 33, fp);
-    }
-    if (!p->is_del) {
-        int c = p->qpos < p->b->core.l_qseq
-            ? seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos)]
-            : 'N';
-        if (ref) {
-            int rb = pos < ref_len? ref[pos] : 'N';
-            if (c == '=' || seq_nt16_table[c] == seq_nt16_table[rb]) c = bam_is_rev(p->b)? ',' : '.';
-            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
-        } else {
-            if (c == '=') c = bam_is_rev(p->b)? ',' : '.';
-            else c = bam_is_rev(p->b)? tolower(c) : toupper(c);
-        }
-        putc(c, fp);
-    } else putc(p->is_refskip? (bam_is_rev(p->b)? '<' : '>') : '*', fp);
-    if (p->indel > 0) {
-        putc('+', fp); printw(p->indel, fp);
-        for (j = 1; j <= p->indel; ++j) {
-            int c = seq_nt16_str[bam_seqi(bam_get_seq(p->b), p->qpos + j)];
-            putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
-        }
-    } else if (p->indel < 0) {
-        printw(p->indel, fp);
-        for (j = 1; j <= -p->indel; ++j) {
-            int c = (ref && (int)pos+j < ref_len)? ref[pos+j] : 'N';
-            putc(bam_is_rev(p->b)? tolower(c) : toupper(c), fp);
-        }
-    }
-    if (p->is_tail) putc('$', fp);
-}
-
 #include <assert.h>
 #include "bam2bcf.h"
 #include "sample.h"
@@ -112,7 +75,7 @@ static inline void pileup_seq(FILE *fp, const bam_pileup1_t *p, int pos, int ref
 
 typedef struct {
     int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
-    int rflag_require, rflag_filter;
+    int rflag_require, rflag_filter, output_type;
     int openQ, extQ, tandemQ, min_support; // for indels
     double min_frac; // for indels
     char *reg, *pl_list, *fai_fname, *output_fname;
@@ -305,7 +268,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
     bam_hdr_t *h = NULL; /* header of first file in input list */
     char *ref;
     void *rghash = NULL;
-    FILE *pileup_fp = NULL;
 
     bcf_callaux_t *bca = NULL;
     bcf_callret1_t *bcr = NULL;
@@ -393,139 +355,122 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
 
     fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
     // write the VCF header
-    if (conf->flag & MPLP_BCF)
-    {
-        const char *mode;
-        if ( conf->flag & MPLP_VCF )
-            mode = (conf->flag&MPLP_NO_COMP)? "wu" : "wz";   // uncompressed VCF or compressed VCF
-        else
-            mode = (conf->flag&MPLP_NO_COMP)? "wub" : "wb";  // uncompressed BCF or compressed BCF
+    bcf_fp = hts_open(conf->output_fname?conf->output_fname:"-", hts_bcf_wmode(conf->output_type));
+    if (bcf_fp == NULL) {
+        fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
+        exit(EXIT_FAILURE);
+    }
 
-        bcf_fp = bcf_open(conf->output_fname? conf->output_fname : "-", mode);
-        if (bcf_fp == NULL) {
-            fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
-            exit(EXIT_FAILURE);
-        }
+    // BCF header creation
+    bcf_hdr = bcf_hdr_init("w");
+    kstring_t str = {0,0,NULL};
 
-        // BCF header creation
-        bcf_hdr = bcf_hdr_init("w");
-        kstring_t str = {0,0,NULL};
+    ksprintf(&str, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
+    bcf_hdr_append(bcf_hdr, str.s);
 
-        ksprintf(&str, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
-        bcf_hdr_append(bcf_hdr, str.s);
+    str.l = 0;
+    ksprintf(&str, "##bcftoolsCommand=mpileup");
+    for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
+    kputc('\n', &str);
+    bcf_hdr_append(bcf_hdr, str.s);
 
+    if (conf->fai_fname)
+    {
         str.l = 0;
-        ksprintf(&str, "##bcftoolsCommand=mpileup");
-        for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
-        kputc('\n', &str);
+        ksprintf(&str, "##reference=file://%s\n", conf->fai_fname);
         bcf_hdr_append(bcf_hdr, str.s);
+    }
 
-        if (conf->fai_fname)
-        {
-            str.l = 0;
-            ksprintf(&str, "##reference=file://%s\n", conf->fai_fname);
-            bcf_hdr_append(bcf_hdr, str.s);
-        }
-
-        // Translate BAM @SQ tags to BCF ##contig tags
-        // todo: use/write new BAM header manipulation routines, fill also UR, M5
-        for (i=0; i<h->n_targets; i++)
-        {
-            str.l = 0;
-            ksprintf(&str, "##contig=<ID=%s,length=%d>", h->target_name[i], h->target_len[i]);
-            bcf_hdr_append(bcf_hdr, str.s);
-        }
-        free(str.s);
-        bcf_hdr_append(bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
+    // Translate BAM @SQ tags to BCF ##contig tags
+    // todo: use/write new BAM header manipulation routines, fill also UR, M5
+    for (i=0; i<h->n_targets; i++)
+    {
+        str.l = 0;
+        ksprintf(&str, "##contig=<ID=%s,length=%d>", h->target_name[i], h->target_len[i]);
+        bcf_hdr_append(bcf_hdr, str.s);
+    }
+    free(str.s);
+    bcf_hdr_append(bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
 #if CDF_MWU_TESTS
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
 #endif
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
-        if ( conf->fmt_flag&B2B_FMT_DP )
-            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
-        if ( conf->fmt_flag&B2B_FMT_DV )
-            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
-        if ( conf->fmt_flag&B2B_FMT_DPR )
-            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
-        if ( conf->fmt_flag&B2B_INFO_DPR )
-            bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
-        if ( conf->fmt_flag&B2B_FMT_DP4 )
-            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
-        if ( conf->fmt_flag&B2B_FMT_SP )
-            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
-        if ( conf->fmt_flag&B2B_FMT_AD )
-            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
-        if ( conf->fmt_flag&B2B_FMT_ADF )
-            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
-        if ( conf->fmt_flag&B2B_FMT_ADR )
-            bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
-        if ( conf->fmt_flag&B2B_INFO_AD )
-            bcf_hdr_append(bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
-        if ( conf->fmt_flag&B2B_INFO_ADF )
-            bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
-        if ( conf->fmt_flag&B2B_INFO_ADR )
-            bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
-
-        for (i=0; i<sm->n; i++)
-            bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
-        bcf_hdr_add_sample(bcf_hdr, NULL);
-        bcf_hdr_write(bcf_fp, bcf_hdr);
-        // End of BCF header creation
-
-        // Initialise the calling algorithm
-        bca = bcf_call_init(-1., conf->min_baseQ);
-        bcr = (bcf_callret1_t*) calloc(sm->n, sizeof(bcf_callret1_t));
-        bca->rghash = rghash;
-        bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
-        bca->min_frac = conf->min_frac;
-        bca->min_support = conf->min_support;
-        bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
-
-        bc.bcf_hdr = bcf_hdr;
-        bc.n = sm->n;
-        bc.PL = (int32_t*) malloc(15 * sm->n * sizeof(*bc.PL));
-        if (conf->fmt_flag)
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
+    bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
+    bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
+    if ( conf->fmt_flag&B2B_FMT_DP )
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
+    if ( conf->fmt_flag&B2B_FMT_DV )
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
+    if ( conf->fmt_flag&B2B_FMT_DPR )
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+    if ( conf->fmt_flag&B2B_INFO_DPR )
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+    if ( conf->fmt_flag&B2B_FMT_DP4 )
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
+    if ( conf->fmt_flag&B2B_FMT_SP )
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
+    if ( conf->fmt_flag&B2B_FMT_AD )
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
+    if ( conf->fmt_flag&B2B_FMT_ADF )
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
+    if ( conf->fmt_flag&B2B_FMT_ADR )
+        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
+    if ( conf->fmt_flag&B2B_INFO_AD )
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
+    if ( conf->fmt_flag&B2B_INFO_ADF )
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
+    if ( conf->fmt_flag&B2B_INFO_ADR )
+        bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
+
+    for (i=0; i<sm->n; i++)
+        bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
+    bcf_hdr_add_sample(bcf_hdr, NULL);
+    bcf_hdr_write(bcf_fp, bcf_hdr);
+    // End of BCF header creation
+
+    // Initialise the calling algorithm
+    bca = bcf_call_init(-1., conf->min_baseQ);
+    bcr = (bcf_callret1_t*) calloc(sm->n, sizeof(bcf_callret1_t));
+    bca->rghash = rghash;
+    bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
+    bca->min_frac = conf->min_frac;
+    bca->min_support = conf->min_support;
+    bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
+
+    bc.bcf_hdr = bcf_hdr;
+    bc.n = sm->n;
+    bc.PL = (int32_t*) malloc(15 * sm->n * sizeof(*bc.PL));
+    if (conf->fmt_flag)
+    {
+        assert( sizeof(float)==sizeof(int32_t) );
+        bc.DP4 = (int32_t*) malloc(sm->n * sizeof(int32_t) * 4);
+        bc.fmt_arr = (uint8_t*) malloc(sm->n * sizeof(float)); // all fmt_flag fields
+        if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
         {
-            assert( sizeof(float)==sizeof(int32_t) );
-            bc.DP4 = (int32_t*) malloc(sm->n * sizeof(int32_t) * 4);
-            bc.fmt_arr = (uint8_t*) malloc(sm->n * sizeof(float)); // all fmt_flag fields
-            if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
+            // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
+            bc.ADR = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            bc.ADF = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            for (i=0; i<sm->n; i++)
             {
-                // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
-                bc.ADR = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
-                bc.ADF = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
-                for (i=0; i<sm->n; i++)
-                {
-                    bcr[i].ADR = bc.ADR + (i+1)*B2B_MAX_ALLELES;
-                    bcr[i].ADF = bc.ADF + (i+1)*B2B_MAX_ALLELES;
-                }
+                bcr[i].ADR = bc.ADR + (i+1)*B2B_MAX_ALLELES;
+                bcr[i].ADF = bc.ADF + (i+1)*B2B_MAX_ALLELES;
             }
         }
     }
-    else {
-        pileup_fp = conf->output_fname? fopen(conf->output_fname, "w") : stdout;
-
-        if (pileup_fp == NULL) {
-            fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname, strerror(errno));
-            exit(EXIT_FAILURE);
-        }
-    }
 
     // init pileup
     iter = bam_mplp_init(n, mplp_func, (void**)data);
@@ -547,94 +492,30 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         if (conf->bed && tid >= 0 && !regidx_overlap(conf->bed, h->target_name[tid], pos, pos, NULL)) continue;
         mplp_get_ref(data[0], tid, &ref, &ref_len);
         //printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
-        if (conf->flag & MPLP_BCF) {
-            int total_depth, _ref0, ref16;
-            for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
-            group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
-            _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
-            ref16 = seq_nt16_table[_ref0];
+        int total_depth, _ref0, ref16;
+        for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
+        group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
+        _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+        ref16 = seq_nt16_table[_ref0];
+        bcf_callaux_clean(bca, &bc);
+        for (i = 0; i < gplp.n; ++i)
+            bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
+        bc.tid = tid; bc.pos = pos;
+        bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
+        bcf_clear1(bcf_rec);
+        bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
+        bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
+        // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
+        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0)
+        {
             bcf_callaux_clean(bca, &bc);
             for (i = 0; i < gplp.n; ++i)
-                bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
-            bc.tid = tid; bc.pos = pos;
-            bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
-            bcf_clear1(bcf_rec);
-            bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
-            bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
-            // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
-            if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0)
-            {
-                bcf_callaux_clean(bca, &bc);
-                for (i = 0; i < gplp.n; ++i)
-                    bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
-                if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
-                    bcf_clear1(bcf_rec);
-                    bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
-                    bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
-                }
+                bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
+            if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
+                bcf_clear1(bcf_rec);
+                bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
+                bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
             }
-        } else {
-            fprintf(pileup_fp, "%s\t%d\t%c", h->target_name[tid], pos + 1, (ref && pos < ref_len)? ref[pos] : 'N');
-            for (i = 0; i < n; ++i) {
-                int j, cnt;
-                for (j = cnt = 0; j < n_plp[i]; ++j) {
-                    const bam_pileup1_t *p = plp[i] + j;
-                    int c = p->qpos < p->b->core.l_qseq
-                             ? bam_get_qual(p->b)[p->qpos]
-                             : 0;
-                    if (c >= conf->min_baseQ) ++cnt;
-                }
-                fprintf(pileup_fp, "\t%d\t", cnt);
-                if (n_plp[i] == 0) {
-                    fputs("*\t*", pileup_fp);
-                    if (conf->flag & MPLP_PRINT_MAPQ) fputs("\t*", pileup_fp);
-                    if (conf->flag & MPLP_PRINT_POS) fputs("\t*", pileup_fp);
-                } else {
-                    for (j = 0; j < n_plp[i]; ++j) {
-                        const bam_pileup1_t *p = plp[i] + j;
-                        int c = p->qpos < p->b->core.l_qseq
-                            ? bam_get_qual(p->b)[p->qpos]
-                            : 0;
-                        if (c >= conf->min_baseQ)
-                            pileup_seq(pileup_fp, plp[i] + j, pos, ref_len, ref);
-                    }
-                    putc('\t', pileup_fp);
-                    for (j = 0; j < n_plp[i]; ++j) {
-                        const bam_pileup1_t *p = plp[i] + j;
-                        int c = p->qpos < p->b->core.l_qseq
-                            ? bam_get_qual(p->b)[p->qpos]
-                            : 0;
-                        if (c >= conf->min_baseQ) {
-                            c = c + 33 < 126? c + 33 : 126;
-                            putc(c, pileup_fp);
-                        }
-                    }
-                    if (conf->flag & MPLP_PRINT_MAPQ) {
-                        putc('\t', pileup_fp);
-                        for (j = 0; j < n_plp[i]; ++j) {
-                            const bam_pileup1_t *p = plp[i] + j;
-                            int c = bam_get_qual(p->b)[p->qpos];
-                            if ( c < conf->min_baseQ ) continue;
-                            c = plp[i][j].b->core.qual + 33;
-                            if (c > 126) c = 126;
-                            putc(c, pileup_fp);
-                        }
-                    }
-                    if (conf->flag & MPLP_PRINT_POS) {
-                        putc('\t', pileup_fp);
-                        int last = 0;
-                        for (j = 0; j < n_plp[i]; ++j) {
-                            const bam_pileup1_t *p = plp[i] + j;
-                            int c = bam_get_qual(p->b)[p->qpos];
-                            if ( c < conf->min_baseQ ) continue;
-
-                            if (last++) putc(',', pileup_fp);
-                            fprintf(pileup_fp, "%d", plp[i][j].qpos + 1); // FIXME: printf() is very slow...
-                        }
-                    }
-                }
-            }
-            putc('\n', pileup_fp);
         }
     }
 
@@ -653,7 +534,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         free(bc.fmt_arr);
         free(bcr);
     }
-    if (pileup_fp && conf->output_fname) fclose(pileup_fp);
     bam_smpl_destroy(sm); free(buf.s);
     for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
     free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
@@ -798,19 +678,12 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "\n"
 "Output options:\n"
 "  -o, --output FILE       write output to FILE [standard output]\n"
-"  -g, --BCF               generate genotype likelihoods in BCF format\n"
-"  -v, --VCF               generate genotype likelihoods in VCF format\n"
-"\n"
-"Output options for mpileup format (without -g/-v):\n"
-"  -O, --output-BP         output base positions on reads\n"
-"  -s, --output-MQ         output mapping quality\n"
-"\n"
-"Output options for genotype likelihoods (when -g/-v is used):\n"
+"  -O, --output-type TYPE  'b' compressed BCF; 'u' uncompressed BCF;\n"
+"                          'z' compressed VCF; 'v' uncompressed VCF [v]\n"
 "  -t, --output-tags LIST  optional tags to output:\n"
 "               DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR []\n"
-"  -u, --uncompressed      generate uncompressed VCF/BCF output\n"
 "\n"
-"SNP/INDEL genotype likelihoods options (effective with -g/-v):\n"
+"SNP/INDEL genotype likelihoods options:\n"
 "  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
     fprintf(fp,
 "  -F, --gap-frac FLOAT    minimum fraction of gapped reads [%g]\n", mplp->min_frac);
@@ -850,6 +723,7 @@ int bam_mpileup(int argc, char *argv[])
     mplp.argc = argc; mplp.argv = argv;
     mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
     mplp.output_fname = NULL;
+    mplp.output_type = FT_VCF;
 
     static const struct option lopts[] =
     {
@@ -885,6 +759,7 @@ int bam_mpileup(int argc, char *argv[])
         {"bcf", no_argument, NULL, 'g'},
         {"VCF", no_argument, NULL, 'v'},
         {"vcf", no_argument, NULL, 'v'},
+        {"output-type", required_argument, NULL, 'O'},
         {"output-BP", no_argument, NULL, 'O'},
         {"output-bp", no_argument, NULL, 'O'},
         {"output-MQ", no_argument, NULL, 's'},
@@ -902,7 +777,7 @@ int bam_mpileup(int argc, char *argv[])
         {"platforms", required_argument, NULL, 'P'},
         {NULL, 0, NULL, 0}
     };
-    while ((c = getopt_long(argc, argv, "Agf:r:l:q:Q:uRC:BDSd:L:b:P:po:e:h:Im:F:EG:6OsVvxt:",lopts,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "Agf:r:l:q:Q:uRC:BDSd:L:b:P:po:e:h:Im:F:EG:6O:sVvxt:",lopts,NULL)) >= 0) {
         switch (c) {
         case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
         case  1 :
@@ -931,9 +806,9 @@ int bam_mpileup(int argc, char *argv[])
                   break;
         case 'P': mplp.pl_list = strdup(optarg); break;
         case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
-        case 'g': mplp.flag |= MPLP_BCF; break;
-        case 'v': mplp.flag |= MPLP_BCF | MPLP_VCF; break;
-        case 'u': mplp.flag |= MPLP_NO_COMP | MPLP_BCF; break;
+        case 'g': fprintf(stderr,"[warning] bcftools mpileup `-g` is functional, but deprecated. Please swith to -O in future.\n"); mplp.flag |= MPLP_BCF; break;
+        case 'v': fprintf(stderr,"[warning] bcftools mpileup `-v` is functional, but deprecated. Please swith to -O in future.\n"); mplp.flag |= MPLP_BCF | MPLP_VCF; break;
+        case 'u': fprintf(stderr,"[warning] bcftools mpileup `-u` is functional, but deprecated. Please swith to -O in future.\n"); mplp.flag |= MPLP_NO_COMP | MPLP_BCF; break;
         case 'B': mplp.flag &= ~MPLP_REALN; break;
         case 'D': mplp.fmt_flag |= B2B_FMT_DP; fprintf(stderr, "[warning] bcftools mpileup option `-D` is functional, but deprecated. Please switch to `-t DP` in future.\n"); break;
         case 'S': mplp.fmt_flag |= B2B_FMT_SP; fprintf(stderr, "[warning] bcftools mpileup option `-S` is functional, but deprecated. Please switch to `-t SP` in future.\n"); break;
@@ -942,8 +817,16 @@ int bam_mpileup(int argc, char *argv[])
         case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
         case '6': mplp.flag |= MPLP_ILLUMINA13; break;
         case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
-        case 's': mplp.flag |= MPLP_PRINT_MAPQ; break;
-        case 'O': mplp.flag |= MPLP_PRINT_POS; break;
+        case 's': error("The -s option is for text based mpileup output. Please use \"samtools mpileup -s\" instead.\n"); break;
+        case 'O': 
+            switch (optarg[0]) {
+                case 'b': mplp.output_type = FT_BCF_GZ; break;
+                case 'u': mplp.output_type = FT_BCF; break;
+                case 'z': mplp.output_type = FT_VCF_GZ; break;
+                case 'v': mplp.output_type = FT_VCF; break;
+                default: error("[error] The option \"-O\" changed meaning when mpileup moved to bcftools. Did you mean: \"bcftools mpileup --output-type\" or \"samtools mpileup --output-BP\"?\n", optarg); 
+            }
+            break;
         case 'C': mplp.capQ_thres = atoi(optarg); break;
         case 'q': mplp.min_mq = atoi(optarg); break;
         case 'Q': mplp.min_baseQ = atoi(optarg); break;
@@ -980,6 +863,19 @@ int bam_mpileup(int argc, char *argv[])
         }
     }
 
+    if ( mplp.flag&(MPLP_BCF|MPLP_VCF|MPLP_NO_COMP) )
+    {
+        if ( mplp.flag&MPLP_VCF )
+        {
+            if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_VCF;
+            else mplp.output_type = FT_VCF_GZ;
+        }
+        else if ( mplp.flag&MPLP_BCF )
+        {
+            if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_BCF;
+            else mplp.output_type = FT_BCF_GZ;
+        }
+    }
     if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
     {
         fprintf(stderr,"Error: The -B option cannot be combined with -E\n");

From 303cc365e2d450119a3453c2e0f11255d0e52817 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 26 Apr 2016 13:59:05 +0100
Subject: [PATCH 193/211] import mpileup tests from samtools

* mpileup.1.out, mpileup.2.out, mpileup.3.out and mpileup.4.out
  are from samtools with mpileup.1.out and mpileup.3.out converted
  from the text output
* mpileup.5.out a new test with the newer AD, etc annotations
* sam/bam/cram test files all stored. perhaps there is some
  way to store one version and convert within the test ala
  the vcf-miniview in samtools?
---
 test/mpileup/mpileup.1.bam       |  Bin 0 -> 67789 bytes
 test/mpileup/mpileup.1.bam.bai   |  Bin 0 -> 96 bytes
 test/mpileup/mpileup.1.cram      |  Bin 0 -> 49113 bytes
 test/mpileup/mpileup.1.cram.crai |  Bin 0 -> 42 bytes
 test/mpileup/mpileup.1.out       |   70 ++
 test/mpileup/mpileup.1.sam       | 1016 ++++++++++++++++++++++++++++++
 test/mpileup/mpileup.2.bam       |  Bin 0 -> 27928 bytes
 test/mpileup/mpileup.2.bam.bai   |  Bin 0 -> 96 bytes
 test/mpileup/mpileup.2.cram      |  Bin 0 -> 20072 bytes
 test/mpileup/mpileup.2.cram.crai |  Bin 0 -> 45 bytes
 test/mpileup/mpileup.2.out       |  523 +++++++++++++++
 test/mpileup/mpileup.2.sam       |  248 ++++++++
 test/mpileup/mpileup.3.bam       |  Bin 0 -> 27569 bytes
 test/mpileup/mpileup.3.bam.bai   |  Bin 0 -> 96 bytes
 test/mpileup/mpileup.3.cram      |  Bin 0 -> 19643 bytes
 test/mpileup/mpileup.3.cram.crai |  Bin 0 -> 43 bytes
 test/mpileup/mpileup.3.out       |   30 +
 test/mpileup/mpileup.3.sam       |  250 ++++++++
 test/mpileup/mpileup.4.out       |  527 ++++++++++++++++
 test/mpileup/mpileup.5.out       |  529 ++++++++++++++++
 test/mpileup/mpileup.ref.fa      |   71 +++
 test/mpileup/mpileup.ref.fa.fai  |    1 +
 test/test.pl                     |   19 +
 23 files changed, 3284 insertions(+)
 create mode 100644 test/mpileup/mpileup.1.bam
 create mode 100644 test/mpileup/mpileup.1.bam.bai
 create mode 100644 test/mpileup/mpileup.1.cram
 create mode 100644 test/mpileup/mpileup.1.cram.crai
 create mode 100644 test/mpileup/mpileup.1.out
 create mode 100644 test/mpileup/mpileup.1.sam
 create mode 100644 test/mpileup/mpileup.2.bam
 create mode 100644 test/mpileup/mpileup.2.bam.bai
 create mode 100644 test/mpileup/mpileup.2.cram
 create mode 100644 test/mpileup/mpileup.2.cram.crai
 create mode 100644 test/mpileup/mpileup.2.out
 create mode 100644 test/mpileup/mpileup.2.sam
 create mode 100644 test/mpileup/mpileup.3.bam
 create mode 100644 test/mpileup/mpileup.3.bam.bai
 create mode 100644 test/mpileup/mpileup.3.cram
 create mode 100644 test/mpileup/mpileup.3.cram.crai
 create mode 100644 test/mpileup/mpileup.3.out
 create mode 100644 test/mpileup/mpileup.3.sam
 create mode 100644 test/mpileup/mpileup.4.out
 create mode 100644 test/mpileup/mpileup.5.out
 create mode 100644 test/mpileup/mpileup.ref.fa
 create mode 100644 test/mpileup/mpileup.ref.fa.fai

diff --git a/test/mpileup/mpileup.1.bam b/test/mpileup/mpileup.1.bam
new file mode 100644
index 0000000000000000000000000000000000000000..e95bc3a6825eac324fa406f24c037728b2858010
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diff --git a/test/mpileup/mpileup.1.bam.bai b/test/mpileup/mpileup.1.bam.bai
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literal 0
HcmV?d00001

diff --git a/test/mpileup/mpileup.1.cram.crai b/test/mpileup/mpileup.1.cram.crai
new file mode 100644
index 0000000000000000000000000000000000000000..e43adff45f568d186be74353902cf104beff5cc7
GIT binary patch
literal 42
tcmb2|=3oE=X5$AYPfQF=44#;n8yG$}F*IfP<l}pG2Sc}Q*+~hY5&-8E3<>}M

literal 0
HcmV?d00001

diff --git a/test/mpileup/mpileup.1.out b/test/mpileup/mpileup.1.out
new file mode 100644
index 000000000..41340661d
--- /dev/null
+++ b/test/mpileup/mpileup.1.out
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	100	.	C	<*>	0	.	DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0	PL	0,27,189	0,9,108	0,15,134
+17	101	.	C	<*>	0	.	DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0	PL	0,27,182	0,9,99	0,15,132
+17	102	.	C	<*>	0	.	DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0	PL	0,27,188	0,9,111	0,15,139
+17	103	.	T	<*>	0	.	DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0	PL	0,24,189	0,9,108	0,15,147
+17	104	.	G	<*>	0	.	DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0	PL	0,24,178	0,6,89	0,15,133
+17	105	.	G	<*>	0	.	DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0	PL	0,27,170	0,9,97	0,15,125
+17	106	.	G	<*>	0	.	DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0	PL	0,30,190	0,6,85	0,15,124
+17	107	.	C	<*>	0	.	DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0	PL	0,27,192	0,9,108	0,15,136
+17	108	.	C	<*>	0	.	DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0	PL	0,27,190	0,9,108	0,15,135
+17	109	.	T	<*>	0	.	DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0	PL	0,27,195	0,9,110	0,15,150
+17	110	.	G	<*>	0	.	DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0	PL	0,27,194	0,9,104	0,15,136
+17	111	.	G	<*>	0	.	DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0	PL	0,30,167	0,6,88	0,12,118
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+17	124	.	T	<*>	0	.	DP=19;I16=17,1,0,0,626,24802,0,0,987,56523,0,0,279,6003,0,0;QS=3,0;MQSB=1;MQ0F=0	PL	0,27,154	0,9,104	0,18,154
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+17	133	.	T	<*>	0	.	DP=15;I16=13,2,0,0,584,22816,0,0,838,48482,0,0,282,6196,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL	0,21,163	0,9,105	0,15,150
+17	134	.	C	<*>	0	.	DP=15;I16=13,2,0,0,607,24653,0,0,838,48482,0,0,283,6267,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL	0,21,177	0,9,105	0,15,152
+17	135	.	T	<*>	0	.	DP=15;I16=13,2,0,0,600,24178,0,0,838,48482,0,0,284,6352,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL	0,21,173	0,9,106	0,15,156
+17	136	.	G	<*>	0	.	DP=15;I16=13,2,0,0,574,22258,0,0,838,48482,0,0,286,6450,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL	0,21,172	0,9,105	0,15,134
+17	137	.	T	<*>	0	.	DP=15;I16=13,2,0,0,563,21377,0,0,838,48482,0,0,289,6561,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL	0,21,160	0,9,104	0,15,139
+17	138	.	C	<*>	0	.	DP=15;I16=13,2,0,0,584,23088,0,0,838,48482,0,0,291,6637,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL	0,21,172	0,9,108	0,15,142
+17	139	.	C	<*>	0	.	DP=15;I16=13,2,0,0,554,20790,0,0,838,48482,0,0,292,6680,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL	0,21,161	0,9,106	0,15,143
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+17	146	.	T	<*>	0	.	DP=14;I16=12,2,0,0,514,19484,0,0,778,44882,0,0,289,6573,0,0;QS=3,0;MQSB=0.583333;MQ0F=0	PL	0,18,152	0,9,103	0,15,128
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+17	148	.	C	<*>	0	.	DP=14;I16=12,2,0,0,541,21019,0,0,778,44882,0,0,286,6542,0,0;QS=3,0;MQSB=0.583333;MQ0F=0	PL	0,18,157	0,9,106	0,15,146
+17	149	.	C	<*>	0	.	DP=14;I16=12,2,0,0,512,19326,0,0,778,44882,0,0,283,6471,0,0;QS=3,0;MQSB=0.583333;MQ0F=0	PL	0,18,148	0,9,109	0,15,140
+17	150	.	T	<*>	0	.	DP=13;I16=11,2,0,0,511,20251,0,0,749,44041,0,0,280,6362,0,0;QS=3,0;MQSB=0.5;MQ0F=0	PL	0,18,153	0,6,84	0,15,152
diff --git a/test/mpileup/mpileup.1.sam b/test/mpileup/mpileup.1.sam
new file mode 100644
index 000000000..65d9095af
--- /dev/null
+++ b/test/mpileup/mpileup.1.sam
@@ -0,0 +1,1016 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:17	LN:4200	M5:a9a06ca09c111789d92723fbf39820f6	AS:NCBI37	SP:Human
+@RG	ID:ERR013140	LB:g1k-sc-HG00100-A	SM:HG00100	PI:450	CN:SC	PL:ILLUMINA	DS:SRP001294
+@RG	ID:ERR016352	LB:g1k-sc-HG00100-A	SM:HG00100	PI:450	CN:SC	PL:ILLUMINA	DS:SRP001294
+@RG	ID:ERR156632	LB:3815246	SM:HG00100	PI:352	CN:SC	PL:ILLUMINA	DS:SRP001294
+@RG	ID:ERR162872	LB:3815246	SM:HG00100	PI:349	CN:SC	PL:ILLUMINA	DS:SRP001294
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+@RG	ID:ERR242963	LB:6503965	SM:HG00100	PI:457	CN:SC	PL:ILLUMINA	DS:SRP001294
+@RG	ID:ERR242967	LB:6503965	SM:HG00100	PI:457	CN:SC	PL:ILLUMINA	DS:SRP001294
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+@PG	ID:bwa_index	PN:bwa	VN:0.5.9-r16	CL:bwa index -a bwtsw $reference_fasta
+@PG	ID:bwa_aln_fastq	PN:bwa	PP:bwa_index	VN:0.5.9-r16	CL:bwa aln -q 15 -f $sai_file $reference_fasta $fastq_file
+@PG	ID:bwa_sam	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1350 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.1	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1056 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.2	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1047 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.3	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1044 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.4	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1377 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.5	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.6	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1368 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.7	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
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+@PG	ID:bwa_sam.9	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.10	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.11	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.12	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.13	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.14	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.15	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1368 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.16	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.17	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.18	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1368 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.19	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.20	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.21	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.22	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.23	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1368 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.24	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.25	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1368 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.26	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.27	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1365 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.28	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.29	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1365 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.30	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.31	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.32	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.33	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1368 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.34	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1371 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.35	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.36	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1377 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.37	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1374 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:bwa_sam.38	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1368 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:sam_to_fixed_bam	PN:samtools	PP:bwa_sam	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.1	PN:samtools	PP:bwa_sam.1	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.2	PN:samtools	PP:bwa_sam.2	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.3	PN:samtools	PP:bwa_sam.3	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.4	PN:samtools	PP:bwa_sam.4	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.5	PN:samtools	PP:bwa_sam.5	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.6	PN:samtools	PP:bwa_sam.6	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.7	PN:samtools	PP:bwa_sam.7	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.8	PN:samtools	PP:bwa_sam.8	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.9	PN:samtools	PP:bwa_sam.9	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.10	PN:samtools	PP:bwa_sam.10	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.11	PN:samtools	PP:bwa_sam.11	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.12	PN:samtools	PP:bwa_sam.12	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.13	PN:samtools	PP:bwa_sam.13	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.14	PN:samtools	PP:bwa_sam.14	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.15	PN:samtools	PP:bwa_sam.15	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.16	PN:samtools	PP:bwa_sam.16	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.17	PN:samtools	PP:bwa_sam.17	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.18	PN:samtools	PP:bwa_sam.18	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.19	PN:samtools	PP:bwa_sam.19	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.20	PN:samtools	PP:bwa_sam.20	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.21	PN:samtools	PP:bwa_sam.21	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.22	PN:samtools	PP:bwa_sam.22	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.23	PN:samtools	PP:bwa_sam.23	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.24	PN:samtools	PP:bwa_sam.24	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.25	PN:samtools	PP:bwa_sam.25	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.26	PN:samtools	PP:bwa_sam.26	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.27	PN:samtools	PP:bwa_sam.27	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.28	PN:samtools	PP:bwa_sam.28	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.29	PN:samtools	PP:bwa_sam.29	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.30	PN:samtools	PP:bwa_sam.30	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.31	PN:samtools	PP:bwa_sam.31	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.32	PN:samtools	PP:bwa_sam.32	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.33	PN:samtools	PP:bwa_sam.33	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.34	PN:samtools	PP:bwa_sam.34	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.35	PN:samtools	PP:bwa_sam.35	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.36	PN:samtools	PP:bwa_sam.36	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.37	PN:samtools	PP:bwa_sam.37	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:sam_to_fixed_bam.38	PN:samtools	PP:bwa_sam.38	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:gatk_target_interval_creator	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.1	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.1	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.2	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.2	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.3	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.3	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.4	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.4	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.5	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.5	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.6	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.6	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.7	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.7	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.8	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.8	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.9	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.9	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.10	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.10	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.11	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.11	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.12	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.12	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.13	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.13	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.14	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.14	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.15	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.15	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.16	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.16	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.17	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.17	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.18	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.18	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.19	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.19	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.20	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.20	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.21	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.21	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.22	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.22	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.23	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.23	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.24	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.24	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.25	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.25	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.26	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.26	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.27	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.27	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.28	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.28	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.29	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.29	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.30	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.30	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.31	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.31	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.32	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.32	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.33	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.33	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.34	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.34	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.35	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.35	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.36	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.36	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.37	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.37	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:gatk_target_interval_creator.38	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam.38	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:bam_realignment_around_known_indels	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.1	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.1	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.2	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.2	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.3	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.3	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.4	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.4	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.5	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.5	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.6	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.6	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.7	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.7	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.8	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.8	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.9	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.9	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.10	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.10	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.11	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.11	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.12	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.12	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.13	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.13	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.14	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.14	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.15	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.15	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.16	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.16	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.17	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.17	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.18	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.18	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.19	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.19	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.20	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.20	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.21	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.21	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.22	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.22	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.23	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.23	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.24	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.24	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.25	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.25	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.26	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.26	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.27	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.27	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.28	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.28	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.29	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.29	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.30	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.30	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.31	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.31	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.32	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.32	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.33	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.33	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.34	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.34	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.35	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.35	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.36	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.36	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.37	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.37	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_realignment_around_known_indels.38	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator.38	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_count_covariates	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.1	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.1	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.2	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.2	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.3	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.3	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.4	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.4	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.5	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.5	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.6	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.6	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.7	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.7	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.8	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.8	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.9	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.9	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.10	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.10	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.11	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.11	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.12	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.12	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.13	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.13	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.14	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.14	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.15	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.15	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.16	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.16	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.17	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.17	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.18	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.18	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.19	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.19	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.20	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.20	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.21	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.21	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.22	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.22	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.23	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.23	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.24	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.24	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.25	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.25	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.26	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.26	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.27	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.27	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.28	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.28	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.29	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.29	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.30	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.30	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.31	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.31	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.32	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.32	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.33	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.33	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.34	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.34	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.35	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.35	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.36	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.36	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.37	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.37	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_count_covariates.38	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels.38	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_recalibrate_quality_scores	PN:GenomeAnalysisTK	PP:bam_count_covariates	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.1	PN:GenomeAnalysisTK	PP:bam_count_covariates.1	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.2	PN:GenomeAnalysisTK	PP:bam_count_covariates.2	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.3	PN:GenomeAnalysisTK	PP:bam_count_covariates.3	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.4	PN:GenomeAnalysisTK	PP:bam_count_covariates.4	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.5	PN:GenomeAnalysisTK	PP:bam_count_covariates.5	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.6	PN:GenomeAnalysisTK	PP:bam_count_covariates.6	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.7	PN:GenomeAnalysisTK	PP:bam_count_covariates.7	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.8	PN:GenomeAnalysisTK	PP:bam_count_covariates.8	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.9	PN:GenomeAnalysisTK	PP:bam_count_covariates.9	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.10	PN:GenomeAnalysisTK	PP:bam_count_covariates.10	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.11	PN:GenomeAnalysisTK	PP:bam_count_covariates.11	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.12	PN:GenomeAnalysisTK	PP:bam_count_covariates.12	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.13	PN:GenomeAnalysisTK	PP:bam_count_covariates.13	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.14	PN:GenomeAnalysisTK	PP:bam_count_covariates.14	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.15	PN:GenomeAnalysisTK	PP:bam_count_covariates.15	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.16	PN:GenomeAnalysisTK	PP:bam_count_covariates.16	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.17	PN:GenomeAnalysisTK	PP:bam_count_covariates.17	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.18	PN:GenomeAnalysisTK	PP:bam_count_covariates.18	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.19	PN:GenomeAnalysisTK	PP:bam_count_covariates.19	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.20	PN:GenomeAnalysisTK	PP:bam_count_covariates.20	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.21	PN:GenomeAnalysisTK	PP:bam_count_covariates.21	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.22	PN:GenomeAnalysisTK	PP:bam_count_covariates.22	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.23	PN:GenomeAnalysisTK	PP:bam_count_covariates.23	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.24	PN:GenomeAnalysisTK	PP:bam_count_covariates.24	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.25	PN:GenomeAnalysisTK	PP:bam_count_covariates.25	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.26	PN:GenomeAnalysisTK	PP:bam_count_covariates.26	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.27	PN:GenomeAnalysisTK	PP:bam_count_covariates.27	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.28	PN:GenomeAnalysisTK	PP:bam_count_covariates.28	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.29	PN:GenomeAnalysisTK	PP:bam_count_covariates.29	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.30	PN:GenomeAnalysisTK	PP:bam_count_covariates.30	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.31	PN:GenomeAnalysisTK	PP:bam_count_covariates.31	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.32	PN:GenomeAnalysisTK	PP:bam_count_covariates.32	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.33	PN:GenomeAnalysisTK	PP:bam_count_covariates.33	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.34	PN:GenomeAnalysisTK	PP:bam_count_covariates.34	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.35	PN:GenomeAnalysisTK	PP:bam_count_covariates.35	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.36	PN:GenomeAnalysisTK	PP:bam_count_covariates.36	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.37	PN:GenomeAnalysisTK	PP:bam_count_covariates.37	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_recalibrate_quality_scores.38	PN:GenomeAnalysisTK	PP:bam_count_covariates.38	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_calculate_bq	PN:samtools	PP:bam_recalibrate_quality_scores	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.1	PN:samtools	PP:bam_recalibrate_quality_scores.1	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.2	PN:samtools	PP:bam_recalibrate_quality_scores.2	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.3	PN:samtools	PP:bam_recalibrate_quality_scores.3	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.4	PN:samtools	PP:bam_recalibrate_quality_scores.4	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.5	PN:samtools	PP:bam_recalibrate_quality_scores.5	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.6	PN:samtools	PP:bam_recalibrate_quality_scores.6	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.7	PN:samtools	PP:bam_recalibrate_quality_scores.7	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.8	PN:samtools	PP:bam_recalibrate_quality_scores.8	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.9	PN:samtools	PP:bam_recalibrate_quality_scores.9	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.10	PN:samtools	PP:bam_recalibrate_quality_scores.10	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.11	PN:samtools	PP:bam_recalibrate_quality_scores.11	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.12	PN:samtools	PP:bam_recalibrate_quality_scores.12	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.13	PN:samtools	PP:bam_recalibrate_quality_scores.13	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.14	PN:samtools	PP:bam_recalibrate_quality_scores.14	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.15	PN:samtools	PP:bam_recalibrate_quality_scores.15	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.16	PN:samtools	PP:bam_recalibrate_quality_scores.16	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.17	PN:samtools	PP:bam_recalibrate_quality_scores.17	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.18	PN:samtools	PP:bam_recalibrate_quality_scores.18	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.19	PN:samtools	PP:bam_recalibrate_quality_scores.19	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.20	PN:samtools	PP:bam_recalibrate_quality_scores.20	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.21	PN:samtools	PP:bam_recalibrate_quality_scores.21	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.22	PN:samtools	PP:bam_recalibrate_quality_scores.22	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.23	PN:samtools	PP:bam_recalibrate_quality_scores.23	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.24	PN:samtools	PP:bam_recalibrate_quality_scores.24	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.25	PN:samtools	PP:bam_recalibrate_quality_scores.25	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.26	PN:samtools	PP:bam_recalibrate_quality_scores.26	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.27	PN:samtools	PP:bam_recalibrate_quality_scores.27	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.28	PN:samtools	PP:bam_recalibrate_quality_scores.28	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.29	PN:samtools	PP:bam_recalibrate_quality_scores.29	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.30	PN:samtools	PP:bam_recalibrate_quality_scores.30	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.31	PN:samtools	PP:bam_recalibrate_quality_scores.31	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.32	PN:samtools	PP:bam_recalibrate_quality_scores.32	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.33	PN:samtools	PP:bam_recalibrate_quality_scores.33	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.34	PN:samtools	PP:bam_recalibrate_quality_scores.34	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.35	PN:samtools	PP:bam_recalibrate_quality_scores.35	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.36	PN:samtools	PP:bam_recalibrate_quality_scores.36	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.37	PN:samtools	PP:bam_recalibrate_quality_scores.37	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_calculate_bq.38	PN:samtools	PP:bam_recalibrate_quality_scores.38	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_merge	PN:picard	PP:bam_calculate_bq	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.1	PN:picard	PP:bam_calculate_bq.1	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.2	PN:picard	PP:bam_calculate_bq.2	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.3	PN:picard	PP:bam_calculate_bq.3	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.4	PN:picard	PP:bam_calculate_bq.4	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.5	PN:picard	PP:bam_calculate_bq.5	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.6	PN:picard	PP:bam_calculate_bq.6	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.7	PN:picard	PP:bam_calculate_bq.7	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.8	PN:picard	PP:bam_calculate_bq.8	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.9	PN:picard	PP:bam_calculate_bq.9	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.10	PN:picard	PP:bam_calculate_bq.10	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.11	PN:picard	PP:bam_calculate_bq.11	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.12	PN:picard	PP:bam_calculate_bq.12	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.13	PN:picard	PP:bam_calculate_bq.13	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.14	PN:picard	PP:bam_calculate_bq.14	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.15	PN:picard	PP:bam_calculate_bq.15	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.16	PN:picard	PP:bam_calculate_bq.16	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.17	PN:picard	PP:bam_calculate_bq.17	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.18	PN:picard	PP:bam_calculate_bq.18	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.19	PN:picard	PP:bam_calculate_bq.19	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.20	PN:picard	PP:bam_calculate_bq.20	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.21	PN:picard	PP:bam_calculate_bq.21	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.22	PN:picard	PP:bam_calculate_bq.22	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.23	PN:picard	PP:bam_calculate_bq.23	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.24	PN:picard	PP:bam_calculate_bq.24	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.25	PN:picard	PP:bam_calculate_bq.25	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.26	PN:picard	PP:bam_calculate_bq.26	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.27	PN:picard	PP:bam_calculate_bq.27	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.28	PN:picard	PP:bam_calculate_bq.28	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.29	PN:picard	PP:bam_calculate_bq.29	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.30	PN:picard	PP:bam_calculate_bq.30	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.31	PN:picard	PP:bam_calculate_bq.31	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.32	PN:picard	PP:bam_calculate_bq.32	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.33	PN:picard	PP:bam_calculate_bq.33	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.34	PN:picard	PP:bam_calculate_bq.34	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.35	PN:picard	PP:bam_calculate_bq.35	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.36	PN:picard	PP:bam_calculate_bq.36	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.37	PN:picard	PP:bam_calculate_bq.37	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.38	PN:picard	PP:bam_calculate_bq.38	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates	PN:picard	PP:bam_merge	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.1	PN:picard	PP:bam_merge.1	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.2	PN:picard	PP:bam_merge.2	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.3	PN:picard	PP:bam_merge.3	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.4	PN:picard	PP:bam_merge.4	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.5	PN:picard	PP:bam_merge.5	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.6	PN:picard	PP:bam_merge.6	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.7	PN:picard	PP:bam_merge.7	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.8	PN:picard	PP:bam_merge.8	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.9	PN:picard	PP:bam_merge.9	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.10	PN:picard	PP:bam_merge.10	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.11	PN:picard	PP:bam_merge.11	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.12	PN:picard	PP:bam_merge.12	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.13	PN:picard	PP:bam_merge.13	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.14	PN:picard	PP:bam_merge.14	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.15	PN:picard	PP:bam_merge.15	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.16	PN:picard	PP:bam_merge.16	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.17	PN:picard	PP:bam_merge.17	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.18	PN:picard	PP:bam_merge.18	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.19	PN:picard	PP:bam_merge.19	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.20	PN:picard	PP:bam_merge.20	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.21	PN:picard	PP:bam_merge.21	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.22	PN:picard	PP:bam_merge.22	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.23	PN:picard	PP:bam_merge.23	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.24	PN:picard	PP:bam_merge.24	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.25	PN:picard	PP:bam_merge.25	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.26	PN:picard	PP:bam_merge.26	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.27	PN:picard	PP:bam_merge.27	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.28	PN:picard	PP:bam_merge.28	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.29	PN:picard	PP:bam_merge.29	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.30	PN:picard	PP:bam_merge.30	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.31	PN:picard	PP:bam_merge.31	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.32	PN:picard	PP:bam_merge.32	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.33	PN:picard	PP:bam_merge.33	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.34	PN:picard	PP:bam_merge.34	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.35	PN:picard	PP:bam_merge.35	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.36	PN:picard	PP:bam_merge.36	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.37	PN:picard	PP:bam_merge.37	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates.38	PN:picard	PP:bam_merge.38	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.39	PN:picard	PP:bam_mark_duplicates	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.1.39	PN:picard	PP:bam_mark_duplicates.1	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.2.39	PN:picard	PP:bam_mark_duplicates.2	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.3.39	PN:picard	PP:bam_mark_duplicates.3	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.4.39	PN:picard	PP:bam_mark_duplicates.4	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.5.39	PN:picard	PP:bam_mark_duplicates.5	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.6.39	PN:picard	PP:bam_mark_duplicates.6	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.7.39	PN:picard	PP:bam_mark_duplicates.7	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.8.39	PN:picard	PP:bam_mark_duplicates.8	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.9.39	PN:picard	PP:bam_mark_duplicates.9	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.10.39	PN:picard	PP:bam_mark_duplicates.10	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.11.39	PN:picard	PP:bam_mark_duplicates.11	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.12.39	PN:picard	PP:bam_mark_duplicates.12	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.13.39	PN:picard	PP:bam_mark_duplicates.13	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.14.39	PN:picard	PP:bam_mark_duplicates.14	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.15.39	PN:picard	PP:bam_mark_duplicates.15	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.16.39	PN:picard	PP:bam_mark_duplicates.16	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.17.39	PN:picard	PP:bam_mark_duplicates.17	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.18.39	PN:picard	PP:bam_mark_duplicates.18	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.19.39	PN:picard	PP:bam_mark_duplicates.19	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.20.39	PN:picard	PP:bam_mark_duplicates.20	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.21.39	PN:picard	PP:bam_mark_duplicates.21	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.22.39	PN:picard	PP:bam_mark_duplicates.22	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.23.39	PN:picard	PP:bam_mark_duplicates.23	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.24.39	PN:picard	PP:bam_mark_duplicates.24	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.25.39	PN:picard	PP:bam_mark_duplicates.25	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.26.39	PN:picard	PP:bam_mark_duplicates.26	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.27.39	PN:picard	PP:bam_mark_duplicates.27	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.28.39	PN:picard	PP:bam_mark_duplicates.28	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.29.39	PN:picard	PP:bam_mark_duplicates.29	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.30.39	PN:picard	PP:bam_mark_duplicates.30	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.31.39	PN:picard	PP:bam_mark_duplicates.31	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.32.39	PN:picard	PP:bam_mark_duplicates.32	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.33.39	PN:picard	PP:bam_mark_duplicates.33	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.34.39	PN:picard	PP:bam_mark_duplicates.34	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.35.39	PN:picard	PP:bam_mark_duplicates.35	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.36.39	PN:picard	PP:bam_mark_duplicates.36	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.37.39	PN:picard	PP:bam_mark_duplicates.37	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.38.39	PN:picard	PP:bam_mark_duplicates.38	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+ERR013140.3521432	99	17	1	29	22S86M	=	226	313	AGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCA	@AEDGBHIIIIIFJGIKHGHIJJJEJKHJKJKGKLLIFHKLLCJJIDEFFHKHEHHJIIIDJEEEJEIKGJIHCGKHFKFE9BBDIAJAHF4?DE@I:DD48(86D=>	MD:Z:86	RG:Z:ERR013140	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@iidijgijijfjkkhegjkkbiihcdeegjgdggihhhcidddidhjfihgbfjgejedXaach`i`geS^cd_hYccSWGWUc\]
+ERR156632.12704932	163	17	1	29	36S64M	=	195	293	TGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTG	BFAFGFEIGFEFHHEIDKJGHHHJIIE=@KKGGKJGIBLLMFKMDIIHJKKHFELLLKFIHMHIHHIHLKJFCHFJIJAID=JHKFGHJIHKKCH:@HD?	MD:Z:64	RG:Z:ERR156632	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@hakklejlchhgijjgedkkkjehglghgghgkjiebgeihi`hc\igjefgihgjjbgY_gc^
+ERR156632.9601178	99	17	1	29	62S38M	=	279	377	CTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGA	DEEEIIHHKIJILKHLHIKEKHHMKLKKJGKKKKLKLFIHEKIKL=KLJLKIILHKMH9LJJJJLHLHJJKJJKMLKJD>MJKLEHIGHIH=FFCHF>BE	MD:Z:38	RG:Z:ERR156632	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@iikgkgiijiijlkjic]lijkdghfghg\eebge]ad
+ERR162872.21706338	99	17	1	29	10S90M	=	246	344	CTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCA	BHBFH<EIFGGGJFEGJJJI?JJKLDGAHJKJIIILHFCJIAKKEJKIJHBIHJBJKDJHKMKJGJLKHIGJ8IGHKL=JGF8KCHKK:HAD4IIDFFFB	MD:Z:90	RG:Z:ERR162872	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@ffiedfiiih^iijkcf`gijihhhkgebih`jjdijhigahgiaijcigjljifikjghfiWhfgjk\ifeWjbgjjYg`cShhceeea
+ERR243039.1049231	163	17	1	29	43S57M	=	269	367	TGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCT	AEEFIFHIJDGIGIJHHIAGGGLGJIEJHJHHFIJGJJDFJIGKJIGKBKJKKIDIHIDFKCDJJFGEJEHCHJEKHIHJGGIEGGGJFIEIAHEFFFA0	MD:Z:57	RG:Z:ERR243039	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@jihfjajijjhchghcejbciiefdidgbgidjghgiffhdfffiehdh`gdeee`O
+ERR243011.373069	163	17	18	60	100M	=	483	564	CCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAG	@?DEBGGDIFFDGFELJHGJFIGGHEIIHIE>DKHGHJFJIFIDFDIJHHJHHIICKKKIJIHH?JJKEKGHGJCGGEHFIHJHFK;HGIHIJGICIEDH	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243011	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@J
+ERR162875.9416595	163	17	23	60	100M	=	239	314	ATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGC	DBDIGHGHIBKJIIKIJJGJGKKIKILIKKLJLLKKJJILIJJLMKKIJJHIKLLKJKHDELMJHFKIKDKDKIHHILFKLHBMKGLJ7KGDJHBBFFGD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.23732910	163	17	25	60	100M	=	299	373	AGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTT	DFEEGGHGJDIHKJIIHHHLKKLHIILLKKMILLKHKMIMMLJLLKLIGJFIKMJJKEMMLHKGDIJ?CILGIIJJLKLL6KMKLM7IIGJGJF?CFEG?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@
+ERR162872.5127873	113	17	28	37	100M	*	0	0	TAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAAC	.BDEFHG?AEFGHIFCEHLGIIFJIA@LCFKAFJDJDEIBHELKIJMH8FJJKHAMG>GHGKHAKFKHHGGEL=LIJJIILCJHJGHJIHEFIFI9DBGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.19056012	113	17	32	37	100M	*	0	0	TGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAAC	DFGEGFDK;HFFHJJDJHFJJKILKDMIJFDKJMIMJKM@HAMIL=KKMHHLHM8GKKECMHJLHGM=BLMJIKKJLHJJKGHKIJJ@IHJFEEGHDBGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.19886608	177	17	33	37	108M	*	0	0	GCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCA	%CCD@AC<DAFAAD>F?E@DBECDF@<EE@HEDABGH>FHGFEDHEHGABBCC>@FFD>FCGKEELCIHLGKJJGCHHJDBCIIJJIFIJJGDGHCCGGEFFCAEGD:	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243079.1328786	177	17	33	37	100M	*	0	0	GCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACA	DEDDICIGFGFIJHGFJGG?KGJCHKCHFICIKEHGFHGJDJ@ICIFEAGKBKC@CHFBKFBHFEGEDEJHHHIFJEGHHEDGHDHJHHJFCDDGCADE?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243079	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243027.254838	177	17	36	37	100M	*	0	0	TGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCT	?B.F)9:GCFJ=CGBD0DFG0AL5;;CHIH?<GG*(JDKBIGB7*8.CG=3=@I3;=DG?D?J0<GG=C@<9AFAJDCGJDE4CDAJ@AFAJ??CHBCE=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243027	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.13071468	113	17	37	37	100M	*	0	0	GACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTG	=DHEDFDJIKIDGILIKJIMDJAHJGJKMI@HJ@GFHGJHIIL@JB:AK9CEJHDH2EFFEGB=KLGAJJJGIJCC1IKJJJJJI=EFCFHDDEGEEGEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.15521446	163	17	41	60	100M	=	314	372	ATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCA	ABDIIIJGKGKJKKKKLKJJIIIMKLLLMJKLGMLKMMJLHGMLLJIJKKIDIKKHIJKMJLLGKKKLOMHLFIIJIKHIMIMHDJJHHIJJGKJIEGFC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.15487245	177	17	43	37	100M	*	0	0	TGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGC	B9,5:EHA%37IG1F5<F:*H?BEI6;KJEC:A9:4?ECALBGC09@G2KH0:F=C89B:<LKD=KG@E2AA<E<KC=;>8/F?C65G=E0=BBFD>BD?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.3774900	177	17	48	37	108M	*	0	0	TTTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATC	4&4%4-<'CH>+GD8<6<<;85562@>C:>310155<+/4568-&,)8*7=6,9;D261>CG@6?@>/H=8@HB:F<FFFFF;ACAEE>EFED@<>DB?-2?@=>BA9	X0:i:1	X1:i:0	MD:Z:1G106	RG:Z:ERR016352	AM:i:37	NM:i:1	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.8688512	113	17	48	37	100M	*	0	0	TGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATA	DCF.<IH=AG5:AH>AGFCKCGDBJILEK@CEKGHL9:B7GM<3F<:BH=FC0KC;HM:K;DKGCHLM?IG>@GMJFECHHGCDIIBEFI:GAHBCBDCD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243063.860385	113	17	58	37	100M	*	0	0	GAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCC	AA@@FADGFKI?HCHFE@IFI:?GGJHFIIJIEBHFFKGFHIIHJ@HJHCLGIKGDHJHHIIJJIGFGEIGBGIGHJGGEGHJH@IEHEFGIFHIEBB>A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR162872.19371403	99	17	64	60	100M	=	413	448	GCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAG	BDGFHHEEGFIIHKJIIJDJKKHIKKIJEIIJIIIKLKLMKKILLLKJKIJLJMLLIMKKEHEGJFJKGKLLMJKJIMLCJIHFKJKIJEDKEGIEHD?F	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR162872.10929052	163	17	69	60	100M	=	429	459	GGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAG	E>EFFIJJKKIIJIHKKIJNLIIDKIHEKJLLMLLLKKJKJLJKGJNJIJKKMLIIIKGIKKKKHMKLHMKILLAJJJIKLJLLGILLJKJFDHDEGFD1	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:F@CA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.10099033	163	17	87	60	100M	=	384	396	CCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACG	D?DEGBHHIIIJKGHKKIGJKLJIBLJIGIFGJHGLEECAJIJCFJIKLGHI@KCFEJCJJJ3IJLGJKJLLIHHEGGJD?H4EHIADJE>D>7FCF@8*	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.753594	99	17	95	60	100M	=	555	559	CAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTC	?ECDFG9FGH8EIGFHAIEHFHJFGG@JF?DGGEDEGGEKHIAJGFJI@GGFEGIEHEFHJHGEDHHHE@>@EK>HFHC@JFFDI3CEHHGAGEEECF@B	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR013140.20277196	163	17	97	29	34M74S	=	339	349	ACTCCCCCGGCCCGGGGCCCGGGGGCTTTACAAAAAACTGTCCAGCGCATACCCGCATCCCCCCAAAAGAAGCCACCGCCCCAACACACACCCCCCACCCGCATAACC	824475'$-2)*#(/#%(/#(/-%-%-/%0/88800($,+3(*+..,%%+6%*#%2,/001)%%$2%%/$.%$00(,%+,1'*.%7(%&$&#'$$$#%#%#($+%+)"	XC:i:35	MD:Z:6T0G4T2C0A2A3A4A5	RG:Z:ERR013140	AM:i:29	NM:i:8	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.19887184	113	17	99	37	40S68M	*	0	0	GTGTGTGTCGGGGGTGTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGA	%$($&$*+#%%#1'$$%2-'0&3*/$/$-73/69:7=1%2135??3C<6;:9@<46<?GDDKGMIIIIIHHIIHKIKGJJIKJ@JHGHDIHJIHFJHHGFJBFIBEC@	X0:i:1	X1:i:0	XC:i:68	MD:Z:68	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR013140.25967365	99	17	105	60	108M	=	372	374	GGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCC	;???BDC??BAFFAGJHIH7GGDIIJGKGJIHHIFHEHBBKFIHGEHIHGHKLKHHG:HEHIGKGLIID=IIFHDGH@EIH@FHC7<CA6?F>@G@EBB=FEBF<@95	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.4461044	113	17	114	37	17S91M	*	0	0	ACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATCCCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACC	/=1:/=44-348<0(910@955>D;??@=>>=<<A5<BA=6DEB999<@<'B@;1@;<C@?=D9?A9@38@1<@.C8<CGACBG>@DE?IIIHFJFJHGIHGHECCB@	X0:i:1	X1:i:0	XC:i:91	MD:Z:33A57	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245034.1618692	163	17	124	60	100M	=	510	485	TAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAG	>ABDECDGFEHGHFHFFJF@GGGDGHHGJGFJHHHDKH@I@JGEGHGGJHBGHGHGCLGIHH@IGIFGKGHIAJIHHGEGHHIJFHIHHHEIECFCFBCE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245034	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR245038.421367	177	17	131	37	100M	*	0	0	CATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGC	A>7EBHBFIGE>JEJFC/KFCKGEHGKFIJ@IEHD=JJJJCGACHEJGEHDFFFBGFFJHEGFIIKILHFFHHKGKJGFHHJEFJEHIGGEIGIIEE?C@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR156632.396790	177	17	133	37	100M	*	0	0	TCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCC	>FDAGAHKICK>IBHJMJD?IFKILGEKAEJKLE:LKLGGCL1@KHGHKDMGCIKII@DH:KKHGLFIGCFLIJIHHGKJGJJHHHHJEIHGIFB@FA@B	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR243011.687269	177	17	133	37	100M	*	0	0	TCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCC	,G<F-GD.A59E:<=G<B5IF:00<;<@>0I=C718G?2IB91/1FACI1?319I=IHADEF@DI<?<EF5FGLI?F93HACE4HGHJCICHF3E=E;:=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243011	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242939.81544	99	17	152	60	100M	=	565	512	CATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAATGCACCGCCCAAAGACACGCCCATGTCCA	=A@D7EF@IDG;:GH9E13ED?>5GBH5DJFHF=7;9G@G2DB5F?K2C;F.7G>7GCF9H=B<<G0FF8G)C6EB546)ID==BEFE5<>'GF?:BA1*	X0:i:1	X1:i:0	MD:Z:71G28	RG:Z:ERR242939	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243083.1184095	177	17	168	37	100M	*	0	0	GCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGT	CFG1F@CBDD>9HICI:@F=HIHIGDHPJBDFFG@IFEHKBDIJICJIELH?DEFHEHCGA8:@GB<EIDICAEHHIFGGE?IGGIEDGDEGFFA@FFC?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243083	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR162872.15901000	163	17	175	60	100M	=	399	323	CCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTC	EBGGFGKHIHICKLLHJKHNMJNLMHIIJLLLMJILJLMIMHIMHKKJMJLHKLEKLILIKMJKKKCLLKKKLJLLJLKLGHIHLLLKKJKLCFJGGGGG	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:D@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@I
+ERR013140.10132183	99	17	182	60	108M	=	413	338	ACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGCAAGGCTGCATG	@?EB=GIIIFGGIJJHIKGGJGKKHJKGJKKKHIIKIGIKKCJJKHL=JLLLFDGIILF<KHKJGFEDGCGGHBDHGIJGHEECFC6=5FFID==<(6486;BA2<=@	X0:i:1	X1:i:0	MD:Z:96A11	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR156632.12704932	83	17	195	29	100M	=	1	-293	CAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGA	DCEHFGFAGLELL>IJELIJ@HLE:LHKHEL:FDLKHE8IJGHJHDDLJLJIKFJLLLLJIHLGMHJJLLKJBJ8MIK>GLKK6HLKHJG7IEHIG@FCD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.15310883	163	17	201	60	100M	=	519	417	AACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA	BCDFGHGFFGIIJGKHFKGKIILIJIIKCHLHJIILIJIJENHMGHLGJKILLKHIHHLKJMKKJHIHLKLJKJMJHBFJMFLLKJIIKAHHFFGGFFDB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245053.675620	163	17	213	60	90M1I9M	=	408	294	TAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGAC	?AHDDHEHEGJEIGGH@HHHGHGIFHGHBIIIHGHEIHHJJHGFFFGJLJGIEIFEKFJKHIHGKHEHHG=JJJGGJKFEJBHFJGGFICEHGCGGE=C8	X0:i:1	X1:i:0	MD:Z:99	RG:Z:ERR245053	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.3521432	147	17	226	29	19S89M	=	1	-313	CACCCCTAGAAGTGACGGCCCCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTGCCTGCGACAAA	71%??A9A792/7-2%(&:$::+BC@<=E>=EFCFHILHEDJNKHLFJFGGIMGGMMGKBKFMLELFMJJDEEJFJLIJIHIJFJHIHIFHEHIEGHJIFB<CCE@?:	X0:i:1	X1:i:0	XC:i:89	MD:Z:0A88	RG:Z:ERR013140	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245049.908854	177	17	232	37	100M	*	0	0	CAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTGCCTGCGACAAAGCTGAATGCTATCATTT	EB=FE?H=AGHIIGGGHJJJDKB@HGGKHGKFJGHFBHLGLGHJIIFDICHKFBJGGIIGHHEJ@JEKIIEIIJEJAAEIFFHHJFDDGGIJEEFICDAA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245049	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR242975.1375007	113	17	233	37	70M1I29M	*	0	0	AAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTT	<AFG@H<BIFHKGHIHGKJLHCEGGHHHKKJKJIHFHKFKAIJIIFFHHIKFJHIFIIIHJDJEIFIGIEIIHKFI>GEJEFJIJGIDCFHICEEGDCA?	X0:i:1	X1:i:0	MD:Z:99	RG:Z:ERR242975	AM:i:37	NM:i:1	SM:i:37	XT:A:U	BQ:Z:@@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242943.1259162	163	17	236	60	67M1I32M	=	565	428	GACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAA	<ADFDAIHFFFJEGHGFIHBE=ECHDHHGIGD9H6IFJHD<<GG6H2JGJHHBHG=EH:BCAHIFG>ED?HCII?>H76E;=CDG=FJHDEDIAE?AB9@	X0:i:1	X1:i:0	MD:Z:99	RG:Z:ERR242943	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D@G
+ERR245049.65948	113	17	237	37	66M1I33M	*	0	0	ACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAA	?F@>HAHHFDBGGIGAIDCGFHJFKBDHHIHAMKGEGGDHIEEEHGJHJJHEHHGFJEJFHAGHJ@HIJJFIAJEJEEGJHHIEFGHHDFEIFCEBBA@?	X0:i:1	X1:i:0	MD:Z:99	RG:Z:ERR245049	AM:i:37	NM:i:1	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@DFFG
+ERR162875.9416595	83	17	239	60	64M1I35M	=	23	-314	ACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAAC	0?FGAHFHI?IKEHLFCK?DLH/?EBLIJEHKIMFKJLLHDFLJGJGLGHLFGKCHLILHIHJGHKBKJJCKGHHGGKJHJDEHIKGGGIFDEEDDCCFB	X0:i:1	X1:i:0	MD:Z:99	RG:Z:ERR162875	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.21706338	147	17	246	29	100M	=	1	-344	TGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCT	BB7EHGIKJJIJGFIIKFMKGIKKIILJBLKLEJ9IMMKKKJFLJGKKIHDLGMLHIMKMILEJILDGLLMKHIIKMMIJHLIDHJH>GHHKHIJFGEEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243047.1018873	99	17	254	60	49M1I50M	=	653	498	TTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGA	@=CDDGGGI@HGJEEIJGIIJGEJFHHKIKHJJGGKBDEGDJEHGIFHEFKGHIHKCGCDFFFLJGGHHIKGF@HEGFBEDFHC=DJFCEHFFHECBC:/	X0:i:1	X1:i:0	MD:Z:99	RG:Z:ERR243047	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243055.2002258	1187	17	254	29	49M1I50M	=	653	496	TTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGA	A>A?DDH:HD>CGDBCE<FIGEIAHHFH7:ICJF=@FF7F<A=C<C<<F:B7G>>65H9BGIK>JKFH<92.>J.;95FE3353+8839?/4H/.9CAE/	X0:i:1	X1:i:0	MD:Z:99	RG:Z:ERR243055	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245032.1218650	163	17	255	60	48M1I51M	=	543	387	TATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAG	?ACAFFGGFFFJDFJHHJIJIHKGGHKHHIJHHHJ7FFHGHFJHIGLEDIJIIIKBGIHGHIIJLGIFLJJEDKH@FBDHHHHJIJIHEKGHHIEACICE	X0:i:1	X1:i:0	MD:Z:99	RG:Z:ERR245032	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR243071.874302	177	17	262	37	100M	*	0	0	CCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAA	@EEIGGEEIEIGCJGJFEIFJIICKHGLG?GJ3JEI<HEHGJEKAJ=HDIEEJJJHGDFEIJDGFJDHHEDE?@EIEGIHGJJFHH@FGHHGHEFG@E@?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243071	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BD
+ERR242983.1848957	113	17	265	37	100M	*	0	0	AGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAAT	<DD61@@;+HGII<FJDGCFJGECDFF;JDEBJDKHICJE3HIBEFIGEFH=BHFFF<GFB<JECDDEGAA@J;=HGGGIGBEB@FIHHID?HGGCA@D?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242983	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243039.1049231	83	17	269	29	100M	=	1	-367	CCTCTCCAGAAAGGCTGCATGGTTGACACACAGTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATA	8GCGDDGHIEFJEJHHJKIIGKFBJGKFJFLGJFJHLHJBJFIEGGJKIJFHGHKEHFGGHGEEFEFDLFIKFGKKGBGEIIHGGIGIJHHDDDEEEDA?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243039	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.9601178	147	17	279	29	100M	=	1	-377	AAGGCTGCATGGTTGACACACAGTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTT	=GEEGHJFJIJIJIF9JGKGLJJELDLJJAKHLHIMKMHMHIILMIHJKHIHHHGIGCLJKLIIKKIKIIJI:JKKJKLKKGFEHHIHFFGHG>FEGDCB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@I@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.6409758	163	17	293	60	100M	=	651	457	GACACACAGTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCAT	ECFGFHHHKFJJKLKJBIIKJ<LKKCKJHLILJILHIFJIJJIIJLELIHDLCLC>CHKILFM>HHNKJF??I<AIG@LLFJC9IGDHLHCEHFFE:E=:	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.23732910	83	17	299	60	100M	=	25	-373	AGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGATGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTA	E?EFGGJH?>IHKHHLJNIEHHJJMFJILBIHHIEHIHMJJLJHEMCJIJJHLLIGJKLJLHHHJFKIIJILIHIHLJFHEKIHH?JGGGHIFEGCBCCA	X0:i:1	X1:i:0	MD:Z:0C0A0G0T52G43	RG:Z:ERR162875	AM:i:25	NM:i:5	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:d^de@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR162875.15521446	83	17	314	60	100M	=	41	-372	AGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCA	EEEEGEFHLKHCJLDIDHHBIGHMJDMIGJLIJJJAELMLKKLMMKIGHGFKHHJGMJLHIKJIJLLDIHHLHIIGLIIIHEHGGGFEGGGFHIHDDEGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.24509474	99	17	325	60	100M	=	581	355	ATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATA	BDEEFDEEFGGFHKKJKGKKKKIGHHKJMJLBKJLJJHJHKHIJIKMLJJIMIIHJKIHHIMHIJMJIGJGHBHJHIJFLIKHJLFDKIJKIIFCCDBEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR162875.16695705	163	17	332	60	100M	=	647	414	AAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGG	79@(D+JGDCD7@KI&%=/HGC/BBA9<7>JH:1HI9=FFJI:;0,6H5D)A6I<F4LFD:CF@4G443HBBB:J4FD1=LFFBC?>HH29EBAAB@DC(	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.20277196	83	17	339	29	108M	=	97	-349	CCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCA	4AB@(8G1B?AFFFHJ>HGJJHH@HJHIGIHNIHHHLHKLHJKJIIJLKKGJHIHKKJIIIIHKKHKKIIKKLIGKKJIGHHHGHHGHHHJJFIIGFIFFGIHFFDA@	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.8214205	99	17	346	60	108M	=	676	437	GGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAA	@BCCFGIGIGHHIHJIJJGHKGHGJKJKGHIHHIJLIHHGLIIIJLHIHIIIIKFKIIIIJLHLIIKKHIKKKHILKHHJHHGKLMJHGGHEGDIGIHFEHCHDDFCB	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@HHH
+ERR243007.996298	1187	17	357	60	100M	=	683	425	CAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATG	BDGEEFFFIFGEHKIKFHEKHEJIIAFFJIHDJIGFDHAFFEHHIIHJHJHHJDFIFFJIHHHFHHEEGJEJHIHGGDEHFFHHKHIKHHHIFIEGE?DD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243027.1412318	163	17	357	60	100M	=	683	425	CAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATG	ADGEFFGFJHHEGJIIHGEJFEIIJEFDIIEGIIIGEGEFEEJHGHFJFJFHHFEKHHIFJHGGEJGDIIFHIMHGGFEGIFHHKIHMJGJFFGDFDEBD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243027	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.23475567	163	17	362	60	100M	=	503	240	AATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGT	B?DHGBAHGGDGCHGFEIIEIEIFLGH=7G<G=IJIJ=JHJDBI<IDK=>:DACIIJJ>AJGB<GE>BAAD5JA8E=F<EA?:3=FLGA491H,F@F8CA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.25967365	147	17	372	60	108M	=	105	-374	CATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTA	;C@D3B>(CEBDFBB>CEDGDGEC1CDB=DAFCFEFHJACEFF<CCDE@@IADE@CCD=@E-@G@CBCFHDHHC@CAGE@@9D@;BAF>F>@ACCACG=BCDBBBC@9	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.11659627	163	17	375	60	108M	=	645	360	AGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTTATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGA	:FD@CDEABEEHCCHIHGGGDDDGJJJHEIGIJGJEE/HIJMKJIIKKIILIIHKKMGFEJJFIHKMLLMLKHHINKLLLIHKJGKGJFFAJCH1GFBFBHGD>BDB;	X0:i:1	X1:i:0	MD:Z:37C70	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.7259970	163	17	378	60	108M	=	660	377	TGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAG	:DEE??CCGBCGHGGFGDDDGJJJHEIHIJGJEEIIIJLKJIHKKIIKIIHKKMDGFIJFJIJMKJMLJHJJMKHJLJHKKGJGIIIGJGDDGF>JFDHE?BCECEEE	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ABE
+ERR162875.10099033	83	17	384	60	100M	=	87	-396	ACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAG	6BD0@6?BH;6BCHFE>6JJHHAEMJBALKIM18KBCHJB?IFIMJLBDKIHBFDGGEFJIIDIJHKFHAIJKKBHFJJGCHHFF>HGCDEEGED>DFGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR156632.5355545	99	17	398	60	100M	=	640	341	AAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGAC	C@C=FFJGGHHKGGLGHIJKJIHDJIIHIJJLNLHHHDFHIJDMFJLGMILHKGJKHILIJGJHLFJJJIJHLGIMMIHGGHLIKKHNJMIGFHIGEFBA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:D@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.15901000	83	17	399	60	100M	=	175	-323	AAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACA	CBD7GGIKHKHH@KJJLJHJHFHJHHKJHMKLKJHJHIJIMLMHKLLLNGJKJIHJJKLIHKJLKHMGIILIIIIKLIIIKHJJJJJJHFEGFGDHFFGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:HGF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245053.675620	83	17	408	60	100M	=	213	-294	CTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCAC	FCEDHFEGGJGEEGEGFIFBKHFJIIGICEDJKKFHKKGLBJKGFDGEJKGHHGIKEHFEFGH:HIHKEGEIJKJJJJIJFEHGJGHIFIGEFGGECGCA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245053	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.15069550	99	17	412	60	100M	=	742	429	CATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAA	AEEGDEFFAFCEEDH5HGHHDG>HIG7IJBCDBC?HI>F<@GJFAED@MGJI<FHG2?EEHIBF4GCHNJEG2GG?BAH68<=C;J=;?HJ?EDFFF?AC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CH
+ERR013140.10132183	147	17	413	60	108M	=	182	-338	ATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTT	CEECDEECDFFEFEFEHFGHHHIHIIKJJFLKLGMILHFFFHKKKGHIJLKJKFFFKHKJKKJIKGKKJJJJIFIEEHIIEJIFIHGGHFIKHDEDEBBBABFEDBE:	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.19371403	147	17	413	60	100M	=	64	-448	ATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAA	?EGFHGGGIFHHIJILJLJH@IJEJIMLMELLLIKIMMIHHKKMLGKJKLKJLIIKKKJBKLLIJJMLLLLLLMLIHKILIKKIJHHIHIHHJGJFHD@E	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@FEL
+ERR162872.10929052	83	17	429	60	100M	=	69	-459	TGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAG	CF?BEF,?H@LJKHGJLEJCKJ@<GIIKLJJHEKLFMHIHKJJIKKJIJHEJLKILHKLGGGJLELL>LIHHII?JKHKHJGGGFGEJFGGGIGDEFGHB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.7627281	99	17	434	60	100M	=	618	283	TATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTC	BCCDDEFIGGJIGIJHIFIIBGKGIGKILIIHIGJJMHIKIKIHHIMGJLJKCMGDIJLIIMIKGKIJJIMBIKJIJIHIIJILKKHK@IDGIGIGH?=D	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.15927236	99	17	441	60	108M	=	653	319	GAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAA	@CEDGIEJFGIIIIFHIJGHHHIKGGGGJIHHIJJLHHHIJKJLJLJLJKIJLKJLHLIIIJJKJLHKHKIHGJEGJJGFJLIEIKKFFJFGFIGC;HHEHACF@BB=	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@AC@
+ERR162872.257723	163	17	452	60	100M	=	628	275	AAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTG	DAEFIIFGKHKIIJJIEGMJILKKIFIHNCJLHMJMHHJILJILJJHIEJKHMKJJILJIEEEEKLFIFKJGIMKJLLLIIKLJJKDFLEIJHC>FEEC>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:IFG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242971.1689116	163	17	452	60	99M1S	=	861	508	AAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCAGTGCAGCTTTCTACCATCACCAAAACTTC	:>9A>6CGE::3ADE?G>ECBHGA12.AKC;I;?C>;D6;+F8JFBH.C<=2F@H.AF)G7H@,*9I;$9000F>9;3;4)D@E8(?8?:EDD?;B*C%/	X0:i:1	X1:i:0	XC:i:99	MD:Z:71T24A2	RG:Z:ERR242971	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@PNLT@W@@
+ERR156632.4899095	99	17	457	60	100M	=	835	477	CATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAAC	DEDGFJIHHGIIILEGJJJJHHHLKILHLGLGIJHHJILJJJGJJKHLJKKIJJKIHJKMMMHILJIELLIOLLFIKLFJLGHLJJKJHJFGFDIHFCD=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242943.1830749	163	17	457	60	100M	=	890	532	CATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAAC	ABCBGIFCFFFHHJEDIGGBFDELIBF>J0IGGHGJFI==GCCABKBKHIGHLG?H?BH@HJ;?JGH;IIGLJIGDJI>HFIAEHEGEFEFGF>EFCDC<	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242943	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.29762488	163	17	466	60	108M	=	716	350	AAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAA	9@>:?A=BAA??7@AGBABCCBD?H@?EA@B;EDADE<E:EBDAC@@?AB=??=<?D@;ACFF;DA98EA>EABEFG:GAB>>::?>><@@HDDCIEGD:A)BD<>C<	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242979.1294369	163	17	468	60	100M	=	781	412	AAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCC	?AGDCGFGEDCBIGFIFJGJEHCGIGCHFFDEADIEGHHGFJHGGGGGJJHFFJGGAJHHKJJEGKCBGIHHKGHJFBIEEEFGJGHFIFFHFCFE6<FD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242979	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@HI
+ERR162872.26172147	99	17	478	60	100M	=	569	190	TAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGG	BCG>EG9GGICC@;HHILIHIICFEKJ<9JI9I<3J7I=EKBDF?A2FHIK2BFFJJ<F2CHFIGJJCGJJF;83HC/KE?II9IH0>D(J5E@F697?@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AE
+ERR243011.373069	83	17	483	60	100M	=	18	-564	GAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAAC	<8BFHA>DFDHIC:H;D?BHHGDAH:JAH>FDHHEHHFJGHIIIAJJGFGMCB;JFGI2HHFFFAECG9H9ECIEEEHEJBAIEGJDEIDEIFFCBEAB?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243011	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@BB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.18011293	163	17	488	60	100M	=	748	359	AAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATC	EAEFIHHKHIIHIIKHKLJJKJJJIJJKHLLHILJIIMLIMKMGILNJJKJJMIKMIHKIHJILLJKGJJJJKJJJIEKLLMHLGAJKLEJEHHHHGFDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:D@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.8507187	99	17	498	60	100M	=	764	365	ATATGTCCACACAAATACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGCAGTCATCAACAACAAGC	B>8C1E0+B,;BG5<-+);K0<GK7HHF6FH+GIG-J3I4?H5+BI+A1>EI@AI,(HEI2C2+J+F<)9KL1DDHG-=#2F1G)E:9HA?DICAGDE)B	X0:i:1	X1:i:0	MD:Z:15A66A1C13A1	RG:Z:ERR162872	AM:i:37	NM:i:4	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.23475567	83	17	503	60	100M	=	362	-240	TCCACACAACATCCTGTTCATTGCAGCTTTCTGCCATCACCAAAAAGTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTG	C.=7?7F7C.A1<83<H28JJ498@C6CJI9+).:8@9H&/:JI(:5>K9D299HH?@CM12C=<E35;5<G7B4BAG0<5HB7;GGDFF>B6>DDEECA	X0:i:1	X1:i:0	MD:Z:9A1A20A13T53	RG:Z:ERR162875	AM:i:37	NM:i:4	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR162875.21460873	99	17	505	60	100M	=	796	390	CACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGACCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGT	5E;:AD>BEF-7IJEF;6HBE3,IJGAG/J7I)GDKHF7B2;J;H2DICH1BBE(?>*4BB*@>L2>H<FL8725G@DK,EJ5A12G('HH015AH=E3E	X0:i:1	X1:i:0	MD:Z:61C38	RG:Z:ERR162875	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR245034.1618692	83	17	510	60	100M	=	124	-485	AAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACC	9B@ABDHEEGGIGFFHKIJL=HHLGFHIGGKFHIEGEGFIFKIGCFJCHIFCJBBIFEIHHHFEJHHIHKFDMFJGEIGGJFFJEBEJFHGFEFGCCE?@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245034	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AE
+ERR245028.442278	1123	17	517	60	100M	=	913	495	TGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAC	?=FAC,EA,DGB-HG=HH0H;20F5<:F>G,,G*2:/87<F7.*0C<,4JA<JF/>+8@21''.FDJ/AH;=*-C+6B*B70=IFD=D>E759'85?5<)	X0:i:1	X1:i:0	MD:Z:99A0	RG:Z:ERR245028	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245045.954816	163	17	517	60	100M	=	913	495	TGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAA	>FDAFFCCGHGJGJEFIHEHHHGIFGIEHHHFGCILHHGJGGHIEGIDAHHIIEJFGGIKIJIFEHGFFGKGGEHIHH?FKHDEFHIFGCDGEHFFEEEC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245045	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR162872.2317332	163	17	518	60	100M	=	701	282	GTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAAT	DDCDGGGJJILJKHHJLGIKHJKJILKJJJJJGILJJJJIGJKJHJHDLKLJHLJCJKKIIKFKJLJHHKKJGJIGIHIKLHLFJJIHEDGBJGHFEFBB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245038.1576181	99	17	519	60	100M	=	949	529	TTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATG	?@ECECHHFJHHFEIHDIHFFJGIGGGGGGGFGHGHGHEHJJGGFIAIHFKFLHHJIJCHFG7IJKGGJGGIHIHHH@EGDKEGG;ADFHEGDEEEDDCF	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H
+ERR156632.15310883	83	17	519	60	100M	=	201	-417	TTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATG	BGFEFHHIJKMAJJLJIJLIJIGJLGHHIIHJLJDHILHHKJHMGEILJMKIKFHMJ=LLLGFLJMIIHHHKHHLHHHIJJHJJJJGHGIIJGIFIEDCD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR245032.1218650	83	17	543	60	100M	=	255	-387	CAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGG	EDBCBEFFKKFGFIFEGJEJFBLIILGIHDEJHIIHJFGLGJHIJGFLGFJEFFLFIKHEHIGFFGIKEJEJEHGGIEIKDGJFLIEIJIDFIDDEDFBA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245032	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.753594	147	17	555	60	100M	=	95	-559	ACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTG	BE;A?IEHEAIIILADGFGAHGFIKFEIIIHHLFFJFDHEDDKGEIHIDHHEHIIHEIEIGGCHIFHI?EIGLHEJIJEFJFCEFIIJEHIECEIFEGC@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR242939.81544	147	17	565	60	100M	=	152	-512	GCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCTCTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAA	+./6&=F=9A-0H1)GD:@:C<C3E/B=<<?==4GB<%E6+;>(AD-ID=?/>7C)>0@B@(I7/HGH?46GBE8G9C-<H@95A*EJB30@DB4:1E04	X0:i:1	X1:i:0	MD:Z:61A38	RG:Z:ERR242939	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242943.1259162	83	17	565	60	100M	=	236	-428	GCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAA	'/8BD2889IEB22FADF=99D9AE>DBIGC<@IFDE49DG.B;BJC??JEDHCCF=<EGEDL@;IGHDC>FDDDG9E3AIAD4IEG;FDCCDAEEEH??	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242943	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.26172147	147	17	569	60	100M	=	478	-190	TTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGA	(7=C87CDG?6BAFIH8JDGBLHJBHA;JE@2>;I/AI=0=LEMEMI;KDD7;E3'=I;?B<7GHI7HEE7L4K65GHGJH/BLFDJHHIIIHJDC;E<A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.14588577	99	17	571	60	108M	=	807	343	CAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATC	@CEBIGHHHIIFJIJFIJJFKJGJJJGKHIFIJDIIHGFLKGJHIHFKJJIIFELLFIFIEIII@LHHKHGGKFGIBICIECIF?FFEHBFEIA=JGHBIDECCDCCD	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR156632.3225464	99	17	579	60	100M	=	749	269	GAACTCATCAACAACGAACTTGTGGTTTACCCACACAATGGAAGTCCACTTAGCAACAAAATGGACGTAACTCCTGGTACATGCAACTGACAGATGAATC	=C?>F2H+8@IHIE@%/FEKGLFI8@?CHA6JIH?IBAFF@MF20L4IDBGHBDJIIJJB%)%>G@#/IGGJIHJL?8GJAGK6GJJJJG;HHEAHGCBD	X0:i:1	X1:i:0	MD:Z:15A28A16A4C0A32	RG:Z:ERR156632	AM:i:25	NM:i:5	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR162872.24509474	147	17	581	60	100M	=	325	-355	ACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTC	DGFGCGJGHMHHKHHHMJKKEKJDJIDJKNJLIKIIKLLIKMGLMJMAJMKLHJLKGJHMKMILLHIIMJKNILJJIKJKLLHIKJLHKKKHHJFFFHCE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245024.739014	163	17	584	29	20M1D80M	=	935	450	CATCAACAACAAACTTGTGGTTACCCACACAATGGAAAACCACCTAGCAAAAAAAAGGACCCAAATCCTGGTACATGCAACTGACAGATGAATCTCAAAC	?CCEEDGGGHFG2>H/C6J8EE<:HH080=2G03I.G,,;E0()I(0&:H,,IJDJ0J.-H)G@*./I0>I;D6;/0*/G8;09+.<-./7I9...8DD9	MD:Z:20^T17G5T6C10A2C35	RG:Z:ERR245024	AM:i:29	NM:i:6	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@I@d_@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242959.1635151	99	17	588	60	100M	=	998	509	AACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCGGGTACATGCAACTGACAGATGAATCTCAAACGCT	@?EBE@G?DHCBA>E:;FBFGD=@ECHEE=@6:72GIGEIIA;EJE8FHH5F6K6:AHGA??EK5(:D0BCEFG2IIHI9?G7E5GHAAAA8EFC3><1(	X0:i:1	X1:i:0	MD:Z:65T33A0	RG:Z:ERR242959	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.14628028	163	17	612	60	108M	=	865	360	CACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGG	;D@DDACFDGGHCFGDIEFHGHFDHIFIJIJEEHGJJCHEHJIHBHDGHII8HFIGI9J@IFIGKFFBHAJJF>GIAE8IF=B<JGG>:EE@G4F@@9:EAH@C;B<E	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR016352	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@J
+ERR243015.17606	163	17	618	60	100M	=	982	463	GGAAGACCACTTAGCAACAAAAAGGAACAAACTCCTGGTACATGCAACTGACAGACGAATCTCAAACGCATACCTCCGTGTGAACGTAGCCGGACTCACA	A<?BIFA6DFHE8GCGB4>F?3C<9320E-DGDJ*>EA@D<H>F8369I1:D>D/-6F,H;H0EC?,AJG?.I)=/I%=FE/C*%%1<06F)#GECD:,<	X0:i:1	X1:i:0	MD:Z:26C28T15T12A1A13	RG:Z:ERR243015	AM:i:25	NM:i:5	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.7627281	147	17	618	60	100M	=	434	-283	GGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACA	<FAGHD.J?KCEKDIFILHGIHLLKIFLIJIMKGLKMJJDKKHLLIHJGLILLJJHKJIJLHMHHICLGJJJLMHDDJIJKJHHKJHKJICJJGKGHFFE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.257723	83	17	628	60	100M	=	452	-275	TTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACA	@BFEI:DIFDEF=?HG3JF<8GBEKJAGBIEJIKK:HMHGBHGKIGLIIFACIIHCBFFDHIGKJABIJIIJGHLGHKKICJJHKHKHIIGHHHDFGFGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.5355545	147	17	640	60	100M	=	398	-341	AGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGT	FE;D:FFBBHFJIIKIJIMFELHHC>HKBLLHIHFEGJFIGHHHCIKFIDJKIIDIIGIMDHKJGDAKBLGHLJKHJEHJIJ@GHFGGJFFGIFGEGFCA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR013140.11659627	83	17	645	60	17S91M	=	375	-360	TTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGA	%5?-$)89<=;9>(.144==2@>BD@>DBCDFIGFFIIEBF@HDFFFFCABDC@BC;CFFLCJGEJ<HFCFCIILJHLJJ@KJHIKHFHKKJIHGGGGGEGFEHDEC@	X0:i:1	X1:i:0	XC:i:91	MD:Z:91	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.16695705	83	17	647	60	100M	=	332	-414	AACTCCTGGTACATTCAACTGACAGATGAATCTTAAACGCATTCCTCCGTGTGAAAGATGCCGGACTCTCAGGGCAACACACTATCTGACTGTTTCATGG	)9H1&B2571,7,%&*(88?,9C7H62,2,4A('(A/<3/-14M.>F15E*?:E2JCB(I/2)80DBH*G;K)**)-L0H<DF<FJ;;@F.F5A51C<4-	X0:i:1	X1:i:0	MD:Z:14G18C24A9A31	RG:Z:ERR162875	AM:i:37	NM:i:4	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.6409758	83	17	651	60	100M	=	293	-457	CCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAA	@B?CAFCDFB76?7JCHGKE>CC<GI3HIEC28=E86I?DKJ<<E=FJH>?IGHBGFDLC<I<IHKLKKIKFFKDFGHHHHJDEDJHHGGGIGEDCFBAB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR013140.15927236	147	17	653	60	108M	=	441	-319	TGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAAC	6:@>EDDFBE<FED9AEJEFIKHEEFFFG=FCGHDEGJHEH=FFBIHGFIKFJKM=KKGLKJGJKKKHJEIJHJBLHHJKIIEKHFJJIHGHIIGCCHDGHDDC@@C:	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243047.1018873	147	17	653	60	100M	=	254	-498	TGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGT	2D;@@HED1I:CJC?EAGHE:7A@BECJE:@AGH9>8@KBC?FEC9?FECFFHFH>HAFI@FEHFHEHIEDG@GBJDF;GEHEHFIFBFJFFFBGBAFC?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243047	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243055.2002258	1107	17	653	29	98M2S	=	254	-496	TGGTACATGCATCTTACAGATGAATCTCAATCGCATGCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTATATCATGGGAAACT	A)+5C7EF18?'9C,8H-<-GD2-59+EDG,;HI9GC0K,1)5F789A3.-4.)(4<,?=,GFIHI**<*4>EF2E2CF>0.4GE0)>E@110EGCBCD?	MD:Z:11A2G15A5T48G1T10	RG:Z:ERR243055	AM:i:29	NM:i:6	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D@@
+ERR013140.7259970	83	17	660	60	12S96M	=	378	-377	ACGCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTG	40&/81&8:/<<79B<BCC=DCH@FH=DEGJGHGDI?MJFIHJGIJ@HGHGEFIIFFMJJALKHILIGILKLJIEHIHIIIHGKFJJHHJFJIJHFIIIHFFIDFCC@	X0:i:1	X1:i:0	XC:i:96	MD:Z:96	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR156632.18988851	99	17	667	60	100M	=	822	254	GACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAAC	=EEFIFGGAHGJKKGIHJCKII@LEHMLAGH@MIIIK>IILCEL:JKLIKGELFHIKJJJFJFJJLEMGIJLHHGOBGLL?CIJM;KLJEHGFGAFGCDB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.8214205	147	17	676	60	108M	=	346	-437	ATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAA	:;A>;:9685?>@CCECD;@D@H@EDI>CGLJCLFFMIKFKHIKKFHJKCKFMDFHMJJFLJHGKGJIJJKJEEJGJLIJIEEHAJIIDHHEKHFIGGGFEDDC@@?:	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.996298	1107	17	683	60	100M	=	357	-425	ACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAA	?>CE?D@HJF:?>EIFFFGGHEIKFBIKGJHJEJIJIHJFFJEIFKEGIJGJBJGIHJGJGGIHHEEIIFIGHIEGF@IIIFEIEGHGFGIGHDGFEA@?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CEE
+ERR243027.1412318	83	17	683	60	100M	=	357	-425	ACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAA	A7?E@DEIIEJ@GGIDFFEHJGJJHCJKGMIHGKHHIIJHFIFJFJGIFHEJEJIHICDIHGGBHGFIIFIFHHFFD@IHHAFIEEIGFFHHIDHGEA@?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243027	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CEE
+ERR013140.3773682	99	17	697	29	108M	=	1064	389	GTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGG	@ACFHHGIHGCJ?HJFKJJFKFDBIHJEHCEBHHHCHEFAJDF>DFFGFDEB?ADDBEEAFD@;;DDG@8A>:CB=DDBB:CCD@>D?HA42A>?8?/%3@,(=<986	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:29	NM:i:0	SM:i:29	MQ:i:22	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.2317332	83	17	701	60	100M	=	518	-282	AAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCT	CGD8BHH@AGFKCKHKLIKKG>ILFLJJIGGJILJJIJJIILHIL:LIEMJIIECKGHGCJGLIHMHJKHHIFKJDJKKGHGGKKHIHIIGFGEDEF@FB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EI@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.29762488	83	17	716	60	7S101M	=	466	-350	GGACTCACAGGGCAGCACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTT	)/4/1429@99+@?%BBD<AA>D<;:;=:6?84=<7<=;?7G=?869::6?8B2<?177;;;=:>C;==>0:841>.,5C0?7DB4@@2@FGCBBC5AFCHGAC?BC<	X0:i:1	X1:i:0	XC:i:101	MD:Z:7A93	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR013140.11567710	163	17	728	60	108M	=	984	356	CTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTAT	:DCCCDDFCGGGCCHHGHKKDJJKFIJIHJKJG=FJIKGJGKJIEKKLKHJMHLHGCGIH?GFF<FFB=GFFIFFIHJ>BHDD7BAF>?BHFHFD>D66>7<CF@F??	X0:i:1	X1:i:0	MD:Z:100T5G1	RG:Z:ERR013140	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@SPP
+ERR162872.20029780	1123	17	736	60	100M	=	981	342	CTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGATGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTAT	BHG?C8=:GI<(2D)CGJKJ9GHG6D0*G@4.*4I9G9I:I>+AECC)CB?.BAB98G<(A9DMHDJI/&F@D&/H(861<:G6..2/39681K36EH2:	X0:i:1	X1:i:0	MD:Z:59T32T5G1	RG:Z:ERR162872	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@I@@
+ERR162875.14341769	99	17	736	60	100M	=	979	342	CTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTAT	BGHFCDGGEIGHGHCJGJJKGHDJFCILHIJJJKHJELJLHKIJGGKKJJLI9LHJILJHHLHKLLGLIKJGLJJ2<GKAEFM@IJLDJHHHHIHEGHC@	X0:i:1	X1:i:0	MD:Z:92T5G1	RG:Z:ERR162875	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@KLKHJYWT
+ERR162875.15069550	147	17	742	60	100M	=	412	-429	CATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGAT	BED9A@A>JJH9@D?GHGEKKLHGJGIKJIKKIL;JLJH44ILGI@KHJIJKII8CKMGJBHGAKLIIJ?HLCIILGDKKHIHIEHDIKGKHFHHDFDBD	X0:i:1	X1:i:0	MD:Z:86T5G7	RG:Z:ERR162875	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR162875.20069376	99	17	747	60	100M	=	975	327	GAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGG	ADCDHGGHIHGGHHCGIHHHIIKGHGLJLIJHMIIJIJJLMILFMILLHGLKJLKNKMIKJLKJJJJMJGJLKLJJHMHJFJKJGMKFJLGHJGGEHHFC	X0:i:1	X1:i:0	MD:Z:81T5G12	RG:Z:ERR162875	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AB
+ERR162872.18011293	83	17	748	60	100M	=	488	-359	AAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGT	:BDFDI?JEG77D?LLH8KFJGJFHKKLIILIGIJIKCGFILLJCKJGDEIMFMLEKILKIHKIHLJIIMFKLKJIJIGHKILIKGGHGGGHGEEGEDDB	X0:i:1	X1:i:0	MD:Z:80T5G13	RG:Z:ERR162872	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.3225464	147	17	749	60	100M	=	579	-269	AAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGATTCTGGTG	=DD1HEG%@;?7HH28GFCGLD>GDDCCECKDHGGBLAJHEHDJC63AK.BHK<?LJGDIKAH=;IBII?G37:9<D;>FHGIIHH<<7FCE=FE?BDFA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@F@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR243083.371418	163	17	750	60	100M	=	1106	455	AGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGATTCTGGTGG	?EEFEGCF@EG@<CHFEGDFFDDIFJ>FFIFGH<GFHH=JEJ1KGEEIDFHCHEDEIGJFEGHEGDFJHKBHKFHGD@CEDJHII;CC?GF9BH?H;BGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243083	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BA
+ERR162872.8507187	147	17	764	60	100M	=	498	-365	AACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTG	9BE:FI?CALKLFDLC?EH7<?;DJLJJFJJ?H=7MIHLFK?:GGJ8EHMI6JKJJ66G5HI2HK*K7<9IDICJFI0=4FKGIKGHKHDGHJDJ@FE>D	X0:i:1	X1:i:0	MD:Z:64T5G29	RG:Z:ERR162872	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242979.1294369	83	17	781	60	100M	=	468	-412	AAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATA	BB<EDFGGIHHGMIIHJJJIJJJHIJIIJJG>FHIIJHKIHJGJFDDIFMGJEGIJGHLGHFKGGIHGIGHKEFFHGILEJGIGHCJHHFJGGGGFGCA@	X0:i:1	X1:i:0	MD:Z:47T5G46	RG:Z:ERR242979	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.21460873	147	17	796	60	100M	=	505	-390	TGCCTGGGACCAGGCAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATC	E0:ID<=A,5AF/F/H0BEE3LJ&:1EA*G4<:FKAJBC8@CJHH4ICD@,EJ9F4CIHFLH=LEM;AHBJIEKIMGDHDJDGFIJK1CDGCHH/HIEA=	X0:i:1	X1:i:0	MD:Z:8G5G17T5G61	RG:Z:ERR162875	AM:i:37	NM:i:4	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.14588577	147	17	807	60	108M	=	571	-343	AGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAA	<AC79>BCCDGIKFF?HGEFAGGGKLJFJHLLHEIGFDFHHHIIKDGGEKDKKFMHHFFMJKKMLJKKGIJIHIJJJAIJIILLKIGIKIKGDKHCCCBBDEB?@@?:	X0:i:1	X1:i:0	MD:Z:21T5G80	RG:Z:ERR013140	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.18988851	147	17	822	60	100M	=	667	-254	GTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTG	?CD@E?GAJILHIIIJHEJJH:FKKIACJGIHHFKGLLGMIKJKHHKLJLFJKJIKDICKIKDJKKGJJKKIHFFIGEKJFGFEFGHHEFDDFEEGFGF?	X0:i:1	X1:i:0	MD:Z:6T5G87	RG:Z:ERR156632	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR156632.4899095	147	17	835	60	100M	=	457	-477	TGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGC	2@FGIB?>JIKIJK*I9BEC=:HKLHKIJHKDFJJFLJIMIFKIHHKLKDKJKHGKLLHILILHEMKHGGIGHHHGFFEHGGJKKGJJIIFGFEGFDFDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.21635478	99	17	854	60	100M	=	1075	320	AACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTA	BBEECHEFIIFIIFHKIAKKGJ<JHGHIHLJ>HJEAKKKJHILLLCKIHHCIH@JFDJIDJJCIIMLHLJKJIKJIIHFLEGIKELKJHGKGIHGDHEF?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:DD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242971.1689116	83	17	861	60	100M	=	452	-508	CTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAG	0>?=B,..4&.9D)B=A--EG97=I;;E1&'::7/:=@-;>3+5BCGGF=HB5I6-F6GGC*+D/1EG=-.2+@/?')?0.C@>E*=A@=2?E3A@:BC>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242971	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.1140280	163	17	863	60	100M	=	1156	392	GTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTG	DEFHIHJIIJJIIIKHIHIJMKDIMIJKGKKHHMMKJHKJJJHIIJGHJJKGICJMLLLCELJJMKFMIIJHIIJELLLFIEGKJMJMHKDGDHFCFCBD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.14628028	83	17	865	60	108M	=	612	-360	CCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGG	AB?E?D@A>>=DBGBGHFB?BHCAHEH>FIIEIFHCIHGGGGJLCEGDGIIFKBG@JJIGIHICJIFHIBIJEKJJEIKFBDKJKIJHIJJIIFJEIH@IGIGBECBA	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR016352	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR242943.1830749	83	17	890	60	100M	=	457	-532	CCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAG	B=D7EG5KCF>GEGBDDAHDFEFFF7FHIKEEEJJ=HIJHII:EDEI9E>GGBHHCLFCDIFCGAEKEIHIGCIHJGGGEGHGDGEFGHG<FHF;A@GD?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242943	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GBF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR162875.20797205	99	17	895	60	100M	=	1190	394	CTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTT	BGFGDEEFEFFGHGGGHIHIHHHKLKHKIKIDJJILKFIKHJJLKLIGHKJKKGHMLLIKHKAEJMIKMLMJL?IJLDHIIIILELFDILBJJGIAEHC=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.3985724	99	17	899	60	108M	=	1182	390	ACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAAT	@?EFHHHHHFFGIIIIGHGHIHHGHJKGIJCIHCGJKIIJLKHFIJGJILIJJIJIEIIDHHFJJIHFEBHIHJHFNKGGIJAFJHH:HIECCE><BGAA6:DC?A<+	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245028.442278	1171	17	913	60	100M	=	517	-495	AATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGGAAGGTGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTA	>8BB/4.?'BEH9.'HHIH9LIF9@%;AH(:A-0AJ=E=7A,EIF@=;IG<0KH6@F4)H9IG-E,2:G1E;GCAFIBHAGC6FHDGHGGF=CCDE,@A?	X0:i:1	X1:i:0	MD:Z:63A36	RG:Z:ERR245028	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245045.954816	83	17	913	60	100M	=	517	-495	AATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTA	AD>CGHAFFIKGIFIFHGJHIJAIIHJIGDHIGGJK=JDECHGIGKJHIILHKBIJFGIJEIFH>EK<HIKIGHKGGJJIHFIFIIIKFHIEFGIGCGAA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245045	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:DF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245024.739014	83	17	935	29	100M	=	584	-450	ATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGG	@CFBHGGEGFGGIJINMEHGFJEJLHHJJGJEJJIIILFIMHIIKGGKJJHGJIHKGJIGHEJIJKGIHHGGJHHKGGHJGHGIAHGIFKFGHEIFEFBA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245024	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245038.1576181	147	17	949	60	100M	=	519	-529	AGCTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAG	BFGBDAFGEHHHIKJIIIHIEEGJGIAHGKJ=JIHKIGKJFJHHHFJAHHIMHHJFGHJCFIFHGIGFII?HHJ@LGIFFMEGFHIGJGGIFHDEIHFEA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.17780862	99	17	951	60	100M	=	1308	456	CTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCA	BH8F9F;DEEHIF<:4IJGD@175:F9;6E20IF>)=BI>)A8FAI1F@K@9FI1A>J9CC3@@2@E8CB)GGILA>+DK0BE-@8J<:I*97CCGD70D	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR162875.20069376	147	17	975	60	100M	=	747	-327	GATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAA	BEGHGFHLLJKFLLMKLKIJLHLLLKIKJDIJMLLMIJJLIJJLDJKMHLKKKIMKIHKLKMKMMILIGMKKKKLIFHFLJKJJILJLHGGGGFFIHDAE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@FFK
+ERR162875.14341769	147	17	979	60	100M	=	736	-342	CTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAA	DDFHJHH>JKKKIKJJLGMKKKJIMGIIKMLLJIKJJJJLAJKIIMKMJBKJIKHKKMIDLIJJJLLLJLKGGHIJJMAJILJLHHHHGFGKIFFFIFAD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CI
+ERR162872.20029780	1171	17	981	60	2S98M	=	736	-342	CGTGAGCCGAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAA	%2,G.I.6,B6H8@)):=8I3>F*0AAD6B?:=86/.BG5?5=L>DG6L=<64JJ6II-;;>FI>I>EE7DD58C5CM?IDFCL@HDHGFGECFFEHD@E	X0:i:1	X1:i:0	XC:i:98	MD:Z:6C91	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BJ
+ERR243015.17606	83	17	982	60	100M	=	618	-463	GAGCACAGGAGTTAAAGGCTGTAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAACCCCTGTCTCTAAAAAAAGAAAAGAAAAG	:B@:.D9EBI53,(1:E3;E?74</-**.B.08A=13)JIF-00HJDJGHF36/01);>>*3+E=>B>B*-(@1*1H/1?GE+++0+,33:0C-,=BA9:	X0:i:1	X1:i:0	MD:Z:4C8C7C49A28	RG:Z:ERR243015	AM:i:25	NM:i:4	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.11567710	83	17	984	60	7S101M	=	728	-356	TGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAA	/36>+5/+ABDF7EF9=DF>D;=C@9CCEIHGHGEBHCDFDH=?BE=A@AF=AGD@F;C>FJBDEFGHFEHFCBCCAFLHH@EJGEDEHGHGGEIGGFG8CBBI?=>?	X0:i:1	X1:i:0	XC:i:101	MD:Z:101	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CF
+ERR242959.1635151	147	17	998	60	100M	=	588	-509	GGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATA	6*?DFC8@>7.4ED9-DH=DB9)/I1:C6HC0BG:478)I8C=GDF1B/G*<F6A-H@.::-?9>-GFC8+8H>9+D?I:8F2*,:D<?IFI.GA<AD;@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242959	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245041.487129	99	17	1004	60	100M	=	1368	463	AATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATG	?BCGEGHGDEHEGCIG@IHEHHJDHIHGFIHJGGIGFIEHIGJFJGGHBGIHHJHEJJLHFCJGGHBLGI;GKEHIGIFHFF?DGIFHHIGDEDEG8EAC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245041	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.11973614	163	17	1020	60	100M	=	1163	242	GCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATC	BDCFDFGEGGIDDJIIKJJGE<JHEILIGHIFIF@KKDHHJJCDHIHIHIJLHIJCLGKIFJHJFE3/IKCJKJLBI@DLGKHJJCHFFLE>GIHDAFCC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR162872.1587020	163	17	1024	60	100M	=	1273	348	CTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATT	EEGHGHJFGKIJKLLJIJIIJIMJNLKJKJJNMKLIJMMKHJKLLIJMKIJKMKJKJOIIKKGKLLKKLMMJGJJLJHILJIJJJLKHHKKLHGGHFCDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.9494189	163	17	1031	60	100M	=	1277	345	TTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATNCATTATCTGAA	BAFDFFHIFGGFHHGHHKHIHJGHKKJKIIKKLHIIIIIHNIJGILJIHKMIJIJJJLLILJLKKJIILJJIJJIIJGMCHHLELKIF!IHGGEGFED-E	X0:i:1	X1:i:0	MD:Z:88C11	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:DC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@J
+ERR242943.1490060	99	17	1031	60	100M	=	1433	501	TTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAA	?@G@FBGH>>DAFDEI>KGFDBBB97DH?=CIGE@FDED+K@776KDDEGGFGCIF7HDG7<C/F8?BDGI?;H<6@FKHF3F6K5>>JDFCBE@=CGBB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242943	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@DG
+ERR245038.1101322	1187	17	1055	60	100M	=	1338	382	CCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAAT	@AGIEGIIGEGDGGGGKGFFHJGEIGGFHHGIGIIGEHHFGHEGKGFFKGGDHHKHEEJIJJGFJHHJDEIIJJFHHGKBIFJGHFJCJAEIEEDCCCCB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR245049.1671108	163	17	1055	60	100M	=	1338	382	CCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAAT	A@FHEHHIHDGGGGGHJEGHGKGHHHHGHHHHJJJGJIJJFHEHJGHFJEHFJHJHE@JGKGHGIGIHEGFHIJFHHCIJJFHGHHHGKFEHCDCDGCDB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245049	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR013140.3773682	147	17	1064	22	85S23M	=	697	-389	GAGCCCCGCTGAGCGCAGAGGTCGGCGCTGCATGGAGTGGTCCCCCCCCCCCCCGTGTTGGGAACGAAAAAAAAAAAAAACCCCCAAAAAAAAAAAAAAAAAAAAAAA	%3%$$$3(+8$$$-&7526&%4=$''%+7.2*,"&1%,/1#$$###$##%%%$$%1$+%$"%$/'##########$$$$$$$$##$#$$&$67%%$$$#$#$#$$6*/	XC:i:35	MD:Z:7G4G4G5	RG:Z:ERR013140	AM:i:29	NM:i:3	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CBCCECUVDDCCCBCBCBCCUIN
+ERR243091.615703	99	17	1066	60	100M	=	1497	530	AAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTT	?BB@CHEE@EICFGGJGGHFGGGKGIFJHDGEGIDHFIFGEDDJFBFGBHICDKGIGFEIJHIEHEFKGGEJHFIHHLHHJC?CEJF<GDDFHH;EB:B@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243091	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GJIEE@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GG@JI
+ERR162875.21635478	147	17	1075	60	100M	=	854	-320	AGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTT	GFCAFHFGHHDHMGLGIHKLIHG?JGKFKJJEMLLJFHLMBMJIEKJKGJKLIKIHJHGKEJLJHJJLMHIEHI@HJHIIJIHKKIEHHIHIJGGGFD@D	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AB@E
+ERR162872.18681977	99	17	1084	60	100M	=	1234	249	AAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTT	@BCDGEFFIICGHDEJFEHJICHHFLJIHKHMEHG?EHCGAHFHB<CJGMGKHLDIJJJKJJLH:GBGBBAH(ADIA<FCBDGH@IHF;H@JHF<A,FC?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EGE@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AA@
+ERR243079.816750	99	17	1096	60	100M	=	1452	455	TATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTA	@ACGFGFHFFEGGJGFDJHKJEHKBHDFDHKIKGGGFHJIFIDFJHFKGFIFFHDFHHHGFHJHGCEEHEGHFFGHGFEIEECHIIHEIJEKECG?EBCA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243079	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243083.371418	83	17	1106	60	100M	=	750	-455	ACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGC	=E@EB=EFAH@HG<HIG@FFLGJGFHHJBGEFGBHJKIIIBHGHJABGHGFH@DAHHGEGEJ<DFGEHHIDFGHJGHGJKJHFGDGGHD7BIHGFEFGC@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243083	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.4998889	163	17	1122	60	100M	=	1385	362	TTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAA	A>EEBHGFFEFCIFFF@FIHFGDGHECEGI>=>GAGKJGEGF<A=DFHBEHGFKGBJCKKDHGKGAIEAIFFGHI0INBFLEDJIHE8JGH9IHJ?=D>:	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C@@
+ERR243003.852165	163	17	1147	60	100M	=	1483	435	TTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGC	@?ACHFGFDEEIGGDFFGFFJGGDGFGFJFEGHKHFGKIHKEEGFHGFEIGHKGGJGKKHIKIJHGHIIHHDIHHIEKHG?IIHIFJGGHFGEHEEEF=A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243003	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.1880433	163	17	1154	60	108M	=	1476	392	TTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCC	:?@@CFEDBBCCCGHGGGDDDIEGJHIJEEJJILFHIBHEFHGKIMJFJJMKJIJLLKIHILKJLMLIJFLKLLLMIJKKLLHGJLLIKGGBH>JFJDFEGIGFC>CC	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@EH
+ERR162875.1140280	83	17	1156	60	100M	=	863	-392	TTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAG	AA=GGFGHEHBIHDHJI==:?G???EJI@GK?BHIJJIIGJHHHJBBKKDCFLMDB<DMHIHHHHCDHCIGBIGFICADGHHIHJGCGBH6GEHDFDCGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:DC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.11973614	83	17	1163	60	100M	=	1020	-242	TTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCC	BACGHGGFGDJHJIGJJLIAGHLIBJIIBHHIIGLBKGGMGKLEGLLNHIHK9KHIH9DJIKHHHCH7IIDHHHJKJIHGHC>@AILDCIEJJIFG<E8C	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:IHHI@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR013140.3985724	147	17	1182	60	108M	=	899	-390	TTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAAT	<D@BE;CF@?AACDBEG<>@B@0A?:BC><9=C?@DAG<@;=>CCC>AABB:@<?=EFCB?=<KBKMHEHHEJEJDJILLKJJHIIIAFIHGHEH@HEFGHECDD@B:	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@F@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.7178739	99	17	1187	60	100M	=	1434	346	GTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGG	DBEDFFFFGHEGKGHGHJKIJKHKGFIHKIJHKIKHHKKGJJIDEKIIIKGKJMKKHJ?LCLMJJFJFLJCJGKKBKHHIFGD9ECHE8BABC0.BH5G6	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@
+ERR013140.17777881	163	17	1188	60	93M15S	=	1524	397	TATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGCCATGTCGGGGCTTGGAATGTTTGG	:BCCB?@ACGFCCCFECCGCHIJIGH9GGGEGFFE>=IIIIJAECEHGF@DCAEHIF<B9+;F5=FAB?FB263:76;:>6>9),<>B9<76$*)=2?5>8:7/*+2&	X0:i:1	X1:i:0	XC:i:93	MD:Z:83T8T0	RG:Z:ERR013140	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.20797205	147	17	1190	60	100M	=	895	-394	TATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAAT	@ECFEGHKJIFHHBJJCAKKLHHGNHMHEIIJEJMIIHFJHMJEIHHKLKMHHGEHDJKMIIEELLMJJHJJMEJLLLLEJHLIIJIDJIIIKEHIHDBE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR242939.1378819	99	17	1202	60	100M	=	1582	479	CAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTT	=C6:EADGG?;FGCIGFHHGF5IG?H>GCICJD;G?DG9HHHE4@AJDCCEAGIAFD5I,6H=5JAHJ4EJCHK2DAG=JEEDK8836E@ECH///A?=*	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242939	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243035.1352953	99	17	1224	60	100M	=	1563	438	CAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCT	@D@EEFGHFIG?DGIHHHHFBAIBIFHHEFBJHHHEHIGGGEIDMBBFJGGFFEAGEMHH<HIHHBKFBG<=0CBEFFGGC?E@BFGIG<3EGB5EF>F>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243035	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.18681977	147	17	1234	60	100M	=	1084	-249	AAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTAC	0@75A@E9F:(18K.@;I@2L2E:B?DJHCEJJKL36IIIB7B?CK?*KJI+LGIJ9=JJAL?BJJGJCJGJJGHILGLJI<HGJHCIKIHDGGJG;DDE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR156632.10970255	99	17	1238	60	100M	=	1440	301	CCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCA	=<8FGEAB1CCLE>CB@AGDD<>ED?9@?DD/=>=0I>=:EA2L7;3ECK5;G=>@MKL/0A2>A89?<2>KF@>L<9;/7>I@4:5:AFD7I@5A@G6E	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR162872.9427750	163	17	1249	60	100M	=	1421	271	CAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGAT	ECDFFGKJIHHJKLLHHLLLLDIMGILHMDKHLLLEKKHIIDGIILGKJDIIEIK@JHIHIKNMMJIMKJJJDLLLJDILLMI@HKIKF>FHCAFGGHBD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR162875.5181154	163	17	1266	60	100M	=	1395	228	GAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGG	BCHHBGGFHIFJDDHJJLFJJ?DJMIHHKJGGGDGGHB9KGDBF@FKKHBJ6BI@DJJMIJC@IJIIKKLGAIKGHIHKJLIHHGGG=?GIFK8D:CA@=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@EFGE
+ERR162872.1587020	83	17	1273	60	100M	=	1024	-348	ATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCC	@EED@HGGII@IJKIJIHIHILKKIJIIIKKKHJHFILLNGJJKJLDEMMILGJLLKIJHIMJJHJIGHGIMGKIIIHHHGGGGKIHHGHIHGGGFCE>B	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR156632.9494189	83	17	1277	60	100M	=	1031	-345	CGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTA	3EDF/DGGHKHHJJEIJKMJJJJJKM/IKGKGH@LMGEJ1ML<ELCJKHILKJKJHINI=IIIIHGLMJKIIJBIHHHHIKBJJILK?LJKEEHIHHGCD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR242963.315564	163	17	1289	60	100M	=	1708	518	TGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCC	@FD>BHFG@EEEFIHEGFFEHHJKIGGJHGGI;JIJHHHIIIDEJHKJHGIEIHIHFJFGEEGGGFGIHIFE@HIDBFHGGIJHHHFDGFIFH@GECDC>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242963	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR156632.10697401	99	17	1297	29	54S46M	=	1427	229	ACCCCAAACATTCCAAGCACCGACATGACGCTCAAAGGGAATGCTTATTGGCGCGTTTGGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAA	DAFCIHHGHHFGCKHFKGIJMDIIJHKGJALCKDDILKCCEHKLLGIJGLIKEIADIHLKLJFEHFJKLLMFGIK?IGEHLE@EIBGLGFDHIHHFCD:;	MD:Z:4T41	RG:Z:ERR156632	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@NQVUYXY@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.17780862	147	17	1308	60	100M	=	951	-456	ACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTT	5EGF<FAIG?6@A1LH:H03@452F=9J><E6<)12B?GJ3*FCI?=4@IF6E:CJDM*9IH84?AI8HD@?EEI5I8EC@LGLCF4KHA<5HHGG=EAD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR013140.23901775	99	17	1316	60	108M	=	1621	379	GGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCT	@BDFD>HJHIIDJJHEAFJKJHHGHJJGKKIFGGGFEHCIEEFDEIJJJJAHFFIFLLLLILJHHK>ILKHIL?DDFGA5DA;A<C4>7:DD?CF<D>I:BAD@@B@B	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242951.1253490	99	17	1327	60	100M	=	1717	489	CCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCT	@BEFEDGGGIGFHFGGGJKJGHFFFFHGFHIJDEEKGFHJIDFEDKJIIEIJJDJAJJIIHIB@HJCJGJJBG?G=EGJGEAJKEEGHCEFH>BHCCFED	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242951	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR162875.7604876	99	17	1336	60	100M	=	1673	436	CAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTT	BECF-@EFHIIGHFGGGHHHHEMHHHKKDJIJCFCLKKKKGIJDK9AMJJAELCCJKBHIBCDFJ@IGJKKHBBIHDJKDFIK2IJFLJIGEFHDG8FB?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@@
+ERR245038.1101322	1107	17	1338	60	100M	=	1055	-382	ATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCT	DAA>CEGGHFHHGDGHBFFKFHHCI>GEHIH5HGIHKDFIBHHAH=JCII?EEHGEJIKAGHGGCEEJCEGIGEEJ:DFIEGGIJFDJHGFEEHCECDE?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245049.1671108	83	17	1338	60	100M	=	1055	-382	ATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCT	CBBB@GICHFG?E7FEGFFIHHIIIJGLIKHHHJHKKFFHJHFAKIJFIHBGJHIGIIJAIJHGEDIJHDIHGEEKGDFIEGGIIGDJFHGHEHEDCEE?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245049	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245041.487129	147	17	1368	60	100M	=	1004	-463	ATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGA	?DCEGGJCAHGHHAJHJEEHCKKHHEKIIBIINGGFDLIBJHHFGKHFFKEHHIKGJIHIHIJIGHGFKFLFIIHEGGFIIDEFGHGHGICJGHIGGEDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245041	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR162875.4511615	163	17	1375	60	100M	=	1652	376	TAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCC	EA9IHD>CAD6A>K+A=23J>5:?K+0G?17<+G;<79:F=?CCH;<6/J6KCG0JB@HH)EKIF<MEI4B5ND?G@FJI5GB7?9?JL=F@-1*9F/E<	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.20508653	163	17	1384	60	99M9S	=	1673	377	CACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCCTGGCCTGTTTGGTGAG	:CBED;GFHBEGJA@KIGDDHIICGKEEGGJEHGJHCJFHJKE>DMBDDB@EKDDGADAABECFDFDHBHBDGFEBE?DEC>@=@:GB@96#E?:42<72%9764;2(	X0:i:1	X1:i:0	XC:i:99	MD:Z:91T7	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.4998889	83	17	1385	60	100M	=	1122	-362	ACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTT	.@2AGHJG8EHJ?JJFHIC/MFGEB<A<KJI:IGJJAMJ=IDHDG;HCIIKGILBGMHBIKDK@HHJIJHCIEJGJGFGHFJHHKHIIFHHHFHEJEE?=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AB
+ERR162872.25518652	163	17	1387	60	100M	=	1632	344	CCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTG	E5?FGJ@GJKGC:HIGHKJAG=MI@=HMBJJNH=CJGDIK@<:KLEFHHKDILJK:FBBHLDCJ/IIIJG/JKMIHMLFEII?EEFBGL?ELEJJA:<=D	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:G@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR162875.5181154	83	17	1395	60	100M	=	1266	-228	AGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGG	C;):EE0EGIHHFEIIHAD?;BLHIJJLDCL74LGKH@@GFHFK<BABHKACL=AA>AG6J;?@MCKH@FIBHDID7J?E=I;I9=HGG@EGFFFF?CBB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR162875.16344032	99	17	1402	60	100M	=	1670	367	TTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAG	ABFDHDCIFEFGJFEGFFGHBKLKKCG=KKIJFHFLDIFJMCBJHG6GEIIIGLHLGLKKKM@GL4JEKKDLKMEJCJJFIGI>CLF<DH?DEEFBFBDD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245032.1136878	99	17	1416	60	100M	=	1713	396	ACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGG	ACFCFIGHIGHFJFHGHHDDKIJICLGFAGGJHDFFFGGIFJEKGJIIIFIFHJJFEIIIGEHKHGJFEFHGBIIIAJE=JDJGAKHGJHIAFFIA@G>C	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245032	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@C
+ERR162872.9427750	83	17	1421	60	100M	=	1249	-271	GCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTG	;FA@GAFJJHF;>:GMIEHLKIIJHJLKIJIHHJKJKIMKKMHJJMIIIHJJJJCEKFKLHIGJFNJGKICLLIGKKJKJIKKJJKGIIIEIGGFECGDB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.25752000	99	17	1426	60	100M	=	1789	462	TTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCACGGACAGAAGGCCCCTGCGTGC	B@=>FC/=CEF>G<5CE+HHECIGCHHEFICHH9J/C9><.=;3H.G79M>D/=K.8CFHNB:BEA9G/8:&7E3K9C)8JDH2C2:-H,&.(>./(BG;	X0:i:1	X1:i:0	MD:Z:78G10G0T9	RG:Z:ERR162872	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242963.327784	163	17	1426	60	100M	=	1781	454	TTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGGGAGGAGCAGGGACAGAAGGGTCCTGCGTGC	@<FEGEFGEFHHBHEK@EB@>GGDBGCGFIED>EJ@DIFDJAEGG?EKG>?J(JIIHBEEJ:D0F,?FG#G9J.FIFHGGF?HEGAH/F82-H9AB98==	X0:i:1	X1:i:0	MD:Z:69T30	RG:Z:ERR242963	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.10697401	147	17	1427	29	100M	=	1297	-229	TGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCC	CEF=8DGGHHIKEKKHHIGELJFHDGGIHJJDKJMKJKKKH=LGJJJKADKJJMFJKBHIFDEGCKDGIKIK;JKCJK2FGJJHFHEIHFGHFG@BFE@B	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BG
+ERR245024.1107845	99	17	1428	60	100M	=	1785	456	GGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCC	@:EDEFDEHHHIDJGDDGDIE>EEDF?JDHEKIIIIFCIE@H=CCFH>EDHJIGG>E<JEFJFI929<GAEEEKAGJHD9G@J>AGI<-FF?FD9A@CD8	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245024	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@
+ERR242943.1490060	147	17	1433	60	100M	=	1031	-501	TTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCT	BADGDG?HGIFFDHIGDHGEGJFGHFKHGADIIJ<FLGF9IJIGHIAFIKGEIIJGID=FHGHIFHH?DHEFEHEGDHCIJHHBHIDC@CFFADDGG@EA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242943	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR156632.7178739	147	17	1434	60	100M	=	1187	-346	TTCTCTAGGTACTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTT	CEGGDDCJ??8"DEIHGFIJIF>IILHJHGJJEE;BEEFDLIILKB:EIEEHK>IG;AM5FAKKKDKIFK@KBGKKIFFHKICFKFFBDFHC@@GFBGCA	X0:i:1	X1:i:0	MD:Z:11T88	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.10970255	147	17	1440	60	100M	=	1238	-301	AGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGACGGGTCCTGCGTGCCCTGCCTTCACAAG	+>DC7>>0HE,A+37HHA9HIDBA?H.A1A.F8?N5HKDJ9FJ54:D>EK2C2)>I9:=FD=<<K*FH;@?B$L@@A<-?B3->8IH=GH)/1EF@>;FA	X0:i:1	X1:i:0	MD:Z:72A27	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.9078489	99	17	1452	60	100M	=	1710	357	ATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGA	C@BGFJGJJJJKHGHIJIKLIKJKHJHKKJLGHGIJ=MKHEKF>HJGJKMLIKMKDHDMFINLL<LLLLIEAMHHIKILLEIKHIJDKJHKHIJDGEF5E	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR243079.816750	147	17	1452	60	100M	=	1096	-455	ATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGA	5<BGDF:IGAKFGBJDBK7GGFLJHKFIHHFFGHHHCJE9HHGGGJJGCHEDIGCCKIGFEHFI@HF8G>BEIGIEG<GIFGIDFEHH@GAIEEGBECD?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243079	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR242983.836867	163	17	1460	60	100M	=	1849	488	TGCTGTGAATTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTT	@EDEHEIDGGEJDJHGAI>BIBHEFEDI@JEI>JIFKBJHEKJFIIHDGHAGGHIJBIIIKIBDJDHHJIKI>5GGCGGJJHHFHEBFDKFE@;IC=G?=	X0:i:1	X1:i:0	MD:Z:9C90	RG:Z:ERR242983	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AB
+ERR245034.324906	163	17	1469	60	100M	=	1786	416	CTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCT	?DGCFDFDHFHGGICEGJCEJFIABG=GBJIFKHGJI@GFFHDGKHH3LHHJJABHHFKGMKKICEFGHGJGHHKFKF9FKI@HHB=FJA2D;:C@DC7@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245034	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.1880433	83	17	1476	60	37S71M	=	1154	-392	TGGGTATTGGTATGTGGTGTCTGCTGTGACCTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGG	0%.*1%?0+(3+7%;#'2%8=44222;76%51(02/+5B/:<E;@??@494:0C9<;?=A:A==8A?=@>C@<>CA6CA<?:7<D?DD@B@BAGAABCFIHHGGDED@	X0:i:1	X1:i:0	XC:i:71	MD:Z:71	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.24601969	99	17	1483	60	100M	=	1707	323	TTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCC	BABG<EHFEA?E0G4CEF:IGL2D?FFJIHHHC=GFJGGC:FK:IBDLMJBB6>=I8JELF8F.G18.3F)GDEDAE70G--DJJGHK@)+=B<FE3>0=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243003.852165	83	17	1483	60	100M	=	1147	-435	TTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCC	9DBGG@F;<IGD<J<IDHCJ=GIG?LIGFHHI;BIKEJ?IHBIGFHBGKGGJBIFIKJIIMDIKFIHKFFHHGGGHGFFHIJGFIEIGHHEHGHEHFF@?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243003	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243039.1011454	99	17	1490	60	100M	=	1670	279	ACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAA	?C?@DDHEIFGJIFJGGGHGJFCKIJEIDJJI@EJHGHHJFIICJE@JIJFJICKLGHGKIEHFJCHJDGBEEFGHAJHIKKKHGEIIJGJFGGGEBFC;	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243039	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243091.615703	147	17	1497	60	100M	=	1066	-530	AGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGC	;@EEGGEIIJDGIJGIHGCBGEIIBFHHIGJF8EBHEFHGGKIHIIKGHIGJHJGEIHIHGGGHGGHJHHJCJGHHEIJJFIJIHJHGJHJDEJGFFEDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243091	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR242947.484791	163	17	1499	60	100M	=	1858	458	GAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCC	?BGEEIEF@FGJFGIFGDIDHI9AFHJGGHIGGGFHGIGIJAIIHIECIFLIHHBKEEJEFCGKGCGHIKHIFIIIGIDGGJJIHIFDHFFHHDH?BBD>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242947	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@
+ERR242999.1133728	163	17	1503	60	100M	=	1901	495	AGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACCAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCT	>F7ABHDH;F?FAFD08<BD:;?EHH7/GB;@2>&@L>0HIG5IH=JFHI8?58F58A62;<BDI2IGDNGH+GIH0IGHCH'A@:H8C5CCH4;F>>G)	X0:i:1	X1:i:0	MD:Z:34A65	RG:Z:ERR242999	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.15752406	163	17	1509	60	100M	=	1804	394	AGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGAC	EEEFIDIGJJKKKCIKKKLKKLLLIL:IKJMGMLLLLKHIMFIIJMJHLIIIJIKHIKLKMLKKKKLLMKINLLLLKFIEJKJ?JIIKKJIDJJIFBDBC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR013140.17777881	83	17	1524	60	46S62M	=	1188	-397	GCGTGTTGGGAGGGGGGGGGGGAGCGGGGACAGAGGGGCCCGGGGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGG	&)%%*$$$%##%#(##$$#%$*#-%$01-893-%#11$$2##$"&1*86><?>=<<?@;@EDCBFEIKIDLLFB?GCEEGGDHDKKJGCEDHGHHBHHBIGFGGDED@	X0:i:1	X1:i:0	XC:i:62	MD:Z:62	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.7109038	163	17	1534	60	108M	=	1854	427	CACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGCCACCAGACTTCCACGACAGGC	;D@DDCCDEEHFCHFHHHFIEGEEHEEEHBJ>FGIGJHHIFHHJEIJHEJD4JCIJDJGDHFG9G=HCIB:FGBA8;9E@JFJBHBB8IBBCEC=EJ@B;8;C;@CC6	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR016352	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.28180864	163	17	1536	60	108M	=	1849	387	CAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGCCACTCGACTTCCACGACAGCCTC	:B?>=595B?<==??CA>BA=BC4@9B=<C=4B7@>=?A0:C>EB=@AB@>8=>8E;?A@E7;CF;B@=<DDB8&;F>?.GADBA<@9$'17.?2B3C66@386&298	X0:i:1	X1:i:0	MD:Z:88C0A14G3	RG:Z:ERR013140	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.18201416	99	17	1557	60	100M	=	1954	496	GTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGCCACCAGACTTCCACGACAGGCTCCAGCCTCGGCACC	DDCEEJF;HFILHKHLJJIKLLHHLIMJJGIDGIJGLHK9LHJDELM@HLKILMMKIFKLLJELGJJGDEHHKHM;IJAJIGL.BLKDHMIHIIA5GFA?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243035.1352953	147	17	1563	60	100M	=	1224	-438	GGATCTCTGCCCCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGCCACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGC	D986>>D=2B&HFI6I/D/A8EB@I3EA5GHG*FEH=C:;HIDD1/G;IFD3EFJ0D?D44I<:=FG;2H3<=@HIH;@>@JIIGH>?EII5CDDDGDD?	X0:i:1	X1:i:0	MD:Z:10A89	RG:Z:ERR243035	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:F@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR242939.1378819	147	17	1582	60	100M	=	1202	-479	CTGGGCAACTTGTGCCCATTTGGTGACCCCTCACTCAGCCACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGC	0>D/&9C98=AG73#/8.4+0H?H,0'10K@=2G(+<:'C1(20.207D?C2+B?11H&==<II;5A>79J@B:A8>2GH)4@F;H7BB4<FD?/BBF=?	X0:i:1	X1:i:0	MD:Z:4A14C80	RG:Z:ERR242939	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243023.1620289	163	17	1585	60	100M	=	1908	422	GACAACTTGTGCCCATCTGGTGACCCCTCACTCAGCCACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTT	?C?EDDECABH>F=GGHCE0FAGHCBH?JGGE=<ICIFHCGJEHF@IHFFBBHHKHJKHGFFFI=I*GABHDDBE.;IDAE:IGBH:1FCF@3/.AD=C(	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243023	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.23901775	147	17	1621	60	33S75M	=	1316	-379	AACTTGTGCCCATCGGGTGCCCCCTCACTCAGCCACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTC	%;41.*8%1);:<*#'3?$%??C5%94699:%/1C?>F;==;1@9<5:.>>0'/,6<=*0;<4:2?=@<>D@B1:<=:?@E@F?BD>8GHBHF;DGGEIBHEECBCD:	X0:i:1	X1:i:0	XC:i:75	MD:Z:75	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.25518652	83	17	1632	60	100M	=	1387	-344	CACGACAGGCTCCAGCCTCGGCTCCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTC	;C0C/;)@F7,:KK@KGH(CJ<03-G;J.JFF@DC5/:8?GE@DF.A.EA3FI2AGMIMI?E3;F4JBJ@JGEBCK8EIKFHGJ@FDEH=FE<AIEBG9B	X0:i:1	X1:i:0	MD:Z:22A77	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243059.1079565	163	17	1638	60	100M	=	1995	456	AGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGA	@F?HIHFHJIHII@IJIJHJGJGKIHHGIFFIHKEDIHBJHGLJBHGJJEGDJJKFCJIKIILEBGFJIJJFHHHKHHKEIKJIJGJGHIJFGIFEEFE/	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243059	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.4511615	83	17	1652	60	100M	=	1375	-376	GCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTCCCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAA	EB0EBB.J-<>7,405,0?GG%E1:D.8115<='E&82A6*IJE53:,*C:)HII:H#D;:D3FKC*8I;368?<0GMHHH?:.-GCJ3<8<-5'+/+BA	X0:i:1	X1:i:0	MD:Z:57A42	RG:Z:ERR162875	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR242959.484376	99	17	1656	60	100M	=	1972	415	CTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCC	ADBGGJGIFGJGGCGKEFJH@KGGJKAGFHHGGIGFIEEIJHIFLGGEFIJGJEGHGKIELFLFECHEIHIHHJGIIHHJGFGIGHHJGIHDGGFDEFB6	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242959	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@@
+ERR162875.16344032	147	17	1670	60	100M	=	1402	-367	AGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCT	AC=@>A8:IJKBGJEJIIJFLHJIGKEKMHIEEE<KGKJG:KLKIKDKIEJLIFK9MHCHCLDHMJIILMDKJLIJ?KHGHHI@AIIKLIKHGHJG=BFD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243039.1011454	147	17	1670	60	100M	=	1490	-279	AGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCT	9@;=F@HEIIH@EGIIDIKGJHICHJJJLGJGGHELGKFAHKIKGHKGEEJMJFJHKGIKGIDGLHJFGJFKGKGHHHIGEHHHGJHIHFIEHEHFFBF@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243039	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.20508653	83	17	1673	60	19S89M	=	1384	-377	CCCTCCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCA	)/,;%>9(4986(1$75&8+B:?>EBD>FHFFIGGIFHBIIJMFGIBHHEEGFGCBHDLJHLEGFCJFC?GGEDFGDF@ELFECFEBFFHDJJJIGGFIHHGIFFDA@	X0:i:1	X1:i:0	XC:i:89	MD:Z:89	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.7604876	147	17	1673	60	100M	=	1336	-436	TCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAG	DE?E:IFD7JGIK>KKJMHJIGDHHKGJEKDJMJMJHKLLKILIJLKLLFDJILFEM?L<HJHJGLLGJJLJKKLLIHIGJJMJKLLKGJILHHHJGGFD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.24601969	147	17	1707	60	100M	=	1483	-323	CTACCAGAAGTGCCCTTCGCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAA	:DCEA@H9KHCJ5J?IJ2:K?II=L0/M@?D;:I9INEGB@A3<BHKEBEFELM3:@DCLJKHJIEIDE?KEHICJ=NEGIKAHFHIJIIDBDHAHFC@D	X0:i:1	X1:i:0	MD:Z:18C81	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR242963.315564	83	17	1708	60	100M	=	1289	-518	TACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTCCTCTGGCACAAGCCCACCCTGCAAAG	/;0FED:GG@4FG:G9CFIGAIEH:GLIIB=FFKGIHBD7GC?<8AFLFEFHH1>@KGI4DC=EHIG<D6DJ.(?EEGHJJ>ABH=?9G6F8JFGG@<8?	X0:i:1	X1:i:0	MD:Z:73A26	RG:Z:ERR242963	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.9078489	147	17	1710	60	100M	=	1452	-357	CCAGAAGTGCCTTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCC	CFHD9DDHIJF"*6JJMJJKEAFLMFLBKHCMFJELEEIFHA:KKMFLKFFBJKLCLJLIKLKKHHGJJLFFLGIGJKKFKGIHIIJGHHIGH@CCFE@B	X0:i:1	X1:i:0	MD:Z:11C88	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BG
+ERR245032.1136878	147	17	1713	60	100M	=	1416	-396	GAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCT	?BFAE@FF@FABDHABKGKCHIHFDID<KHKGIGFIAEHGHIKGGJIG>HHKDIHKGHGJJFECIHKFEK<JHHKHDHFIKHGGEGEIFHIDCFF@A>F?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245032	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242951.1253490	147	17	1717	60	100M	=	1327	-489	TGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGG	B4EFFE5FAI7?K5JAHHFJDBKAJGIEIIHHG?ADIGCFIHJK1BJLEGJKG=H@KFDBFIIEAKFHEHIJEFDHGF?IAGFJGIIEEGGEFEHFEFB?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242951	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242991.1183757	163	17	1719	60	100M	=	2047	427	CCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCC	?=?FDI@@HHGFJEHGIIGGGDHEHFJDHBEHIEEHHJHFBIHHJFHJDFHJFGGHC@IDHIEJJJIJCK<GHAKCHHGJ>HFJKEGDL@DIHHADF<E?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242991	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GD
+ERR242991.1577744	1187	17	1719	60	100M	=	2047	427	CCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCC	?@DFAIFGHHEBCGHHIIHEIHHAJHGHDBEFECK@HGIFHEGEHIJJ9JHJHK<HHEIDEIDHJDIJIHFIHH=JHHGJDHIJHJGGIG??FHGDF8FE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242991	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@HJ
+ERR243059.892087	99	17	1719	60	100M	=	2042	422	CCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCC	@BCECHEGHHGHIGHGIGFGGFGHIHJFGHHHHGIHHIJGIIFIGFIEIFILIJHHIGIHEIDIIJIHFCGHHHJHIFHIHIFJIIHGJAGGGCG?CDFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243059	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@HG
+ERR156632.9766143	99	17	1732	60	100M	=	2017	384	ACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGT	DB=HGHGFIHHIKLKKKIIJFKJKHLKGKIJLKKLMJMKIHKJHHJKLKJJKJLFLLJ=HIIIMGJJMJLJIJFGILKALMFIKCKKKBKKHKEHHEE>5	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.9045126	163	17	1733	60	100M	=	1981	347	CCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTC	EBHHGHJHIKKKKIKIIKNJLKKJMHJKHJLNLLLLKMJLLJKILKLLJJMLMLKLJLKILLLMKKILKILJIJLKLLKLKIMKKKKDKJIKGGGFF@DB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.16941332	163	17	1735	60	100M	=	2041	405	TGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTC	BFFDE4EHIHHHGJHHFHJHJKKHKKHGKKKKLKKKILKIIHJMJKGIJLHKLJHHJJMFMIJJMILLLJJBLLKKJLLHMKILLEKEJIGBIII@FEGA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C@
+ERR162872.10053578	99	17	1777	60	100M	=	1965	287	CCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCTCCCGGGC	BADGDEGEHIBGFFGHIAJKGIJJIJKHGHL7KFKKIJ=GJFJBCKJKADLBBEBJGMKJ;GLHLMECMLLLHH>BEBDI;H=38EEKCB?EK;H(===,	X0:i:1	X1:i:0	MD:Z:92A2G4	RG:Z:ERR162872	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@RBO@DDD@
+ERR242963.327784	83	17	1781	60	100M	=	1426	-454	ACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCTCCGGGGCTCAC	4:<9CC1GEHC?69HI0?FD<713E9EFD<HAAE=@D;6EGHFHC/J98F(G:G@@EK.G3J9=HEHFEIH@<EGF=>H=B=HFEGDJ/E9FEE/DDFC?	X0:i:1	X1:i:0	MD:Z:88A11	RG:Z:ERR242963	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245024.1107845	147	17	1785	60	100M	=	1428	-456	TGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGCCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAG	6DEGCEDF>HJC1BBIGHIE4;DHB>FGIHHICGBB<CIFDBGD6BAI.K8H:DCIGIGCHJHF#FH8D@HHAGGHC)HFFF<IB>>GFEGIDHD?ADD?	X0:i:1	X1:i:0	MD:Z:64T35	RG:Z:ERR245024	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.3514928	99	17	1786	60	100M	=	2012	325	GGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGC	C?EFGFFIGJEHFKLKJKIJJLDKLLKKIKHGHM6GLK<H=JFEAIKKJKJKJFGKLB?IJF/ALGEL7JIKIMJ<CIBLEFKFIK7GI;C?AHF<EABB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR245034.324906	83	17	1786	60	100M	=	1469	-416	GGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCTCCGGGGCTCACGGAGC	CAC2F5F?GHKC?FIGKJC=IIHIHJGIHHJFJBJFGKJJFJIBJHKDMGHAKBFGJIFJKFHGIJHKFHOJFFHFIJIHJHJFHAGHHIIFIFBFGFD@	X0:i:1	X1:i:0	MD:Z:83A16	RG:Z:ERR245034	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR162872.25752000	147	17	1789	60	100M	=	1426	-462	ACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGC	/C>9C@:>GJEMELI1EL:-6IE>L>B>3'2E/BBECJ;DDKINKDG:0H+3BM6@KNJH7<HA;GKLDJEC@EKHKK8DHFDF?A9HEKHCGGIH=@25	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.15752406	83	17	1804	60	100M	=	1509	-394	AAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACC	:ADEDGHKEJJJKJIEKHJMIKCLJ<IELFNJGJMJIJM@IKMIJGLKJKFMLIIKDEKLILEHKFKDKLJIMILGDJJKJJAHIFJHHGIGAFFEDF>B	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR243039.1277921	163	17	1809	60	100M	=	2171	461	CCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCTCCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGA	<<=GGB40FE;BA>HHI7K:F4AIIABJHGGI:IHD?IHBACCDF@AD<>GADI&ED:)I<9AB10;I/IB6?EF:>3;AGGAHEEI9@9/051EEG@??	X0:i:1	X1:i:0	MD:Z:60A39	RG:Z:ERR243039	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.8706087	163	17	1811	60	41M67S	=	2105	373	CTGAGGCCCGCCCTGTGGCGCCTCTCCCTCCCTTGCTGTCAAGACAGGGGTCCTGGCCTCCGGGGCCCATGGTGCCCCCCTTTGCCCAGGAACCCCTGGCTCGCTCCG	8C>@?>=;;4;>40<BA='-%#,,7=8>465.<986B1?<5*:%'%).%".,#23$%*+0'$#%"%#)%+,$/.+(#&)#,%&%%'$,)$5$($'%%,&/%.%/5)%(	X0:i:1	X1:i:0	XC:i:41	MD:Z:20T20	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.241318	163	17	1823	60	100M	=	2171	447	CTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGT	=EHCIEH@EICJHK@IHJHHIEFI@EFIIK4AGGKEIBEJ7EC;:IHJF=1?<HIIJGAIFKJI;DIHFJEK6HA>KD.IHG8IGCJ>FHCIHHHFDDF6	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243015.41290	163	17	1834	17	100M	=	2189	454	CTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGGGCACCTCTGAGCCCTCCTCACAGTGCCTTCTTCTT	<@BB3:GC>H>9II>1FGF26GB.B5:/>93?2&GD<8A2G3:EB3@*B:=8G)A652K40%?6&'&<IDC9G0GG&CFJD1098D9/-<D;F(-*(9E1	X0:i:1	X1:i:0	MD:Z:64T1T14T0G13G3	RG:Z:ERR243015	AM:i:17	NM:i:5	SM:i:17	MQ:i:17	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243031.1324865	99	17	1847	60	100M	=	2047	299	TGTCAGGACAGTGGTCCTGGCCTCCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTG	?EDEFHEFGGIEIHGKHHIHIHFIHAGHFIGJHHBGGJAHBIHJIJEKHJ>CGBDIHHJJ;FLIGFIIGIIGHBJGJJIJDLGIIGBEHGFJB@DEF@>D	X0:i:1	X1:i:0	MD:Z:22A77	RG:Z:ERR243031	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.28180864	83	17	1849	60	33S75M	=	1536	-387	GCCGGCCCTGCGCCGTCTCCCCCGCCCTTTCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTG	'&1$$/-6%'((&,*%+%$$%.(%/36/+%1;06>?168<>2<;;:@D:79=><A7<</2>;@C9A:D=E9CBAAEACDE9?DCEDFCDEEGIADCBADEHGCGE?C@	X0:i:1	X1:i:0	XC:i:75	MD:Z:75	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242983.836867	83	17	1849	60	100M	=	1460	-488	TCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAG	AFE@?CGHGBF@F2I-D4HED@@HD7BDGEEB>GDHBCJI5IHGEHE>HGCFEDEFHGEFG=EKGGDFGBAFCGCHJDGCFEHGGH<IFFGFGCCBEFD?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242983	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243019.556608	163	17	1851	60	100M	=	2294	542	AGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAA	AEADFGJEIGEJHHIIJHJGIBBHGGJJGH@IFJHGAIHGDJDJKH6CIEDEHIIIJBKJHHJEGFHIFIJGKKJJCKIIKH5IIIJJBJIGHDBFDECA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243019	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.31190318	163	17	1854	60	108M	=	2162	415	ACAGTGGTCCTGGCCTCCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTC	9?CCBABCDCGBEFGECD69>EGCFF@:>@ACH7D@EB@BDDC;BD=?;7D>FDCF?<DAECCID=A>3@%=?;8B@5?8?59@A5B@5D39?::9A?>1%$,-#9.1	X0:i:1	X1:i:0	MD:Z:15A92	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.7109038	83	17	1854	60	108M	=	1534	-427	GCAGTGGTCCTGGCCTCCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTC	$>;0776;<A3<9CB5C;<=;7BADE96:F?E6AFAEC?E@B9=@;FAA??@?AIBEDDCFAAEFFEDEFH>FECG5GGJIJJJFJIIJGDJHJ;FJCFEFCCF@ECA	X0:i:1	X1:i:0	MD:Z:0A14A92	RG:Z:ERR016352	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242947.484791	83	17	1858	60	100M	=	1499	-458	TGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCC	2EED@IGEHGJFHBHGJHMGLFAGJDJC?KG9LHHIIGCIHHFEJJIIGII9AJLEKHJICHIHFIFJIHKGJKHFFFKGIHDIJHFHJGIEGHCDEB?A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242947	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@DDG
+ERR162872.17554044	99	17	1863	60	100M	=	2053	289	CTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCT	BFHBFFFFGCCGJJJIHHCGIKDI>KHKKIHLKKCDLHGIJJKKKILLKMJLLJIIJGMHKKIKHLLKIL@LLJJKGLHJIHGL?JIIKBDGEGHCECGE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242975.1004165	163	17	1881	60	100M	=	2290	508	GGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGC	@>EHGAAIHGHIEIJGAFIFEIGHJHJFKJGGIFIJKHJGLFJIFIGJKKJJFKJIHLFJIKJGFIHKIGIGFGIIIIIFJKHJGGEEDHGDBGIDFDGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242975	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR243031.1705886	99	17	1881	60	100M	=	2179	397	GGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGC	?@DGFDAHGGHIEIIHAEIEFGHHIIIGKIHHJHGIJGIIKFJIHHEJKIIIGJJIJIFGIFJGCHIKIDJDBHEIIHJEJHIIEFGFDFCHCEGEFDFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243031	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR162875.23402552	163	17	1882	60	100M	=	2021	238	GAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCC	DCHHICIIIJKHLJKDIKHIJKLJIKJLLKLJKHMLIKJNILJKLIMKLMMHKLLLMILLLLHIMIMAILKJIKILLLGKLMLIIIIGIGIIGKCGFGF<	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR162875.5605685	1187	17	1882	60	100M	=	2021	238	GAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCC	BAHEIAIIJJJGKKFCIKHGJLLJLK7LLKLFLJKJGHIKCLJKJGLKLKMFMLKJIEK05FFIJ@MD@N5E;III3IGKLMLECJAFGHHDDKCGD9C<	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242971.738250	163	17	1883	60	100M	=	2315	531	AGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCA	AEDA@HEHHIDIIIAEIGEHHGIIJGLIHIKIHIKIBILGJJHGIJIJIIGJIIGJFJEHIFFLHLHGKGHGIIIIHEIJJJCF?GEAGFDHKGDEHED?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242971	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242999.1133728	83	17	1901	60	2S98M	=	1503	-495	GTTCCTCTGAGCCCTCTGCTCTGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCC	)+,7@CDG8F4'0>6066E%?/@;9>;5:?.816IK)2//DIBL97;EHC+@0,+2)4?1DG4GC<-E?D442EE3JB6H-%CHBCB;7G,,7F@C12*/	X0:i:1	X1:i:0	XC:i:98	MD:Z:0A16A1A78	RG:Z:ERR242999	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242955.454193	163	17	1904	60	100M	=	2322	517	TCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGT	ABFFDIBGDHCGHGHFGGDJJIFFHGHIDEHJHHJGHJJFHFJBIFHJHHAI9DAHGHIKHGDAH9CHHAILAJ?JLAFJEJGHIHAFGF9H<G7DG?C4	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242955	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243023.1620289	83	17	1908	60	100M	=	1585	-422	AGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCA	=DF?HEEHIFDAIIEAEJHELHGHGFJHKHHGGGIIHG;KJEIKD@EH=JKHFKIHAEFE@EIE<G?IDFGHEDFHIICGGGHHHGFFHFHDFFFF?FEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243023	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243079.862248	99	17	1921	60	100M	=	2274	452	GTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTG	@CGGFFDHIHIHEGIGJCGFFGJCFHFKFHCEFHFJFFIBJEE=DADHEIFCFGBCI@BKHGFGJFGJ=FGIDAFJBHDCG>EG9GG7GHJCE;CBGFGC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243079	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.17357143	163	17	1931	60	100M	=	2079	247	CTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTG	BEDHHIJJHH5J>HEKHLHIIIHEILKLJHLKKLGHHIJIJDEIMIKJMKDKNGM@IIKIKMIILH<LJIJHIMJDJKJJJIJDICLHLJLGIKFE@FCD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243011.1711788	163	17	1951	60	100M	=	2265	413	GAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAA	7@?AEG?@H>GEGED?ACDBG5>GG=.E@J8CHEFC?K<F:=>FIK7HG2&E>D0IIJ=>9D-6FE>ACHIE0<649F<G6G<1DD;BCB0<-4GA:C>C	X0:i:1	X1:i:0	MD:Z:90G9	RG:Z:ERR243011	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR242975.806680	163	17	1953	60	100M	=	2127	273	AACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATG	@AEDFGHEIHJHEFFGEIGGEHLHIHLIIHJFJGGJHIEKDGJIIHILEJFKIJHJGMJIIBFGJJFJKGGKFEFIJKKHEJDGFKBHHJGHGHIDDEDF	X0:i:1	X1:i:0	MD:Z:88G11	RG:Z:ERR242975	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H
+ERR242991.1140440	1187	17	1953	60	100M	=	2127	273	AACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATG	@@EEHFGEHHJHFEEIDHHGHGKGIGJJHGKGLFHLGIGIFAIJHIGKJDEJGKGIHKJIHBHEKJIJJGJJFFFIDJLIHHEEDJHKGKDJEDIDCEDD	X0:i:1	X1:i:0	MD:Z:88G11	RG:Z:ERR242991	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR156632.18201416	147	17	1954	60	100M	=	1557	-496	ACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGG	36DEAGCKDKIIIIHHJFJGLL7KKH?K;LLH?IIMKLHIGHK0:LKJ?KA7KBJIIK>EFIIFMHHBEGBIFGLIIBKCIDHHJ@HHCCH>FFDCCEBA	X0:i:1	X1:i:0	MD:Z:87G12	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245038.798432	99	17	1958	60	100M	=	2312	453	CTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGAT	?DAEFG9CCCFCGFFEFHEGIIHEEHBJCEHGGFHBEDIG7DJEF3HHIFIHHIHFAFFIIJGJIF;EDEGHBFH9CDBGHFC>G/E:??FC@FBC@BCB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243087.1122947	99	17	1960	60	100M	=	2366	505	TCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAA	?DGFBC?D?DFGGDF>FIFGIHFK@KLGFGGEJDD<IHGGKF/EF:AEJG:FEIAB5;IIKJ@EK;EEKHIIHHDDGGIEICKGJBGICCGDIFFH@C?A	X0:i:1	X1:i:0	MD:Z:81G18	RG:Z:ERR243087	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245024.1210272	163	17	1962	60	100M	=	2280	417	TGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGATAACA	?E@5ACC>FFFDFAFAG<CDEHGFGCIII=@E8@C4EGF:2BH?7BCG;F><><7I8>HG?AKEFEFFILCAHF<6B;IAIHCGBK@<5GIABDDAB5DC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245024	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR162872.10053578	147	17	1965	60	100M	=	1777	-287	TTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACA	.>@@DJHGBMKCHIK.LJKHHALILLFJDILHBBILGF>JKLIGDJFDCKIGGKEL;LEKIJIKJLBMGJAJJJFIIKKMHIDHGGIKJKIHFGGI:FFD	X0:i:1	X1:i:0	MD:Z:76G23	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242959.484376	147	17	1972	60	100M	=	1656	-415	TAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGATAACAACAGGAGCGA	6BEFBHFHCGCIHKEIAJJJJGGIEIIFGHEEDICEJKIKF?IJHKFHIILGHGBGDEKHIHGGHFICBHHIHHGIEEEECIHIIEEEIDEIGFFFE>D@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242959	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.2168867	99	17	1981	60	100M	=	2205	323	CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGG	AEGEHEEIGIGJGFJJIKIKJECLCFFJFLLHJDIILKILMLFMHFHKKLMKICIJIMJIDMKLJIJKIIILIIMDHIHHGJKILEJLH@HFCAJFFDGC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BA
+ERR162872.9045126	83	17	1981	60	100M	=	1733	-347	CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGG	EC?HEBIEDELDIIJIJJKKEIGKJLHMLLLHCJJJDMJKGLKJJIIKJKLDKIJHJKFCIJJLIILGHJJKLKJHEGHIGFKIJKJHBIFEAGHFHGAB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243003.755522	99	17	1982	60	100M	=	2281	398	TGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGC	?FDGE>GFDFFFECIIHGKHI4HCHDHDKJEHAFFHIAIGHGHFCEHGHJBGGGDEJFHB5IJGGJFFCGFHHFBGECFIGHGKCEK@?@G?@IFE@;E5	X0:i:1	X1:i:0	MD:Z:0A99	RG:Z:ERR243003	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:ZQ@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.15198869	99	17	1987	60	100M	=	2229	341	AGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTG	DD:=GKGFJJJHHJKKHIHKI>HLLGIDHHKLLJJMFLIIGJDJJKIJGGHKDKDJBLHFLJJJGLLGJJ?JDIAKJKMLJL=CIIJEC>IHLGHIEAED	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243059.1079565	83	17	1995	60	100M	=	1638	-456	GCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTC	@DCGFEHG?EHJCJJIJB?HGHGJHIIHIJGEEKGHGIGIHG@ICGJGKKIHIEGFFIHCJGDEEJD?GHHFIKAIEGAHHDIGGIIFHJFHHG?E?DB@	X0:i:1	X1:i:0	MD:Z:46G53	RG:Z:ERR243059	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.4987821	163	17	1996	60	100M	=	2242	345	CCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCA	DBDFJHHGJIKHIJMKJJDIEKKLLLKJMHIJJLKJMFIIGJJIKINIKKJLKFJJMBJNKJIJKKJKJKKJNJBKKKCKFKHLJMLLBKIHJIBGABFC	X0:i:1	X1:i:0	MD:Z:45G54	RG:Z:ERR162875	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245024.420543	163	17	1999	60	100M	=	2317	417	AGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACAC	?D@@EH@FGFFBHGG@ECAJFIJH@GDEEGEEIG?GFFGHGHFJIIHGKGHGEKFFJGHDHGGIIFJICEIA:HH;IHIGGHCHHHE:@:C9??BGE>A9	X0:i:1	X1:i:0	MD:Z:42G57	RG:Z:ERR245024	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.3514928	147	17	2012	60	100M	=	1786	-325	ACGTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGC	34F=D2JFAJF*>BBHKGKIEDEIAI@H@LKHJDKCHIGJKHLKHIGGKCHJCLGJIBK=KAKFHEHLKLGKLGEKI?I?GHIGFGBHHHHFFEG@F?DB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.9766143	147	17	2017	60	100M	=	1732	-384	GCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGTAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTC	<BDC.BKCHEEKFFJCHCIGH:HDLKCII:GHHAIB8LIHC=GLBGKLKFFJCDD:@CHIKIK>HHKGGEFE5FBIHLHHEAFIGGHJEFAH@DFGFGFB	X0:i:1	X1:i:0	MD:Z:36G63	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.21458070	99	17	2020	29	90M18S	=	2301	388	GCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGGCACACGCAGCCCTCGCCGCGCCCCGGGGGAGTAC	@BEFFFFFEJGCJJFGGHIJGJHIIKGIFJFGICCIKHHGEHKFIJJGJJALHLAGIDJEDFGHABFC>>1*128CBC:/1-=&1$1*'($('92%$#(7&%$%,%1.	MD:Z:21G51T11A4	RG:Z:ERR013140	AM:i:29	NM:i:3	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242983.1365156	163	17	2021	60	100M	=	2397	475	CCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGG	AAEHDDDGHIJHHGEDFJHHHKFIHGIDHGGGHHLHGEIJFHIILIGLGADHG@JGJHLILGJK>JGKKBJBEJFIHEAJHJIFFFIAJAHCJ=GHBEFB	X0:i:1	X1:i:0	MD:Z:20G79	RG:Z:ERR242983	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@DB
+ERR162875.23402552	83	17	2021	60	100M	=	1882	-238	CCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGG	:BFFBFBKIJKLHIIIFMDLKJKLIGEHHIIMMMMJIHIHHINLLLFJDLEJCKL;LHLILJCMJKJKCJCIILGKEDIHKIJJGHBIBHHIGIFHHCBB	X0:i:1	X1:i:0	MD:Z:20G79	RG:Z:ERR162875	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR162875.5605685	1107	17	2021	60	100M	=	1882	-238	CCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGG	CFH>B6BII68FHC>B@@GLFJKFHCA?FIDIKLMJDC:LH9HLKGHFAM;JC2LHJHLILHIMFIKFADCFEKHKIE?HKKDJHHBIBHIIGFEHGCBB	X0:i:1	X1:i:0	MD:Z:20G79	RG:Z:ERR162875	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR156632.16941332	83	17	2041	60	100M	=	1735	-405	GGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACA	?EEGEHIEFHCJKKJIGGFLHHLKLKILELHCEIHHLJLCMJLMKNLJDLEKKI=IHEKLKJKLIKCLDLLKKNILLLLLHHIJIHDIJHHGFIHAHFED	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243059.892087	147	17	2042	60	100M	=	1719	-422	GGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACAT	DFGDEHEDHEHJHJHFGFJEFKGIKKIBKEDAJIDIJJJJHIJHJIHAIAFIKFG>@JFJJHJGFBJAJIJJHHJHHGLIFHIFF@GGHEGEJF@IDGB@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243059	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:FH@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242991.1183757	83	17	2047	60	100M	=	1719	-427	GAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAG	EB?CDGD<IEDDHBEE<<IHIKBK?H>KK?KHJGKE:KFJHBBGBJEJ?J?BJK>IHJDH@H?GDDHGEHIHHHD>CADE@EHHEDEJFADFIEEEDGD?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242991	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242991.1577744	1107	17	2047	60	100M	=	1719	-427	GAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAG	0@?C7GAGIE@F<JECGEBF>HAC?H<KK?@>JGK<CKCIFH?GBG:JCJ?BF@FEHHCG@J?G@DPK<GIBH@GDFGDE@EGEBBDE@?HFIECEAFA>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242991	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243031.1324865	147	17	2047	60	100M	=	1847	-299	GAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAG	ECCE@GEIJGEFBIFFJHKHJHAIHIBKJFILIGKIKKHJKJBJAIFIGKEAJKJIKIHGAIAJLKLKGKIIHIHDHGFF@GGHEFDKGAIEIFFGEHDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243031	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.17554044	147	17	2053	60	100M	=	1863	-289	GAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTG	EGGEE?GJIIKLKKLLDLIKEKLJLLLLNKKMK?JLEMBIIMEMGELMJLJLIJDLDMLMKKIKLJLLJIIJJICIJJIEHLICKIK=HFIKJJCHFECD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.360692	99	17	2070	60	100M	=	2206	235	GACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACT	8DDB5DF:E=?BH;GKDFK5B?)GAF6@H2CIL?KF;J>JC3E8GHK?@.42I4BG<F2D:94FE8ECHJFFA/DHH?<I5B8DAD?3;-)AE>HE7AC.	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.10955775	99	17	2073	60	100M	=	2419	445	CGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCT	B?EEDEHEFHHHHIHIECJCHGHDIFACGKI7CGAD62LHLCHH6?IG3@CJCHF@K@:HIFLH8G@IHG1KEE@CG58@/HHJ@JJF@C@5JCFAHGF;	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242979.559120	99	17	2075	60	100M	=	2431	455	CACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGG	@CEEIGHHIIGIEJIBIBFJHGEGAIGOJDGHIBJAIDKJHKHJGJFGDHHEJCGIFEJGKLBFJHGJFHGKJCEHGHGLGIHKIKGMIKHHDGGEFDEG	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242979	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GL
+ERR162872.17357143	83	17	2079	60	100M	=	1931	-247	GGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTT	AGFFIIFKH5=?DIJI>JBCKJLLIDHGDLEIMLEMGLIKJLIHHKIDCHIKJIFMJ?JHMIHJJMLBEI@IGBGJGKKJIKGKHIKHF>CBIFFEEE?B	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AG
+ERR243063.1642219	1123	17	2084	60	100M	=	2462	477	CTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCA	AEDEIG<H@EHHIGH@IHKI=@GJ?G9JFHLHKGJEHDGCG?DH?-KEEHHJIBEHHEF@J:>EAFECKHI-ACAGHI=HHHEFKB@HH1..F8=;76D4	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243063.246578	99	17	2084	60	100M	=	2462	477	CTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCA	AEGFIB@H@IJEHGICJGKIHHGJAI@JBHJDKDJEHHCE>B?HBAKFEHIGIAFHHHH@JHJHAFEEIFKFIHIGDIJJJHHEJIIHCIEFBAFABF=B	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.8706087	83	17	2105	60	28S80M	=	1811	-373	CGGGCGGGTGGGCGCTGCACACGCAGGCGTCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCAT	$$$&$$%&%%#(1-5-(4.=5:C=.&%8%C:F?CFH=GFCG@G?DAFFCB;=G<EACFD=EEFEHGGI@A?DD8>5?.@BDGHACAGGDGCJGDECJHHDHHHFABA=	X0:i:1	X1:i:0	XC:i:80	MD:Z:0A79	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242999.1001077	99	17	2110	60	100M	=	2438	427	GCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGG	@CEGFFGFIGGEFEGDEIAEIEEFIJJBGHFEJFJHKJBGGEJCI=IFLDHHHJJKJDIKLIIIFIID>G7DIHGIGJIIEIIJHGJFKKHGHGDGFFF=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242999	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@HKC
+ERR013140.30331713	163	17	2120	60	108M	=	2444	431	GATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCGGCCTGGG	:DCCA?CC9FEDCGEI@@CFHGIBIEDB?EBDDEIIDIL=>FGE>DCDBFH;@ADBBC;=ADAC==CBBBC1;;A?BC>?FD>BF:DD8>/47=:AB:94;?@9DC?B	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@EDH
+ERR242975.806680	83	17	2127	60	100M	=	1953	-273	CGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGG	<EDFCDCFFAJEJIHGGKJI@IKHGGDJEJJGKJGKHJJFFJEFKHHHHIHFHHGHICJFFDIIKGIFIJIIKGGGHDKGHHJHFIEDJFFFGGGDGEB?	X0:i:1	X1:i:0	MD:Z:93G6	RG:Z:ERR242975	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@DD
+ERR242991.1140440	1107	17	2127	60	100M	=	1953	-273	CGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGG	;EDDB?DIFAIEIHGJGJHJBJGIIGIKFKIILHFKHLJEFLGHKGIHIEHHHHIGGFJFEFGIJEJDHJIIKGIHIHJGIIHHFJDEJDEEIGFEGEB?	X0:i:1	X1:i:0	MD:Z:93G6	RG:Z:ERR242991	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@DD
+ERR162872.12579188	163	17	2147	60	100M	=	2456	408	CGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCGGCCTGGGGAAACTGGGGCAAGTATCA	E=EFEJGJHIIKJKIILLLLJILKJKLLKKFHIILLJKJIGJJKLLLJJLJMKLMLJMMKMKKJIMHJJGIGKEJLLLLKKLJJ?JIKEIEKIHKEDEF7	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.31190318	83	17	2162	60	108M	=	1854	-415	CTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAAT	@E@@A8B=:F6@@A=BCC>;CC>7<34<7=;.9??EECCH=FABGGFHHLJIIFHIHILJJJLLLLKIIHIKLLKJIHKGHGKHHIHKJKJGJIJHGIHFEFFFCB@@	X0:i:1	X1:i:0	MD:Z:58G49	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.241318	83	17	2171	60	100M	=	1823	-447	CTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCGGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATA	CADB=EDBCB,H8GG2:08@<?IA?GD>HHFAI1;DCG<CGHEDMI?HA>G1HG=@CLAA?IG>GEFG=GHF?EH@>HGFGEDAHIEF9FDECDCC<CA?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR243039.1277921	83	17	2171	60	100M	=	1809	-461	CTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATA	GA?EE;;?:G?IEE:F?C7:G>IBAHI>MGF3<0GFFA;6HC==;@6:H950BCG6>:E?BE:CGDFH?CDACDH2HJ;>HGA>CH:I>BD@BC=4ADA?	X0:i:1	X1:i:0	MD:Z:49G50	RG:Z:ERR243039	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR243031.1705886	147	17	2179	60	100M	=	1881	-397	TTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCT	@D:EFEGCFEI@KHJDJIJHKHHGKIKFHIJIHKFELHGFJJJHKHGIIKEDFKIGHJJJFKIGJIJCIKIJIIHGIIIKFGEGEFEDGHEEFHGGFFEA	X0:i:1	X1:i:0	MD:Z:41G58	RG:Z:ERR243031	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.1719649	99	17	2188	60	100M	=	2533	444	ACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCA	?CC@FGEFIFIHHH>EHGIHH?CEIGCHIBJGEJHIHIHDFGFHGFCEGHHGHKEEGIGDHHJGLGGJIDJJCE=GGGG?IHC@HEDAIIGDIHFGGED@	X0:i:1	X1:i:0	MD:Z:32G67	RG:Z:ERR243007	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243015.41290	83	17	2189	17	100M	=	1834	-454	CCCTCAAGACCTGGGCCTGGCCACAACTTCCGTCCTGGGCAAACTGGGGCAATTATCACCAGAGACGAGCTTTATAAAAATAATGGTGCTAGCTGGGCAT	@9>7D(.@B&.A111//.(4':-E4=/7,.),'DB=;0)1E<-E<<=3*1$B%'C/D-JH>H1-4*=1+>8D<B<**8@GC+C++*+<G32,,73<<D0:	MD:Z:9G10G0G0T9G6G12G12T34	RG:Z:ERR243015	AM:i:17	NM:i:8	SM:i:17	MQ:i:17	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243019.804639	163	17	2190	60	100M	=	2558	467	CCTCAAGAGCTGGGCCTGGGGTCAACTTCCGGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATG	AAFGFGHGJGHIGGIHIKJIIEKHGIJFKHBFJHIJHHHFFHIJJHJIHHFLFFFIIHIHJGKGIKBIGJEFC@GJEIHF@GFJHFHIJEKGHGGGFECE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243019	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR162875.2168867	147	17	2205	60	100M	=	1981	-323	CTGGGGTCAACTTCCGGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGT	GEEGIFHKHHJIHHEJKLNJKKDKIGILJKJKLLILJIJKLIKMLMJKKKLLKNJKIHJIJHIJHIJBLHIKLIMLLJKKKLIHKJJJJLHIIJHHIECE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.360692	147	17	2206	60	100M	=	2070	-235	TGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTA	1FBF2D8C0E1FBICAK@DIH7CE=BJJ6?KA:ICKDBKLH:LM;MLJFGELIB>HCEHHHFH9GIJBIHGFDFF>GFJFKAG>IIKKK=GHJGAICEB@	X0:i:1	X1:i:0	MD:Z:14G85	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR013140.20581831	99	17	2212	60	108M	=	2526	421	CAACTTCCGGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTG	@CEBIFHI>HHJJHIIIJJJGKHIIJIKJIGHGJKHLKIJJKHILJJLFIFGFDFEHJEGHJHGJKLIJFIGEFGLHJKGJJGHBGGG>AHGFCBB?99=EBC=C70>	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.15198869	147	17	2229	60	100M	=	1987	-341	AAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGA	@BAHGDDDIKBKJ7HDJEKKHLLJIIJKGLHFJHHIHFFIEGCGCEILLHKJBBFKKIIIKIIKJLEJEKGJLFGFFFGIIJJJJFJGHGGIFHEDD?DB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.4987821	83	17	2242	60	100M	=	1996	-345	TATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCG	DCDFHFIIHJIHIKJKKDIGIHGGHIJBIIDMKHKMIKKMIKLILHJLIJLJNKIKLFKJJGIHJHJHLJKLFLIHIJKJKIKHCHJIJFIHGIEFFE?A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243011.1711788	83	17	2265	60	100M	=	1951	-413	AAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACC	?2B=,;EB04@BJ=:D9.40=I;<DA9E>:497E12=JHA;9:00>JA12<B50G5;?D9'@DCEK:DCE@C=?/A<A8DFBE08AB<H3FE>FB@1D;:	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243011	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:F@G@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243079.862248	147	17	2274	60	100M	=	1921	-452	GTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCC	CCC@?GEF4H:IE8G0JD269>G6H@/EFE6EGE?=DBII;;A2-G@;GJ7?8H;HGEJGLIFDF@>,H=ADDH:=EF;?F;@FFIG?EGGHF>FDCF9?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243079	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.7043507	163	17	2276	60	100M	=	2525	348	GCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAA	ECHBIJJJIJKHI?HILJJKGILGKLHIGJJJILGHKJEIMHHM?JJMJK5B*ILLINGILKJGKDFIDFEHILEJG=JMCEHAAIJ2JIJ@K8JFFG<(	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245024.1210272	83	17	2280	60	100M	=	1962	-417	GCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACG	6FCDCGI:FF@@HGAI@IEE&<@:E@;GE;JJKF2GIJHHGJBH7I@F=IDAIH;BHFAG@BIFFGHBB@F?F@IE:HGEH@:CEDHBFF@F<?ADAF=A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245024	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR243003.755522	147	17	2281	60	100M	=	1982	-398	CTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGG	BCFFCEG8FGHHF=HGCFDBKGIFCHHIIFGJIDMGCHIIIGJI6CKGGJ=HIKGIJI<BEGEGJHHGGJIKCFIGGGJIHCHJGFGJGGIAJDFDE??@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243003	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243019.1623189	163	17	2285	60	100M	=	2569	383	GCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAA	A9BD>FEGCAH;GDFFGDGDBF?C;IFIFFGB?EAA>?I?;H8DA<JFG5FGDFF;A?8GH=L5B*GIAD?BDE>HHAH7GBA2DIH6HHDEBA>EFE=C	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243019	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GBI
+ERR242975.1004165	83	17	2290	60	100M	=	1881	-508	GTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCA	DCCD;BFHHDHIGGF@D@IGIIIJEBEHGHIJJFJIBIHFLFIHJJHHGGAIHHFIKICIJKJHHGGGEIIIEIIIHHKGHHDIEGDDAGHGCCBEABD?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242975	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243019.556608	83	17	2294	60	100M	=	1851	-542	CTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCT	D?DEEBFEEECF9DHDIGJIEC;BHHAADIK;@KJIKFIFLHJKGD@HGHHFFJEGHCCJGGGGHKDH>GIFHIJGGHIFEFEGAHHHDDDFBEFGDDF?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243019	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.21458070	147	17	2301	29	108M	=	2020	-388	CTGTAATCACAGCACTTTGGGAGGCGGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAA	920<'/7<1>?48/307$9C721:2$2A/9<226;<66=5<ABE7C=B;>?@?:6?AC=>=3DD?-?@E9BB@CBA@;?FDCDC:DEFCACC@FCCC?BBA=ABB@?:	X0:i:1	X1:i:0	MD:Z:8C16C82	RG:Z:ERR013140	AM:i:29	NM:i:2	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR162872.23671856	163	17	2311	60	100M	=	2618	406	AGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAA	BEGGFJGFLJIHLILKDGKKMIMKGMJHHLEHIGLJKJMKJMMIMHJHLIKKKLJLKMLKILLICHJKEJGFJJIGLLEMFKJLLHJJHIIHC?DFEFDD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GKKL
+ERR245038.798432	147	17	2312	60	100M	=	1958	-453	GCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAA	BE?GE3FEGGDGE9>KI5HDFGIGI6:EAIG4IID9:GG@J;HHH@EIHJ?@F=JCFFHIJHDEE5>IKJFDDEFHIBHGHFGEEHEFECEGEEID@B?>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@FEHGG
+ERR242971.738250	83	17	2315	60	100M	=	1883	-531	CTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACA	ECAAEGDGDHG=6DIKAIIJHHIE7@9FH;JHGHIEDKGJGHGFAEFEHJEIJJGJHIJFGECAHIFFFAEHIJIHEIGIDEHFFDEAECEHDCDBBEE?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242971	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR245024.420543	83	17	2317	60	100M	=	1999	-417	TTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACAAC	DCEEHEC?F?FEC:88F<J=:FFAEA5FJHI70CGH==DCKHEIKAFHDJHJHHIIJGGF5AIIHFDBDGIJBIGJGJEFIFFEEEGAFJDDEDDFG>AA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245024	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:FE@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242955.454193	83	17	2322	60	100M	=	1904	-517	AGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACAACTAGCC	:D)8=CE3J<E?I;DH>??7E+:9I59BEI5H<@E8A?GD2HJHHFHFFHFJFCACAE+IEFD>HIHF=DJDFB?I8A@AFGDEIEFECDDICCHAEE;?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242955	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243059.1325819	99	17	2332	60	100M	=	2706	473	AGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACAACTAGCCAGGCGTGGTG	?E@CH@E@G@ECBGGHEIGFIIFI?FCIE?CDBEIIHBI:@>F@F@D:IGHHGAJHJF9<KFIIDH<HGFACDAHHGHIIGHGFE9>HFEE8GG<BG/0G	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243059	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@I
+ERR162875.18309473	163	17	2350	60	100M	=	2674	423	CAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCC	EDHHGJHFGKIKIIKILJHLL@KLIFIHJDKIJJJIJLFIMHJLLFIIIJ@GIHIDKJJKJJJJHJJLIAIKIKHL@IICCLLE?JJGIDKCIFEBBEFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@DB
+ERR243087.1122947	147	17	2366	60	100M	=	1960	-505	GCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCT	?E:GFGGIFBFCBEIJDEEBGGA:IFLFLHGDEFFFFICEKFAGFGCIGGKEIFEKGJH?HGIIHHGGJI7IDGJGGEIGFGGHHIKECKFHHGHHFGEA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243087	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.12984374	99	17	2382	60	108M	=	2636	361	AAAACCCAGTCTCTACAAAAAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCGGAGGGGGGAGGACTGCTTGAGCCC	@CEEDBIEDDIEEJEFJJJCJJGHGKJGFFHAIHFLHIFLICEF;ECB>C:0?2;2073>C@=@B7980@<8;:=82?2=?;3+>=D??34$1C#%*3<&4)67;39,	X0:i:1	X1:i:0	MD:Z:83T7A16	RG:Z:ERR013140	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:ABC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.5601349	163	17	2389	60	100M	=	2710	420	AGTCTCTACAAAAAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCC	BFFHJIJHIIIIHIEIIJIJJIJHJJIJNIKLKHNKMEIMLGMKFILIJIKKMMIIMIMLLJNLLEJLKILIINHLLLALKKBIHILKJIKJHIFHFFFC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@HH
+ERR242983.1365156	83	17	2397	60	100M	=	2021	-475	CAAAAAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTT	;BABAEE>DJEFECB<IGDJCEGCKDIHBHGIIEIGJFJDH?FLHHFJHFBJIIJJ@EJHJIIIHIJKGJHHGGHIEGIHEIF<IFGIHJFEHFDDFDA?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242983	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CD
+ERR013140.13475139	99	17	2401	60	88M20S	=	2680	386	AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGCGTTTGAGGCTGCTGT	@CEBEEIHHHICFJIFKGHIKJHII>DBC:CE>A8C>C>7DBA=BEDDB4=9;:<C><??>@=;@D@@=B@E.3?972<>6@8=>?1$0:95%5%*1=8;0%4<228%	X0:i:1	X1:i:0	XC:i:88	MD:Z:88	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EHG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243035.1445358	99	17	2405	60	100M	=	2748	442	ACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTG	@CFEEFGFGGGIGEJIHHKFKADLGAJFELIEIHJIHJEELFJIIGKHIHGJJIKGFKJKJJGLHGJHHHLHHIEJJJEIFMKJIHJFFLFEEIAHGF@>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243035	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.22794881	99	17	2407	60	100M	=	2639	331	AAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCT	@BCCDBEFCFHAIGFHI@JAHK2>F:E;C>HIIKFF>CLCK;&+B2M4CLG=EH<H.EJBILHL<@DIJF<DLK=GHE1L6C:2EEA=+C1HC4GBG?9.	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BDDBB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.13634813	99	17	2414	29	100M	=	2713	398	AACTAGCCAGGCGTGGAGGTCCACACCTGTAGTCCAAGCTACCCAGAAGTCTAAGGGGGAAGGACTCCTTTTGCGCAGAGGTTTGACGCTGCTCTCAGCT	8?*HD>E+FH(+(F/'60<D-E),7+3D*:4)8DD,&G1<3C(0J)&3./G.*%./&.&=28&GJJ,(91(2.&()+M1.&=188@)$?>.JB+),FB04	MD:Z:16T3G14C6T3G2G2G13G3G0A2C3G0A6G6G1G4	RG:Z:ERR162872	AM:i:29	NM:i:16	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.10770274	163	17	2415	60	100M	=	2690	374	ACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTG	ECHFJHIHLIKEIKJIKIHLKIJIKJKLFIMGLIMKNILHJIJINKJL@KMLIMKJKKIKM?JJFMKLHKKLKJIKNKGLFJIIJMJHLKKJIGJEIGFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.10955775	147	17	2419	60	100M	=	2073	-445	GCCATGCGTGGTTGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGAT	'9DA,J8DDL:>+JIILCKCKLJ6>LCJBCIKLAEHII;MJJKKEI?KJLKLELIGDMGLIJKHJLGDKKLJ6KLGIJIFJJHLIJKFIIFKJHHFEFAE	X0:i:1	X1:i:0	MD:Z:4G7G87	RG:Z:ERR162872	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242979.559120	147	17	2431	60	100M	=	2075	-455	GGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCA	@ADGG@H2ILDCEIH7HIHGKKEDJFGJIKJHIJGKHHIFHJEIJJCKJIJJGJGHJGIIGJIFIHHKIGKJGDJGGFJIHJGIFJGF@HIFEHCHEEF?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242979	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243027.576419	99	17	2434	60	100M	=	2778	443	GCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTC	>DB@DD<BCHCAF1,9AJG?DD?=GFGB?FIJF<F@?G;;BH0CH=E=>FIEFD;BH;?BHFEF?:JECGBHE1;9EIK.F1:G-DAH9I,.=>EF9D@E	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243027	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR242999.1001077	147	17	2438	60	100M	=	2110	-427	ACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGC	5CJDGDHGCIHIBJJDEGEJIJHKHJLIIIHJHGFGHHJEMJBKHIHIKHNKDGIKIIFIIJIJJIJKHIFKGKKHIGJGHBIIFGJEHGIIDFGDGFCA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242999	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR013140.30331713	83	17	2444	60	108M	=	2120	-431	AGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTG	938:(A@??<8>>>GBGIEFFIGDHLGKJDLIKGFJIGKLKJKCIEJ@LJDIELKLLKJLJFLHKKLJIKGKKHK@GIGKIDIJIHGJJIHKIIF?JEIHFGIHFAC@	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.474429	99	17	2447	60	100M	=	2812	464	CCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACA	BAD5=FHEGHFFHIBC;HFJGKD1JIFGHIHJKJIKGKGK2F?BMHE9,HEDK9HFKJFELHJ2BJL.0@FHC1K3DE3ELE=GGBEBIFB6BA9CE9?1	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.12579188	83	17	2456	60	100M	=	2147	-408	TCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTGAGTC	;DGGIIGJKILJGKJJHGKKJHM?JLEIKMMKGLMLMLKIGJMKJLMELIIJIMIKMIHIJJHEKKGILHKGLKIIJIKKIJJCJIHIGIIHIFFFHDCB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243063.1642219	1171	17	2462	60	100M	=	2084	-477	GGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTC	DF8AH9?GHHCGCHJBKAIK>HJDC=HCIIJFGGAEJGIJKCADDIAI:IC8H9HDB?IG@GC=;87GAHB=G>H;2@GEHIFGHBGGFFFFDGDHDDB:	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243063.246578	147	17	2462	60	100M	=	2084	-477	GGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTC	A@G;HFFFFF9CHHHFDEE@3HJHI/HIIDJJH?DGDFIJJHIKEIGIHDKEGCCDE?EGEGHBK?IFFABEGJCH2@GEHIEGHHGGF>HF<H>GDDB?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.7043507	83	17	2525	60	100M	=	2276	-348	ACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCGAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTG	<F:IIBEH>KCJIE;J@>LIKJLLIJMKIFLHKJLEJIEKHHBHKKIGLLKILMIGKDHGMMGGHGHGGJHHGHHJHDHFLIIJJGJFIFEEIGGBHCDB	X0:i:1	X1:i:0	MD:Z:39A60	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.20581831	147	17	2526	60	108M	=	2212	-421	CTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCAAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTA	@EBBBAC@DG@C@6FCHEEDEBH=B>EECCFDGBCC@FFFHGGKDFGLEKFKDFFI@FFHFFFEIJFFIAEEEEHDDHHGGFJIIIHIDDDIIIJJHGFEHGCBEFB:	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.1719649	147	17	2533	60	100M	=	2188	-444	CCAGCCCGGTGACAGAGTGAGTCACTGTCTCGAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCT	DEFHGFAGHHJDJGGJIHKIIFH>LHHF<9CFEGFEJKFEJJJHKIFBGFFHIKFHEEIFGGFEEFEICDHFJHHJIIJFJEFEJIIEJFGIEEEIEDF@	X0:i:1	X1:i:0	MD:Z:31A68	RG:Z:ERR243007	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.5990783	163	17	2544	60	100M	=	2843	398	ACAGAGTGAGTCACTGTCTCGAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCC	BCFGFHFHGGFIGHJIGJIIBIHHIILGIFLJGIKIIIFIEGHJIIKIHIJHJIJJJIIIHGLHMCJMKJJHIILFKKLHLKJJ?FHLKHLIKF=D=GED	X0:i:1	X1:i:0	MD:Z:20A79	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BCD
+ERR243019.804639	83	17	2558	60	100M	=	2190	-467	TGTCTCAAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGC	DEDIAFDFFFCHJCBCGKDJMFGGAFHCLFDDEKFGH@FGGHHFEIDIHIICIJCJGFFIGJGJGCK@HGIGFHEIIHEGGHIGGJGHIHIFFCBEA>D?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243019	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.17163139	163	17	2564	60	100M	=	2828	363	AAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATA	EACFFGJHHIHI3IMIGIJI>>GJIJKKJ?JKBJIJHIJIHIMHMJJMKJJAFKMJKMNHMKJM=GKMKINLLIHI>LKGKMJIKGIHJIJGCIJ?HFD-	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GCDEDB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243019.1623189	83	17	2569	60	100M	=	2285	-383	AGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCC	EA?<DEHCGIFFFEFEHG>C?F>=D@;FBFB<B<HBHIGI=A:6E@D4IIJ?GEGA2H>GFD?B?AH8H?6@G4JDIIGEFFF:C9@@CDGHCCE<BE=>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243019	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR243091.852212	163	17	2575	60	100M	=	2967	491	GAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCT	ACDHFEFGDGEJGDIHHHDIHDEGIHCFHHD<EGGGIDHHGIHJHKGIFGDJHJHDKIFJIFF;JFKJEIIIELHHFI=CIAIHEHEDEI?BFFEHCAEE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243091	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR162875.26247502	163	17	2581	60	100M	=	2858	376	ATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTC	DBDFGJHGHHIJIIIHJJJJIHJKHMGLKKMJJJJCKMJLMMGIKJJJIIMMHMJLEHKLLLKLMKMLFJLHKIIBMLHLHIKJCIFGJKJKKJFCHG@D	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.1508798	163	17	2587	29	100M	=	3006	518	AAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGC	??B@AE;=EFA786=F8DDD3G8FKHE=A;CIB86<;1IHM5B,:;9>7=:@<&I4L;C?/AJ9JK>J2DHKAK5,H29=,=0,E9?H.GKJGE78&,6A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.20693133	99	17	2588	60	100M	=	2892	403	AAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCA	A:CEECDFEDGGHGF@GE<<HDHEFJDC5IK?4@JB;HGG2FJFJ3I;HI?:6CJKLGC9GFJFDEEB>=D2F?BF?>HI<KKDCI8GBI=FHFB&B3E+	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:F@E@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243063.876263	163	17	2589	60	100M	=	2900	410	AACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCAC	@ADDDDFCFDGFFCFBEKFJGGJGHHFGEKFJGIDJEFHIGGKHEIIIBFIGJIIIJFLIGHLCFKI@IJEJGHHH@EJGHEHGIJCELHCJHHFFGFBE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243039.1477734	99	17	2595	60	100M	=	2955	459	TAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCA	?ABBEEEDFEEKFHJFIFIEHHJKIIGHFKGEGHGGIIDKIHEHJEHHIIJIKGJIIDFJHBIGEKIHCIBHD?HKKFGIHGHJGGGJ@HH?DGDE:8F;	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243039	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.1633327	163	17	2618	60	100M	=	2786	267	GGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATG	D?FHHFJHIJIJGKKHMLKHGLKLLLKJKLLHJMJIIL?MLJKIKIKCIJLMKLJLMBGKMHMIJKJKKKJGLI:L7HHJLIJMLGLLJGIGICEFCDAB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.23671856	83	17	2618	60	100M	=	2311	-406	GGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATG	CB9FB2HH>CFH7EJIK<CIIJHKILBLLLMHKLGGIDKLHJMIGGEEJKLMCMKMIIJLHJKJKKKKKFIMKIGLGI<LHKIKHHHKIHGGIEH:FCDB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.1511398	99	17	2622	60	100M	=	2951	428	TTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGC	?@DEEDDFCHGDIIIDEI@IFIH?GIJDEIFGI6>HHCIGFEF@BJHFKJGEHDCLGEHHIFGGHHIGIFDKDIJGEJJHJGJHFKHFDF>JEE?GDCEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.12418699	163	17	2634	60	100M	=	2962	427	GCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCC	BDGBCGEHGHHIGJGHFJHIIKDIHHIGIIICHKJKFKLKKF@KMDKJJKJJLIEHMK=KIJJEMMJKIHLJJKJILKJJKHHJJJFHKIIJAIGFH9E>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@JD
+ERR013140.12984374	147	17	2636	60	108M	=	2382	-361	TTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCAT	'??98:CD@B<<CCDE=9B=>CDI@CCF;>DEFCACDD?@BDCFBFFEAB?>BDGACDDECDCEDFAADDFBB@CHFJICIJIEECDFEADGDHHCAJBDBDA>CA@9	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.22794881	147	17	2639	60	100M	=	2407	-331	GGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTT	6?.97*GGD:-:810C?IIEJKBCFDJ>HCFFG<IC4DMAAMFKKJKIDHLIJDK3MGDEH7IJDAKKJJJKELGKBJKKJILFGHJKJIIFDGHIFFAD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR242971.169330	163	17	2649	60	100M	=	3021	471	ATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAAT	?AEFGFEAHHDJFEDHBEIIHIIIGHEFJGEJHIJDDIHIHII?IHFJJIKDJIHHHHKC=LDCMDHHIIHGJJDHJIGGDKHHHHIJHFAHCGEGCAC:	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242971	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243039.71589	99	17	2654	60	100M	=	3030	475	CCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTG	?@@DBBHEFBG?EFEGHHDGIA6?JC@EJA>EIFIGJ:<GAIG8FJHEJAIJEFDDIJ@HIGEKDHIJGH@KHDACBGG9=GKH;DFEDFBHA;?FCF:1	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243039	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242943.897194	99	17	2661	60	100M	=	3015	453	ATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTAT	?ABD?DFFGFGFFIEEHHFIHHGH=HGHGGDEIFHGHGIHJHEHGBJJDIICLIGGIJFJJJJEMFJHCGJIGIIEJFDHIDGKIHAGIHJCGGDFFC?@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242943	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR162875.23244382	99	17	2668	60	100M	=	3014	445	CCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCT	BBHEFEHDEIIFHJH=HBJIBDKIILIHJIJLKKJBLIJJFFJJFHEHHHFFKLJLJMJJJBLFKKLKMKIJILGIMLHJGKMHC.F;JKGEBEAGDCEE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:DD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR162875.18309473	83	17	2674	60	100M	=	2350	-423	TTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTA	3<1EE>JCJJE@<DHKJF<LIC8HDJKLFEFJALGJDIKKKEJKLLLKILLKLAGGBKKKLIJIJBJKJ?LGGIIKGJHJHHK@GHHH9GJFIFGHBCCB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.13475139	147	17	2680	60	108M	=	2401	-386	CTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCC	95=-2>:2>@2+4B>E>BBDDDAD@DE:=D9CG<AD=ADDHBH>D;'<EIGMBADGFCIEMJIBIGDE<HDFHEELAKDCJJCEKIKHIJJIFIEGGHGFAECDEEF9	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H@
+ERR162875.10770274	83	17	2690	60	100M	=	2415	-374	GGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCC	=DEHFIFKGFILFELLKLJGKHKJHGJKJKHKILIKK?JCMGFKJJKHEALLJJMHFCIJJJGKKIHIHHIIIILHMJKKEHIJIHJJIHDIHIGFB@>A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR242943.312088	163	17	2694	60	100M	=	3037	442	ACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGT	ABEEHHIIGEIHGL9FIIEMEFGKJHJIGKEJGEHDKJIDFDIHEGIGFGLKEIGHJJEGJIACGDHGFJHCHIIIIFDELGIF9HFD;EKFHFFEEFC.	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242943	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.5443750	99	17	2699	60	100M	=	3006	406	CTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATG	AAFG?FE9<3/IDDJIHBDEIL5;JHGH:/>LJHD?JH@F*CJ8H@.GII>IHB:EJL82B81I7?BA?E;8H>;J:CHK@2(HDH.7C/47.48A(+8;	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243059.1325819	147	17	2706	60	100M	=	2332	-473	AGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGC	2DDDGDFFH?DIIIGHGJAHGJJ;JJ8HJ>IIBBIJIIJE@GGJHIGIHI>FFDJIEHJFKHJJIH@IHFJIIKFIGICHIHBHHHGFHJFGHDHFFAB@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243059	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR162875.5601349	83	17	2710	60	100M	=	2389	-420	CTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTT	D@HHHEGEJJJKGKDKJLIJKIJHMGLIIIKKIJMIIJJMIJKJKKOHHGJI@MMIHJIJIGILKHKLKJGLKKKKKJKLIKIHJJGHIEIHGFGDHCBA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR243019.480835	99	17	2711	60	100M	=	3135	523	TAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTC	??GADDHDFIHIHFJGDDEHIHHGHIHEFHGDEGF?GEHGJEEGHGGFFBFEEFEIIJHH@FFKEIHKIEHHGKHGBIHIHFFIHGHKCGKDHFFEFBCD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243019	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.13634813	147	17	2713	29	100M	=	2414	-398	GGATGCAGCTGAGGGGTGCCCCTTTTACCATCTAATCTGTGCCATTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAG	F,7?1D.JK>H@80DJA3.K6LJ%7IHJH85ADIDFB8K8300(66AAGK;<JGAL<=5IGDJ<L;<G=/HIKEKIJJJJJ6IDBGGKD<DJI7>;:EEE	X0:i:1	X1:i:0	MD:Z:23C19C56	RG:Z:ERR162872	AM:i:29	NM:i:2	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:D@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR245049.1543898	99	17	2735	60	100M	=	3077	441	TCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCC	?DFABEFFFHHEGGJHIHJIHHHEFGEEJHHIHJIJEF@IGGGJFFFKHKCFHIIIKFFJGHHJIHEMAJJGIGAKIJHGFE5EII76IDG>;?FE<D@C	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245049	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BH
+ERR243035.1445358	147	17	2748	60	100M	=	2405	-442	TCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCC	AEEBAGFEEG<GHBEHGBFFKHGEFEIHJIDHBHIGGHDAIKCHF?HLGGKEGGJIDGJDHGGJIGJC?HGGJ@GGGJFIAHGHIEE>AHGIIFFGFE@?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243035	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243027.576419	147	17	2778	60	100M	=	2434	-443	GGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGCCCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAG	:DCC@>DCC1HBEEBE=>/;:4;>*E?FBGB-IGEC@>BIHH9#F<AJDHBH;37GH4>0H+2?@FCI4A>HAGHBEDFI<J>JDHDEDDDJGI>BAECA	X0:i:1	X1:i:0	MD:Z:43A56	RG:Z:ERR243027	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.1633327	83	17	2786	60	100M	=	2618	-267	CCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAG	=DB<FG@HKFADLFJCJJ1ECHFGBIJKL9DMJLHEJJ=HIIHLKKLKIDEKLKLIILLIJDJIEIIJJKILHKKKLKKIFHHKHJFGFIIHGFEFCFGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR243007.788439	99	17	2789	60	100M	=	3067	377	CTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTC	?FGCDGDFEIFFIEGGGGIEFKGJFKGEAFGIDGHIHHJDIGFJBHHF@FJGHK@HIIG>CJ@DHEHGJHBIEHHFA<ICFIJ=IHHGIG9E;CFBJE3E	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR162872.9718342	163	17	2810	60	100M	=	3044	333	CAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGA	ECGFIHHCIJFHFKIJLLLLJ=LKKLKDGMFGFJJHJL?3MDGKCKMGHJ4KGKKD;FHBIDDJC?E9AIE0IL2MC1KJG8KG9L@L5)B0GC:=GAC&	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.474429	147	17	2812	60	100M	=	2447	-464	GAGCCGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATA	E.E'AHIIB:I5JC;F9)K>':'>:;BHHLKJKJ<?EDEIDJFG7MI?F<LIAH:JIIJLHFIKKHJEIJLEDKJHJIDEHJGKKDI@IGKJIGJIHDBB	X0:i:1	X1:i:0	MD:Z:3A96	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243067.1030440	99	17	2824	60	100M	=	3191	466	CCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCC	?@E?<EBEFFFAEAFGEFIBEEGG?<<;<J2<E=IF;GG:F8E=29B;?FB75B7HA-:=*F92?AG</0C*49>6=BH7FII->G9DF5?.;*7A0?==	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243067	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR162872.17163139	83	17	2828	60	100M	=	2564	-363	AGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACA	4CGHB?HDB8CJDKHLJJJBJHDJHJJMIKAFIEMLKJJJIMJKGIILLMJFJIKJMGJIMGDIKKJHLLHEGFKJLHGKKHGGKJIII?EEGGCCGDEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.20228886	99	17	2837	60	100M	=	3084	346	GAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGAGTGGCTCAGATACAGGGAGGGGCCCACAGCTCGGCCT	@CG8DHF:=7?5GBAGDGAL9I9JB,BIHHH=5<FCJ?@-LH>B,8;4M./MK7E/.GL(B.*.88J1FBFJA6CDB;H57L&K:)(GI1B405B.-17)	X0:i:1	X1:i:0	MD:Z:62C19T17	RG:Z:ERR162872	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.5990783	83	17	2843	60	100M	=	2544	-398	CAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTT	DFEEAFH@HGJHLHKFKJLJLLJKKIMKJFHGIJLIEJJJLGLKDNHCKJKJLKLLEAILHLHJHKIFHLLKLJLEHLKKKKHJJKKICJJGIGEGIEBD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR162875.26247502	83	17	2858	60	100M	=	2581	-376	ACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGAC	<DEHIIBHFHEKJKHBIMJLIHJIKIKKGIMH@LGJIHM=MDJILDKJKMMIJGHLLCLCJ;KKILKHHHKLICJKIHIIIIDDGJFCIHHGHF@EEFFA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR243015.596677	163	17	2861	60	100M	=	3240	478	CAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTG	?CEDDDHHGHIFG>HGGAGICIHGJJEHGJ@E>?ICJAJ@EIIDBIHLBF@IHKI2DKF=EIHKFIHLJDK=CHH<KEHJF?D@3IFFIDGF4EDEEB<=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243015	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.13236661	99	17	2887	60	99M1S	=	3218	430	TCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAG	DCGHBIFGJIKJKDEJLKKKJLIIIJJLJLHMFLJGMKDIJMLFKDKKLMLHJMJIJJKJMKLMGJE:JHJHKMALLMHJFLJ8KJFFKK/JFG?FGD.*	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243051.1973649	163	17	2888	60	100M	=	3111	322	CTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGC	>DD<B:7C@F8B95FFIDGGE-F:CD?;EDCD;:55EH?EI?=JC>J@G:>@C?F;,<D=FJI;?9<HE*<IC0HG1D4<IDA:82G./0*FF,@DD8:3	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243051	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.20693133	147	17	2892	60	100M	=	2588	-403	GGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCA	BC6HF<DAGEGHJJIAGKG1?DKKHJK>CGI8G;HDHBJ:BJDGHJ>LIKA*@GIIF@BF::FF1JJBLCJDKGBJJJIFFJIFIIJDJ:IDJJHJGDFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:DE@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.13732136	163	17	2900	60	100M	=	3298	497	GTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCA	DDHBIJIHLHIHJJLIJIMILKKJLGJ:JKLMBKLJLM?AHFJGIGALJKLHIEI<GJLMM?LLLKJDIJMLLJHJI1I<K*?:L5JG9:1HHHHB1EA1	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243063.876263	83	17	2900	60	100M	=	2589	-410	GTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCA	2?EDG@DCHAE;F:IIKHGHIHHHIEJEHKHCHJJJFJHKIIHJEFI<IHKFBHHIFIMGIECHLE?IIKIIJIGHJIGHIEGIJHIKHIIHGFHFEBDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245032.287858	163	17	2905	60	100M	=	3258	452	TCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGC	?DEHEECFHJGFBKDJGHHIGIHDGGJBGJHGD@IHEAHGGHFD?HFI@FFDIGJFGIICHJAEIGIIGGC<CDIIECGEE:GG:EH:GHGCIFGGB8B9	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245032	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245038.1772750	163	17	2917	60	100M	=	3261	443	AGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGC	AFEIEIFGGHGJIHIAHIHKIEIICEIGJHIIHHGIB@HDDIHJGJIHGIAGIJKGGFKH@GGK-CHIHF6:J@G:GGJ1HHDCFGJEG>FIEHC94ACB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR162872.24480599	99	17	2922	60	100M	=	3229	406	CCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCG	BADEEEIHHFADFGJKEJHHGCHEBGJHIIECGFKJLLIBJFJGE<.KFA;JHMHBGCFCJMKC7;LKI49J@>1KD2G)BC1AC>KAHF77+4HC3:@$	X0:i:1	X1:i:0	MD:Z:99T0	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243007.1511398	147	17	2951	60	100M	=	2622	-428	ACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGG	-;EDIBBIHHFEEHC?DIJ:IIHJIHCHJB2G:HIELHJIJHI?HCHEIDJGDJFIHHEFGIJIIHIEIIHJGHIJHHHJIIIHHKIHHHGGDEHFFE>@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243039.1477734	147	17	2955	60	100M	=	2595	-459	GACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAG	@BCHBEAED@C8EIH7EJICIIIGFH0GGKJIJGL<IHEGGHH=JKJIKKDHJKEJFHJJDFKBEKHGGILIHGHIIHIJJKHHIG>GAEIIGGFHEGDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243039	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR156632.12418699	83	17	2962	60	100M	=	2634	-427	CCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGC	6:FFAGIJHKKLMLJKLKL;9KLIGIGLJIJKK>JKLFDMMKLHJKFHKLLLJMJLHLMFJKKLNKMKLLMKNJ>JIKJIJHH5KIHFLH=JJJIHIECD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR243091.852212	83	17	2967	60	100M	=	2575	-491	GGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGA	AFBAE<@GIG@H7I@5=?HCIEFJDHG?DBFAJDHJIFE0IDCFJIJFI@HAGJIGDCHIHGGJFCEGIEFHHGFHE?G>GGBGDIEFG=B>GHA=FFE?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243091	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243043.1629476	163	17	2977	29	100M	=	3421	543	TGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCC	?E?>CEEFDIGHHFGG>FFGJEGJGFJHFHGECHG=FGJHHFGIFI@K>IEHFC8DAGLIF>JBHE:AJHH:I:G*>BCDCDB8GHF6.5@FF10;@E92	X0:i:1	X1:i:0	MD:Z:99G0	RG:Z:ERR243043	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C@BOU[PL
+ERR156632.1508798	83	17	3006	29	1S4M1D95M	=	2587	-518	CCCCAAGCAGCAGCCGGGGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTCCCCAGATGCCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCT	<'&*(-+/?*88'-%%(((+KB/N.G)9.5E39>/;,F</*?*3K20GK703/('0'1G9)/,'2KIL6A8.G?I8LFC@>BHLI?CKH=BJ?FEE==DA	MD:Z:4^C6C0A2T1T36G8G36	RG:Z:ERR156632	AM:i:29	NM:i:7	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@FEIG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.5443750	147	17	3006	60	100M	=	2699	-406	CCCACAGCCCCCACCTGGGGCAGGGAGGAGCTTGGGGTACAGTGCACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCT	@6F1-8/B%#K/,H/4A3EA9@KI7.1F049E82))G61;/,-H*C<)9*JB;.*E=;;9/.E8IGG>H*K3GJ6F2<DGEKDLHEJJGHIKHH;IEBFB	X0:i:1	X1:i:0	MD:Z:8A0G7T16T9G55	RG:Z:ERR162875	AM:i:25	NM:i:5	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.23244382	147	17	3014	60	100M	=	2668	-445	AGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGC	.;CF8@5GG4K=9.?L@/KB8)9G>56:D6:AGJ6H:CA;L5KK;@5IGBKB;:>5KHJLKDGHMDLJJKIJJLGLJJJLIKKKKHIKHIKIHHJGIHDD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242943.897194	147	17	3015	60	100M	=	2661	-453	GCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCA	+EF0D..G8E:D9FIA?GB;3;ECG:HG@2DBJ/F;;;CG?GFC;7H@*DFA=I+FGGJE?IILHIGJGKIGJEJIIGHEFJIJFHKGGJGFGHEIGEEA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242943	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.25542568	99	17	3017	60	100M	=	3110	192	CACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGG	BDDCHHFFEEGJHBEII0KGKE<GIJFGJIHEKKEJFGIFJF883?JJIDJKLJ@E:JKC=GLKLGLMHLJGILHGIFIKD;HGE<DFGD8ED?2AGC?@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242971.169330	83	17	3021	60	100M	=	2649	-471	TGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCCGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAG	BDBAAF>GEECF?D4?H9GGHH@:I;EFHB=GBI6GGE<+AIEGJBDI:9IGDJAKEHEJHCBIGHJDGHGFJFHIGHFAIFFJGHGIEIGHHGFEBBD?	X0:i:1	X1:i:0	MD:Z:62T37	RG:Z:ERR242971	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243039.71589	147	17	3030	60	100M	=	2654	-475	GAGCGGCTTGGGGTCCAGGGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTT	<A8(((2=79-0E60>.2*D-E;*DH>GCHF<H1/8-;C5?I?IC@@FLGEHIHGGIIIJHGIJBIJJJEAIFEKHHFJEJIIJIHIDEIGEJEIFHGA@	X0:i:1	X1:i:0	MD:Z:3G0A5T3A3T81	RG:Z:ERR243039	AM:i:25	NM:i:5	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CE
+ERR242943.312088	83	17	3037	60	100M	=	2694	-442	TTGTGGTCCAGGGGACAGCCCCGGCCCAGCTGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGC	+A4.GB,#*)(%=80?.D&?H514A<1*4)/E42JFBI56GGHIHKGIHIIGEHBFJEFJIJ3GHCFJFIEIDHJGHHHHDDIHDJFIFHIFFEHEDDC?	X0:i:1	X1:i:0	MD:Z:7A3T6G3T6A70	RG:Z:ERR242943	AM:i:25	NM:i:5	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.4053670	99	17	3038	60	100M	=	3280	341	TGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCA	CDDIHGGHILGLKJJJMLKKLKMLLLILIIHKIMKLMMEKLKLJLLKJNLKINIIGKJLJNGJMJDLLLHKHJILKINFFGJLHILKMLKKFHIIHEBFD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR162872.9718342	83	17	3044	60	100M	=	2810	-333	ACAGTGGACGGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAG	/?.2+B;7$&E)2$?@/;F.8>,+@3IEA;IBAJKHHDKFHJIKDJJDFKI;IKIIAIHIKIIBKGLJKLJIJHHIGGJGKIDKEHHJGHGHIEEBAGHB	X0:i:1	X1:i:0	MD:Z:9A90	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243063.161207	99	17	3057	60	100M	=	3124	166	CCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGG	AAFHGFFFIFGIGIGFHHHAJHIHGHIJFKGFHICDJGHIGMFHGBIJEKEHIIFJJHLHBGIIGJJIIJKHABIIKHJHFFHIHIMIGJEDJFEFFBFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR243007.788439	147	17	3067	60	100M	=	2789	-377	TGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTC	>=4EGDHEACGIHKIKHHHHJKGIIHJCIIIJHIJG;LIHHKGLKIJJHIEJKLFMGJGJKGGGJGHIJJFEFHJJIJHHIHIEIHKHHJEFFFGIFEC@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243007	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR245049.1543898	147	17	3077	60	100M	=	2735	-441	CCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAG	CF@GAHEHDEJFHHGHJFJKHHG=KFDKHHIIFKIKEHACHDJJFJEJBJKIIHJHHHJIFDFJIGGJIHIFJHAIKGIJFHHFIKIHGHIGFIGGHGDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245049	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR243031.650799	99	17	3080	60	100M	=	3507	526	GCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTG	?DBFHDH?DFIBCIEGEGDFHAGCIIIE=GHGGFHIDD@IHCHHJDFEADDE>C8EGG6:JIEL?GG8BI@G2EGIHGI=GIHEIDKJDGJIFEFC@>BD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243031	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR162872.20228886	147	17	3084	60	100M	=	2837	-346	GTGGAAGTTGGCCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCA	6+0GEG;HD?)'@8K0/GJ89>B=:GILFGD3HB<<H2:>LG>GC5GBGD?7<I>CIE<BHMEJEL?:@IJMHCE8EILGE:BDDGLGGGKKJEFH@GFB	X0:i:1	X1:i:0	MD:Z:10A89	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.10091814	163	17	3092	60	108M	=	3418	391	TGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAA	:?EBDCFFCGFFGHHHHHFHAGFGGCGJKEGJIHJJJEEJKJE?DJEHKFJMDJME>ECAHADBFDCBDAKFGEEGFDEFC@AED?DDDD'>><B22B.<C?D:=6BA	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GH
+ERR162872.25542568	147	17	3110	60	100M	=	3017	-192	CAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACAC	;EEBDCFGFKH@HGLJEJBE;LILLKBIGJJLB=MMBJGKHKFLKJLFHKICMJJHIMIGEH@JKLLFILLKLJGKMHHJJIKJIJGHGHGHGHHIHH=<	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243051.1973649	83	17	3111	60	100M	=	2888	-322	AGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACC	@FCFJGCEJJ1FEJIACIDEFFDCGE@;B?EJHJ<CHCEAJKG:=BDAIHHFEHAEJHEHF?:H?IADF7DFCHHE>>CKGBF?HE@EB@CF>FGDED>@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243051	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.1328730	99	17	3121	60	100M	=	3494	472	ACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGG	BDHEHHGIDEIHHAHJDDEFIHIDAKI<<5IJ;JKEB3F=CFCJHIJHEJIKCLFLBEC<JKG6=IEH7BBLCIEHF=ADFF88>D2GIEH5A4FCH53=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243063.161207	147	17	3124	60	100M	=	3057	-166	CTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCAC	EDFGEDEJGH@HIBCMHKJIICHGGIFIGKDGIGIFGCKGIHGIHFJCHIJJHHFICJIGGDJDFDKGHIEGEFFFFGCHEIEIEGHDEGGGC?EEEFC?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243063	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243027.47729	99	17	3134	60	100M	=	3547	512	GGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCAC	>?FEDFFGGIHGJGAJEHHFHIHFIGFJHHJEJIDHKCIIJFKIFJHFJBGCIEFIHIGJGFEAGGJFFLHJHGAIIBIFKGIEAGG?IIFFDHCFDE9C	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243027	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243019.480835	147	17	3135	60	100M	=	2711	-523	GCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACG	EFB;GBGHGKIHHFJBHEBIGJGHHHJLIG<FIFHLHHLKJIHGHGJHEFHIFGEJIIHHGDEDGFGGBGKEIECJHGIGFGAHIIIFIHGGHIHFHB=A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243019	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245041.246570	99	17	3137	60	100M	=	3462	424	AACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCC	?BEAEEBGFH8BDFIDGBJEFBHEFFHJEIIFHJHIFHFHB>?BFGGDEHGB@:H?>?=H@CGHEBJDHDFCEEGH98AJHB?GAGEEJ9EDGHBE736?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245041	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.19273677	99	17	3143	29	99M1S	=	3488	443	GCAGGTGACCCTGGAAATCCAGTCCAACTGGCAGGAGGGCATTGAAACTGGCTTAACAATAACAAACCATAGGCCCAGCACAGTGGCTCACTCCTGTAAA	A.<='.HF8B@>I<H3*H/4.CH94I*+*0'K,:/))'.B,-G041A*)/@3L(=I*61-4)*4)2E8K()8.L0>45)D3I.,8&;J;(174HBHEE).	XC:i:99	MD:Z:16T3T5T8T15T4A3G0T2C10G0G14G7	RG:Z:ERR162875	AM:i:29	NM:i:12	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@Q@@
+ERR243031.386955	163	17	3144	60	100M	=	3511	466	CAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATC	ADHDDHGGGGIKIGEGDIGHJEIGGHKIJDJHKIBLIGIHHFKHFIHJJGDGEDHHEHHJCJBDFDHIEDGGBH:JCGGIHIEJHEGEFHAGC=D@C3=B	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243031	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR243091.881299	163	17	3174	60	100M	=	3491	416	CAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGA	ACHCFJFGHGEFJFIHHJIJGEFEIHHFDJDKHIGHHGGEKIIGAJJIHJHNCKHJJJHJCKIHJAGJHJIHGKJGHJEEEIGFJIIHHHDGDHEDBGEA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243091	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243067.1030440	147	17	3191	60	100M	=	2824	-466	TGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAG	@?BD=<9$=>-74&C<L;>I@7FIE8AHA5E>HFIDFKJ8H0<JG:CD8HE=F1ID9H:G>BCDHJFGHHH=ACHE<GIFHDGHI;JEFGI>GGDHEDD@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243067	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.18600710	163	17	3209	60	100M	=	3375	265	CCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCC	EBFFFKIJJCIIKIHILILKLLLJIDKJGHIIGJLLJCKKLKLGIKGKKLKLLIKJLEKIL2LJKBLKHLIHJIJIMJLKILEHLIFLJILFGJJEHGF3	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR156632.13236661	147	17	3218	60	100M	=	2887	-430	GGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTG	>ECDFFGGBKJKGK@CLKJHJJ<HGJKKKKKKIBHKKLIGKLKLKLKHIKKIFHKHJIIHIHKHKIIEKLGKJGBKFLFFGJJHIKHJIEGEFGFEEDFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.22586072	163	17	3226	60	100M	=	3490	362	TGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCG	EFCHIIHH@KJKKHJIJLJKKLLKLGHIH3EFL<LICMKJEHDI=LK@GKJHJFKJLGEKFMDGL:ILJEAHJKIBLBBEGL?JIJIHIB:I9CD>F;F<	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.24480599	147	17	3229	60	100M	=	2922	-406	CTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCT	B7H:=HFGAGBHICJCLLHGEHK>?KHKIMHI:MEDGFLBIHIEIJLJM=IGLLJFHLKIKIJHLHFIHKLJIEKIKK+KHHIJILJAJHGHDIAAFEED	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242963.1107552	1187	17	3234	60	100M	=	3565	430	GCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAA	@ABGHECGEFGGEJHIHHFFIHGDKGKGHLHHEHHHDJHEHIHGLIKFKGCJHK=ELFEKHGKFHIGLJJKKHJGGIGIGMKEGHHHHFIG?BGF?EF?C	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242963	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AH
+ERR242963.383553	163	17	3234	60	100M	=	3565	430	GCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAA	@DEGGEDGGJGGGKJIHIFFIHGDKHKGHLHHEKHHDJHHHIHIJEHHKGEJJKFGLFEKHGGIHIILIFKKJJGGDJHGIKDGGGGIFIG?EIF?DEAC	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242963	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CH
+ERR162875.6771266	99	17	3240	60	100M	=	3423	282	AATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATAC	ABEEDEFIHFHIGFHGHHKHKKHIIG>JIJGKHIHLIJIHJIMKHLKNJFN:HLHJMJJMFLKKILKMMK?GIGIJHI@GFGJELEAHFIFKGGFBFCC?	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243015.596677	83	17	3240	60	100M	=	2861	-478	AATCGCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATAC	5@C>*8FI6<K3DEC@H9E>D:EBAG:GHD>F8;FK;G>FIIJH:0C<9IIAAIF>J>JIFJEE?CHHJD@FCGHIFJ@CA;G@:GFG@EIDCCCBC@B?	X0:i:1	X1:i:0	MD:Z:4C95	RG:Z:ERR243015	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245032.287858	83	17	3258	60	100M	=	2905	-452	GGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTG	CCDGCEFFHIAJGGFG>JCKHFKIIJGLGFIHH?HJFIJ>HHHHDLIJKGKEFMHFJKHJEGEIIGAIHLEEKDGEFGG@DJEEEGGGFHHFJGGG@ED@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245032	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR245038.1772750	83	17	3261	60	100M	=	2917	-443	CAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTG	EEDEFEDFIBGGBFK;DGHHGIIGFIJCHIGGGEIG>IJIIHJGHIFHFEJHGHIFJECDGHHAIGIEGJCEGEEGEEIDFEFGEEIHCIFFH@EEBDC>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245038	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.4053670	147	17	3280	60	100M	=	3038	-341	GAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCA	DCEFGFCJIHCIGIFKL@LKKLKKEKL=LHHIIJMKHLFGHKKKCJIMHGMGGHGIJIGMHHHGHIHLHKMIKJCIHKIHKJCHJGGIFJFFFCFFBAFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.18994301	163	17	3289	60	100M	=	3627	437	AGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGG	EFFEIGGKHIKHKKKKLJLKJJJKILJILIJJJLMLDJLKHKMIKJJIEHIHKJJJEEHH?LKCKJDJLHDLLJBLJGJKKHHIIIIHKKI?JCCGHBGD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@II
+ERR243003.1151913	99	17	3289	60	100M	=	3442	253	AGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGG	?EDBEFFIFGGFJIGIIHJGGGGEFIHEJFGHIHHIBEKHDIHDEHIGGFJGFIFFGFFLJIIJHJBFJHFJJJCKGGJLHHKEFFGDIHFJIEAFGBEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243003	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GG
+ERR243039.1531670	99	17	3295	60	100M	=	3652	456	AGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCT	?CDDDEHGFHFDGEHGGGIHHEFHHJHGHCABGIEIHCGHG>F@HHGHHECFDJGIICEFBFJDFK0FBGGDKJEJIEEGIGGIEHHFAID38FDDADE<	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243039	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.13732136	83	17	3298	60	100M	=	2900	-497	CCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAG	=FHG?JAGGA=G8K?GJ@=EFG@LEDAAGNJHMEEHIHIIIJHH:FF:HA@EKDL<>?FIJJEKEFKB@GJKIIHHGHCGKJJKG?HGFIHHEHGGEFGA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR162875.12766080	99	17	3309	60	100M	=	3630	420	AACATGGTGAAACCCCGACTACTAAAAATACAAAAATTAGCCTGGCGTGGAGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACT	BB;EEG(>HFFD,F>24*HHG4;GEII3;@IDD3??GDFJ4AF;/K1BK:)B6G2GFE9K2G98IF,J?H=JK=2GI9K.-<98HJK0<H-1<A)77@?;	X0:i:1	X1:i:0	MD:Z:17T32T49	RG:Z:ERR162875	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.14666027	163	17	3312	60	100M	=	3577	364	ATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCT	DBHBFJHGHIKJJDGKLHJLI@JJJIIJKIJJJJJJNLKLMMJDILIHLGLCMKJLLKLMKJHJMLKILMMFJKGLLDIIMKMMIKJKJHKJLGAGHFFG	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@I
+ERR013140.11093052	99	17	3330	60	93M15S	=	3585	362	CTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGCTGCAGG	@DBEHHHEFEIIIIIFGGCIKKHII@DDG7CC@9=ABBAAGBDCGCADBAB?EC?G?ACEB@@;EB<ABD<<A=@CB9DEAG<BFC:53>:9-=4$1;/12%27+28,	X0:i:1	X1:i:0	XC:i:93	MD:Z:93	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242963.128219	99	17	3359	60	100M	=	3766	506	TGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGC	?EAE?GFFHHGHIECDGJFHGGHJDEDEIHFGAKKHJHKBGFGJDEFGGHKJJHKGHIJIJIGGLGJBKGH@DBIJ8I==FIIFJGIE@JFG?G>>@CB>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242963	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.18600710	83	17	3375	60	100M	=	3209	-265	TCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAA	-EDHDFJ@DKH@JKHIGJJGCMGLEIFL9GJ:KDJJAIMAHJKIJLJELILLLDDJIEIKKHBJKLMILJJHGKGCIIKHLIJJHKHJIIIEIFGEFGBB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR156632.14578469	99	17	3384	60	100M	=	3677	391	CTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAT	=A7AH;9<AJHD9GC<,3CJ2AGKHDJHHDE:AAK1E=I;':<KJC3=*;7;;F;A;6L08;,J9/,EBHJH;;JI7DL(/8D:K@JG=*2A9DH@FD:*	X0:i:1	X1:i:0	MD:Z:99G0	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.10508568	163	17	3407	60	100M	=	3608	300	CTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAA	BFFFGDGGDDJIJIIHLIJGLJGBFGIHIIHKGLJKKILIIMFKDKLIIKMKJILJKILKMLLKKMJIKJLHLGHJKICKDIKDILEJII@IIHGGCDDB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@EGIAKKKKKHIIH
+ERR013140.10091814	83	17	3418	60	42S66M	=	3092	-391	CCCAGCTACGGGGGAAGGGGAGGGATGAGAACGGCTTGACCCGGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAG	/$7<2<<8-)$316+$&$#6>;.55-+.&132$*8344:$:)$88<?@2@@;;67?<;>07;:B<>A=@=A;@@:CDB@EDBCCIGBIFIIHJJJHGFFGJHIDCBD>	X0:i:1	X1:i:0	XC:i:66	MD:Z:0T65	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243043.1629476	83	17	3421	29	100M	=	2977	-543	GAGGCGGCCGTTGCAGGGACCTGAGACCCCCCCACTGCCCCCCAGCCTGGGCAACAGAGTAAGCCTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGG	B.C;((:#?3H.3*.11-1').:.8,&#'/'9J1;.5B7((F004D9/GHD0>D>=/;-;EG6#F@2E9/>/3CFCFDEFFEFEFGFJCJDHHFFF@E@A	MD:Z:5A1A8T2G6T1A1G7A1T22A36	RG:Z:ERR243043	AM:i:29	NM:i:10	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.6771266	147	17	3423	60	100M	=	3240	-282	GGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCT	@@0AF,6EG4<:.>>F.?H6F8B.4:1@5JH<G6CF.F4KHHEGK8LJKB>GEHDCBBFKA?KG;A:JEA>HGHIGIHHIHIGIILHLHJKIGGGGHFFE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR243067.219795	99	17	3430	60	100M	=	3486	155	GTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATT	?CAFFDHDHFHHIIFJEGIHGAIHHHHIIGGFIIFJIGHIIJJGIHGKHLCBHIFFKJHJFIIJHFHGFGDIGGHF9BH?A7G9AC@HDI-FG9DB9A@>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243067	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.12181062	163	17	3434	60	100M	=	3613	278	CAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCAT	DDHFIHJJJKIKIGKJHBKKJILLGIJLKKINKLKKLKJIJJKMJMGHJKKJMLLLJLLMKJHJJJJEIKIJ;@?EIGH@JJGHCIB?HAFDC1>@H3C3	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.15307937	163	17	3442	29	98M2S	=	3853	510	TGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATAAAACAATTTTGGATTTAGATAGAATATCATCTG	BEEEAEIFH@K?BIGED@HJ@/HI9LIKJJCHAEKFGM?EJ:CJCC=EI:FKK<4FB@H=H=45)-*;I2+.;IGB</&&8($4)3A*$G1E;5@,F7.3	XC:i:99	MD:Z:66C1C2C7C2C4T1C5C2	RG:Z:ERR162875	AM:i:29	NM:i:8	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@FS@@
+ERR243003.1151913	147	17	3442	60	52M1D48M	=	3289	-253	TGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTG	0>B@A7I2:AFI==73B2G9HGFEHL-IDDHCCDEI>?DFJEDIGAEEEJ/5FGFGFGGFFFFIHIFJEHJGGHHHIJKHGJHFHCGIIFEFFHIFFGC@	X0:i:1	X1:i:0	MD:Z:52^A48	RG:Z:ERR243003	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@efefefca`_]]@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245041.246570	147	17	3462	60	100M	=	3137	-424	CCAGCCTGGGCAACAGAGAAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGA	?8/5F*9EA40GD0G8/:$DC:2G-C;7A1.;@E@E=FDD7EFDCHKCHAIFDGHBFFIIG=JHJ?CGJICF5GGHGGKEIGBHBHGCFCDEEAGAGED@	X0:i:1	X1:i:0	MD:Z:18T81	RG:Z:ERR245041	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR243027.1264030	163	17	3470	29	40M1D13M1I6M1D5M1I23M1D9M2S	=	3836	465	GGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCAAACATTTTGGCTTCCAGATTCAAATCCCCCCTCAAAGGATAAAAACGCGGAAATTCAAAG	A?FGFGGIGLFEGJGHIIHHFIJJIHIFIGGGGFJF&*0>.*J*1G>F1?**6.)1%/G$/<%*/*E*(I4*)0B+=&-/-*7545)*55.GG)C./E*)	XC:i:99	MD:Z:40^C1C17^G2T4T3G0C7T1T5^T9	RG:Z:ERR243027	AM:i:29	NM:i:12	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:CA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IEb@@C@@@@@@A@HL@JfC@@@@@@dICcL@@EU@C@@@@@@@@@@@@@@DC@@@B[@@
+ERR162875.18637663	1187	17	3471	60	100M	=	3780	408	GCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGT	BDEDGHEHLHIHHJFKJJ:GKLGKDHEJCIJGJJIJ=CHCFHJGGGGCH@EJIFDGK@C;DJJ8:?KIK;;LFE=E4<-I8AA4C=F71AIF8H9=FC8,	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.6808869	163	17	3471	60	100M	=	3780	408	GCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGT	DDDFGGJHKGGHKFIKJLLGKKLIIJIJIIJHHJKICBJJJFJAGIHBLGBFIIIKGJ?CLFFIJJKIKDCGKEHND<GA8JAJJCIDFHIHI=D=F:E6	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.15409720	163	17	3484	60	100M	=	3810	425	ACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCA	DCHHIJGHKKIHIIJHDKIJJJIGKHJIHIJJIIFHIGMA@9IEJ7KLGJDHKFIKKGKKJAL>6DDICEHHAIDBIJIFJEIJDL@FFCFF9HH>EEBB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243067.219795	147	17	3486	60	100M	=	3430	-155	TCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGA	/B7E4=5:DGFFFFFEFFFEHFKGKFIIGGGHHHJJJIJKLIGHJIHHGFIIFHKGJJFIIKGEGEHFEAJAJGIFFGHFIHLIGIEIGIEIEEEDHFDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243067	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR162875.19273677	147	17	3488	29	6M1I93M	=	3143	-443	TGTATCAAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAA	+CC-*98FHHF;I@(:DC1FIJ:J16A8>)2J3KC3G;ALH<@L<J>F61G6ICB?CI;DACEIBIGG4JDAI:GHGJDB>JFJEBIBC:BGFHHHFD:B	X0:i:1	X1:i:0	MD:Z:3C95	RG:Z:ERR162875	AM:i:29	NM:i:2	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@eggeZh\CT^[HY@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR013140.22233344	163	17	3490	60	108M	=	3784	401	TCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATA	:CEDCDEGGHHHIIIIIGHHEHFJHHEEEELJJEIILHDDEKJIHIJKGJKIEKIHGMGGFEFFFI>LCFHLLHF?DIGEFFJGCFE;HEE@AGCJHIIIIHCF?F>@	X0:i:1	X1:i:0	MD:Z:97G10	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.22586072	83	17	3490	60	1S99M	=	3226	-362	TTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGA	.*71578ED=H6?H>D?,DLFJ7B7A=II5C=@JGHEAFIHIGIHBHCDHBL6EAHKB@IGCCEBCDB@CIJDCHEDGHGHEIECFFGI@CGFHGEBGE@	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR243091.881299	83	17	3491	60	100M	=	3174	-416	CTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAA	C5;=CAAEFDFEEEEBCI;JFIKHGHGHIIKGEKGJIGGIJG=GDIKGFIHIJEIHJFFFFDDDAI>IDJDFGFEIFGHGIFGFJFIDFGEHGGDB@A@?	X0:i:1	X1:i:0	MD:Z:96G3	RG:Z:ERR243091	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@PSRW_`_^
+ERR162875.1328730	147	17	3494	60	100M	=	3121	-472	AAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAA	0ACDFDC9GCF?CGKF:GHLIHJKJIJNJIKIEI2B6FJJJIALHIJKLKHLJKIEJHIH>DGBKJLIIJIIKDIGGLIIALIKHGGHKIJGJHFFDC?E	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@GHIJHF@IDF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ADCDAH
+ERR242955.586810	99	17	3506	60	100M	=	3917	510	ATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACG	?@CCEAEDBDDDEG6GG-IFFCC8FFGEADFHFIHFCA<GJEA<FHGECG@J@DIEIFGCJIDI>JFDFI9EI6HE>F;BBFGBF4FEAEC>ACEA7?A7	X0:i:1	X1:i:0	MD:Z:81G18	RG:Z:ERR242955	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243031.650799	147	17	3507	60	100M	=	3080	-526	TCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGC	>GCH1GFFHGHHHFGFGIHHHEEIIIFI;GIAADHIDFFI@HDHAGD>BIAHHIEFBID>FIEFHHFGHDIFFHDEGGEFDEEEFFEJHEGEF@FDD?CA	X0:i:1	X1:i:0	MD:Z:80G19	RG:Z:ERR243031	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.8738223	99	17	3511	60	100M	=	3914	502	ACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATAAATATACGCAAAC	BDDCFBAAIEBIDBGKHE=8DDGGHGHJJDFHHD;LC<=>C=GHK<E29JIFGJHJDDH:7JAEG;>I:?IJB@@H7AHHB0:)J@H(AF:C@HA/378@	X0:i:1	X1:i:0	MD:Z:76G10T12	RG:Z:ERR162872	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR243031.386955	83	17	3511	60	100M	=	3144	-466	CCCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATATATACGCAAAC	$FC@@D>FJJJAFIJIHEJKJHA@GHKHKKHKJCIGJDFHCHFEBJAJHLGEFHGHEIICJEGGJGHFFGGJIIFCIEFCDDEJFDGEGDFDEAFHBAB?	X0:i:1	X1:i:0	MD:Z:0A99	RG:Z:ERR243031	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@IB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR243059.116527	99	17	3516	60	100M	=	3914	497	TTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTA	@@AFCGGDGFJFGEJIFFFFIGHIHHIHGIKIGEDGCGEHAI@EIEEFHCJG@JEJFHHJFHFHGJJEJGIHEGGHHAJGGEGEGDHEH?JDFHE@CDB@	X0:i:1	X1:i:0	MD:Z:71G28	RG:Z:ERR243059	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EEC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.4686821	163	17	3525	60	100M	=	3871	445	AGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATATATACGCAAACCAGTATCCTACTGT	EEEFEJJGHHIJKKLKLLJIHLMJJJJJKJJFLEILHJJIIKKIMHNJJJMKKKJIJJKLJKMKKIKKJKKGHGIIJJIKCKJJIJKJMFCHEIGEEGG<	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR242971.1136963	99	17	3535	60	100M	=	3893	457	TCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTT	?DDEFFDHGFCI5GFCFDCBGAI@?IF9A>AJHGKD<EHGKGIHE=BHBFCDGHHFHDFJF<FEDAC@7JAAGG5EEGADEHFG?<B?B8IC@DCB7>@@	X0:i:1	X1:i:0	MD:Z:52G47	RG:Z:ERR242971	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BE
+ERR243027.47729	147	17	3547	60	100M	=	3134	-512	GATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTC	DB?FDE?CAH@FFJGFAGGIEIIGKFIIICKFEGIDJIFJJFFIHE>IHDHFHEDEDCIJFEEJIIIEFHGLDFKCHHGHHIHEBHCHHHFHGGGDFDCA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243027	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.1106475	163	17	3557	60	108M	=	3858	408	CGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTAT	;:CCDDCDCEGHGGFHIEGIDHIIGGFH>IIAFJ?JDEIHHHHH?HHF8HJEK3HB<JGHHIJD<HI<GC?JIJC@EEFIFGHHIJG@H@<E:ID@JHJ=@=EEHEBD	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR016352	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242963.1107552	1107	17	3565	60	100M	=	3234	-430	TCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTAT	=:BFGE6DEFD;BDFBCJHHFGCFEEGDCJHDC:GEFBF>GFADFIKEI;F;HGFEKDGHGHAFGH?FHEH=AGHFIFGHG@JFIGGJGFGE@FEEBAB?	X0:i:1	X1:i:0	MD:Z:22G77	RG:Z:ERR242963	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242963.383553	83	17	3565	60	100M	=	3234	-430	TCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTAT	B>DAB<GDGFJAGDFGEHIHFGGFEFADFJEEHEIBHBEAJJFGCJKJIGFDILFFKHIFIHIGGF?GHGHHEHHGIFGHFAIEIHIJGHFE@EEECAB?	X0:i:1	X1:i:0	MD:Z:22G77	RG:Z:ERR242963	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.14666027	83	17	3577	60	100M	=	3312	-364	CAAATCAGAAGAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCT	BB@FDHFJFJKGHHGEIMFFIHHIIFBCHMGJFKILJIKJJLJIJJJJIJJHHJDJJJIKIGJIJJIHIDKILKKKIJJJCIHHIGGGFGFEFDEDHEGA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.11093052	147	17	3585	60	108M	=	3330	-362	AAGAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCA	:.(=>9>7>CD=C@B<D@>;@EC<DDEHBECGGGHGJHHJHKIJHHCFHLJELGDGHIFJDBJCJKKLJGEM=GHCJCHGEHGCCDAGKEFEIEIEGCBEGEBBFDD:	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243087.1477801	163	17	3600	55	100M	=	3909	408	TATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAA	A@DCG@HFFFGHGKFFHIHGDHHKFIFIDJFKBEFEFEEFFIFDGFGAGHHLIIJFKHBGIFAFHFDGEACGJIJKJ;JEEJGFGHEFBHFJGGECECA>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243087	AM:i:18	NM:i:0	SM:i:37	MQ:i:55	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.10508568	83	17	3608	60	100M	=	3407	-300	AACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAG	>EBGIFGFIJMJBLIIKIJJJJHDJIKKKJJJJJFJJIELIMLLLJJFJDKKKKIJJIIIIHIHJMIMILJIIKHHIGJIHIJLIFJIIHFGJHIIFAED	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@G@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.12181062	83	17	3613	60	100M	=	3434	-278	GTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCA	BCFB?IFBLHIHGB<IJFBGAHGHJJIIGHJHH@LILKKMIHJKBKHIIJJEIJIHJFFKLJMILIFHKGGJJEHHJJJHAHHHHGGKDGIGFHEDG@GB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.20934779	163	17	3616	60	100M	=	3855	338	TCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAATTTCATAGTACCACAT	BD?HFHI8HKHKHKIC<IAHMGHJ@JIBIH'ACBJM+IJHCD<DGE>7JI=.>EJI8&FKF+IGB7H2JI<FIHH8DJ1IIHJ?(=E>F7F=?CF5A2+?	X0:i:1	X1:i:0	MD:Z:84C15	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR242975.161746	163	17	3623	60	100M	=	4004	480	GTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACAC	@CGEHDIEIAFEFIEEIFIDFFFI?FIEIJHIEIGBEJEFDCFHGFIDHKHJJJELEBHGHBHGFGHFLGHEFECFHJHEJHFFKGAHDEAHGCIFBFD>	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242975	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.18994301	83	17	3627	60	100M	=	3289	-437	GTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTG	?DEE=HCEFHIHJIJBHJIDGHLLKIFIJCDKJKEIJIIIIHJJFJMELHHKKJLHIHIKIIIILHIJIHIHHLIHIIIKHGGHKHJGGGJFFIFHFGEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.12766080	147	17	3630	60	100M	=	3309	-420	TCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCC	:==>CF@1DIH4=GCE2L9:8A9EB4/:8JKJHC5CIH3CKE<L>;7<?FIL=D.@@HJ36==KDA?DIGLHEDJEICDI9J8LIFFDA:K:IEIBC<5@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.9446395	163	17	3647	60	108M	=	3871	331	GACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCT	9A@?C@DEEEF>EGGE?EDI?=IGEG?IGGG@HFGIHGGFFGHFEIGF6FG6H:CFGAIHJIFAA<=?HBGKGFF8FDHF@?GGIJG9CGHAGH>I.HH?;><;BA<A	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR016352	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.11081426	99	17	3652	60	100M	=	3977	424	CTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTG	AEFEHGAGJGGHFIGCHIIHIFJKGD>FHIHEKHHHAIILFDIHIDGKIGGKFJJLHJJBJFJAHGJKHLJHJADKKIDGDEKL;<JEH2EIIFH?GDHF	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H
+ERR243039.1531670	147	17	3652	60	100M	=	3295	-456	CTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTG	0=DD>=DEF;EFFEH>CEGAAKEJFHHHEKEDG?IFGAGJCIHHIGGFHDFIFEHJB>HKDIHHAK=?JEKGKHJHGIGIEH?EHHHIEGGIFF@D=GC@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243039	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR156632.301185	163	17	3655	60	100M	=	3885	329	TCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCT	BDC@EHFDFFFHGGDGGJJJKKIKFGFIIFHGEHHHJFHHIJGIIILGJIHHMHIJLIKEJIKLKEFJJJLLHLKJIHGLLLKLKDIMFKGIJJHHDD@:	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.9849990	163	17	3663	60	100M	=	3854	290	ATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAAC	EADFFGHGGKJKKLJKIHJJKIJHIJJHMHJJIIHGHKMHMJJIMHKJLIKJJIMMCILIKKLLKLIEHLJMKLKNMK@MJKHLLKLKKIKKJIIHFCDE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR156632.14578469	147	17	3677	60	1S99M	=	3384	-391	TAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGTCTCCTGCAACCACAAATCTACTC	/.D1G.8'@12H+3IKHF>JJ@';7II::8LK80HME:-)8;I=:,:1BIL0.J;I6EM2'//H4<8>I/70G1.I-005L=JI5@F>>2EE2?@E5A:?	X0:i:1	X1:i:0	XC:i:99	MD:Z:75G23	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243079.290863	163	17	3688	37	100M	=	4062	473	ATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTG	?BAFCDDCDCEFGGEIEGEIDDGHFGHGFGICHGDEILIGJIHIJCHIHHJMGEKIJEGHGGJHHIIKJJBIHEIHIIJEHGJIAHJLIJHDJFCFGDAE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243079	AM:i:0	NM:i:0	SM:i:37	MQ:i:7	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR016352.12571677	163	17	3692	60	108M	=	4043	458	ATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATT	:BAA@@BFBGDFGFFHGFDGHDHGEGIG?IEEEIHHHHIHIIHHFHJHIFJDJFGFHIJFIIJEIID8AFEGIEIIIGEIGFJAJ@F=?IK=JH?FBFDFF@;;<@ED	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR016352	AM:i:23	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR242955.298650	99	17	3708	37	100M	=	4076	467	TACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACAC	?ADCFFFDBGHDHGIGHGFJHGFFI?IHHIHGBFJKIGJDGIEKHKGJJJHJFIGHGIHIGFIIGIHJJJEJLHIEFIDJGHGAHFHGGBFCCFH?CAEA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242955	AM:i:0	NM:i:0	SM:i:37	MQ:i:0	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.16735015	99	17	3713	60	100M	=	3988	374	CATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCAT	B;ICDHEF4BBFH0GJC.:F<K6JK;I74A=0(ID3EL.>;MKK.AH6FEL=5IGIFA9GFILF5J8<@G7AH/LI&+>.CDIJF,7K669<EIC@>G;,	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243031.299961	163	17	3714	37	100M	=	4080	465	ATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATA	?B@EGCBHEHFEFEHHDGIEIGHHCK@HDBG@IFFD=?BC=E@CEHEH;HHICGHHGIEF>FJIIJAIBIIEGG=DE@<@I;H=HBFIC0F7FF@1DAA:	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243031	AM:i:0	NM:i:0	SM:i:37	MQ:i:7	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243047.429920	163	17	3715	37	100M	=	4067	451	TTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTAACCTATTCTGGACACGTCATAG	@ADEBEFGCGGIJFHFGIGIGHGHHFFJI=?JGFHGGGGGJGGJFHHHDIGDHGDJIDIJJIJKKJ;JHFJ;DGDCEGNHDBDHEJIICGHFF7DAE@5>	X0:i:1	X1:i:0	MD:Z:77G22	RG:Z:ERR243047	AM:i:0	NM:i:1	SM:i:37	MQ:i:7	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.12000443	163	17	3721	57	108M	=	4045	401	ACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCCTAGAAATAGAGTCCTGC	:ADBDCAFGFFGA?IGGAABEBIF=?DBA?AD@B@B?@AB?49B?B??<>?@;B687?96BDB?177)43:@?28B>6963%842;(->,1<3:33?21/24%3,A@0	X0:i:1	X1:i:0	MD:Z:90A17	RG:Z:ERR013140	AM:i:20	NM:i:1	SM:i:37	MQ:i:57	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.3552250	163	17	3731	10	108M	=	4051	394	TGTCCCCTCAAGCTTCCCCTCGCTCCTGCAACCACAAATCTACTCTCCGCCTCTCTGGGCTGACCTATTCTCGACACGTTCTAGAAATAGAGTCCTGCCAAACGTCGC	/<@70(/>3061&A57-(#.%23.,4>@01B95B>>3</71:7A/>:#/&AF@D+B/;%&FCB1+F3@<6B)-,:7%)9'8B<+0D7359F@7@49?@$>/B3(//).	MD:Z:20G26T6G4T11G7C0A17A1C4G2	RG:Z:ERR013140	AM:i:10	NM:i:10	SM:i:10	MQ:i:10	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.7468652	99	17	3733	60	100M	=	3865	231	TCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACA	AECDFHGFFJHIGJJIIJJ0KJKJGKJIIIJHHIGHJKKIKLLLLLLIKKLKKEKEBIHKJFLHIKIKMMHJIJJDHLHIFMIIFJDJIMGIJIIGFDD@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245049.438880	99	17	3734	60	100M	=	4134	499	CCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACAC	?BAEFGFFIHHEJGHFHIDIHHGDGIHGHGEIGHGIKIEJHKHJGIIHDKIJFEA@EEJGHIGEFFKMJG9JFJAGKGCDHDHIGFI?KDFHH?IF?ECD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245049	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.10931516	163	17	3750	37	100M	=	4074	423	TGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCT	@FBCBIJJKJFHFCFJFEDHLIHDMILFJLBLLILI?MH<HHIEJJGJJHJIIJHJJ>E;J8BFL=CJGFMJMDDK/LKGHJBGDIL<HD?9JJIEG>F)	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:0	NM:i:0	SM:i:37	MQ:i:0	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243075.758288	163	17	3764	60	100M	=	4186	521	ACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTT	ACECFEHGFHHIIIIJHHIIIJFJJHEEJFHHIFGGKJLHHBGJBGIFGELGHHHEJGLELIJIKIHMGIAELIIIDGJKJFJFKIIIHHDGHIGH=EF@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243075	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR242963.128219	147	17	3766	60	100M	=	3359	-506	AAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAG	=>AAICDJEJEJHJIKDKHGHHGJBGGCFJHAIHLGGKFJDBHHJDFKJFCGFIILG@JKHIHFDJEAIDJFG@HGGGFGIGKGGHJFFJFIF?JJBBD@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242963	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.23480670	73	17	3771	37	108M	=	3771	0	TACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCC	@?@@DIEHB>GHIJHEBKKFDGGFDKGEEIGCHJGFF=FEKHHGHDFG>FDD?F@DEDGEDKHAIFGCH@EEHGGC>@EC@-G=6D+8(9?F?4B=>E>GAFA@);9#	X0:i:1	X1:i:0	MD:Z:107A0	RG:Z:ERR013140	AM:i:0	NM:i:1	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.23480670	133	17	3771	0	35M73S	=	3771	0	TTCTCATCAATCCCTCATCTCTTATAACCATTTCGGTCCTTTCGGCCCTACAGCCACCTTGTTTATACTTGGTAAGACCCACACCACTCGCCAACTTACTCTACTCCC	8+7?5>09:),/%81,$,7<+?)+1+*+),3%5+)#%(4B%$&'%'/*@,)*%%&,%(/0%-&$$*$-,$3*.%/$:%$+.$*%&+.,.%%,%(%7(-.-',1*6%&$	XC:i:35	RG:Z:ERR013140
+ERR162875.18637663	1107	17	3780	60	100M	=	3471	-408	CCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAA	0GBCBHDJFC6IKG.?HA?>F:JM8LECJIAEHMHHFIBLK8K=E:6<KEGKD>DAIGH:JBFIJJG>MIKKMIIIJKG=E<AGKGJGFJFGFEDEBHBA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.6808869	83	17	3780	60	100M	=	3471	-408	CCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAA	4DFHDFGCAFGALHJGCFIGKHBAI@GCKIMKIGMDIIILKHJKNJJJIGGKGEJGL;KCJIMIHFJHKJDKKIHLHKJCGLEGKJFHGJFGFDDE@HBB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.12122315	99	17	3781	37	108M	=	4070	375	CTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCC	@DDFFFGHHFFGJFJKGGGJKHIKGKG@HJKGHIKKKHHILIFKLJJJLKGLH=GC>??<ECD=CDC?CBECE?<E>DC8DCABCGGFDH:BA::<>>8<67=8?>0A	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:0	NM:i:0	SM:i:37	MQ:i:7	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR013140.22233344	83	17	3784	60	108M	=	3490	-401	TGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACA	3:;8-9?=@=;AA<?AB=9=>CF==EEG@H@@?A>DCF=?@ED=@9@CB:=BBJG?FHFLHLHIIHLJIKKIHIH@JIJHKIIGKHJKFJJGIHGJJEIHGIGGDCA@	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.15409720	83	17	3810	60	100M	=	3484	-425	CATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCT	CADGGEEIHKKDIIIIIJKBIJIDIGGHJ=JKNJIJJILJIKMIIEFLJEMLJGILIIJLHJJHEBIKGJGJJJIIIIKHKKIHIGJJIGGHIFFHEEGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242975.1167526	163	17	3819	29	100M	=	4160	433	AGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTT	@EDHEHGIIHHGIEI@GJHHHAFGJKFIFJHIIIIDKJFIG@JIGALJCIJJFKEDEJEHHJJGJIFJHGIHGKFJEFJKEJHJGHGIIIHHDEGFGDEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242975	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR013140.9944053	163	17	3821	60	92M16S	=	4143	402	AGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCTTTCTTACGGCTG	9AABCCCDEA=EB:CBBD?>EIIEACC;DDE@F@9F0@>45C7:<2=>6CFACE@6<C>@7=50>93&=-48693<@89AA3<*,=A58<44352/%)'/'$%,$$70	X0:i:1	X1:i:0	XC:i:92	MD:Z:92	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.26059461	163	17	3830	57	100M	=	4037	306	ACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGA	DACBBH7-AG=HJK=FKDIIB9:M1;GJ=DC@IFBBKGHDLH;GHGK:I>J129CJEFJ8G>M=<J=MGFG;M,HLIAH8GKBJALKC2KAE?FH>D99A	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:20	NM:i:0	SM:i:37	MQ:i:57	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243047.360466	99	17	3832	60	100M	=	4185	452	ACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATA	@-=CG<AF=DEHIDI<JC6BFBEBIJF17EE@AA82>EEAGEFF;5>CL31D5CC@JHCD/>G26@JGHECFIE7G>BC>GG;III2D@24/'.G>6,90	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243047	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243027.1264030	83	17	3836	29	100M	=	3470	-465	GGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCC	9<?=FFHFCFEFIBGLHE?KBL:8HJFFIHGFEJ?HH@B@HIDIIHEGKFG?GEIDIHGEBIIGCGH@EJGIKDAJ@JGFIHGHFEHGGHBGGFCEBE??	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR243027	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242979.1160824	163	17	3844	60	100M	=	4206	461	GTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCT	?CGDGFHDHGCGGIHI<IHECIIGGJEBIEGEHIEIHIEIHJKGGFHGFDJDFKEGGHJDIIJIKJDGGIJJIFELGEBJG3JIJF<BEDG@ED7FAAE=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR242979	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.6951269	163	17	3853	60	108M	=	3896	150	TTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTAT	:?DECDD=GGCFJHHGHIDIHDDIJIJKLEIJJIJJIGILAJCHDDFCDGJHKIFLHCDGEGGJGCCEE<CFF@DEEDBB?F>>B=A@=>ABAA@@>9;7>5<=?:29	X0:i:1	X1:i:0	MD:Z:83A24	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.15307937	83	17	3853	29	100M	=	3442	-510	TTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTC	=>B)IDA7FC8D/DHIF1GJ11J?G=L6DEA>HEE:AGKJ>?AJIJJ4CD;=8HKFIAFDCGBI23EHCLKB5C@JIHG6IDC+BGF>HJ;+IEGGFGDB	X0:i:1	X1:i:0	MD:Z:83A16	RG:Z:ERR162875	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR162872.9849990	83	17	3854	60	100M	=	3663	-290	TCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCC	CHFHG=HKHHJJKBGKIBJICHJLGLLEIMMHKJMIKLKKHIIKKJJJMJJLILMGGKFLIKMJJMGGLKKKMIKJHIGIJCICJJGJJGIIEFHFHE>B	X0:i:1	X1:i:0	MD:Z:82A17	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.20934779	83	17	3855	60	100M	=	3616	-338	CTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTTTAGCATACACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCT	C:>>A6-'07KJDD7D92002-I&K(G2&92/;B98MFH)HB2BCA-E/4KI>.DIG8AIB=HE:C7J+@3KHJB6<HFDDF<JI;IFG7HEFHEG93GB	X0:i:1	X1:i:0	MD:Z:39G6G53	RG:Z:ERR162872	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR016352.1106475	83	17	3858	60	108M	=	3557	-408	TCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTATGGCTG	?9>CDDHDEFGGAABEHDHHIKBFJGKHIJIIJJGKGGK?JFK=B@HDKJHBGJHGKKJKHKHHKIIIJJEGHIKKIJIAIIJKJJIJHIIIJGIIJJIIGGHEDDCA	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR016352	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.8064738	163	17	3861	37	108M	=	4107	353	CTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTATGGCTGATA	:B@AA@CCBEDDEDDCDFFEGDCDGDDDFCG@EFGEGEGGGFA?@IGFHE@DDHEFIGFIHGHFI7E?GAGHIGBIE9FHEHKDEJF6FBJ=BFC?HIEAH9AGFB5?	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR016352	AM:i:0	NM:i:0	SM:i:37	MQ:i:8	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.7468652	147	17	3865	60	100M	=	3733	-231	GCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCT	DF@FJFHGGIDILFLJKHJMIIKKEJKIJHHLKLJKLLIKMEKMIIMJLEGLIIMGIMKLLMGHJIJJHKDJDKLEJMGLMIILIMFKKDHKGGHGEFFD	X0:i:1	X1:i:0	MD:Z:71A28	RG:Z:ERR162875	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.9446395	83	17	3871	60	108M	=	3647	-331	TGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCAC	A8ABBFFFFB=GIHEHIHHJKBH?EKBJCGHJFEFGDHGHJHKGEJHLKKEKFJJKBIIII=KKAIAIJHKJG@JEFJIJEJJHGJFCIBHHJGGHGHDCIHG<DDBA	X0:i:1	X1:i:0	MD:Z:65A42	RG:Z:ERR016352	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR162872.4686821	83	17	3871	60	100M	=	3525	-445	TGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTATGGCTGATATT	CED@DGIGHJGCIH@IJJHLKDIGFKLLJFMMJJKJMJJKKIMIIMJHNEIKMMELGKJHHJHKKHEKLHKKJJLIDKFLHJLHHKHFGGIHIFFFDCBB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162872	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR245028.1420999	163	17	3874	60	100M	=	4187	412	TTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCA	A@FEGFJHDJIIIHHGFHKFJEDKJHHIJGHKIKKIEGHIHIGIGJJFEIIHKIIGGEIGJIAKAKIHGJJIJCIHGIKIJEKJEGGJGHIIFFAEBG<@	X0:i:1	X1:i:0	MD:Z:62A37	RG:Z:ERR245028	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.739324	163	17	3875	57	108M	=	4054	286	TCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGC	;BCDDCDEDEHFFFGDHHGGGFHGFGHGIEHEHHHGEIEHHHJFEJGHIJJCJIIB:IGHA1C6AG:FI@HFGFHECD8IF9KED:H<BIIE@>GHA>D@>AE9>E?:	X0:i:1	X1:i:0	MD:Z:61A46	RG:Z:ERR016352	AM:i:20	NM:i:1	SM:i:37	MQ:i:57	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162875.919124	99	17	3879	37	100M	=	4109	329	AGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCAC	BG@FFFIHGHGGHJHKGHKJIHLLIJJKLKLHKIILIKKHMLHDJKMLKDGIHJILLJBDKJIKIILFAKJDAEH@BKKFF6KIEJK&G8HEB>DB;EDA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR162875	AM:i:0	NM:i:0	SM:i:37	MQ:i:0	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR013140.17460076	163	17	3883	60	108M	=	4144	368	CCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCC	:DEDDDDCFEBGCFCFE?CBHFJGBDEGGEGFDJJEJHEACGGDEFDA?EBBC1B:@ECDFB@EA>?=E?CAA@F;98@9AECDCA@>=;C@7;=7-2?>A=99.@84	X0:i:1	X1:i:0	MD:Z:53A54	RG:Z:ERR013140	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.301185	83	17	3885	60	100M	=	3655	-329	TCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTA	:CBGFIIGHIIJKJHKLKFLKJLLHFECKIILKJMFJMLMLMJLKLIIIILHEKKILNJLLEHJGMJLMJJLIJIJKLMKKIHIIIKKGCJJFIKGHGCD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242971.1136963	147	17	3893	60	100M	=	3535	-457	TGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTT	0EA=GFDB3F<ILEJKA@IBJGIJHHIF=EHHJJFIEFDHFIAJ@AHFG=H:KECIDFGHJIGIBB>BDEIGJHGGDGHIEBJJDFK<IJDGJCJCEGA@	X0:i:1	X1:i:0	MD:Z:43A56	RG:Z:ERR242971	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR013140.6951269	83	17	3896	60	108M	=	3853	-150	AGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTACGACTGA	65>72+?./;6-6->D8ABFCCFHAEJEBAGHBEEFCDE=>:@DBHGHAHDEEBCDFDDHJDFHILJLGCHEGDCEFD@JICJHJIHHFHEHJDHDEGCBC6EFDEC@	X0:i:1	X1:i:0	MD:Z:40A60G1G4	RG:Z:ERR013140	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR243087.1477801	83	17	3909	55	100M	=	3600	-408	TACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTC	0?F?HBFJGGK:DHHII@FGHDFEEHJFBHJHGKICJ@BKEFGFH@EJGCB:HHJHGGEGFDEJD@HFDGKGIH@FJ?LFA>EHJGDIEEHKEGDBCCB?	X0:i:1	X1:i:3	XA:Z:17,-4057,100M,1;17,-4094,100M,1;17,-4168,100M,1;	MD:Z:100	RG:Z:ERR243087	AM:i:18	NM:i:0	SM:i:18	MQ:i:55	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR013140.18542909	163	17	3912	60	108M	=	4185	380	ACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGC	:AEDDD@EGBFIJJIIHIGGGDIJHG<JIGJJDBJDGFGKCKHCFKFBCE?DBFCCC@;;EDA5>;<<?C88=8?@E@@;==A,,;2(5:372-92:5>9+&$&$&-.	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR162872.8738223	147	17	3914	60	100M	=	3511	-502	TCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACAC	-E8?FIGCF:AKEDCFFH>JADKDDL:9JIHKIIJII>DC@GA3F;GDJHFLIJFEIDLHDLLEKIFMMGGJ>JHLJIIMIEJKKLLGJIHHFHHIEGDB	X0:i:1	X1:i:0	MD:Z:22A77	RG:Z:ERR162872	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CAB
+ERR243059.116527	147	17	3914	60	100M	=	3516	-497	TCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACAC	=EGADGGDIHHGIGKGGIJGICJCJKGHKIIJFDJFLIHJIGJEFHIHIJLIGFIIFHIDBJJ?EKHKKDFKDKGGKGGIHFJHHIJGJGCFHFCHEGC@	X0:i:1	X1:i:0	MD:Z:22A77	RG:Z:ERR243059	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C@@
+ERR242955.586810	147	17	3917	60	100M	=	3506	-510	TTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACC	(C7BB7FG28FJ9E><FIBF4CA10I7BDB2FEH9HKGHGF?F;HGGHCHEBGFFI>BAJ3CGHHJEEEDJ>GKGHIHFIEGJCHJHAGGF;IDIBGE>A	X0:i:1	X1:i:0	MD:Z:19A80	RG:Z:ERR242955	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR245032.607478	99	17	3950	60	100M	=	4200	348	CTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCTACACTCCTTCTTAGGGCTGATATTCCACG	ADCDG?GHCDGF<EGJBFEF>JFEG>D@E?@HGDFGHH=EEIHFGFC?GGIIHCIEFED>H>0@CI4(<J;D,EJI9>.=FA;,J/.4./BF7?3.@9B7	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR245032	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR016352.14078817	163	17	3952	60	106M2S	=	4187	342	CCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCTACACTCCTTCTTAGGGCTGATATTCCACGCCCCCGCTAA	:?CA@CABDDEDEE>CCEF@DFB<DF;DHAEBECG7HA?HFEHF?GDHEHGDEEGF6AFDB<G8>'42C;6HBI@9CF8K@6F;E7C>?;D=D<BE=7;&*.+..)2&	X0:i:1	X1:i:0	XC:i:106	MD:Z:99A6	RG:Z:ERR016352	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.17620265	163	17	3959	60	100M	=	4171	311	ATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTA	BAFDEHGGEEFFIJGHBJHCKJJIIHJGIKKKKGKKGHLKLILFIHJHGKEIJ.GJJK=CKLGFGKALMLHJKEHBLEHJLKFH7BK8II@IEDH(A@GA	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR156632	AM:i:23	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR242975.793811	163	17	3966	60	100M	=	4155	288	ATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCTACACTCCTTCTTAGTGCTGATATTCCACGCACCCGCTACACTCCT	@@?EDHGFH5BFB?DEBFEGGICKIH/IJ:DE*:CBJAHE>6JG?;)>FD:,9HI<.:BIDB0GJHA.3.2IH>HC?0E:@9G+BG82*@B;,BFFFFBB	X0:i:1	X1:i:0	MD:Z:69G30	RG:Z:ERR242975	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR013140.11440888	163	17	3974	60	108M	=	4283	416	CGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTGATATT	:<EDADEFGGFEGEIHIIDHIDGKLLJJIJHHHEIJIGACJHFFBGFIDJHIFIDFBJC@DCAFFFHEECEBFJC9AD==:<@AC?G;F9?B>?F>=:+6/@7>>:@2	X0:i:1	X1:i:0	MD:Z:108	RG:Z:ERR013140	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR156632.11081426	147	17	3977	60	100M	=	3652	-424	CCCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTG	#6DGGIHEBALI4LIDKFAIKL1AIDCA@JJ?LIK=I0LG=DBI=LEKI7LHICI:KKJ7;HEHHHCIJKACBIGJIB:JE>J?HHFECGHFFFEFDGFB	X0:i:1	X1:i:0	MD:Z:0A99	RG:Z:ERR156632	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
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+ERR162872.16735015	147	17	3988	60	100M	=	3713	-374	TCCTTCTTAGGGCTGATTTGCCACACACCCGCTCCACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTGATATTCCACGC	-6<2;D9H?:AJLDH7?)K0/LH:FF,&3??M4'N2/&0N@J:<IE<K*N4+CG<E7DH;3EE?KACDKBIGH0'DLADCJH?>7;LFJCG7)@HIF=C@	X0:i:1	X1:i:0	MD:Z:17A1T13A66	RG:Z:ERR162872	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
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diff --git a/test/mpileup/mpileup.2.bam b/test/mpileup/mpileup.2.bam
new file mode 100644
index 0000000000000000000000000000000000000000..82bf2ad29e7aed7b18005aa16c68f92f113d1e06
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diff --git a/test/mpileup/mpileup.2.bam.bai b/test/mpileup/mpileup.2.bam.bai
new file mode 100644
index 0000000000000000000000000000000000000000..4900edf25f72adddf26c6aee4eb8dcb32b3bab49
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literal 0
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diff --git a/test/mpileup/mpileup.2.cram b/test/mpileup/mpileup.2.cram
new file mode 100644
index 0000000000000000000000000000000000000000..758c09202e0d3a556cd3e79f6c973677e856b212
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HcmV?d00001

diff --git a/test/mpileup/mpileup.2.cram.crai b/test/mpileup/mpileup.2.cram.crai
new file mode 100644
index 0000000000000000000000000000000000000000..fbe69e16dc9be39a64f5628e13f5ddcbf9d9ff1a
GIT binary patch
literal 45
wcmb2|=3oE=X5$AYPfQFAOdpt-Y&UsmVq$9i+{DD#*z^e#gH?+OpCnKf00=h=cmMzZ

literal 0
HcmV?d00001

diff --git a/test/mpileup/mpileup.2.out b/test/mpileup/mpileup.2.out
new file mode 100644
index 000000000..00c8efa6b
--- /dev/null
+++ b/test/mpileup/mpileup.2.out
@@ -0,0 +1,523 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	100	.	C	<*>	0	.	DP=18;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,189:9:0	0,9,108:3:0	0,15,134:5:0
+17	101	.	C	<*>	0	.	DP=18;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,182:9:0	0,9,99:3:0	0,15,132:5:0
+17	102	.	C	<*>	0	.	DP=18;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,188:9:0	0,9,111:3:0	0,15,139:5:0
+17	103	.	T	<*>	0	.	DP=18;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,189:8:0	0,9,108:3:0	0,15,147:5:0
+17	104	.	G	<*>	0	.	DP=18;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,24,178:8:0	0,6,89:2:0	0,15,133:5:0
+17	105	.	G	<*>	0	.	DP=19;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,170:9:0	0,9,97:3:0	0,15,125:5:0
+17	106	.	G	<*>	0	.	DP=19;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,30,190:10:0	0,6,85:2:0	0,15,124:5:0
+17	107	.	C	<*>	0	.	DP=19;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,192:9:0	0,9,108:3:0	0,15,136:5:0
+17	108	.	C	<*>	0	.	DP=19;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,190:9:0	0,9,108:3:0	0,15,135:5:0
+17	109	.	T	<*>	0	.	DP=19;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,195:9:0	0,9,110:3:0	0,15,150:5:0
+17	110	.	G	<*>	0	.	DP=19;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,194:9:0	0,9,104:3:0	0,15,136:5:0
+17	111	.	G	<*>	0	.	DP=19;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,30,167:10:0	0,6,88:2:0	0,12,118:4:0
+17	112	.	C	<*>	0	.	DP=19;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,191:9:0	0,9,95:3:0	0,15,135:5:0
+17	113	.	A	<*>	0	.	DP=19;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,176:9:0	0,6,87:2:0	0,15,139:5:0
+17	114	.	C	<*>	0	.	DP=19;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,27,182:9:0	0,9,103:3:0	0,15,133:5:0
+17	115	.	C	<*>	0	.	DP=21;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0	PL:DP:DV	0,30,189:10:0	0,6,89:2:0	0,18,147:6:0
+17	116	.	A	<*>	0	.	DP=21;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,183:9:0	0,6,90:2:0	0,21,175:7:0
+17	117	.	G	<*>	0	.	DP=21;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,183:9:0	0,6,85:2:0	0,21,177:7:0
+17	118	.	G	<*>	0	.	DP=20;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,27,175:9:0	0,3,60:1:0	0,21,162:7:0
+17	119	.	G	<*>	0	.	DP=19;I16=16,1,0,0,629,26439,0,0,958,55682,0,0,267,5553,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,24,175:8:0	0,6,73:2:0	0,21,160:7:0
+17	120	.	A	<*>	0	.	DP=19;I16=16,1,0,0,672,29188,0,0,958,55682,0,0,264,5518,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,24,175:8:0	0,6,83:2:0	0,21,171:7:0
+17	121	.	G	<*>	0	.	DP=19;I16=16,1,0,0,662,28460,0,0,958,55682,0,0,260,5454,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,24,181:8:0	0,6,80:2:0	0,21,168:7:0
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+17	589	.	A	<*>	0	.	DP=31;I16=17,14,0,0,1157,43973,0,0,1798,106082,0,0,568,12340,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,24,236:8:0	0,15,165:5:0
+17	590	.	C	<*>	0	.	DP=32;I16=16,14,0,0,1094,41302,0,0,1769,105241,0,0,549,11951,0,0;QS=3,0;MQSB=0.958545;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,18,192:6:0	0,18,175:6:0
+17	591	.	A	<*>	0	.	DP=31;I16=16,15,0,0,1165,44163,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQSB=0.999805;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,209:7:0	0,18,188:6:0
+17	592	.	A	<*>	0	.	DP=31;I16=15,15,0,0,1114,42144,0,0,1738,102482,0,0,571,12651,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,215:7:0	0,18,182:6:0
+17	593	.	C	<*>	0	.	DP=31;I16=15,14,0,0,1065,39889,0,0,1709,101641,0,0,550,12132,0,0;QS=3,0;MQSB=0.954405;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,18,191:6:0	0,18,174:6:0
+17	594	.	A	<*>	0	.	DP=33;I16=16,16,0,0,1163,42917,0,0,1858,109682,0,0,572,12672,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,205:7:0	0,24,212:8:0
+17	595	.	A	<*>	0	.	DP=33;I16=17,16,0,0,1130,39996,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,198:7:0	0,24,213:8:0
+17	596	.	A	<*>	0	.	DP=33;I16=16,16,0,0,1059,37039,0,0,1858,109682,0,0,590,12952,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,169:7:0	0,24,230:8:0
+17	597	.	C	<*>	0	.	DP=33;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:DV	0,54,255:18:0	0,21,204:7:0	0,24,220:8:0
+17	598	.	T	<*>	0	.	DP=33;I16=16,16,0,0,1214,47104,0,0,1858,109682,0,0,593,13013,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,217:7:0	0,24,239:8:0
+17	599	.	T	<*>	0	.	DP=33;I16=16,17,0,0,1183,43669,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,197:7:0	0,27,247:9:0
+17	600	.	G	<*>	0	.	DP=32;I16=15,17,0,0,1174,44066,0,0,1858,109682,0,0,601,13145,0,0;QS=3,0;MQSB=0.999287;MQ0F=0	PL:DP:DV	0,51,255:17:0	0,21,194:7:0	0,24,232:8:0
diff --git a/test/mpileup/mpileup.2.sam b/test/mpileup/mpileup.2.sam
new file mode 100644
index 000000000..337c037ab
--- /dev/null
+++ b/test/mpileup/mpileup.2.sam
@@ -0,0 +1,248 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:17	LN:4200	M5:a9a06ca09c111789d92723fbf39820f6	AS:NCBI37	SP:Human
+@RG	ID:ERR229776	LB:HG00101_I_bc_pelib_1018	SM:HG00101	PI:510	CN:MPIMG	PL:ILLUMINA	DS:SRP001294
+@PG	ID:bwa_index	PN:bwa	VN:0.5.9-r16	CL:bwa index -a bwtsw $reference_fasta
+@PG	ID:bwa_aln_fastq	PN:bwa	PP:bwa_index	VN:0.5.9-r16	CL:bwa aln -q 15 -f $sai_file $reference_fasta $fastq_file
+@PG	ID:bwa_sam	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1530 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:sam_to_fixed_bam	PN:samtools	PP:bwa_sam	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:gatk_target_interval_creator	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:bam_realignment_around_known_indels	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_count_covariates	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_recalibrate_quality_scores	PN:GenomeAnalysisTK	PP:bam_count_covariates	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_calculate_bq	PN:samtools	PP:bam_recalibrate_quality_scores	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_merge	PN:picard	PP:bam_calculate_bq	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates	PN:picard	PP:bam_merge	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.1	PN:picard	PP:bam_mark_duplicates	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+ERR229776.1434662	163	17	1	29	63S38M	=	189	288	TCTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGA	?FIFEDHEHF@EJEHCFEGIFHHHJIIKIIKFKMHLILKJJJFGCF@DHILJMHMDEKDGBIJJJGGK@HMKKFJHJIHCIHLHJIIIIKEIJFEGGGDDF	MD:Z:38	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@iiffj_gljjeigihgbhgkgihhhhjdhiedfffcce
+ERR229776.44080430	163	17	1	29	33S68M	=	200	299	AGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCT	CEHIFEEEIFFKIHIHEBFHGIKGLJLMKKKKJMLBJKCJLJJGIIJFJKJILJMKKJIKKJLKGFJJKBKJKEDAIKHIFHKLHHLHGLFJJH?CCDFDH	MD:Z:68	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@lkaijbikiifhhieijihkiljjihjjikjfeiijajijdc`hjghegjkggkgfkeiig^bbcecg
+ERR229776.67863896	163	17	1	29	70S31M	=	243	336	TCCTTTCTCTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGTCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAAT	?EEIBDFJFJFGHHHHCA7JII@HIIGHFIIJFILIGDAJLICBIGIGMKLFAFJJILIMILIKF@JGGGJJHILEJMICEGFJIHDIHL?G0=>AH@<AC	MD:Z:31	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@iighkdilhbdfeihgchgk^fO\]`g_[`b
+ERR229776.47122623	163	17	19	60	100M1S	=	316	393	CTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGCCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGG	?HDAAGFFHGAIE?FHEFFJGGF7DCIHKJIEDGILIJMBKEFC1BFJBGI<ECJJE@HJ)BB(40DGGJFKJ>D@GGG@LDAGFDC@GFF?C6BADEA##	X0:i:1	X1:i:0	XC:i:100	MD:Z:63T36	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@@
+ERR229776.5202330	113	17	20	37	101M	*	0	0	TGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGA	FFFHGKHJIHHHJIIKLKIHGHGIHBCCHEHDDFFFDFIAHI@CE@EHIHBJIKJKLGJKJFIHJFAJGH=:A6JIHFEDGGHGIGH=HFABDA@EIDEEB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.96861155	99	17	29	60	38M63S	=	245	315	AATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCGGGGAACTTAACAA	=BE:CD5=@;3BC5<<C1?8DE679H/<D2;I:@-8D################################################################	X0:i:1	X1:i:0	XC:i:38	MD:Z:38	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.10174020	99	17	32	60	101M	=	73	141	TGCATGACAATTGCCTTGGCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACA	CEFEEEDCDDBGGEHHHG(;FFFIJJIJKGHHGCJJKJKKFAAGHKGIKLDJLKJILKJJCLHFGJFKHIFLGA?HGLHFIIFHJIGGJIIMHIGFHFD@F	X0:i:1	X1:i:0	MD:Z:18T82	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.109178428	99	17	49	29	101M	=	278	328	GTCCCTGCGAAATGTGCTCTGGGAACCCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACAAGGGAGCTTAACAAACATCTGTCCAGCGAATACC	6D<*:G<A"&3C*(/2<>/>E&%()4'5+')=1,)4?C3B5D?:JH'.5>BH5A;*0$;<I?%;-;-*)%1=92>666@FCHCIEIHHIICGDC:GDGFD?	MD:Z:8T0G13G0T1T39C34	RG:Z:ERR229776	AM:i:29	NM:i:6	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.18900347	177	17	69	37	101M	*	0	0	GGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGC	DCCBFBGCGFFFHKDJDBGGIC?IIBHHGDLIFJKLJKDGIJJJJLJMMLLNLKLFJIHKBFJJKJJJKLILLBLJIHIKKIKIIJJJIHIHHKEGFGIFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:EBA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR229776.10174020	147	17	73	60	101M	=	32	-141	TCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACC	CEGFHGHHGJIKDBGGIJAIGDHIFGJFIKJJJKFKKMMLKMLMLMMNMMMJKJKKJHKJLKJKKLKMLBKJIIEKLIKJIKKJKIKJIKDGHHKGDFHBC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229776.54549035	163	17	122	60	101M	=	343	321	CTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAA	CIFFIEGJJFFHIKIHKJIKJBJLIIJLMKLJJLLLMJMLNMJJLMMJLKKM<JMMKMLJLIJGAGFGHGGJGKIHJMFFHGHLFJJHIIILIGIGGEEFF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AD
+ERR229776.1434662	83	17	189	29	101M	=	1	-288	CATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATG	EFC?7ADFIHHID5GIJICHD?DFALHDKECDBEB;8BC:KJJDIJCHCBCBJEHHFGHJKHKCIEIFHI<B>FGIJDED=?DA?=FIGGBBCE<DDCEDA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229776.44080430	83	17	200	29	101M	=	1	-299	TAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA	FBAEGIFA@IBEHIMIHLFIHEKGE@?B9CDDHIHH>>C;?EJFGFHFCFCHCHDAHEBCHJHGDJDEADFDFI@GJJE>J@A>D=E>D>:7;@:DDCFA=	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.67863896	83	17	243	29	5S60M1I35M	=	1	-336	CACGCCCATGTCCAGCTTATTCTGCCCAGGTCCTCCCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAAC	######HIJEG0>><<JGDH;)A47330()/$)@'&%7M;A=<3AGFF:>CBCJ9BD:1;.;2>AG;7?8&/7.C8D;>9,>;B87E>A:3:BHBE@A:EA	X0:i:1	X1:i:0	XC:i:96	MD:Z:24T5T64	RG:Z:ERR229776	AM:i:29	NM:i:3	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.96861155	147	17	245	60	58M1I42M	=	29	-315	ATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGC	CD6;=?GB=-EEDH>IG<=?L@DHBBDCDHHMFCDLGEGG?CJFHGF:EAB0CFHLC>MKGFJI?D@FIILH>IIIIHG;F7A69B=;CA7GEFH/=CB?0	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.70166645	16	17	256	37	47M1I53M	*	0	0	ATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAAATCCTTGCTGGTTTGAGAG	AIIAMHABJNHLI>COB?CJPHJGPJIHOKC;EJGQGKKI>CFBLGOLDAK6=2G@HLKHH(NHKGPHKN?K>LPB88?A8'&5=FJIJEKCCIM;3MEM<	X0:i:1	X1:i:0	MD:Z:81C18	RG:Z:ERR229776	NM:i:2	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.109178428	147	17	278	29	25M1I75M	=	49	-328	AAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGT	ACICF>FF=CFFFEDFG-6CFDMHHLFACFJ5LKJK@MIIKLKJJJCGHKAJLLIJJHJFHGIKLHEJI@HGKFHLJLHHIKJGIHHCIHAGH:DB<=CC:	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229776	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@AD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.33489754	163	17	286	60	17M1I83M	=	565	379	CATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTAC	CGFFDGHFIFFGHHHKHGKJKLJKBKJJMLLLMKLMJLKMKKLIJLKJMNNNKNMMMLLMNLMJKKIKLGGHHIHJHHHGIJHIKINIJIIIIFHHKCCE=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.67002924	99	17	287	60	101M	=	567	362	ATGGTTGACAGACAGTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTT	7<937;<B>A%6@AB5AGBCBG4GEE=;?BDHG;9@D@=;BB@GJ@KKKJ<MJI@D8>DB;:@>C?9C??AEAICI6/9@CEDEMFIEDH?C?GC?DD:DB	X0:i:1	X1:i:0	MD:Z:10C90	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@FG
+ERR229776.39811680	163	17	292	60	11M1I89M	=	579	387	TGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCA	?CGCFE@<FH?FGDGKCE?KHILLJILGHKFBILIDJJKKLHELLMAMDHFAIJBFFJCJGJILGBJFHLMJLJHKIIF;JIJIHHHDHJMHHHBHBEEDE	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.96748390	1187	17	292	60	11M1I87M2S	=	579	387	TGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCA	:CGCFEGDFF:8DFCJ8(3A>E;GHC@EFKB=76DDJDI@BGKCLK8JD6JJAIJBGEBBF?>CCAGCDGEIIFCJGGC;FCEDD@HADHE::=<H?D###	X0:i:1	X1:i:0	XC:i:99	MD:Z:98	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@G@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.12857813	163	17	304	29	101M	=	542	325	CCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTG	CEIEF>IEGJIGIKIJKDHFKIILIIJJJLLLM?KJKMJJGMJLGCIHLFLHJLKJLMNFIKJIJJJNJKJGCAFFJMHFIGLHIHIJKFFDCC=9DHEBD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.47122623	83	17	316	60	4S97M	=	19	-393	AAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCATAAAATGATAGCTCATAGTTGCTTTCCTTTGCATATTTTAAAATTGTGACTTTC	#####GA7>;IDG@D5LNHDB>8.0DF.FFC::HAA?DD3-BMA;;6+=D=HDD<75'8=<@F@F@<5(G5(%><DF<;:D76E?:9/>D>;3*6<'62+7	X0:i:1	X1:i:0	XC:i:97	MD:Z:43G9T14A28	RG:Z:ERR229776	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.54549035	83	17	343	60	101M	=	122	-321	GCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAA	CFGFDJKJJOHLIJJHGHHIIILJJJLMLKKJMJMJLMMMIJLLMJKIJJFMLLIJJIHJIIIJHKLKJIGEJJGHGIGGGFCGGGFHEIEBDHBFEIFEC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.24914793	99	17	348	60	101M	=	613	365	TTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACT	A@EEFE>ED?;EHGIEGDD@FGEEGEGGDEFIJKFIFFKJIHGEIGIKJIELMMJKEBJFHIGEIJJJLKIJDILKJNDKIKKEJKKEIKKGJHJLGCEEI	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229776.100438586	99	17	384	60	101M	=	443	159	ACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGA	AACAEC<A?::GGEDEIE?@;EABEGGBA>GDFCHHIKKFCGHGHLGEIJ=GGJDHJDKMFFHELJHHLBEKKHKIHEHEIJLJNNIGAIIEGEHHGBDCC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229776.100438586	147	17	443	60	101M	=	384	-159	AGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACC	HDBEFGHFHFHIJFCELJLKLFFKIGLEJKAIFEJJMJFMJHJKBJKGBJJMJJFIJFGHGAFEHJHBICCAIEFEGDCF@D@@KHEDFG7CHDBC@;230	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.105883979	163	17	445	60	101M	=	610	265	CACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAA	CGEJFGIJJJDHIHHJHFKKIILLLLIJILLKJKJMLKJJKKKLNMKLLMMLKKKKKLKLLKKKKKNNNMJJOKIAKKKFIKLIKMFFIMKGHIHGHDEFD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@HI
+ERR229776.41759951	163	17	452	60	101M	=	681	323	AAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGC	:DEEEG=*BCB.F6FGI==IIF1BDIAIJI,FEH=BFFHD,AECEBFFEF=8DFIGJGF4<++*@KEHDGIJKHHG-?C=DHLIF8GFEIDFGE?BBDBAD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@IG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.103175593	163	17	462	60	101M	=	681	314	GGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCAC	.6:AFFEEB?<8;:IG?DHH?FI9EIIJJHFGK+:BF8DFAF@DGDJEHHCFECHDC6BE@BEEIBGJMJHKOHDEIEFC=BED6:FEEF=G-9AFE=@BA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.28425582	99	17	465	60	101M	=	698	315	CAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACG	ADD=<C@F;8:E2:4.33:>7HEG2;>@CD7C=@C=@E?CF@?4>BJ>;;9FGH=FGDJHJJJBDC;8=DCEGJGGEHIKHHJEE5@B06C?DHBEHED@#	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.445065	163	17	478	60	101M	=	793	406	TAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGG	?FEDFGHFHHDKKEHEJGJ3HHIIIIKKHIJIJLLLLJILAFJJFJKJ?FGIMKIILJHHFEEFH7IFELLDHKFILFGGKGHJGGGAJIIMHEHIEI7;5	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.76793083	163	17	490	60	101M	=	728	338	ATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAAC	?EDHDGHDFHDHHEHGHCHHIKLKJFHJHJKIIIJHIJFHKJJJLJJBFDJKHIJMBIF>AGHGMHIJMIJJJKC=IGDCDGJFHMIE@CKDCMHHFFGB#	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.7941745	163	17	541	60	101M	=	806	357	ACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAG	?>?FIJJJHH?GDGCEHIHEG7H<:IKKLJKJLADHCFIGKGMIICBILHJLBHIAGL6C8BA2*;BAAAFE>CH=.C;5AE,<CJELHBHGGECGEGD80	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.12857813	83	17	542	29	13S88M	=	304	-325	CTTTCTAGCATCACCAAAAATTGCAAACAAACACACGCCCTTCAAACGGGGAACTCATCAACAAAAAACTTGTGGTTTACCCACACACTGGAAGACCACTT	##############IFFHD=?.D:<8=>5)/<4C=3'=8;;*);10*HHH>?CEC(B9)@@(<:(=>;.G762*6JIB>,6(56--/'GF:7D=486A=BA	XC:i:88	MD:Z:17C14C0T17C22A13	RG:Z:ERR229776	AM:i:29	NM:i:5	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.33489754	83	17	565	60	101M	=	286	-379	GCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAAC	:?DFIJHHICIHFELHIHJHJIHEHGKIKKB=JMJDJFG<H90AEGGIJHFIHKIILHHHECKLIKKIHI<HIHFHFB<GDCCGGBHHGFABEEBEEEEEC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.67002924	147	17	567	60	18S83M	=	287	-362	TTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAAC	###################FG98CC@A?EDF=76@?8:BCGDAECBB5FCGDGFDCEA6:C>.>665CE@HFI>G474>9DF>@?FEA=>=JB:GEE@B>:	X0:i:1	X1:i:0	XC:i:83	MD:Z:83	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.89263281	163	17	572	60	101M	=	706	234	AACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGA	CHEJFEEEFIDKIHHKIKIILIILLJLKKJIIIIJJJMMKHJKJNJJLLNMLKMKKMLKKMKNIJMNMMKEKIHIGHGMFHMIGJIGJHHIJIGLGHDGEF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.40976938	163	17	574	60	101M	=	796	322	CTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATG	?HDDDEIJFJFHGDHKIHKIIKKGLJIEHIGIIIIIKJHIJJHIJJKLILJMKKMLJKLKNJKMMMNJHLEGHGGGMIHKIGHIGJIHJJHGLHIFHFGDD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.39811680	83	17	579	60	101M	=	292	-387	GAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCT	DAFCCC7EA@GFGFHC:0KCFBBD8MLJEA;?><=:HB?3JIKBBAFBHD?FCE2CG:HEGJE<<@ACDFA8BGFDEB<(GEHGFCA?E@:@9E=F@D?8A	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.96748390	1107	17	579	60	101M	=	292	-387	GAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCT	FDGFIEFE@@G>B0CC@0>@FCE=F@MIEGJIDIDE@EGFG?K=BIIJGFBJHE@=9C@HFJE@G:@@?E=D<5>8BH<GGC6D<;B<?35<>==@@<;@=	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.65100219	99	17	604	60	35M66S	=	847	335	TTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGCACATGCAACTGGCAGATGAATCTCAAACGCATTCCTCCGTGTGACAGA	15))2*4?0<4CC>A9<####################################################################################	X0:i:1	X1:i:0	XC:i:35	MD:Z:35	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.105883979	83	17	610	60	101M	=	445	-265	CACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGG	CGFGGEJIHIFMIIGIJHHKLHHEHGJJJIKHHHFIIEBHKLLILIHJJIFLIJILIKHJLKIIJJIHHJHEFB?HIHIIIHGI?EFFGGBBGECIEC:EC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.24914793	147	17	613	60	101M	=	348	-365	ACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACT	@D>GHGHFLFCEHJIHILHDFGDIIEDLGIHEHGC@BGDKJHGJGJJJGJIJKIKJLMICIJJIKEJHJIF>GGILGKJJH=HGHGJDIKFHJFE>DEHE?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.50340221	99	17	667	60	95M6S	=	960	393	GACAGAGGAATCTCAAACGCATTCCTCCGTTTAAAAGAAGCCGGACTCATAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACA	=FCDEG*.<?:B+;DEID.>@56BFHG<58&3)1AJ6(>6'=13=.A3:)2DC@:DA(@;D)B@>B89>BG?;8)@EG@3%;A+>GGKHABEBB#######	X0:i:1	X1:i:0	XC:i:95	MD:Z:6T23G1G16C45	RG:Z:ERR229776	AM:i:37	NM:i:4	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.103175593	83	17	681	60	5S96M	=	462	-314	ATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGA	######@E;EBD8+8)1$4:>FAJJKMG?H:*6@<>;:=A@D>9G<AB15)-<BEDG>;0@;06JIG@CA/9F>E??C>F>@AD>DF>A@32>@<BDC=:B	X0:i:1	X1:i:0	XC:i:96	MD:Z:96	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.41759951	83	17	681	60	6S95M	=	452	-323	AAGCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAG	#######BA:FHE64$)*8;=D@HJGBKG>;')8=;.7F70HHIHIC@EA34IHHE@::*-(<:3H7@CF57>F;B3:07C68;,6A8(<;3563C>;E>=	X0:i:1	X1:i:0	XC:i:95	MD:Z:95	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.7320258	99	17	683	60	101M	=	985	402	ACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAGCACCATTGAGACAGAAAA	B+)=AC/=8@4D<6>948=57D;CA@96A;DIB>AG:8>C;;@@EGIA6?FH>EI8CCGJFD=;><AB@BAGHDIGIF>20>)1?@8FHC69BI>ABF=C:	X0:i:1	X1:i:0	MD:Z:82A18	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@B@
+ERR229776.28425582	147	17	698	60	18S83M	=	465	-315	CAAACGCATTCCGCCGTGTGAAAGAAGCCGGACTCACAGGGCAACCCACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGA	###################HD@HDELF6=HHGGIE7DEIGFDBG9%B6FF>:BDF@FF@FJHFEHEEEHHKCG?CHF81I;GC2B>ECCCAEGFKGFED9:	X0:i:1	X1:i:0	XC:i:83	MD:Z:27A55	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.89263281	83	17	706	60	101M	=	572	-234	GCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCC	>D>FHGHJHGFMHHIIFGIHHEHIKLJJJJKJHLLLKJJJLLKJLGLJJIEIEB@KKFHFCCKJILIDFH>AKIIIGFGJIFFII?GHEIB<AEBDDDDBC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.33718464	99	17	717	60	101M	=	927	310	AGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGGTGCCTGGGGCCAGGGGACTTTC	B@?C<;58@3B:A::9B;D<CE--<;B>E>3IJEE;CFHGBJ=8<8IILFEEIIHJGGHDHIF@7CLGH?0094=094%492;>B=CB'%6<A7#7=JBDA	X0:i:1	X1:i:0	MD:Z:78T15A6	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.69497113	163	17	717	60	101M	=	1057	395	AGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTC	CEBDFGJEGFFGKBFIKC@EKIIJIIFIHIIKLLFFHLJJKMMHAJIJKJJJLKJKJLKLJKKLMMNHKKHHDJCJICI=DGHLICCCGFGCAB>BBIED@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.76793083	83	17	728	60	101M	=	490	-338	CTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATAT	<B@C=?CAHJGHKJIIJHCHEGG6<4IJDJCE<DHEIDB:CEI>D=JCDB><HJIHJIFG@HH>CB>EFGBA?E>DGEB?CDBFGCI@BE<A?@:GCDEB=	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.39704494	163	17	753	60	101M	=	1066	394	CTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGA	?HDCFFFD:D=DJ@GFE8DCGKFJFHCJLLJHIJ<AADAFH@G;6(EMA8CAA>HCAJGCCK=C@F??EA16>>DCMII@LE@CGDI;@DIIHCGG?@=1=	X0:i:1	X1:i:0	MD:Z:75T5G19	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.98656758	163	17	764	60	101M	=	1003	339	AACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGATTCTGGTGGTGGAAACAAGACTGT	CHEFDFGHHHHIHEHKJKLLIILKIIKJEGIJJKLLMLLLLMLJMLLLMKNLLMMLLLMFKJKJKJJNJOJJHJJCLIFHMIGHIGJIGHHJGGCGHDJEE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.20493064	99	17	765	60	101M	=	1017	352	ACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTC	CDGCDEBFDCCHEFIGIJIFGIHCGFHCEDBIIJIKHHKKKKIKKKJLJLEJKKIILK?HIGIELHLILHIGGJHIIEJLHFHHGDDGJHHGIHGJEKFGE	X0:i:1	X1:i:0	MD:Z:63T5G31	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229776.445065	83	17	793	60	9S92M	=	478	-406	CAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGTTTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGC	##########CFJE@CG<E9)31A=6B@/A=B@<?HG>DD@EA;G>>GE8?<AA=5*EHC@B<<??FCCB?9=:H<C:CCH<1GJDFEGD:8;14=7CHBA	X0:i:1	X1:i:0	XC:i:92	MD:Z:47A44	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.40976938	83	17	796	60	101M	=	574	-322	TGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCT	=5?=HGHHFGHIHEDCGHHJHHIDCGCE@D<=AJFKECBEJLHDILJJHH?HGCIGAC;8EIKE=IAFDD><EIGFGHCEG@CGGFIH<G@<?C@AC<FBB	X0:i:1	X1:i:0	MD:Z:32T5G62	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.7941745	83	17	806	60	8S93M	=	541	-357	CCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGATTCTGGTGGTGGAAACAAGCCTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCT	#########LF?-)1HJE@BFCEC?E@=EB5G=>9?/;AFCHFJJJGBFIDHHIF411A=9>$FC@?FAHDFEC<:8A=GG@;DI=8>E;5<D><C9CH@A	X0:i:1	X1:i:0	XC:i:93	MD:Z:54A38	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.65575982	99	17	818	60	101M	=	1120	402	TGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAG	A;BC8D<ADB@IGIICCF>:GC4BG:BCE;@A-:>EHJFFHICDGHIG?GEKIHLIIKCHEFB>>=IAIBHHCEE<9BGDA@GBJH8=JD@CGDIJG?FFE	X0:i:1	X1:i:0	MD:Z:10T5G84	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.59614566	163	17	820	60	101M	=	1133	408	GGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCT	:;@=AHGFFKFKIHHIFCHHKBHHLIEIIIAFEKLLJJLKLKDHJJHIIKMMLFJJ7=GGIGJLJBLJLEIIGIEHMILFGHJD?JDDEFFIJHGHBFDEF	X0:i:1	X1:i:0	MD:Z:8T5G86	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.65100219	147	17	847	60	8S93M	=	604	-335	GATTCTGTTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCC	#########FDGFF:DCFDLEA=0D;BBHLF;6GA-6IJJIH=KI9>G@2019BCAB,F>F=AJBFHA?6?DJJDIEH;HCH>BCA;ACA3;;?G>;C8=.	X0:i:1	X1:i:0	XC:i:93	MD:Z:93	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.70908663	16	17	916	37	1S100M	*	0	0	TCAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTCGGAAGATGCCTGAGCCCAGGCGTTCAAGGCTGCAATGAGCTATGA	##J@<:7FM?IMHGLGINGEEJH=>I:MPGD9:NNM?MIQNNMPRJNEMQKLA9D"MLMMM6L2,&PMQJ8?B2I@+:KMN>=2E?AI@HDIFNG8<FI><	X0:i:1	X1:i:0	XC:i:100	MD:Z:0T53G9T10A24	RG:Z:ERR229776	NM:i:4	XT:A:U	BQ:Z:@@E@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.33718464	147	17	927	60	101M	=	717	-310	GGTGGTGCATGCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGC	;@FCAHGCHGGEHJHIJCJEF?LJIHDED@7CKD;HGJFEIIJGDGBAE5A?IMJLMJGIFLGBIBBJF>LEIJIIF@EIJKICFBHFGKBG?FEFAEGB7	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.53110448	99	17	947	29	2S31M68S	=	1224	373	TACCATCTATTCACAGTGCTGAAATGGGAAGATTCTTGAGCCCAGGAGTTCAATGCTGTAATTACATATGTTATCGACACTGCATTTTGGCCTGGATGAGA	B7:11()8:<B+4.,8?(9E#################################################################################	XC:i:35	MD:Z:3G16G0G9	RG:Z:ERR229776	AM:i:29	NM:i:3	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.50340221	147	17	960	60	101M	=	667	-393	GTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTC	9FBEHGIEGJIHIFMIIJIHHGGH:EECIHHGDMJJKLDFJKLJJHHJKMMJJKLIMJJ>:@A?IJIHJJLKIGJEJFHIIGGEFKHHGGFCB0>EEFDG?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.7320258	147	17	985	60	101M	=	683	-402	CCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAA	?CEIDBKGJJIFLFIIJIIFHCGLCCFFJGDDHJBK?GKGIH=GBCFACECHJHJJIFFJKGJJIJIIFIIJIHGJJJHJIIGBHKHFAGFHHHHKFGCC?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IHIG
+ERR229776.98656758	83	17	1003	60	101M	=	764	-339	CAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATG	EGGHGLIGIIJIIHJIAIEHHHIIHIHMLJFJIIIHMIJJJHLILIGJJIDLKLIHJCHI>JJJJJJIGIFEJJIIIJIHHFCFGBFAHFABDEBEEEEFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.50998015	0	17	1012	37	100M1S	*	0	0	ATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTT	327C$2FG8CGM@H?563@3I@%2==H;?*@H;E?BF;M>N7FFHGA8<GCP:GKPPQP<HOIJ8LJKC25OKLKKOGI?ME87;MHDQQ=CLD8DM=?##	X0:i:1	X1:i:0	XC:i:100	MD:Z:100	RG:Z:ERR229776	NM:i:0	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.20493064	147	17	1017	60	101M	=	765	-352	TGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGA	EF>GEGHHJIIJIIHJIIFHLCLKIIKKOJNKIKKKJMJMKJLKLKKLLLLLKMJLLLMILKLMKJKJJJJKIJGIKLIIIIKIIIKHHIFKFEJGFJEFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.2114306	163	17	1033	60	101M	=	1337	404	GGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATG	:;D=IFE9@FED@DHIJGKJKEGELGF>JELIHKKHLLEKLMMKKJLMKGLDLM<JGIFHFDG.>EGJFHHJFDEKGF@6HJHEKGIHJHDFHFHGCCGDD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.69497113	83	17	1057	60	45S56M	=	717	-395	ATGATTGCGGAACTGGTTTTTGGAGTTTACAACAGAGCAAAAATGTGTCCATAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTT	##############################################@J:+B@;91-=/4*GHF9:H<:04+'751:<48A6:0FC4D;A?;<8==CGD>BB	X0:i:1	X1:i:0	XC:i:56	MD:Z:4T0C50	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.83355002	99	17	1066	60	101M	=	1294	328	AAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTT	ABD>CCDHGD<EICICHJIEHGFFHHKGGDEHG>HJIJJB?>DCDHIHDI<HEIHGIHIJLMJEJLBGJMIHJKIJJJIH@CHKKIEEGFFFHGJHDDCCB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:IJKCE@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CBCDEE
+ERR229776.39704494	83	17	1066	60	19S82M	=	753	-394	AGCCAAACCCTTTCTCGAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGT	####################CG5B7KJC8D<J>D,;5(A:@23?838</,>D87<,<7;-EJH@JHCCC>ED<:BKGFBEB98;F?D8AE11665G6DF:+	X0:i:1	X1:i:0	XC:i:82	MD:Z:82	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.69297552	163	17	1080	60	101M	=	1344	364	AGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATC	?CHADJJDJHFGKEHIHDAGHLCIIIIIJJIEHIKJILJLLJJKJJLMJLMMJJLMKJJKILJKGDKHKJLKGLJKKIKIKHHKKLFIJIFIFJEGECFEC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.44123845	163	17	1082	60	101M	=	1361	379	AAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTT	CHHIIEKGGFIHHJHIHFJLIJKIIJJJIJJIJJIKILKJJKJKLMJLMMJJMNIHJLILKKCGIKJKKJLLKJKIKKMFLLLBILJJKKKKKHFGHFGCD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EIGGD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@EI
+ERR229776.59579091	99	17	1088	60	101M	=	1308	320	TCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGT	CBGCIE@GEBBGHIGFIGCFGIHFGCGHGFEKIFIJIHJLHIKIIHJLJKFLHLJLKIKJKKKKLKIIKKJILJKKKKKJKKKJFKKHKIHIHMEEGGGFF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229776.33511586	163	17	1116	60	101M	=	1421	405	GATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTC	CGFFEGHHGHFKHJKKIFKLJJKKIJILKIKJJIJIKLJKLLKLLKKLKKLMKKKKLLLLJJLKMNLLLLKMKKKKKLJIJEJIKLLLHLJKIJHJGDAIC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.65575982	147	17	1120	60	101M	=	818	-402	CATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAA	ACGFDCGIIFDGJJJNLHIH@=NKKKJLNJKKKKMLMIEFKLIGINLJJJHLMHJKJKJEFLLJJHMJIIJILKGIIILHLJGIFFCDEEGGCFHIFGFC?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IKIG
+ERR229776.45364215	163	17	1122	60	101M	=	1385	363	TTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAAT	CEFFFKHIJIFHIKIHHJHKIJJIIIJIIIKLJJKJILKHKLKLLJJJJJLLLLJJMJMLKKHLJKKJJKKKKKKJKILIKLHLKLLKINKHGKHHFEEDE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229776.59614566	83	17	1133	60	5S96M	=	820	-408	GAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCTCTAACTCAAAAATTCAAAA	######GJJ@=GEHICDIFNGCFDA@MMLE=AJLEEIIGA5@D>GLICGBAC>EJCD3IA@6F9KH:;BHF=JH@H=@?B=69FF@>GGG7BEEEGC<B@A	X0:i:1	X1:i:0	XC:i:96	MD:Z:76C19	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GFI
+ERR229776.74203814	99	17	1171	60	101M	=	1408	337	TTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGT	CEEEEFB<DBEGGGE?A?>EGGGFACEF:CCB@DCHHEGJHEJCLFCBJEGIJJH;CGCIJIBELGJJ<FCLLECF<HGBCHIHHCJHFIHHKHEGB>C8F	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:DDC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.10204227	99	17	1173	60	101M	=	1423	350	TTGTAATCTGTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCA	:5=DC<<=G++:?>GAF=88=BDFFA9-.8:D9@FJHJE<EDHFA>JAB?=D@BCKKFJKJLMCCB:FH68B8@3<;<CBEJEIJIHIHELHDAF4@8GC:	X0:i:1	X1:i:0	MD:Z:9T91	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.95913538	163	17	1208	60	99M2S	=	1542	368	CCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTA	4<EIAFD@FG>FJHH@D?B?@CBDJFJJC,6,?9BJ?:8:ICICIIMK?IDJDDIKIIJ@;@<AAB,=A87=A@A2??/?IFECDFC0##2->@B?HC###	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR229776	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@@@
+ERR229776.53110448	147	17	1224	29	4S97M	=	947	-373	AATTAAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGAC	#####C@CEE6,JC+6.I7CD5:22;1A&=FBFABA<BCC@6CGBG@CA<G?BJIGG@DCFF=LIFDFBCFLKIGD>DLKKG><CKEFE+F:;BFHDEFC?	X0:i:1	X1:i:0	XC:i:97	MD:Z:0C96	RG:Z:ERR229776	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.78137857	99	17	1262	60	101M	=	1530	368	CTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTG	AHEEEGBE<BBFGDGG?B??HJGIGFJHGBFIDFKHGHIIJKHAJJIIILDMKKGIHCH?GEFDD@BJFGFEFKGIIHHIHGHMDEHFKHIJHJGGBCCDE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229776.83355002	147	17	1294	60	101M	=	1066	-328	GGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGAC	7?87?DCFEFEHKIHFHG@JKGHHHI@HHJGHHEGIACADFFGGFGBFFA=HGFH==ECCBFAEBBDFEGGGHIGKKKKKIIJIJEJ=GEFCGE?FFJFF?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.59579091	147	17	1308	60	101M	=	1088	-320	ACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTA	EEJGGGGIHHIG?JIKIFIGIGGIJFHJGDHGHCHEFGFIFFFFCDCDDKDEEGEFFFEFFEGCCCEHILILLBLKIIKKBKKKKIIKI@EHGJJIDFHFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.50673799	163	17	1336	29	101M	=	1617	367	CAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTTCTTACTATGCTCCTTGGCCATTTC	?GEEEJJDEKFIHCHHHKLKKLJIJJKIIILA:CFGHEEJDEFGFE8CEFDFE?;HB7=IFF>DGG<GHFKHIDB9:DI@HGLIJHILIFLFIGHFHFCBD	X0:i:1	X1:i:0	MD:Z:76A24	RG:Z:ERR229776	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.2114306	83	17	1337	60	101M	=	1033	-404	AATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCT	A?>?5H:ACCEJJH>:=C8662CC;E?E6);,4-20,)=(B44316)92:4@DAH<AC>H8HF;@CA>?>9ADE8/<8<D?<>BF:F57C3:9><;C?A2=	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.69297552	83	17	1344	60	101M	=	1080	-364	CTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTA	CGFFIJIIFFHFFLEDBCFFDAAC<D<:?7=G?B7C>;F9:1EG>CKLIJDLJ@IHIGKIHIKGIFH98I<7.GB6GEBHBHFFF=BAFH8>>B<CGC;>1	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.31884178	163	17	1349	29	101M	=	1660	348	TTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGT	&<B9DFCEIGCGAACED<+79FGGEEJEH945:-54CA;$.4;;?BBBF>BH>7GDDFGHF@=CDKC@DKHGEILJEJHC&88F=GFIHDIIHC?.@DEA6	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@AD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.44123845	83	17	1361	60	101M	=	1082	-379	TGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTG	FECDEEFDCGGGGIIFIIBF@FB@=BHAJKMDJJLKCLMIMMLKLMJKHJBFIJI=JGHFJGJGIKIJIDCBDHJFHHEJIFFGJEHFGGBBGE?DCFEFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.72241554	163	17	1365	60	101M	=	1597	332	GGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGT	CBBHFHGFEGIHKJJJJ"1BHGJJ@GIJKHJJIAIKJKJLMKJHKJJIIMIIGMIJGILIFKCFDGFHGDDKMHLJCFBAFHIGHIIIILIJIHHLGFIBE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:HGD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.45364215	83	17	1385	60	101M	=	1122	-363	ACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTT	/>=?GHLHICII?EIHMJLEHGHGFDDDGI=EJGG?GIKLJDIIKEIFKKDBKHIJHIHGHH>HIHF?JH@EDGJGGGCEG;DGGEGFFGE@CA:CECDBA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.26840652	99	17	1389	60	101M	=	1635	346	GGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTG	<<FEFC8E@9:GGBFCAIA:HDAEEIF>?ABECCIJJLJ@BCFAHIJILLCGJIDDGDGBEDJ@+>EGFKHN@CMKIJ;1+C?C3@ICF=D@I?GBA<<E@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.74203814	147	17	1408	60	101M	=	1171	-337	AGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGAC	DCFDC>IEGHIHJCDHCDJIB@DFHKJJHKHJLEIIILJFHJJJJMKJJGK@JJFKJJLJFKJJKCHLJKKIHIIKLIJHIEA&GHHFIKEHJF:KDEFG?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.33511586	83	17	1421	60	101M	=	1116	-405	GCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGC	CCE@GGIHF=D:EHKEJHHKHFHDBHJEGDEFKIFHEDJGH@IEDIIIKIEKIJKFJHCIDILKIJHCFE7IIHHHJJGIH<FIIDFDJGBECD@GCEGFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.5880975	99	17	1423	60	66M35S	=	1658	298	TCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGGTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGT	B:?H;C6;>;BFA:E>F(15.)1'0%1?EB1E(/;3?HHJ5)=CE>5=/8:D89;;EDF=%:A6=####################################	X0:i:1	X1:i:0	XC:i:66	MD:Z:60T5	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.10204227	147	17	1423	60	101M	=	1173	-350	TCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGT	D>AGEGF@8EBKKDH?DLDB=@HKGCHFGJGKIHDGFFEDHHFHC7KKJKDHMFIHGCJELLFKHIJI>IHCIILC>LGIKHGEHEJGIKEGFIEGFE:C?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.66536220	99	17	1466	60	101M	=	1680	314	GAACTGTCCTGGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGAT	A@DBIE==>>/<>>HHEDD@GGCDHH8BG>?JE:DIJHGDBD=AIJLJHH0G(>;D;=DHF:G?BEHFEEDHICFGD=6A;>EB=?KJD7>E13?EA2=CD	X0:i:1	X1:i:0	MD:Z:10T90	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.46562341	99	17	1476	60	101M	=	1781	398	TGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCC	AABECG<A8<BB:;F=2<>5A8>E@C;FD>3F=;=CCEDGCHFC7C6D?@?F@B>CK=EC?ACB?=;6@93E*A??B690<<935:FB>1--?@KC@HE7=	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.93812627	163	17	1518	60	82M19S	=	1829	411	CTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCA	CHFF=GHHFHIHIGKJKGIIKJKKKKLICKMJCKMLMJJJJKKKJLJLD@C?:<>@=DIH,GCCEEBA+6DGC0BCBADCH####################	X0:i:1	X1:i:0	XC:i:82	MD:Z:82	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.9004658	163	17	1520	60	99M2S	=	1782	362	GCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGC	7E:EEGFEHFBCKFHBCFAFHHHGKIFJHJEGLKHIJHEJKHJJGFFFMJMGHJHIILLKFCEKDEGCEBCIHHHIIIHCHILH2@?CFHFFIDHBJF###	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.78137857	147	17	1530	60	101M	=	1262	-368	CCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGCCACCAGACTT	ABFCBF?CIG>:EHJIIFMHICFMDKIFGLJGIIJJLKLKJKKHJLKLJLMJMJLJJLJJKBJHIHLEHIJJJLIHIEKIKKJFHKJIKHEGGEHKFGCH?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C@
+ERR229776.95913538	83	17	1542	60	66S35M	=	1208	-368	TTGCTTTTGTGCTACATGTGCAGGGTTGTGTACTCAAGTAGTCGGATTTCCCTCTTTTCCAAAGCTCCTCGAAGGAAAGTTGTTTTGGGATCTCTGCTCCC	#######################################################################>D:3EHI?IE5(9=?>*B7/&<-1%')&(+	X0:i:1	X1:i:0	XC:i:35	MD:Z:3G27A3	RG:Z:ERR229776	AM:i:25	NM:i:2	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.72241554	83	17	1597	60	101M	=	1365	-332	CCATCTGGTGCCCCCTCACTCAGCCACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTG	AFD@BGEBA;"GGBFAB:E>CG@=@@DEKA5AGF?>;:GACD@BADBEGG:CGAEED>G?IDHKJJJFFJIGIKHJII?HGFIH?BIDGCB>FEBCGEEFA	X0:i:1	X1:i:0	MD:Z:10A90	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CH@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.50673799	83	17	1617	29	13S87M1S	=	1336	-367	GTGACCACTCCCTCAGCCACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCATAAGCCCTGAACAATTCCGCCAGCGTTGCCATCTGTTCTGATGTTTG	##############IG@:;@@:B>DC7#8E;D<BHCD?E4:1&2DD;B?;;/.04+4<81.:7(>5,*=:#57*824:?GE@<;,9GAAC53?@<DAC@<+	XC:i:88	MD:Z:40T1C4A2G3G16C9C5	RG:Z:ERR229776	AM:i:29	NM:i:7	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@EEC@
+ERR229776.36734951	99	17	1629	60	101M	=	1873	344	TTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCC	CEFDEC9GC<CCGIIDGGHGFG9BGGHJJEIHHGKGICHHEHI?FHJ;JJFKI?D=GBGHKCJBAEEJEGDF>EGGHLHLHFHIHKHIHHGHHFFHGFJFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AA
+ERR229776.26840652	147	17	1635	60	101M	=	1389	-346	GACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCT	@==<5E?8GIMJCDHAIIHIE?EJ?MHED?IHFAGDBEAB<E=GLF;HLJEGGEAKJHMGIFCJFFLKDKJHHEFIJLJJKFHJHAGGDH@HHEFHE=@C:	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.19859205	99	17	1638	60	70M31S	=	1883	345	AGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGAC	=B.D@C<?755HD&99?@5AEED.D<+8?<=EF8FCFG*9:-9&/A?HH89G>.5:>9A6>BB@)=?EI################################	X0:i:1	X1:i:0	XC:i:70	MD:Z:70	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.76819541	99	17	1638	60	101M	=	1879	341	AGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGAC	A@BDIEAE><ADG2FDGGECHBA:BDCG=>'?CB@FHJ:JJDD==8EIHJ?KJLFCGGKHCEED:BHIKDHAF>FDAIGGGICHIHIEHLI4AFIFDJAHD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR229776.37392358	99	17	1651	60	49M52S	=	1874	323	GGCACCTTCAACCATGGACAGTGCCGCCAGCGCTGCCCTCTGTTCTGCTGCTTTCTCTACCAGAAGTGCCCTGCCCTCCTCACCAAACCACTCTGGGGAAA	+(23:@9=7:':++?;8E:@E?('1*?EFE=2&225(6;=+5::AAEH#####################################################	X0:i:1	X1:i:0	XC:i:49	MD:Z:10G11T9T16	RG:Z:ERR229776	AM:i:25	NM:i:3	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.5880975	147	17	1658	60	37S64M	=	1423	-298	CACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCC	######################################CKEAGEDB@?CKCKLF<JDBI88BLFEICFGJIEG@<GACIGCJ8?C=:70H?KHCKDAA.::	X0:i:1	X1:i:0	XC:i:64	MD:Z:64	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.31884178	83	17	1660	29	63S38M	=	1349	-348	CCATCTGGTGCCCCCTCCCTAAGCCAAAAGACTTCCACGCCAGACCCCAGCCTTGGCCCCTTCAGCCATGGGCAGTTTCGCCAGCGTTGCCCTCTGCTCTG	################################################################C2'<=67'?=/--'0>+35/*:4+&+&/1410')677	XC:i:38	MD:Z:8A5C18T4	RG:Z:ERR229776	AM:i:29	NM:i:3	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.25705936	99	17	1670	60	101M	=	1870	298	AGTTCCGCCAGCGTTGCCCTCTTTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTG	9<F7CC+2815@0;E<<EACIC'39>FD8A?B>;GHIFJC<7@CEJHEBE=HKI@<A;<BJ=D16/*+03:>?AHD;A#@/<>C*5DFGFIJCDAK?A>G@	X0:i:1	X1:i:0	MD:Z:22G78	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.66536220	147	17	1680	60	101M	=	1466	-314	GCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCT	E=DEHEFGIJIJHIKIJIIJGFHKKGJHIHEGKGJKDGJGGKMJILKKIIHC@JKIIFFF@JKKJLLLKJKIKLKJKJLIHCKFIJJJHHFKGHHGDD@CB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.46562341	147	17	1781	60	7S94M	=	1476	-398	ATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGG	########CGDDFFIHD@FC8?DICDBFEHDF<F@BDBADID@BB;EEBKIGCIF<GICECEIFIFFIJJIKJIGJGLGFGGIFHJFHEIBEG7FDC<<D?	X0:i:1	X1:i:0	XC:i:94	MD:Z:94	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IE
+ERR229776.9004658	83	17	1782	60	101M	=	1520	-362	CTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGG	1EBFGGBECEEB>4684;EA>;8EHE<<5CCC=;7@:0<>@:D=CA>7:49*:CIHIFCH><HJIF>?GJ;86/9<;??F=1+A?3(=64;:?:<B9D559	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.93812627	83	17	1829	60	101M	=	1518	-411	CGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCT	6B@BFBDB>:,CABHJIHIFIGLFEHGKBECBGA@FAB>>C<;ADCDECA>:AEIEH>BHHIHFIJH@HHEEFFEFDHGJFGCGECGEGG@BCE<@C?F@C	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.59635540	99	17	1831	60	101M	=	2100	369	TCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGC	=BH<C@9@D<;FJEC=B>99E@;GBAECD9;GFFJJDAFGF=;?DHKFH:4CEJ>C9B@@B?GBD?1083@;AKHLGIGHGFLHMIIAE:?HHIHKDGJF>	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.80549332	99	17	1853	60	69M32S	=	2041	288	GACAGTGGTCCTGGCCTCCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTCCCTTCTGCTTGCCTGTGGCTTTGAGAAGAA	9>;>5D<6:5;?EAD@@98.8??<+:<D-(/?<>4@HG:)./<?,81:>=:GE.)337?BJ:GB=;=E#################################	X0:i:1	X1:i:0	XC:i:69	MD:Z:16A52	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.25705936	147	17	1870	60	2S99M	=	1670	-298	CTCCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTAT	###8DBED@G@G69@8GC<C7$<B8G78,DCD?@7GKGG?;E9HJBBIIBJ>MCIFGFKG;>E<BJHFEFBJGHCKKFD?F2>9=BH>B@0F<FGFCADE?	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.36734951	147	17	1873	60	101M	=	1629	-344	GGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATA	BEFAFBFAFIJJGAJCCIJGGGC?HIIIHEGGGJJMJJFKLMKLJJLMJKJFMMJMJLKLJLLMJJJLLLMLIKKIJLJIHDKJJKKJIIDFJGHGFFFFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GJH@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR229776.37392358	147	17	1874	60	101M	=	1651	-323	GGCTCACGGAGCCGCCCTGTGCCGTGTCCCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAA	@D<@CF:B?B6,6@0C@JDGB8=EHGA+EHKGFGMKBD<FIJFFJJMFID>CEHKIJHEF7@JJHIFIJJLIDGC5D=AAEHC<FKJEHF?ED3FGEEFC?	X0:i:1	X1:i:0	MD:Z:27A73	RG:Z:ERR229776	AM:i:25	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.76819541	147	17	1879	60	101M	=	1638	-341	ACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAG	4;CC@CFAGCCDHDJGA=HJGDHDCHHKJIHAHJMNKJJJKKIKJJILKGJGILJFJKJEIFJFLLIJIIJKIHIFKKHGKJCFJGKFEGBHGGDKEFDH?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.19859205	147	17	1883	60	101M	=	1638	-345	AGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAG	<C@<EAA?JDGGC<B?HIHCD:BGFIE+BGGLFJHKKMIILJFGEKIJIMJLFCJJJBJHLKECFJFLEAAEII>I??EIHD?BGEF:G@CH=AFKEC;E4	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.11564716	99	17	1934	60	101M	=	2208	374	GCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCAT	+9DH=77>D@7G;?E=F:@CJG=BFIFFH:7HDCF?A@CHEIBDH?IHILFHKKDIE;9;9AEECHFC82:AHJIIGHIF@GFCIL>IFJI<DCGKGC>GE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229776.65159506	163	17	1948	60	101M	=	2208	360	GAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGA	4DEEEFCDEEAKDFJCDCDGHHGHHHBJDGFFIKJJIBJLCIJHKGCICIJIKCCDFBJKIJKKJHBIJHIMHIHKGIHDGLEIHJIHFFGJGGGAEEE@F	X0:i:1	X1:i:0	MD:Z:93G7	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H
+ERR229776.44568317	99	17	2014	60	101M	=	2277	363	GTTGCTGCCAGTTACTGCCATTTTCACGGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGC	ADBEEIBEC@@EGAFEFIH@GEEHGGG?GDBHGBJKJGFGHFIFFKGJLFEKJGCFABGG?BGABEDEGFDKGIGH@H@FDGFIG9<CD:FJHH@H=EDAC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.80549332	147	17	2041	60	101M	=	1853	-288	AGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACAT	HA@6/D>7AE@FBH>@D599*/FHEC@47?560FEGBHEA<B@;78;A:A7B?CC=15(*H>:AB6-E1+A8?*+:LGHHCC2>+>2>HEACGFH:A/A>:	X0:i:1	X1:i:0	MD:Z:0G100	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:gPC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.71965236	163	17	2100	60	101M	=	2416	416	CAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCT	BGEFEGHG=H>HHJIKKHKKKKIIIJIIAIGIIKHMKAJJKKJJJKMMCLKLJKKJGGKGJJHLDIKHEKGHKHEBC8C4DHHHJEDCKHEEDBHDDHCFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.59635540	147	17	2100	60	101M	=	1831	-369	CAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCT	AF>>BHJ>G:IHLFDEILDDDCFFFFH>FHGHDELL=JKGKKJLCNJ;EILIGLJJHMHF;5JIFJIFE@CFIKHGFILKJF><FHHC@H@HHFHKFJEC?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.60999876	163	17	2117	60	101M	=	2359	324	CGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTT	&5@CFGECDF?>EEGHG@KI;JHIIGEIFHG>GCBBJEIBJFCGJBGBFLJHMGHNJHAD111AJECDFHMDDHFIHHD;HDCLF9:@CJDCBB6>DCDHD	X0:i:1	X1:i:0	MD:Z:0A100	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CB
+ERR229776.8956867	163	17	2145	60	98M3S	=	2440	388	AGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCGGCCTGGGGAAACTGGGGCAAGTATC	:CE=FGDF9>@BGGD?F@<;GECFLIHKI>FA.>?@>GIIDILLH?EJFFCDKKJIDF<EILGDD<ADJJGL>GF=CGFFDCC>HEDHLHECBFGBB####	X0:i:1	X1:i:0	XC:i:98	MD:Z:98	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.11564716	147	17	2208	60	101M	=	1934	-374	GGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATC	BDDHFEGHHJGIMJDCLIKKICHLJKMJLLILNJJJECBJJLMMLJKLMLJLMJKKLLKKKJJKJKIIHLJLLLJJJJGHIHHGJKIHHG?CDHGEFGFG?	X0:i:1	X1:i:0	MD:Z:12G88	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GIF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.65159506	83	17	2208	60	101M	=	1948	-360	GGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATC	B@?IBDAGFFGIMIGIJHHF@JKKDKJGJJFJMGEECBBBFLIFKIIKLKGLJIIIJIIJHIIHCJE>GGBDFDFDBE>GB<<DAAGDEG<;>1=CEEEDA	X0:i:1	X1:i:0	MD:Z:12G88	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GEA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229776.13912851	0	17	2209	37	101M	*	0	0	GGTCAACTTCCGGCCTGGGGAAACTGGGGGAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATCC	<?>G>@GOFHFC>LGG@95'JIG;MCHHI"7::5G:FDH3K8LDFFP?IEPG@IHMPOPJBPRH@B?@=,:DLOFDEJQDDC<>?KL=CB0=INF5<JDED	X0:i:1	X1:i:0	MD:Z:29C71	RG:Z:ERR229776	NM:i:1	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GI
+ERR229776.3800945	163	17	2266	60	74M27S	=	2522	347	AAATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAC	4D@E=FG5DGBEJBFF@@'6DGDHBAFCIIIIIIHCM<EDLHFCHAIGJBICB,@:G>AEF>:5<DHGEJGBG############################	X0:i:1	X1:i:0	XC:i:74	MD:Z:74	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@IB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.44568317	147	17	2277	60	101M	=	2014	-363	CTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATA	<EJGGHGHIHHHFGJIJIHJI>@GIKIIJJLIHJOKGFGMMKLLJMHEJ?JLLKJIMMMIJFKAJLMJKKHJEBJJJLHLLIHEF=JEKGEHHFHEFGFFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.68077221	99	17	2314	60	39M62S	=	2563	345	TCTTTGGGAGGCCGAGCTAGGAGAATCGTTTGATTCCAGCAGTTTGAGACCAGCCTGCCCGATACGGCAAATCCCAGTCTCTATAAAAAATACAAAAAAAA	+-;)5(221::@C/3&8F842:3'0.:",+0D;)8+?B###############################################################	X0:i:1	X1:i:0	XC:i:39	MD:Z:0A22G9G5	RG:Z:ERR229776	AM:i:25	NM:i:3	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.60999876	83	17	2359	60	18S83M	=	2117	-324	GTTTGAGCCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACTCCT	###################KF=>C=:%+.80/;CB@30C3==;.G::HD<*(G>4-34(;8<6/2<C7HH:67:?/9;4/0+8%:=>09>(364-/+);7B	X0:i:1	X1:i:0	XC:i:83	MD:Z:79A3	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.71965236	83	17	2416	60	101M	=	2100	-416	CTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTG	@FJEBBBDE:EGEDEFGI@=0<=DHIHJNHIC=@HID@=HHDJEIIKJEI>JDIGEDB@D@CFHHC<FIK>IJIKHIJGJJEHJHGGFGGB@EEFECEDDA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.2016000	163	17	2435	60	101M	=	2660	325	CACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTTAGCTGTGATCGCATCACTGCATTCCA	?GEFDFKHHGGIIJJHGFKHILLIJKGHEILHKHILLFKMMCKJMJLMJBLBHFIJGHLJEGIBJCDHKGFKHIDIIHL?BCHII=FEFEJGMHHHGGFDF	X0:i:1	X1:i:0	MD:Z:74G26	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.101388755	99	17	2440	60	101M	=	2722	382	CTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCG	:A=DCC7@?;<D?>FBBGB::?8*=@5>D7>H<AHF4>BF3B?C?F8@EG?BBCC:??EIE?FH8=:B/<=>HFGGG?CA8G@2AJHKHCF>D@H<=CDC;	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.8956867	83	17	2440	60	7S94M	=	2145	-388	TGCCCACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTC	########JC<E@FCABIICBB8;07ECGCD8=I@=HJIGF?FBE<4HGHACG<<8D9@JH>@GC<>6&):B<F6:8@0;=?>C;<;AA=81?E=DEDD@9	X0:i:1	X1:i:0	XC:i:94	MD:Z:94	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.13231970	99	17	2448	29	6S29M66S	=	2649	301	ATAATGCCAGCTACTCATGGGGCTGAGGGTTAAGGACGGGTTGAGCCCAGGAGTTTGAAGCTGCTGTGAGCTCTGATGGCATCACTGCATTCCAGCCCGGG	+2;*;'0.135EB7H?<.2.=&01>3>B<########################################################################	XC:i:35	MD:Z:11G1A9G0G4	RG:Z:ERR229776	AM:i:29	NM:i:4	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.25467915	99	17	2456	60	101M	=	2477	121	TCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCA	BBFCAGBCDE@HHHFGIIIHIIEIEHJI:@CHIJFKKIGGGIJJJKKLFHDJHHHFGHDGFFHE<FFFFGDKGHIHJHJICIHH:GHCJGJGJEHDIFFFE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.25467915	147	17	2477	60	101M	=	2456	-121	ACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCGAAAAAGAAAGGAA	@EDEBHIELGAGINIIMHKHJFMHIHIFHJIKJNKGJGJKKL@JJDLHJKJLKKMLFCMJIG>KJJJJJLLMJILLIKIIJIFDBG/GIIFHJGHHJEFEC	X0:i:1	X1:i:0	MD:Z:87A13	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229776.3800945	83	17	2522	60	9S92M	=	2266	-347	TGTGATCGCCTCCCTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCAAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGAC	##########G@=CCE>,EA<<>4:JCGBE<==KJGIGID<FGA?>@G<7?IEB@'C@91F>9EB<(5=G?>JGCB@7AGE;41D;95BF<<B>:DCH<DA	X0:i:1	X1:i:0	XC:i:92	MD:Z:0A2A88	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.19017867	163	17	2540	60	101M	=	2857	398	GGTGACAGAGTGAGTCACTGTCTCGAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGG	??EEFEGFHH?GJEGHH@EEIJLK@JCLLMLKKLJFGLFJLLJINLFKLMLIKNIHJMMNKKJLJJD@HGKKLJKFFHH@IHNKIKGDDIHILHHGKDEE@	X0:i:1	X1:i:0	MD:Z:24A76	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.68077221	147	17	2563	60	4S97M	=	2314	-345	GACTCAAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTA	#####BE?EDH:EDHBBGJ:F;CE?@FFEDHHHCFDAIGE<5.GFCKFFBFI>6FC:29('/EBFDE=AA<GEC7'E4J@C2422=FFDGBH?6-@<E=A:	X0:i:1	X1:i:0	XC:i:97	MD:Z:97	RG:Z:ERR229776	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.52739527	99	17	2567	60	101M	=	2867	400	AAAGAAAGGAAGAAATAATGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTC	BGGEEGEED>EEGGIEGJ';FIIKGHEJHEJKKKHILHIIFFJHLKJJLKGKJILMKALILCJJDLIKHMKKKJKJINJKKKLJKJMGHAIMIHJHIE>FA	X0:i:1	X1:i:0	MD:Z:18A82	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GLI@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229776.13231970	147	17	2649	29	101M	=	2448	-301	ATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATC	6F=CA96B-EEGF620>,*965AB>=EF?,DCKEEE><EGKD<:<DGJCLIHFLGFIFFGKB9GD@CFF4IFFEIKHHCE?EGEDCIEJF:D>?HBE@B@0	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.44981660	163	17	2656	60	101M	=	2879	323	GCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCC	?EIFFHHGF?FIIJJIJHLJJKLJIIIICBIIIJHIEHEHJIMLJJMBIIJHFJJKJ>?FGJKKMMNIJHKHBACEGIHFIMFIGIJHILFEHHGDFEFED	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ACD
+ERR229776.2016000	83	17	2660	60	101M	=	2435	-325	GATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTAT	B?C4=DGB8HJCCIKFGBDHCFGGGHHHGLHDGFCEBBKBIJIHEDLKHKDJLKJHGDEGA;GJKJF@GHBBB>C>EDDGF;CCEBGAIGB@DA:=:CE9A	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229776.74190027	163	17	2668	60	98M3S	=	3014	419	CCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTG	CEIFEFKHHHIIIHIJHJIIHIJKFHGGHGKKLKLJMMJKLFJLJKLKJJMKMMMLLKMMJFKJIIINGKJJIHJHJMIFKIMHJIJIIMFIIJJEF####	X0:i:1	X1:i:0	XC:i:98	MD:Z:98	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.31785601	117	17	2710	0	35M66S	=	2710	0	AGGCAGAGACCTGATCACGGATCACAGCCGCCTCAAACTGTTGGGCTCAACCTGAACGTCCCTTCTTGCCTGGTTAGTTGTTCGGACTACAGGTGTGCGCC	########################################################################################B37.<90;7((/=	XC:i:35	RG:Z:ERR229776
+ERR229776.31785601	185	17	2710	37	101M	=	2710	0	CTAGGATGCAGCTGAGGGGTGCCCCTCTTAGCATCTAATCTGTGCCCTTATTTCCTCTGCGTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTC	>AF>>=<GCIH<HEJ=FBDHG4A:8HBE<@)B>C6,*58,CCC(%(,9FB?E8$4EIA7/,E@HCC@G?.IGHGC7FB7FF-C=@E;DGGABBEGEEDEG:	X0:i:1	X1:i:0	MD:Z:30C29T40	RG:Z:ERR229776	AM:i:0	NM:i:2	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.101388755	147	17	2722	60	101M	=	2440	-382	TGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGAC	5BFEDECIICCBFJHKFIEEHEHIIIJHJEIIBA>KHGKHKDFCFBGBALIGIIIILJCIGLIIIF=HIKHKIIIIKJKHHHC8BKJE=JAIF??FDEFG?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.3777343	99	17	2723	60	101M	=	2891	268	GAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACC	A@BCCA28?A:FJFG>FFH>FIHHKGIKG8@HIGIIFHIJFJKKKCGLJJ8FDFHCEEJFE;>@GHHK@DCCGGIGIIGD?@FFIHHIJHJA:?:>E@C9:	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.16418187	163	17	2727	60	94M7S	=	2953	318	GGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTG	?=GEEFFEJFEDGCHG?B8@JHIKG7CFHHGAFIJJKEFJ9=FABI@C1;HIFHEIHIJJ>EILKBE9EA>CLGH7:C(<0EDGJDKFKH:@@########	X0:i:1	X1:i:0	XC:i:94	MD:Z:94	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.60225376	163	17	2734	60	88M13S	=	3018	318	CTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGCGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGGC	4ED@3FDDF@=JG?HEB=2;ACGD>EFJ>>8@FLA5C>BGF*08=&*4<*7%<))4@?:HAFJ><GFH=38>?HD>EJD:@,<:=CC##############	X0:i:1	X1:i:0	XC:i:88	MD:Z:41T46	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.107194084	163	17	2742	60	101M	=	3015	367	ATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAG	?EFJFJHGJGFHIJJKIHIJJKHLILIKMJKHJFJGJJKMMLKJAIILMLMJMMIJLLMIGFDFJMKJKKJMKJG>GGC;@GFFB=E@CC@FEHH@2;AD@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.107791703	99	17	2817	29	1S34M66S	=	3127	380	GGGGTACCCCTGATGAGCCCCGTGAAACAGCCGTCGATTCTCACCCGGGGGGTCGGAAACAGGTGGGGAGGTCTGGGGAGGGGCGTGGCGCAGCTGCGGGG	#####################################################################################################	XC:i:35	MD:Z:3G8G8A1C1G8	RG:Z:ERR229776	AM:i:29	NM:i:5	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.11825404	97	17	2834	37	101M	*	0	0	CCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGC	AE<<BCBEEB<EGH?EI+;=GGFHG@FFA:BH8;;FKHEKLHIGJGIIHDHK@FIJI>EFC?E?>D>GFDFKGIGIHGFIGEGGC5<@FIHFGFCEKG<DF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:FJ@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H
+ERR229776.19017867	83	17	2857	60	19S82M	=	2540	-398	AGCAGCAGGCGTCCTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGT	####################H;FGLDE<A?E;IFCBFBFBDG?==9>5)+9<:AA=E9;7/"FC?D@7CK8BE@FDFEAH;96D=52;AE7-A8<88CGAB	X0:i:1	X1:i:0	XC:i:82	MD:Z:82	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.52739527	147	17	2867	60	101M	=	2567	-400	GTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACG	BGDEGGC9EMIIJHHFIIFDDFHAHFFIGIGH?GIIIGKJMIJIJJMIIJMHIFHLMJJJLKJFCLKEKJIKJMMILJJLKJKFHAHFIH4HGFHEDFF:?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.44981660	83	17	2879	60	101M	=	2656	-323	TGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGG	FEGDHIE?F;G9HHEG>HEA8FIFHGICNGFE<FJEDCJ=D?=@EFGBJG=6:IICA>BJIKJHHH>CBB8:62:A@6?HG<?-B?A5DDCACEBGC;FEC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GH
+ERR229776.49925000	99	17	2880	60	98M3S	=	3075	295	GTGGAGATCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGGGGG	=DCB=C5=4:<>CH37(;9@;?ABD>BF<>CC7,2::8>G)17?GBF-:@CH<;CCHAE=:;DBCAEC@(9>B:?D48AKHFGHFDD:CFIHGFICA####	X0:i:1	X1:i:0	XC:i:98	MD:Z:6G90T0	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.3777343	147	17	2891	60	101M	=	2723	-268	GGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCA	DEAGCHE=>EIHIIKFHDKIIFMHIIIFFFGAECECHFDFAHICGJHLHMKIJJKLHJG<J@FJDJFHIIGIF?I@KKLIKKJIJHHJGIFGGHKGFFECB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.99540436	99	17	2895	60	101M	=	3147	352	GAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGG	BGECE<=@DBEGGHHCGGFHIGGJ@CFFIIEGHJIKK@HDFJHCIJJJHG@LEIFEHB9DEDDCIEDEEFGE=BBHGFF>:<1<@C6*>EA6*07D;A@D?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C@
+ERR229776.16418187	83	17	2953	60	8S93M	=	2727	-318	AAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTAC	#########GAG=;7FE7:)C>E?;:EF</B?DD@;>???JBJCE:GEA=9<77IE@<=F?>@BCJKGGJ>97-<5?A?EA@D;HDI@GI;67A7ECBED=	X0:i:1	X1:i:0	XC:i:93	MD:Z:93	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.89222254	163	17	2970	60	96M5S	=	3189	319	GGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGGGGTACAGTGGACAGGCCCTGCCCAGATGGC	05=DFGE/BD@I+:FG?E6EGIJBFG?DEHFH@AFDBGG:ED;DICIHIGHMF1;@ECBD@+<:+>)@9B&=66<:=BB>>>6>DC*?@EC:BEG######	X0:i:1	X1:i:0	XC:i:96	MD:Z:0T69T25	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CFK@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.25895864	99	17	2976	60	101M	=	3273	397	GTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCG	CECCCG@DEA:DJ@HEGGBB8B@FEHHJAEGII>EBC@D>AGGFHKIIF<@IJIAEA@=>EGIB@EDBCBFA4<<ECE<BEFFIHGIHC?D>D=)8?ACC.	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.74190027	83	17	3014	60	27S74M	=	2668	-419	CTGCGGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGG	############################D?8789?>6?51:D>5.@4:9<:92<E=915A;:B>:5295A3.38;:37:52</@FBHH?GB>DE@CECGEC	X0:i:1	X1:i:0	XC:i:74	MD:Z:74	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.107194084	83	17	3015	60	6S95M	=	2742	-367	CCAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTCCAGTGGACAGCCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCA	#######??68;7GC=7+0FDEED77(+DG76<3/%*=4-<<1+21"A8;<&<43-:6,5@AACGD?>A@9BB>B8:AIHJBDFC@BDJE9ADEDEECFAA	X0:i:1	X1:i:0	XC:i:95	MD:Z:29A10G54	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.60225376	83	17	3018	60	66S35M	=	2734	-318	CGGGGCCTGGCCCTGGGCTGGCAGGTGGCCCCCAGCTGCTGGGGTCCAGCAGCCCCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGAC	########################################################################<?(EB:;CA;+C>7E=CA(5.6;4=DE?=	X0:i:1	X1:i:0	XC:i:35	MD:Z:35	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.4450150	163	17	3027	60	101M	=	3312	354	AGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGC	?C@DCGEFFGFIGFHGE@@HIIIIK?FJIFHKMKKIIJHLJLFJJLHII<FFGFGDJGGCDJDGGGGGG<FCHDAC@GLCBDDDJHGJIC8FJGJFKF<>5	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.49925000	147	17	3075	60	101M	=	2880	-295	CGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCA	<F@AFEBEGGGIIFMGHJLIFCLLKEKKLLKIGKKIMLJLLIJKNDDKLHJJKJMJKKKIFHJJIIKLLIKKHHEFIELIJHGGKJJFHEHGGCIGFEEC?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.26612274	163	17	3093	60	101M	=	3349	356	GACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGG	?GDEFB>DFCCIKEEIHFAJIHJIFHKFKGEDLB>LIJJMACCJJMJIEJGJJIF4FLIJ@HDDLJJKFFNHJKJIGIJCEIJE@@CBCGJHHHGDHCI@>	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.107791703	147	17	3127	29	30S71M	=	2817	-380	AGACCATCTGTCACAGCAGGTAAGCCTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTA	###############################IG++HE>E<12.<CIDCAECF>@99BCEF@6EG6BC,E(BF:>:>GELHDAC9@9GEF><CG>G>CAE;&	X0:i:1	X1:i:0	XC:i:71	MD:Z:71	RG:Z:ERR229776	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.99540436	147	17	3147	60	101M	=	2895	-352	GTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAG	CDDFEFHKHIFIHHGIJGJGIGJHIFJILGHKIIKKKMJJKKGKKMKNMJLKKKJIHJIFB:LJJJLKKI>LLKIIJLJIJHKJIHAGEIFFGHHIDDDH?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.89222254	83	17	3189	60	101M	=	2970	-319	ACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGA	FCEFEJGIFHFHEHHJCGHIDBD@LEB=8@DG>B:>53+14)A:2'DEFGA5-<39?C9DBGK?HEC>ED9#7HA2>C1ED@E<D;>6AH<@GD@GCIDBA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.27664076	99	17	3197	60	101M	=	3465	347	AAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGA	ABGGGEB;@78DCAFCGH8@F<DGIAD@9B<H@C<A=:FH25A;@9FFJ@<DDHJJIGEBICGEDB>?=6;<A8:<AABGFFHHJHE7BG;8B;BGAHFFH	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CCFEB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229776.46260219	99	17	3225	60	94M7S	=	3469	344	GTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGATCAAGACCAGCCTGGCCAACATGGTGAAACCCCG	A?=BEG8A7+7D64.:A7??@F5EF7;2=A>%806CHHI?H018D0;AGH@HHH<;GAB/?AF8EA)9@H@A@??HBEEGCFF<EIDF@DAGD########	X0:i:1	X1:i:0	XC:i:94	MD:Z:66T27	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.38173578	99	17	3262	60	101M	=	3478	290	AGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGC	=@?=7>2>:<:GBBF?IF=BHCEFGCJI?=:GFEAIFGHG8DD@HJKJLFBHHI5AJEJFFEE33?E@DJEFIIFHHFIGGHHEHID5DC<<B:F?AAA?C	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.25895864	147	17	3273	60	101M	=	2976	-397	ATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTA	BBBFGIHHLHGJHNIILHHJHCHBBDHLHEGIJHEGIGJJIHHJIIB>JMMBJLKIEKJLLKJIIFKJKKKJLILKIJIJG=EGJIHJI>DGGGHEFFEFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR229776.31259015	99	17	3281	60	101M	=	3514	333	AGGTCAGTATTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGC	7<8ACD<-.&)9:<<@7;9@HDCI>>/:<@@HFBB<CCH@DG;D@HJKIHDJLLMMBEII=BIIFG<C?IHB?@:BBAEABE?EG@DIHMIGGHFFGFHFD	X0:i:1	X1:i:0	MD:Z:7G1G91	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.109591233	99	17	3310	60	101M	=	3541	331	ACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGC	ABGD:A:@FDEEFHH:BFDCDJE=FGHEEDGKKKLHIIIKKKEFKBIIIC@GIALIIDGGLEHEIGHIHGFGKGELEGFBGHHIMIKIGGHCCJHIGEJFF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.4450150	83	17	3312	60	31S70M	=	3027	-354	AGATGAGTAGTTCAAGACCAGCCTGCCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGC	################################GFDF=;10AB54FF;C?K@BH@B@B=HJJIFE=FJ:>IBAI;=7;DAFC8<HGCDDDF:<8EDCCCHBA	X0:i:1	X1:i:0	XC:i:70	MD:Z:70	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.13454967	69	17	3330	0	35M66S	=	3330	0	GCTTGAATGGACAGGTCCGGTATTTATAATCTCATAGTAGAAAGGGAAGGATGAGTAAAGTTGAACTGGAGCAACTATTATAACACGGACAGCTGTCGAAA	:*=A1?5'117##########################################################################################	XC:i:35	RG:Z:ERR229776
+ERR229776.13454967	137	17	3330	37	84M17S	=	3330	0	CTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACG	7E=DDFFF8CBFFHDF?BDG6K60E;GF<.AA;:5-2*><-@@==+,BFFC7ADBJBGE:I9;)B?CA;;;=3FFHFBD;HLG##################	X0:i:1	X1:i:0	XC:i:84	MD:Z:84	RG:Z:ERR229776	AM:i:0	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.32427229	99	17	3347	60	101M	=	3572	325	AGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGAT	A@FDIE@E<;BFD@?C?IFEHHFIIEGKEFFJHJKKIHLIHKKDLIKLJKGJLIIIJGEJFIIEKGFFJGFKGEEGBFFIHJFAGCDIJIIHJHILGIFGE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.26612274	83	17	3349	60	101M	=	3093	-356	GCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTGCTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCA	#BDDB:FIECE==:A@AJG<GG=+>DA57C;A@='>?CCFEHF?@C@LDF>HHIKHHE4C@DJHH:?FGHAA@?IEDB;D7>@D79G:?BE<9?BICDGAA	X0:i:1	X1:i:0	MD:Z:0C33A66	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@F@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.38128366	99	17	3399	60	101M	=	3700	401	GATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAA	=@ECEC9@>E<EG9>?IDACD8?>HG;C?@=9FCE5?BDC<?D4@FECE7=+1;:GAF9@C>GA>D?>AI=74CH376*:+0;EHKDB->;<B6CIIDGD-	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@KNKOM@
+ERR229776.94969604	163	17	3412	60	95M6S	=	3625	313	TGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAACCACAC	CEHIDFKHGGHIHGHKJHAIJJKILIIJJLLKKLKJKJI?LMKKMLLKJNMMKMMMMJJJKJLGJGKHGHJGIFLHMHIFMILHHHHIHHHHHH#######	X0:i:1	X1:i:0	XC:i:95	MD:Z:95	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@DCEFGHHIIJJJ@@@@@@@
+ERR229776.9018775	163	17	3418	60	101M	=	3756	383	TGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTT	4;@C6?4EFG@:67CE@BFEHJF<F@IEIB@9E4>E;B6,57,I>=FB)20=2490BFGGBDGD?;C,0@07H@0CF10+9D14:CDEEE9@@GCDBD>>@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.27664076	147	17	3465	60	21S80M	=	3197	-347	AGACCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCA	######################CDIGFIBHGBG9C>ECG9:6A;.<4:<=ACIIKKJJHLKKIFEEBAJHHCMKJJKIEJGLHAGHHEHGFIGFHEEFEC?	X0:i:1	X1:i:0	XC:i:80	MD:Z:80	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.46260219	147	17	3469	60	101M	=	3225	-344	GGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAG	B?@ABG;AFE,=D@>;FG7B956B9AABEDDDKKGIKJLGGGKCJJACFGJMKMKJMMKNKJJIJIGEHCLLIKIJLHIIHHGDHHAJ@GDHHHHJFEBHC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.51706669	163	17	3478	60	93M8S	=	3757	379	AGTAAGACTCTGCCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGAAA	BEFFIGIEJHIH:CKHHKGKLLLLLLMLMFBD48?CCC@CHIDHJCGECEDCFAHFAEH@EHGADHIJGAA-6>A@EH6/;3+;CB=DBGJC#########	X0:i:1	X1:i:0	XC:i:93	MD:Z:12T80	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.38173578	147	17	3478	60	26S75M	=	3262	-290	CCACTGCACTCCAGCCTGGGCAACAGAGTAAGCCTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATA	###########################E@FEB/<ICC7G;CBCCCJJKIIKKJKIGCBBFJJILLLIHHHLJKMKILIIFEIA;HIJBIGFFGKFGFFFFB	X0:i:1	X1:i:0	XC:i:75	MD:Z:6A68	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BCB
+ERR229776.40964735	99	17	3489	60	101M	=	3796	407	GTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAA	ADEHEEEHBDEIIIIHJH?9E8=DF:AGE:C8=FGHD79@=39><:=C?A:DB<>EEA8B;?;@6>A632:<EC@EDEIB57AIJIFEBJKEFCG,BD6EC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GH
+ERR229776.94413412	99	17	3490	29	35M66S	=	3754	363	TCTCAAAAAAAAAAAAATAACACCACTTTGGCCTCAAATTGCATATCCCCCCCCAAGGATAAAAACGCGTGAAATTCAATGCAATGACAAATCAAAAAAAA	=>C<DB7579>IICIE#####################################################################################	XC:i:35	MD:Z:18C6T6T2	RG:Z:ERR229776	AM:i:29	NM:i:3	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.31259015	147	17	3514	60	101M	=	3281	-333	ATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATATATACGCAAACCAGT	C@AHHEHGJGFLIAKJIHFEC=BDI?HJJGDIA?DFCAKIF=L?EKLJKJLC;JLJLHKJJDJAJBF:JLIIIIIHJCIGHHD=EHHCGE9HFCDGC>I@:	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.89637749	163	17	3537	60	101M	=	3762	325	CTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGT	?K+=EFHGJH@JHHHIIGIAKBIIKLMJKLJMLIJJMKJLJKMMKLJCKMJLNNNMMKKKJKJKJKJHBKHFGFEJGHHGIHNIGMIMIJIJIIH@HCCAC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR229776.109591233	147	17	3541	60	101M	=	3310	-331	TGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTG	EFECKIJJKKIIIJ?J?GJIFFIHKIELIKHJGKFKJJJJKJMKJMKKLLKKHJJJJJJIIIJAJIJJJLIMIIIJILIIKIHGIHHFGJ:FJJGEIFEGC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.32427229	147	17	3572	60	101M	=	3347	-325	AATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTC	DEFECGJFIGIMIFFFFFFKFDIKHHJJGDFE?HBIIFDGLGFJKGKJHKIKJKKJKJJ?HJNKIMJJJIMMMKBLIJLKKIIHHAHFGKFHGHHGGFEG?	X0:i:1	X1:i:0	MD:Z:15G85	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.40459217	99	17	3602	60	35M66S	=	3843	307	TACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGCTGTGTTTTCGACAGCCGTCCGCGTTATAATAACCCCCCTACCTCAAATTTATTCACTTTCAACTC	=4><E;5@;A8A.7??E94:6;###############################################################################	X0:i:1	X1:i:0	XC:i:35	MD:Z:35	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.22665016	163	17	3604	60	101M	=	3861	354	CGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTTCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCA	49DFDF>@G:=EG=FKHFGG@HE6>FGA?GIIHE?HE6FJFI.:HGFJLJAJ+-5D??B9AAFEEFDD9A1@EBDIDDF?C.CDDHIFGHHHF?8DCICEF	X0:i:1	X1:i:0	MD:Z:52C48	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229776.104546030	163	17	3615	60	101M	=	3837	322	ATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACAT	CEFEJGEKGHFIHGGHH>HIJIIJIFGIIKKHALJJJMMJJKLBJJGJJJJNKJNKLMMNMNJLJKKJMMKKKKKIHKLFKKKIMHMKIJKKHIHFGGDFE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229776.37380040	1187	17	3615	60	101M	=	3839	322	ATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACAT	?EFEIGEJGGAGGCGHC:EGIGIJJEHHIJJIAKIJMIKFJJI?FFGBEIJMJJCGJHJMLMFCECJIMMJKKHHFHILIKKKFEHMKIJHFHHHFFGD:B	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229776.83861944	163	17	3622	60	101M	=	3858	336	TGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACAC	4=EAF@DADF9HDG=E?;DEDAACE@EFIHHLJEEH=4A@BACECFELDIDDJIA8CJJKIFDGIGBGHKIFFEJFDDBCHIHFCHHFDE<BGFCEJFDF@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@
+ERR229776.94969604	83	17	3625	60	101M	=	3412	-313	GTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACT	BGDHBF>GCHJDHJDJJHNNLBKKKNKMJJLLAJJJMJJJKJJHILKLLKGJLILIGIJILLIHLJGFKKJJHIHJKIGGGEAFBBFAGGECEE=DDEGDA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AEAD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.25245101	99	17	3650	60	101M	=	3870	320	AGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCT	A@=H=A<@,5:BF=FAIGBC>G<BJ;I6=8CECBEHII@FGCBDJBHJE>?MAB-=GDEDB>A=GIKJKHDEFJJJB4>DACEIC6F?IEH+?@KEAEDDI	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229776.38128366	147	17	3700	60	101M	=	3399	-401	CTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTC	<DGFFGK@E9C:2CGHKHGB>AHBEKFBFGHFEGCBDFGJJMKJMLFCFKJLLMLIIJKJKJIHJIJJJKJIIHDHJJIHHJJCIIHJGEIGFFEGFEEGB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.45938508	99	17	3704	60	97M4S	=	4005	401	ATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGA	BEECEE@D?@;GGHGBFG@CGD>C>:BEE=8BBC>CEGDFHEGHJJKH@2;?>H>9FFGI.0A?IGJM5B.;IEHGJ=GD:1319:GFBFBHD@FG#####	X0:i:1	X1:i:0	XC:i:97	MD:Z:97	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.94413412	147	17	3754	29	1S100M	=	3490	-363	CCCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGGCCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCT	##?>@E>6AA@CHDGE;FBH<9<->:>BD>CHDC?EC6G-+@CD8IBB/>DDF?;A:FFDMGHFIDLJKGJCCHAIADF?2+D<EB2<IABFGD<GFEEC?	X0:i:1	X1:i:0	XC:i:100	MD:Z:0T38A60	RG:Z:ERR229776	AM:i:29	NM:i:2	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229776.9018775	83	17	3756	60	55S46M	=	3418	-383	TTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAGGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGCCCTATTCT	########################################################F=)5C?7=*@83=>=??G>6?=44:B>>(:F>=97-$65=.6:<:	X0:i:1	X1:i:0	XC:i:46	MD:Z:37A8	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.51706669	83	17	3757	60	101M	=	3478	-379	TGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTTCAACACGTGGCCGTCTGTGTCTGGCTTCTC	<EA?8AHHHHD>H6<6>CDGHFD>AIGHEH?A;HB;.;A12000BC<=:D1FJEIGFEIIGHKHGHH?91'::G@E?FCFD57GHCGFGEDCDD<EGEBDC	X0:i:1	X1:i:0	MD:Z:70G30	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229776.89637749	83	17	3762	60	101M	=	3537	-325	CCACAAATCTACTCTCTGCCTCTGTGGGTTGAAATATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCT	96BFDC?+4,1;:DHCDE<;IHIBIEE>?.<0(,9+<2+7E@@/CAFHHIFJFE4GIICE<3HFFC-CBA<7GFIEC6GIJEFGGGGAD@+DFEDEF<DBA	X0:i:1	X1:i:0	MD:Z:32C0C67	RG:Z:ERR229776	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229776.40964735	147	17	3796	60	101M	=	3489	-407	TATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTA	EEEHFHGBGCGAGKIIKNLFKGIMJMFJFGHHGEFFF>DIHJJAJLKKHJKLKKLMMMKKLMKCLMMJMLKJKJMIILLKKJJKJIJJIJEGGFHKDFEFC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.21787291	163	17	3825	37	98M3S	=	4149	374	CTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATNCACCTGCTACACTCCTTCTTAGGG	?HDEFFDGF>>F6@H?<B?EIGGILIIDLB6LEHD.>IIIHJJJLMKBCFJ@DFLFCGHJJJJIBC757?FHCDFF#67:FH8CIHHJHIDHLHHJF####	X0:i:1	X1:i:0	XC:i:98	MD:Z:76G21	RG:Z:ERR229776	AM:i:0	NM:i:1	SM:i:37	MQ:i:0	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.104546030	83	17	3837	60	101M	=	3615	-322	GCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCAC	C?>EIHIGICJIJFHHHJHHHI@JJMJNJKJLJLJJMMLIJIKIIKIHKIAHHKLHHIILJHIGFF@JJHFIHGD;HBHIJGHJGHHHGGBBDEBGFCCDC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.37380040	1107	17	3839	60	2S99M	=	3615	-322	GCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCAC	###BIHIGICGDG=)HJHDEHI<@GGEIAGBKHLJGMKKIFKJD@DDEEG>F>EK@ICILJJHHHF;JHHFEEGC8JI=IHGDJGAFEGGB@@EBGFBEDC	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.40459217	147	17	3843	60	34S67M	=	3602	-307	GGATAGAAATAGAGGCCTGGAACGCGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCT	###################################CG?+<EFH>GB*7*C;F;4=HF;?F3@ECBCF(ECKHGG>9HB@<@9>9BEACF-8EE907EED?:	X0:i:1	X1:i:0	XC:i:67	MD:Z:67	RG:Z:ERR229776	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.83861944	83	17	3858	60	101M	=	3622	-336	TCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTT	D;GFIF=CD>D:CJHIJJEHGJD:<9:8?<:<EE@?>9JEHEE?<>A?BD6?C>.EJ??>AGJBGFB8694BAHHF@>?<>=9=D=F@B<3+7G@EGFB:9	X0:i:1	X1:i:0	MD:Z:78A22	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.22665016	83	17	3861	60	3S98M	=	3604	-354	TCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTT	####HHI?9>A+CJHJIIA<GB9)*FGG;73B;EDFB@JCFHGBAFDFFG<CCE=:8+40'@CGJB:'9A=6)>377&041;57:=D;=3++.(:>CB=;+	X0:i:1	X1:i:0	XC:i:98	MD:Z:75A22	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.26430745	99	17	3863	60	101M	=	4142	374	TAGCATCTTGCTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTATGGC	BEEEEEBIE>-EFFHEJHH@IFGHJHHHBCBFCCIJIIFJHHKIJKKIGI@MKLMKLJKDJBFFLJKJIDJKIJJCKIIGMHKMKGJGMIHHHHKGGDF;>	X0:i:1	X1:i:0	MD:Z:10T90	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.25245101	147	17	3870	60	101M	=	3650	-320	TTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATT	CDDHHIDHFB@,;@DICEHHEFEHHJLFE?D??ABCCGCDGCFGEJKMKHKJMIICIIFJJILKC?H?EF=IJIIJGFFAH>CB@IIHHHBGFFGGEEFA?	X0:i:1	X1:i:0	MD:Z:66A34	RG:Z:ERR229776	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229776.106927739	99	17	3903	20	101M	=	4098	295	ACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGA	CDEIEEFECAAIGHIFIJGEJIHJJIJHAEHKJ8IAJHFKKHKKIJIILLELKMMKGAJJIIJHGHGIHHIG;HHCGJHHLHGCGLIELFILHC=>BBJ@G	X0:i:1	X1:i:2	XA:Z:17,+4162,101M,2;17,+4088,101M,2;	MD:Z:33A67	RG:Z:ERR229776	AM:i:0	NM:i:1	SM:i:20	MQ:i:1	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
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diff --git a/test/mpileup/mpileup.3.bam b/test/mpileup/mpileup.3.bam
new file mode 100644
index 0000000000000000000000000000000000000000..90b325eeab72c40a2a16ba92c1349085145e2eb7
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diff --git a/test/mpileup/mpileup.3.bam.bai b/test/mpileup/mpileup.3.bam.bai
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Bz!U%g

literal 0
HcmV?d00001

diff --git a/test/mpileup/mpileup.3.cram.crai b/test/mpileup/mpileup.3.cram.crai
new file mode 100644
index 0000000000000000000000000000000000000000..6257e4bb473cac0bcd82851c39704b293449dde3
GIT binary patch
literal 43
ucmb2|=3oE=X5$AYPfQFA44#;nY&UsqVq(ZFly=OmEr!9i-E*BJPz?a@jSH3l

literal 0
HcmV?d00001

diff --git a/test/mpileup/mpileup.3.out b/test/mpileup/mpileup.3.out
new file mode 100644
index 000000000..e0ee45aba
--- /dev/null
+++ b/test/mpileup/mpileup.3.out
@@ -0,0 +1,30 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100
+17	1050	.	A	<*>	0	.	DP=6;I16=6,0,0,0,232,9002,0,0,360,21600,0,0,113,2597,0,0;QS=1,0;MQ0F=0	PL	0,18,152
+17	1051	.	A	<*>	0	.	DP=5;I16=5,0,0,0,191,7317,0,0,300,18000,0,0,115,2675,0,0;QS=1,0;MQ0F=0	PL	0,15,135
+17	1052	.	A	<*>	0	.	DP=5;I16=5,0,0,0,189,7223,0,0,300,18000,0,0,117,2757,0,0;QS=1,0;MQ0F=0	PL	0,15,135
+17	1053	.	A	<*>	0	.	DP=5;I16=5,0,0,0,187,7027,0,0,300,18000,0,0,119,2843,0,0;QS=1,0;MQ0F=0	PL	0,15,133
+17	1054	.	C	<*>	0	.	DP=5;I16=5,0,0,0,184,6852,0,0,300,18000,0,0,121,2933,0,0;QS=1,0;MQ0F=0	PL	0,15,132
+17	1055	.	C	<*>	0	.	DP=7;I16=7,0,0,0,255,9635,0,0,420,25200,0,0,123,3027,0,0;QS=1,0;MQ0F=0	PL	0,21,161
+17	1056	.	C	<*>	0	.	DP=7;I16=7,0,0,0,252,9454,0,0,420,25200,0,0,127,3127,0,0;QS=1,0;MQ0F=0	PL	0,21,159
+17	1057	.	T	<*>	0	.	DP=7;I16=7,0,0,0,269,10389,0,0,420,25200,0,0,129,3133,0,0;QS=1,0;MQ0F=0	PL	0,21,164
+17	1058	.	G	<*>	0	.	DP=7;I16=7,0,0,0,281,11297,0,0,420,25200,0,0,131,3143,0,0;QS=1,0;MQ0F=0	PL	0,21,170
+17	1059	.	T	<*>	0	.	DP=7;I16=7,0,0,0,257,9509,0,0,420,25200,0,0,133,3157,0,0;QS=1,0;MQ0F=0	PL	0,21,157
+17	1060	.	C	<*>	0	.	DP=7;I16=7,0,0,0,268,10392,0,0,420,25200,0,0,135,3175,0,0;QS=1,0;MQ0F=0	PL	0,21,164
diff --git a/test/mpileup/mpileup.3.sam b/test/mpileup/mpileup.3.sam
new file mode 100644
index 000000000..e40039de3
--- /dev/null
+++ b/test/mpileup/mpileup.3.sam
@@ -0,0 +1,250 @@
+@HD	VN:1.0	SO:coordinate
+@SQ	SN:17	LN:4200	M5:a9a06ca09c111789d92723fbf39820f6	AS:NCBI37	SP:Human
+@RG	ID:ERR229775	LB:HG00102_I_bc_pelib_1019	SM:HG00102	PI:497	CN:MPIMG	PL:ILLUMINA	DS:SRP001294
+@PG	ID:bwa_index	PN:bwa	VN:0.5.9-r16	CL:bwa index -a bwtsw $reference_fasta
+@PG	ID:bwa_aln_fastq	PN:bwa	PP:bwa_index	VN:0.5.9-r16	CL:bwa aln -q 15 -f $sai_file $reference_fasta $fastq_file
+@PG	ID:bwa_sam	PN:bwa	PP:bwa_aln_fastq	VN:0.5.9-r16	CL:bwa sampe -a 1491 -r $rg_line -f $sam_file $reference_fasta $sai_file(s) $fastq_file(s)
+@PG	ID:sam_to_fixed_bam	PN:samtools	PP:bwa_sam	VN:0.1.17 (r973:277)	CL:samtools view -bSu $sam_file | samtools sort -n -o - samtools_nsort_tmp | samtools fixmate /dev/stdin /dev/stdout | samtools sort -o - samtools_csort_tmp | samtools fillmd -u - $reference_fasta > $fixed_bam_file
+@PG	ID:gatk_target_interval_creator	PN:GenomeAnalysisTK	PP:sam_to_fixed_bam	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -R $reference_fasta -o $intervals_file -known $known_indels_file(s) 
+@PG	ID:bam_realignment_around_known_indels	PN:GenomeAnalysisTK	PP:gatk_target_interval_creator	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T IndelRealigner -R $reference_fasta -I $bam_file -o $realigned_bam_file -targetIntervals $intervals_file -known $known_indels_file(s) -LOD 0.4 -model KNOWNS_ONLY -compress 0 --disable_bam_indexing
+@PG	ID:bam_count_covariates	PN:GenomeAnalysisTK	PP:bam_realignment_around_known_indels	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T CountCovariates -R $reference_fasta -I $bam_file -recalFile $bam_file.recal_data.csv -knownSites $known_sites_file(s) -l INFO -L '1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;21;22;X;Y;MT' -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate
+@PG	ID:bam_recalibrate_quality_scores	PN:GenomeAnalysisTK	PP:bam_count_covariates	VN:1.2-29-g0acaf2d	CL:java $jvm_args -jar GenomeAnalysisTK.jar -T TableRecalibration -R $reference_fasta -recalFile $bam_file.recal_data.csv -I $bam_file -o $recalibrated_bam_file -l INFO -compress 0 --disable_bam_indexing
+@PG	ID:bam_calculate_bq	PN:samtools	PP:bam_recalibrate_quality_scores	VN:0.1.17 (r973:277)	CL:samtools calmd -Erb $bam_file $reference_fasta > $bq_bam_file
+@PG	ID:bam_merge	PN:picard	PP:bam_calculate_bq	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_mark_duplicates	PN:picard	PP:bam_merge	VN:1.53	CL:java $jvm_args -jar MarkDuplicates.jar INPUT=$bam_file OUTPUT=$markdup_bam_file ASSUME_SORTED=TRUE METRICS_FILE=/dev/null VALIDATION_STRINGENCY=SILENT
+@PG	ID:bam_merge.1	PN:picard	PP:bam_mark_duplicates	VN:1.53	CL:java $jvm_args -jar MergeSamFiles.jar INPUT=$bam_file(s) OUTPUT=$merged_bam VALIDATION_STRINGENCY=SILENT
+ERR229775.22049853	163	17	1	29	80S21M	=	115	213	AGGCTCAGACTCCTTTCTCTATGACAGGGAGGTCATGTGCAGGCTGGAGAAGGGGACAAGAGGGCCCCAACTTCTTTGCAAAGCTTCTCACCCTGTTCCTG	BDBDHECFF@D=DA>CIJIF8E>HBEEBH@AA8>GH@BIJI;<A4(>?CC95@@?*2-67=6?$6ABDGD6GGHKGEGHIJIH=BFIKI:DEADBH>CFIE	MD:Z:21	RG:Z:ERR229775	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ihg\aehjhYcd`cag]behd
+ERR229775.4635304	99	17	1	29	9S92M	=	250	348	TTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACG	BFFKGHHHIKIIIKIKLKIILHMKJJLLMILJJJMLJJNKLLMKKJLJKNKLKILNKLKMLINLMNLMNKJJKLNKMKFAEHGMKPLHFGJIMIKFFFE@;	MD:Z:92	RG:Z:ERR229775	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@jhhhjhjkjhhkgljiikklhkiiilkiimjkkljjikijmjkjhkmjkjlkhmklmklmjiijkmjlje`dgfljokgefihlhjeeed_Z
+ERR229775.76124411	163	17	1	29	12S89M	=	253	351	AACTTCTTTGCAAAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCC	@BDIFEFFEBBGJIHGJHEIJHGJJKIIIIJKHHIIIJKICKHE@<HIIKCJLJKGIIMKBGJ=EGEJMLLMKJJKJLKLK?FCHCNILFEEB?FKAHECE	MD:Z:89	RG:Z:ERR229775	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@ihgfigdhigfiijhhhhijgghhhijhbjgd_[ghhjbikijfhhljafi\dfdilkkljiijikjkj^ebgbmhkedda^ej`gdbd
+ERR229775.72556128	99	17	22	60	101M	=	262	339	CATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGC	BHFGGIHHJHGGIHIJKIILIJKILMKIIKIMMFKMJLMKJJJJMLLHJJMIJMLNLJMMFINLKKMMKKAMHIIKFMHFHMIGGJIJIGJJGHFHAAEAE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.92054104	113	17	25	37	101M	*	0	0	AGATAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTA	IEFFDGGJIIKMIJIHICJGGFHJDHFFHIHGKGDGGDJIFIIJHIIIKKLKKMMMJKHGB=JJJIAJFLJIJJGLLLJKLKHGHJHGHECKGFGLGGHFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:D@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.73749010	99	17	28	60	101M	=	283	349	TAATTGCATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACA	BFHGGHHHHHHGIHHJHHKKJGICGFKCHMIJLIJJJMLJKJJFBJFLJMJJMG?IMLKJJIJJ=LC?GFELIEHICBCGFJD'?BEF8>>1;<=E?CG?F	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H
+ERR229775.71066602	99	17	35	60	101M	=	291	355	ATGACAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCT	BEFHDHJHHHFGLIJIJKKLJKLKKMJIIHJLKMJJLMGGLJMJMMMEJMMKKMMKJ?LKLJMHNJIIMHCFHGMFCIJDHJICAIDJJFIHGGIBBHEEI	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR229775.57643739	113	17	39	37	101M	*	0	0	CAATTGCCTTGTCCCTGCTGAATGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCC	DEEFHE@C?HCHHAIJIIJIHCJEIE;JHFEEFHKFJFJIEGIJGH>9KJD@;EFCJIFA=JFICKIDCFJGFC?IIJHHHKHB@IICIICGCGJGDDH??	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.24343576	163	17	62	60	101M	=	322	360	GTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAA	@DCDHCFB>,,FGDGFHGC@FHFIHGIKH@2JGH@JGJ?EJHCA5?BLIHEJHIGFEB@BG;BBEDGIEDGGGL;FGFI;A37<?FGELHFJIIGEH=6EC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.89434694	99	17	93	60	101M	=	304	311	ACCAACTCCCTGGGCCTGGCACCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGT	AEEGIELGGGIIHJKKLIKJIIHIJELGJKLCHMHJMMKJJJLFGHLKMF?LMJKHIIGFHIFIIODHIIHGFJGIJHJ>F9F2=@JCDKHJGAIGFEEEE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.48988007	99	17	115	60	101M	=	371	356	CAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAG	?GDCCIGFKGFKGHKKHGIKJIIKGJHIACKFGHCKHJJJFIILGFGMK@CKFIHHJHI>JIFJMEGADJG>FEHJIIIFHJHIMDHKGIH?CJGGFFIE8	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.22049853	83	17	115	29	1S100M	=	1	-213	CCAGGGAGCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTA	##IDEBEBHKIDCIFDIFGKD?EHA>BA;GJHIABEGEFGIBDGIKGJMGJIJKHGHKJALJJIJ@DCECE>EIIIHHIKDEFHIEHGHHGHGFEECCD@7	X0:i:1	X1:i:0	XC:i:100	MD:Z:100	RG:Z:ERR229775	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.6535575	163	17	136	60	101M	=	400	364	GTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAAGACACGCCCCTGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAG	@:9<EC6,<909C@??DG3<FGFEABE3.('*.'3D963D<D;19:?)9-$;>D&@9/0<98DBCCGCDG:?E=>D><+/;7A:=HE71)61>4:<CEEE7	X0:i:1	X1:i:0	MD:Z:54A46	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.59467859	99	17	159	60	101M	=	359	300	GGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTC	&5FDGHHJJGDGIEJ>KDDIKLJJGJH<IHEJHAFJLKHLMKHMJMMJF.BGDFKEGJIG8CF.<=EKAE9F'9A=-6G7HH14?=E=DHFAIHGE?D?BC	X0:i:1	X1:i:0	MD:Z:0A100	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.21746912	113	17	160	37	2S99M	*	0	0	TAGAAGTGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATT	###BJFIIFDF>=6GAIGEIHCHGB@?>HBFHGHBGDFKFGKHGFCFFGBBEJFIJMIFIHJJJLID<BJCKLIHJJLH>FF@HDKHEHGFEHLHHDEFDB	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.74734077	163	17	164	60	101M	=	421	357	TGAAGCCACCGCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCGCCGCCCAAAGCCACGCCCATGTCCAGCTTATTCTGCCC	7+>C1A5?-3&B<:EA:(86>A4F8=B<7>7D52@7=<B;?HEEI9B@DG3=*CD:+1+64=$'27AC&9<G<)5:<-@DEG79@:@A,>>CAE5DK.<BC	X0:i:1	X1:i:0	MD:Z:62A10A27	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229775.51284727	163	17	174	60	101M	=	420	346	GCCCAAAGACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTC	:>DCF>(-706B=ACA>D<@IE4:D;CG;@BH9@GH@CCJ@G=<GIBD?C;DDFH;CEHEI>B@;ED9E@BHDBFHGI;5ABFHFIG=FCE/=GHHEJGJF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H
+ERR229775.86942903	99	17	232	60	71M1I29M	=	471	339	CAAAGACACGCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTT	AGHIGIEGD>BGHFHHIKKILKMIIIHIKHJKLCEFJJFMDLJIFHKLLKDJGBEGGJ?@GFIIKIH?GGHDDACIB?>DDJFGII1?,9ED*@>D@FCE=	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C@
+ERR229775.4635304	147	17	250	29	53M1I47M	=	1	-348	CAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTT	EIGGGHHHHCJICGIMGCJGHKCFDJOJJKKIJKKKJIKJJMIIJJJHEHIGILLLLGLBGDJJJLKGIKHGIIKHHJHHKIFHHCG;HFBCGFBEFCDGB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229775	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IG
+ERR229775.76124411	83	17	253	29	50M1I50M	=	1	-351	CTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGA	DDFFFGHJIGHINGDIGDJIJAINKELOIJLKKKKKMJLKKGJKJKLNKKNMMMKLBLJLLLNMMJKKJKKJJJKKJLLIJJHE@KJJJKFHIHFEIIHFB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229775	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.72556128	147	17	262	60	41M1I59M	=	22	-339	CCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAA	DDFJEGJGC@IKEINIFFMHKHIJKKKIIMJKJJJLKKMJJLKKMJLCKKFKKMLLJKJIIKKIIKJHKLGHIGC>HHIJKFHHHGGIJGBEEJAEEIFEB	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CBA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GG
+ERR229775.73749010	147	17	283	60	5S20M1I75M	=	28	-349	AAAGGCTGCATGGTTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGT	######G?<7G9;+@-DEI=CHOHKOFBHE9BHKFE>JHDH9?GHFDCBKCIHA;E=C;9>@A7HA?;AGADHBGHGG@@:>8HG?D9DF6/;@=>:<CB9	X0:i:1	X1:i:0	XC:i:96	MD:Z:95	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.71066602	147	17	291	60	12M1I88M	=	35	-355	TTGACACACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGC	AHGEBHHIHMGIMIGILKBJIKLKMMMKMKIKKHJJLHJMMJKHIG:KLJGLJLLJLILLILLKLKKFKKHHIHIJHHGIJHGGGHGGGGCDBDCEHGGF@	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.73865342	99	17	298	60	5M1I95M	=	594	396	ACAGTAGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTT	BEHGHHHHGKFI@JIILKLKLJKMIILLJJLJJKKJMMNNJMMLNLJMNJMJLLLLMLMMLKMLLMMKJLKKKJMJKIKFKKIIMFFJGNFKIIKIGGCBD	X0:i:1	X1:i:0	MD:Z:100	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BAAE
+ERR229775.89434694	147	17	304	60	101M	=	93	-311	CCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTG	DFGG?JIIHKLILLKLLLILKKMHJMNHKJIJDMLMMMKLMKMIMMJLMKJLLKMLJJJIILIIIJEHIIEJIKIJHJEGHHFJGDHFGGEDBFCFFEDGB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.24343576	83	17	322	60	101M	=	62	-360	GCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAA	?DEFIGIJKEAHC<GIMKHNKJILKHMNKLNMMLLJNLJKKKKMKJKLLLIJKMJNKJHNMJKKMLJKHJIJMMMIJJJIKJHFJIIIJIAGGFHHGGDC7	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR229775.64297521	163	17	324	60	101M	=	598	370	TATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATA	@B4DEDC=EDEAC@HCIJ>BBA;FEFGH:A7E<&<GJK=C9F=EBIKJKJGJHCADIJLKI9I>>HAJEIEKKKJGMIJGILKMGNLLKLKIEIJHDIEFE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229775.65476258	99	17	324	60	101M	=	548	324	TATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATA	BFFFGHHHHKIJKELKKKJJJLKLIIJIKLLJJLJMLMMNKLLKFJMNMKKJMKKLMNLLKKNLKLMKKKKLLKJNNNLILKLMJNLLKLKIEIKHGHGFE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229775.44063798	163	17	331	60	101M	=	608	377	TAAAAACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGG	@92:9C:E>:EFG>H<CCE@G:=;97<@A@EK@@AAD@@9CADEHGFIIHEHHHGHGGD@J36@CIIIM?JFBHJ5E3CGKLKIC'=FH@DJHIEGHFGB#	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@
+ERR229775.78639790	99	17	335	60	101M	=	590	355	GACTCCTTGCTGGTTTGAGAGGCAGAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTA	?GDKFFKHHHIIECHIBHFJGIKIHKKLCBHEFJIKMMKJGIJJBFJJJJDMLKJJKJKKLLLKNNMKKHIILINIGKLIIKILLLNNIIIJKIMGEEE>@	X0:i:1	X1:i:0	MD:Z:0A100	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:ZS@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.59467859	147	17	359	60	101M	=	159	-300	GAAAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCAT	DGCDGIEEDKK>LIKHIGMJFHLNJFHLIJAJIIFMMHDIJHGIHIJLIC?LJIEDCA=<3AJIHID<A?<BDHEE7D<DGCBHJDEBFGEBEFCFFDEB@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.48988007	147	17	371	60	101M	=	115	-356	TCATTGTTGCTTTACTTTGCATATTTTAAACTTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGATAAAAGG	FA=1/@:JFIMIF0:;NLIHEKJGMLKK@>)MJGD=@?<8*4JCCA8@928-=92)2@975E)BFE8-;L>CFC>8K?E=8''?@9A>6C694*%;,/44*	X0:i:1	X1:i:0	MD:Z:4A25A63C5T0	RG:Z:ERR229775	AM:i:37	NM:i:4	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.70199275	99	17	391	29	101M	=	711	374	ATATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAAT	?EFGGHHFFIEIIEF?C@ABICJICEIJJJLLJJM?H>HHCFI:G>AEHJILLFHGCMJGLKEM>-5A8BKE;JIJHFH4AEIAGMJDF@<A@EBGBF7C6	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.47649789	99	17	392	60	101M	=	647	355	TATTTTAAAATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATG	:EFBGHHJJKBIIEDGFIIJLJIKDIJIILLJILIEFMFDJKKJKKHHJAKLIJGCKFILMNNKHJKKLLJ2JIKLDJHBBIFJKLLLIFKIKIJHIHEE=	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.6535575	83	17	400	60	101M	=	136	-364	AATTGTGACTTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATA	CC9CCD3?CDIKJGHDLIIIKGLJE8>EHKJHJLHD9JKJN?JLFAG=GMGKKJIAJAJGHI@JGIKKIMHLIIGDILHIF>CGJJLGDC8DHHLGFGFE?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:FE@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.5711913	163	17	409	60	101M	=	646	337	TTTCATGGCATAAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACAC	<@CDFD<CE@BFHCFCIFD;JFE?<><AB;AA>@A?HIIGFJKJLLIFIFCGIFEEDF@KMC?EI=<<<BHHJJGIGKBGGDAEKKHMJJHIBEHDCGEHB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.51284727	83	17	420	60	101M	=	174	-346	AAATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTT	ABBCB=.9FIDDIEIKDBIFHGKKH@IHJLKLKJIKEIGKJKHDABJJJKHLJILJJJJJLLMKLJLHF@HEHJMIIBHAHIEF;EDEII>GGCDEEFDD7	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.22701711	163	17	421	29	101M	=	699	375	AATAATACTGGTTTATGACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGGAATGAAGACATATGTCCACACAAAAACCTGTTC	<BEEH:<>93:<>>FC'?<A:GG:DEEEF1=J);9C@H@?AFA)=DJB??C))-:4?;<AGCID@KK%;CHJKNGLFKBDE=1@C:DJDGCHBHAEHDGDF	X0:i:1	X1:i:0	MD:Z:16T50A33	RG:Z:ERR229775	AM:i:29	NM:i:2	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@D@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.74734077	83	17	421	60	101M	=	164	-357	AATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTC	A:DBED@DGB7F:FEGIGAH7:CF>IHGIKH7KCHCGJFFJHEFCHJJMCLAHJDHKHMGHMLMEF@IBFIHI@DA:HCIGFA83>=0HH<AGG<<F>EG7	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.52216469	163	17	454	60	101M	=	693	339	ATGCATGTGGACAAAAGTTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAA	@CEEFFBFE<DEGIJHJEEGJJGHIHKKCCGIIGKLLIJKHLKIJIJJKJGKJKJJKLNMMJMMJIJJJKKJKKJJOKKJNKJKLIIJGIJHHCHHDGGGE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IJ
+ERR229775.13748016	16	17	455	37	101M	*	0	0	TGCATGTGGACAAAAGCTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAA	IFEDMGM?J<IGGBNC*PLKJGMIRKLOKRHJJJMJHKLRBFKLNIQEF>:<>:MEMIMED1N?LLQKQD9)@GNLKB<KB18=?87BGILGHGNE8ICF<	X0:i:1	X1:i:0	MD:Z:16T84	RG:Z:ERR229775	NM:i:1	XT:A:U	BQ:Z:D@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D@
+ERR229775.86942903	147	17	471	60	101M	=	232	-339	TTGGGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTC	:HDA8F:ILGILIMIMIFIEA;)D>@GHGFA;>A>D>;A;H=?B5DIEAFEC>-(7@C8BAD<ED3C<=?,3730;D3;HB2&4???/6323/8:"B>5>7	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.82457097	99	17	474	60	101M	=	695	321	GGATTAGGAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAAC	A?HGGHHFIGHIJFJLLDEJLJKIJIIIGJLMJHIHKMNNNJMNLJJMKKJJMKMMMLLLNJJMKKLKJMKNNNNIKKIIKMJMHGFKGHC?FEHLDFGDB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.93698964	99	17	499	60	101M	=	735	336	TATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTT	BFFGHGFHFHEIKKKLIKLIIJLJJKKLJLIMKKMMJKMKKMKKMKNNMNKLLMKNNKKNKMKJKKBKJIOJKKGINHGEGHHGMIJIIJIGJHFIBFDHD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CC
+ERR229775.17900575	99	17	527	60	101M	=	760	333	AGCTTTCTACCATCACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCAC	BEGKGHGLHFDIIGIIKILLLLIKKLJMLIJKILJIKJBMMMNKLKMKNLMMMJLJMMKKKJLIJMHKMIEMJHJICJFDFHIHJGGGKDIIGJGHIDEFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.65476258	147	17	548	60	101M	=	324	-324	ATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAA	BCGGGE@GIAJGDGIHAIGFKNMJKKJKJHKLJGKKJJLKKJJHIKKJJKGJJJKILGGHBHFBHHJIHIGF:KGBJIEJKFFHGAGGHGBBHD;DCEEEA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CA
+ERR229775.83749675	163	17	553	60	100M1S	=	783	330	AAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCT	<BDCFC:8E@3B3/8-EC8;GAF7=<#<69;>?<:GH:?I59=G@JHHDC3D'6@?ACFHI:E?>;BG=BECFIBH:6?E<6?GDEDHDCHDE65?=GE##	X0:i:1	X1:i:0	XC:i:100	MD:Z:100	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@@
+ERR229775.19017039	99	17	560	60	101M	=	839	368	CACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTGTGGGTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACAT	?GDB=1GFFK:GHGH=F<BIJKFIFFFHIJCI6BABKGLCHECG%>?G=CHJJ?DJLGGDGCCC6<CCKFIAGGCFIHF@DDCHE?HDFDE>CIEA?.@E9	X0:i:1	X1:i:0	MD:Z:44T56	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.78639790	147	17	590	60	101M	=	335	-355	CAACAAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTC	CFDGCCHEBGDGFDBKCACBCBC?HKIKDGKLEJJGDHMDG45?IIFIHDEDHIBHA:94'ECEFHC=EH>BFGB<GB<CJADGCCFFHHB@EA9EEEDD@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.63559677	99	17	594	60	101M	=	833	339	AAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCC	?D@CJDHIHHCIIEGHJGHGGIKIIIKLJKHHJGMJJKJJMJJMMMEFJLJJKCCGLLLLKKIJIKKIGHGIOKKIJIJCIJKJINIKKHG:FJI@GEIED	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.73865342	147	17	594	60	101M	=	298	-396	AAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCC	BFGGGIFJHGHHIFCGIIIKKJKKIJKMIIJJGMMJMLJKJKLJKKMMKKAIIJHJJKJIKIIHJIGHIIEIHKIIKJGHJGFIJGHGHG:<EFEGCEHBB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:ADB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.64297521	83	17	598	60	4S97M	=	324	-370	AAACTTGTGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCC	#####FCBBHIKIGCHIHIHI=LLHHKKGJEKGLFKMJHCKCKJKKMIJGCJJB/C?CCDMJIJHCJGIIJFIHGKLIGIIGBHIGHGHH9GE7FICGH??	X0:i:1	X1:i:0	XC:i:97	MD:Z:97	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.44063798	83	17	608	60	101M	=	331	-377	CCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCC	2>@@?:?CEF<DEHIIFEGHFGLKGEJHKKJDI8@G7DCC7IKDBF?EJHIJGHJJJICJFHLECJDKJKKKGBAB>FFBKJG=JD>EIGFGHHLGBE<?:	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.5711913	83	17	646	60	101M	=	409	-337	AAACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGG	AB8=8AGJHCC@FJKIIIIHHAHCEIFICHFGEGEC@EBJKJKGBICJ8DJ>CIKJJ?JLBG=JHGHIIIJMHKKIJGIIC5FGIJGGEIGGFEFIEEHE7	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G@
+ERR229775.47649789	147	17	647	60	101M	=	392	-355	AACTCCTGGTACATGCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGG	68BIAGJE?C?=8JI=5@EIEJHLJJIHGGGBGC?=.?JBAAG=A4EAHJ=FFJJJKJLHH@KJIDHB=HF>?FF>HF@FH;DGI@GAGF7@;@=;3?DBA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.52216469	83	17	693	60	101M	=	454	-339	CCGTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTG	C=DHEIHFFLIANGFAKIJLMIILOKJJKLLKKKKNKKMMKLKMKKNNLLKKMMMLLNHKMKMKJJJCKLKJIJILKIMJLLKGJLKFIIGHKFFHFKEHB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.82457097	147	17	695	60	101M	=	474	-321	GTGTGAAAGAAGCCGGACTCACAGGGCAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGT	?HEFAC>LEAG@C=A@GKKCFHLJJKKJHFCHGKJJJEIGJMJEKFIJJJCHIJKMIFJIFFJJI@FHGH>>;HEEIFCJJ=DJGCGBBEEACFBICEDDB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.22701711	83	17	699	29	3S98M	=	421	-375	TGTGAAAGAAGCCGGACTCCCAGGGCAACACCCTATCCGACTGTTTCCTGGGAAAGTCTGGCAACGGCCACACCATTGAGACAGACAACAGGTGAGTGGTT	####FCGEAFD7::.:DB;'=CB+D@BFFF;2C<,8-%H@C@FI;F-+KIHDCB@57CID<*A4/)G:)ID0IJGKIDIDGEH8<+==FLAEGCKEFEDD?	XC:i:98	MD:Z:16A11A5T9A13A6A16A15	RG:Z:ERR229775	AM:i:29	NM:i:7	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.70199275	147	17	711	29	46S55M	=	391	-374	CAGACAAATGAAACTCAAACAAGTTCCCCCGTGTTAAAGAAAACGAACTCACAGGGCAGCACACTATCTGACTGTTTCATGGGAAAGTCTGGAAGCGGAAA	##############################################CC<+2:::)HD@(8<6C?A;?>=>,'7(>@3>6><=<1;+7:8>A4@9%.*<07*	XC:i:56	MD:Z:12A35A3C2	RG:Z:ERR229775	AM:i:29	NM:i:3	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.93698964	147	17	735	60	101M	=	499	-336	ACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTAT	AEHFGJG:@GHHIHFI@;>JHHEEH@IJJCKJFJJKMJJIIJJHIJGI=HFHGJKLIEFFKICDIDKBIKE@IIIJHGIKKHIGIDIFIG<<?8DEGEFC@	X0:i:1	X1:i:0	MD:Z:93T5G1	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@WWT
+ERR229775.99018716	99	17	745	60	101M	=	985	340	GGGAAAGTCTGGAAACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTG	:?@CDFGAFKBEG@KG@8HJKGIGKIJKIKHK>IFKMJMBGKDFFJF@CGBBIGINHJEJI?FFBDILDLDDILIFGA7)?EEHLIMIHFIFHHHIFDFJD	X0:i:1	X1:i:0	MD:Z:83T5G11	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR229775.92236775	81	17	758	37	101M	*	0	0	AACGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAA	A?>FGG@BDCFFJIJIMIKIMFFIKJILIIKJNIKJILJMJKKMLMLMLMJIIJFINMLFJGLKJKJJHIKKJLJHIJJLIIHDJKIJGIEFGFGHGHDFB	X0:i:1	X1:i:0	MD:Z:70T5G24	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	XT:A:U	BQ:Z:CA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AA
+ERR229775.17900575	147	17	760	60	101M	=	527	-333	CGGCAACACCATTGAGACAGAAAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGA	+EGGCFD>EEFAJIIIJHMHEEJJHKIHJIMDCHHKKJJJJMMEEEKMKIBHBLKLKCIJKLIJGHCAGIFDDF>HFHFIHECEGDF?GEB?EFCFEEIEB	X0:i:1	X1:i:0	MD:Z:68T5G26	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.83749675	83	17	783	60	101M	=	553	-330	ACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATACTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAG	EEICDIHLCGFDCHH>DFHFKGDCNEKJJLHLLG;KIIIDLJEEJD@IC=D=0GMFLIJLCJHHCHFEHIIHHJHIHDFIHKHGHKH>HHAFDE=GEF=H:	X0:i:1	X1:i:0	MD:Z:45T5G49	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.63559677	147	17	833	60	101M	=	594	-339	TATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTG	FDHFHIHEF@<DF?:D=<@,4;0B>FDD;5AC::ELBGCBHE3DKIHEHMFAHLE=BACIGH>IFB7FEHBC=G>KHFCHIFFGJDHEFFBB@BACFCCD@	X0:i:1	X1:i:0	MD:Z:1G99	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:[YZA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.19017039	147	17	839	60	11S90M	=	560	-368	CTCTCTATGTTGATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGG	############GJE:GEE?9)D<=B?09>.>/1?ACBCBIJIA@@?5FEEC9HL<<8?7,B?@@@BGHGC9BHIHGI:GG@BHHCFGGJ<3ED;;CDAB@	X0:i:1	X1:i:0	XC:i:90	MD:Z:90	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.98760722	163	17	840	60	101M	=	1103	363	ATTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCT	<BCDHE@A@:5DBCIFGGFHIGHICEIKIAGJIFKHD?HG>CBG@;DACF=HDJFJJCMJH@JGIKKIFDFFFHHEGEDHKHGCGJJICAB=?AIIIGGEG	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229775.516742	163	17	845	60	101M	=	1152	407	GGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGT	A<ADC<<?FDEEGIIGGJGCJJIFHJKKHIJFEEGHHIJJ@KLJJLLLJJEMJMJJMILLLJKEGHJKJFFCGGHLHFFHIIIGIHCFDIJIIIHKEFGFF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.6073289	163	17	857	60	101M	=	1160	403	AAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTACCAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCA	BGEGCIBFEAAHHFIHHID;EIEGHHIC?FFJIJKKIIKLJLIILJMMMMIJKJKLLIJJJDIIGFDFIIFEFHBFBHIIHIHLHIIIJLIHJIILGGFGD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.36576640	163	17	937	60	101M	=	1160	323	GCCTGTAGTCCCAGCTATTCACAGTGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCT	AFEIEDBFEBAFGHIFGGGHHHGJHEIKIIJK@BGHKKKJFIJLJIKLEKBJKMFJ@DJKMMJFNLLJMKJKKJOKKJMLKHKAIHJGLIIIGLEEGEGEI	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.99018716	147	17	985	60	101M	=	745	-340	CCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAA	><FJGHLDKJHHMIIIJB;<CIHLHGFHIG?:=3;=2CFBGHD:HLKI;@4IFFIAIEHFIIKBHH:82DB>;>HF=GAIHGGH?FIEHGE9EFCIEA=@@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CBFH
+ERR229775.55719080	99	17	994	60	101M	=	1282	388	TCAAGGCTGCAATGAGCTATGATTGCGCCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGG	BFHIGFHLHHEKIIJKKKHIJKIKILAKLJJLJKJJMKKLJLMMJMLKKNKKMLKLKNNNKMMMKIKMJNKMMMNGHHJFHHIKHIIIKHIHCGMGHDIEC	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.77830097	163	17	1036	60	101M	=	1255	319	CTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTT	BIEBGCCHCBCHHH,=FICDJKHCGDGJHJJKHFIIJKLLIKLGLGKLMMDHLJJDLFIKIDIDIKIGJIFHHGFHEHJH?JIIFJFFIIFLIJHGHGGIB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D@
+ERR229775.3695912	99	17	1042	60	101M	=	1118	176	AACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCA	BHEGGIHHHKIKGJKLJIKLLLIMMMMMMJKLMMKLMMNKLNMNNKLLJJNLMLKJKJLMKJLJJHKJHHHHLHFJIHHHIKIKINJKIHJIIMJGEHDED	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.54641833	99	17	1042	60	101M	=	1321	379	AACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCA	BHEGGIGGGKIKGGKKHAHLJLIMMMMMLJKLMMKKMMMFLLMNMJNMKJMJMLKJKJLMKJLJJHKJHGHHJHFJIJHHIKIKINJKIHJIIMJGEHDEF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.90795085	163	17	1066	60	101M	=	1297	331	AAAAAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTT	BGHGHEDHGDCHJGJHIJI?JGJIHHKIKIGHHIKLIFKIIJIHL=HIKJCIGLLHIHKJMLKIEBEHJMLJDMIJKJMIKLDHKCJJGFDHHGGGEFFCB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:JOOLJ@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BCEGEE
+ERR229775.51118640	99	17	1069	60	101M	=	1370	401	AAGAAAAGAAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCAT	BHFHIJJHJKIKJJKKLKHLLJJMKLKJJJKLMJKLJJJKMMFJGKKMLJMMKKLJKMNLMNNKLMNKLKLKMKLMLLIGLLIKNKKLKJCKHFEEFCFGE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EJ@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.57580585	163	17	1077	60	101M	=	1316	339	AAAAGAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTA	BGHGEEE@G>9JHEGHGIFFHHHJKHHIFBAIIFGHHIJKHIJKIIKJIKGJKMLJKKNKKBLDLJKLJLKKJKHLIKLKLKIKLFLKLFIJJEIJGHFDE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CFFB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229775.82642257	163	17	1081	60	101M	=	1336	355	GAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCT	BGHGHH@JEB@JGHHEGGGHJHBJHHIFIICIA>HDJIKJIIJIILLKJLGJJLMJJGLJLGKIHJ=JJKLLMJKKLKFMKLLLLFIJKIKKKKHGGFGGJ	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@L
+ERR229775.30538656	163	17	1087	60	101M	=	1321	334	CTCACTGTATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAG	<F<EAIB-9:5GACICGCCCGDEBHIHIKE@EFCIIJEIGEB@GKHIKMKCFLJH>A?BHJEKFGG??IKKKAEIKJJLLKLLEHKLKIHIJIILEGGEG?	X0:i:1	X1:i:0	MD:Z:7G93	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.87113255	99	17	1096	60	101M	=	1361	365	TATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTAC	?EFGGFHHJHFGIAHIIFKLLKJKLJJKIJKMKLMMJJMNKJMEHHFIEDIKLKLGLLKLLLLKLKJHKJJKKHKFIKD;JCGEIGDIIDK=4CEDEFAEB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.98760722	83	17	1103	60	101M	=	840	-363	GATACAGGTTGAGGATCCATTATCTGGAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCA	EFFFGLHGHJLNKLKJGLLNLILLLIAKKKJLNKJHJMJNIJKDNNNKLLKNNNJMMJMNNNNLKJIJMMMJIJKJKLMLJJEFHHHCIJAGFFHLDIHE?	X0:i:1	X1:i:0	MD:Z:26A74	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.37017046	99	17	1113	60	101M	=	1339	326	GAGGATCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAA	BHDCIGGFIGCGIGKJKIKIJKLIKLKILJKKJFHJKKILJJKKLLMHJJKKLLMIJJKLLLJKJMKMNLLIJKLKKLDFLLKAFHDIIIJHKLGGFFJED	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.3695912	147	17	1118	60	101M	=	1042	-176	TCCATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAA	GDFGGHIJILLFHHMIIMLJKLIJNKKKIMNNKKKKMKMILMJLMMMMLIEIJMLJJIIJIKKLLIKIKIBGHHKJHGEIKFIIHHIGGHBAEFCDEEEE@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GE
+ERR229775.17531023	163	17	1121	60	101M	=	1381	360	ATTATCTGAAATGCTTGGACCAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAA	BEEEDE@EFDEFGFI>GBCBJHFGGIBGFFEJIFJJJJKEFJJJJJKJIHEJKKIEGHJMMKKHGJHFIKJIKKJHJKKKIHJKKLJKHILGMGMHHIEEE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CGDFG
+ERR229775.516742	83	17	1152	60	101M	=	845	-407	AATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTAAAAAATCTGAAATCCCAAACGCGCCAAT	7?ABDGED>DDDDJE?FB9DDCEA.=<>AD=/AEG6ABA8FD>2CGF@GFBJ?>5*G>59@.<*4JKIB;D*)JJIIBHA:8GC>=E4;H7C>F?GCEDE?	X0:i:1	X1:i:0	MD:Z:72C28	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.36576640	83	17	1160	60	101M	=	937	-323	ATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTC	ADEFFKKIJIIHIIJGJIHIIFKJJINIHJJJMLHGHJLIMHGLJIGEFJKGFDKGCLKLLKMLHKKKKJLJGIKJIKLKJJIGBKAJHIGHHHLHGGHGB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.6073289	83	17	1160	60	101M	=	857	-403	ATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTC	<@AFFKKIJIJHIIJGIIJJHFHKJHNIJKJHBEF@HGKHMLJLJJJLMJKIJGKGHLKLKJLLHKKKJIKJJLKJIKLKJJIGBKAFEIEHGHLHGGHHB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.78971137	163	17	1189	60	101M	=	1464	375	ATATTTACCAGTTCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAAT	BBFEFFBCCB@GHHGHHGDHJJJHIGKIHGJLJHJJILLLLILJGKLMIKDFHLKHAE;@HGMGILHFIJIIFGLJJHBCHAGEGIIKIAG>CEMEGEHHD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.87728427	99	17	1242	60	101M	=	1483	341	AACGCGCCAATAAGCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAA	BHE>G?HFHKGIKKKIIIKKLLJKKKHKCEJJJJEJ?JEBDMJJMABJJIJKLJJJFCDCGDHGCCHEHGHLEEHFGHC;IMIJHGINIIIGIMHIIGGD@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:DJ@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BB@
+ERR229775.77830097	83	17	1255	60	101M	=	1036	-319	GCATTCCCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAA	EEFFIFFIHHGINJAGKIJJGHAIJGKKMKJLKKKINMJMMLKNNNKMMKNMJJLNMMMNKMHJEALKKFJJJLJJIIILKJJHIIIEHIFHHJJJGGFFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IKMJ
+ERR229775.55719080	147	17	1282	60	101M	=	994	-388	CTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGCATTCCCCTAAGCCCG	?EIHGEHF@HCJHEFEIHEGGGHIGHHHKG>BGJDEFDBGJKDCEJKJHJELJJIJIGHF@KKIKILKKHHHIIIKGJJHJHEFD<GIIFBAEF9IECB9@	X0:i:1	X1:i:0	MD:Z:85G15	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.90795085	83	17	1297	60	101M	=	1066	-331	GTTTTGGATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGC	ADEFHGHJHHIJINJHHKJHHFIAJIKHEIFGJEGHDFIGCGGCGFEFHFHIEHECCCCCJCDDFDEGGGHJLKILLJIILICA@JHGHEF@GGLGHGJFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.83025798	99	17	1304	60	101M	=	1590	386	ATTTACAGCTTTGGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTC	BFFGGEHHHKGIIEHJF>GLJJMJLLKIIJLMLJMJJMNKLLJLKLKLJNNNNKKHKKLJJJHDHGDGJGGLHGHJIHAGHJGIHAGKIHGJII@FFCCCE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229775.57580585	83	17	1316	60	101M	=	1077	-339	GGGACGCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTA	BEDG?HHKHIJGIKHFHGHKFDIJE?HFHIGJFFFFCCCCCKDEEGFFFFFFFEHDDDFFCJEJLCJIHGLLCLLMKIILK@KKHLKJHIIHKFJHHGHFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.30538656	83	17	1321	60	101M	=	1087	-334	GCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATG	EEHFDIFIJHIHFFCIFIIIFDGIKJJGGGGDDDDCJDECGEDEFFGECGDDDFGBCACJBGIIEJLCLKMIJKLLBLIILLKKIKHKGKFGIEGDGEFI?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.54641833	147	17	1321	60	101M	=	1042	-379	GCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATG	FFHGEHEIJDFGBHKIHHGC<4FHIHHFFFF?BDBEI>G>GDCADCDDDI>AAEE@GAAD>FEB@HG8EGHIIIKHAJIHKEFGHEGGEHB;E@BDEEED@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.29727862	163	17	1327	60	35M66S	=	1641	363	CCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCGGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTT	7==;A97.8+7HA;IE:88;9EEFH8>;?E#######################################################################	X0:i:1	X1:i:0	XC:i:35	MD:Z:35	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.82642257	83	17	1336	60	101M	=	1081	-355	CAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTC	DBEFFGGGIJIKIIIIFFFFFKFHHGHGGGGHD?HEDDFFCKGDGBMJIFJC@MLNMKJLLBMMJMMLLMMJMJLIJLLIILIGIJKJHIIHGHFHGDEGA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.37017046	147	17	1339	60	101M	=	1113	-326	TAAACCTGATTTTAAAAAAGTTTGGGGGGATCCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCT	:DCCDCJFIJHHF9FFHHMFGCFGGEDEC94#455D@=I?7BADBJJIJBCHMJJDMH?HGDLKJAHEHKA@>B=HDBIGHAEHH8ADDF<8DFEHGEGB@	X0:i:1	X1:i:0	MD:Z:31T69	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.87113255	147	17	1361	60	101M	=	1096	-365	TGGGGGGATTCCCCTAAGCCCGCCCCCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTATG	FEFFGGHDCHCC;HIF?15;7A:4#FD>JKG@DGMKBFLFKLKAJ@AMEE9BEBB:GFB?CIEHGJA<<B>>DDH=BJEJIBFGJAF:DG<?BB4GA@9E9	X0:i:1	X1:i:0	MD:Z:24A73C2	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.51118640	147	17	1370	60	101M	=	1069	-401	TCCCCTAAGCCCGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACT	DDDEGHEMFBGAIGDGGGAKKMJKHNKCLLKNMLLMMJMFKC>DMIIMJJCKLLILLILKHIHKKKIJKHHFDFHKHIGHHFFJGEGFIHBBEF@FEEGDB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.48996859	99	17	1381	60	98M3S	=	1659	345	CGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCT	A5FEFEGF?EHHIEIIH8HIIJJIHLJIHGIJHMJJJNA:FAIHGML;0<CFGIDDKBLJCDEEFJ7@7BF6BHDJIJIKIIM?ID;DBE?;DEMEF####	X0:i:1	X1:i:0	XC:i:98	MD:Z:98	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@@@@
+ERR229775.17531023	83	17	1381	60	101M	=	1121	-360	CGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTAGGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCT	;C@A@FFAIINIJINJAKIGNKMIKMKNIJE:LNKHKKKKGKLMMNKMLMJJMMLMLMJLMKJFMJLJJJJJLJJJIJLJJLIFHJICJI@JGHJHEFCEB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.51562629	99	17	1445	60	101M	=	1727	382	TTGGTATATTGTGTCTGGTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTG	?FFEFHHHHIFHIFKLJ&?HIIKMJMKJKKMKKJLLIIJKKHCBFKHAJMACHKJLGJJKMMHHKJKMJHFFGHMIJAE@GHILIFIJIIJGJHHEFFEJ?	X0:i:1	X1:i:0	MD:Z:17C83	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.78971137	83	17	1464	60	101M	=	1189	-375	GTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGG	=DDB?CFEGGFJEFGD?GDHJ?HDIAH>GEDGILGHKHGKHHIKINJKLIJGGFFFF8FFLJJIFEGHLKJGGKMLILLLJKKILKIIILEKHFJJIGEE?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C@
+ERR229775.87728427	147	17	1483	60	101M	=	1242	-341	TTTGGTGACGGGTGAGGAGCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCT	:=;FCD?1/EECJIGHCF>AAFGCIHKEA=BDAF<:EB><JDIAHIDFAL@C:IHEKACDIICJJLKJIJHAHHEH>JFJIDBHHCHAD>+#AFDEIE?B@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.15144424	163	17	1542	60	101M	=	1799	357	CCTGGAAGGAAAGTTGTTTTGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGCCACCAGACTTCCACGACAGGCT	BDIECGEFDCEIHBGCGHGGGJEGHBIFHDJIGHJKJIJJKLH?K@JKFJEJIHILMFJMMHB;>IHIIIMIJCKKIFJHGFHJDHGMFIIJG>JFHBDDF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.83025798	147	17	1590	60	101M	=	1304	-386	CTTGTGCCCATCTGGTGACCCCTCACCCAGCCACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTC	CA;4I?C?9HGCJEBD<08@2<H8=2",J?02/%*H=B4DE66A6?:8HD1?EB@9:4=D.=&EBHAEHDF=;=4@AIGGKBIIG6GA>J<+=@=DB9CD@	X0:i:1	X1:i:0	MD:Z:26T74	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.29727862	83	17	1641	60	51S50M	=	1327	-363	CTTGTGCCCATCTGGTGACCCCTCGCTCAGCCCCCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAGCGTTGCCCTC	####################################################E==>=55;,C:65/9:=5J=C>FF@=GBJCB?5"D1?L;1=EHG;=BA0	X0:i:1	X1:i:0	XC:i:50	MD:Z:50	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.107364540	99	17	1651	29	101M	=	1920	369	GGCACCTTCAGCCACGGACAGTTCCGCCAGCGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAA	?CGGDFL?FHCGFFIAKJIIJGIEHALLJJK<EJBHGIMLLJJACLCGKGHIJFINIKFAEF>GCHGEIEELFIFHMGFGIJDFMFKGIJCMEKHFEAHDF	X0:i:1	X1:i:0	MD:Z:14T86	RG:Z:ERR229775	AM:i:29	NM:i:1	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CBF
+ERR229775.48996859	147	17	1659	60	33S68M	=	1381	-345	GACTTCCCCGACAGCCCCCAGCCTCGGCACCTTCAGCCACGGACAGTTCCGCCGGCGTTGCCCACTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCC	##################################G=:?F3CCE>D:8=64'#)'I<=):7>HIB@=A:CE1;:C=JJHC9A:<7=<E9)J9<;*&C1C899	X0:i:1	X1:i:0	XC:i:68	MD:Z:6T13A9T37	RG:Z:ERR229775	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.22929983	163	17	1693	60	101M	=	1950	357	TTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAG	BEFIEEFEEBCGGIIHGGIFJIHJGEIKKJHKKJKJKLKJIKIGKJLJJMELJJLELLNJMLMMMKKKIIIINDEEMHJHHJIIGHIMICMIMIGHHEGE@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.43533499	163	17	1693	60	101M	=	1932	339	TTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAG	@@EHEE@@E<<ADDGCFDECHBCDAECF?E?I?@BHHHIIBHK@E=IGAEAMHFJJBHIJHFJLLKHJIEIFHGDBECFFHGAE>BCFHCL@LHEHIEHA@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.69874320	163	17	1704	60	81M20S	=	1920	309	TCTCTACCAGAAGTGCCCTTCCCTCCTCACCTTACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCCGGCACAAGCCCAACCTGCA	74J?@C:D@-=C;696/*=;DD8+@*@7C94='04*65:A@860;<J:@1?5=;?95A5?FID?@M5E2DCGIHIE>+9H#####################	X0:i:1	X1:i:0	XC:i:81	MD:Z:32G48	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.51562629	147	17	1727	60	101M	=	1445	-382	TCCTCACCTGACCACTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTG	ADDFD?GHHEBGIGIHIJHHHHGGHGFEGHFJB;2CB?FADDEAJDDFC@8ABCE?A@BCACCB@H@<<?4<?GGEGGHKIHHIJEIIFGBA<E@CEEDGB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.66105707	163	17	1746	60	101M	=	1971	325	GGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGC	B<?GHHCE>AEGG@HEG;ACBGCHFFAFF/?GFJLHILKLHIGGIJM:CECFEIHLBFIDJEHEHILAHB5CFG@FGGLHHHGI3?FFILIHHMHGGKC6C	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GAA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.2494821	99	17	1749	60	101M	=	2024	375	AAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGT	AHHGFFFLHHGIIHKKHHJKLJKLKJJJJLLMJJJJMJCLJJJNFJLMKKMMNLMKLNMMLMIMHKJHJGG<FGHK?HI@H?HIJINIIIMIIHE?<DF>@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@FC@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.15144424	83	17	1799	60	101M	=	1542	-357	CCTGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGGTCCTGGCCTCCGGGGCTCACGGAGCCGCCCTGTGCCATG	@BGGGGB8D@HEHKEJFGGGACGCGKFGGF?EGCCCCDDCGEEFEIGFHDIFJEGGFJDFEBHCEFGEGJKE>LLLKJKII@KKLKKAIHFIHFHHEGFHB	X0:i:1	X1:i:0	MD:Z:70A27G2	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:BD@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@Z\V
+ERR229775.97978507	163	17	1893	60	101M	=	2135	342	TGCCGTGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGT	BEFC<FBFE@AJGIGGJIIHKJJIJHIHKGHJKIJKLHKLIJLKMJJILLGKKHKGJJMLMMJLLMMJJLJJKKJJKHKJKMILJJIIHJIHIJHGFEHFF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@H
+ERR229775.15256528	99	17	1898	60	101M	=	2147	347	TGTACCTCTGAGCCCTCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCC	?CHGDFLGKFDHGGJKJ8DHIHJGJIIKMHFMFJMJIJHMJJJFJLJKJGKFFKLIDFJILNKLLI@2CBJDBKEJDEH>HHGIEFJDFKHGBGCFF7CAD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.107364540	147	17	1920	29	101M	=	1651	-369	AGTGCCTTCTGCTTGCCTGCGGCTTTGACAAGAACCCGCTTCTGGTTATACATAAGACAGCCAGAGTAGGTAGTTGCCCAGGGTGGCACACTACGTTGCTG	<@DE96DJHGG>8CG@:?4$=@*IBB@41AEC<=3+#(B<@6F=287JIG?C8(A@BCIH<F?@B9-DCEBA<I<&86:JF:-3**):03+'."?CED6D:	MD:Z:19T8G5A2C28A3G19G0C9	RG:Z:ERR229775	AM:i:29	NM:i:8	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.69874320	83	17	1920	60	7S94M	=	1704	-309	CCTGCACAGTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCAC	########DG?7?JE=E*5FE:AIIFG=>>MLJFH?C;CJIFGCGDIBIJHDCJCEFFHHIHD?ALEC5CHMD38CECLGCE?45HLCE;BEGFHGJ<=C?	X0:i:1	X1:i:0	XC:i:94	MD:Z:94	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.43533499	83	17	1932	60	101M	=	1693	-339	TTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCC	2D>ADFGGIIHFIKILIFLDB51FCBHGGCKJILFIKKJKKJMIHJMLKJMLMJHLIGIMJMKJGJHGKKIJHFIIFLDHG@HIFIGGGH?KCEGHGGF??	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.22929983	83	17	1950	60	101M	=	1693	-357	AGAAACCCCTTCTGGTTATACATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAA	HEA>CFFGIHKIKIGMKLKJIFKKMEIKLJHKNKMKKNMMLNKNKMJCLMMMJJMMLJKMLHIAKMJLLJKLKMJLJILJJKHHLLKJIIFKGHHHGFFFB	X0:i:1	X1:i:0	MD:Z:91G9	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ADB
+ERR229775.66105707	83	17	1971	60	101M	=	1746	-325	ATAAGACAGCCAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGA	EFCIGFCMICINIMIGJIKKNBJKIHIKMJJKKLJIFINLJKCKMKLMKJJGMJMIGKJHFHIMMLKJIIMLKJIIKKJIIKKKKHHDIIGIHLFGKF:FB	X0:i:1	X1:i:0	MD:Z:70G30	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.105154648	163	17	1981	60	101M	=	2189	308	CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGC	@DCE:EEFD<=H?>>?FF==CCB@1:C=FFGHG;<=?HKICHBC?4AFEE:HEC5<EAHDH;AGIJHKEKEFD@<GDGHBIIEG>AJ3B;H?A>6BCEB85	X0:i:1	X1:i:0	MD:Z:60G40	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.52172354	163	17	1982	60	79M22S	=	2196	314	AGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAAGAACAGGAGCGACCGCACAGGCT	A@?:E>31<61E<;88BG,%/C8/4BAG4;BA1AG92D;D?C9<=)?>;C?B<III@F?JC/>DF+9D+0>>0;DGJG#######################	X0:i:1	X1:i:0	XC:i:79	MD:Z:59G18C0	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.39805220	163	17	2022	60	82M19S	=	2315	385	CAGTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGAT	@94EAE@J>:3GGEGCGD9=ECACGGHHHE;HHB?DFC1E:AA@AJJE=@<H+;C?H8:86<E?@?>C6=43>@CI?8DBC####################	X0:i:1	X1:i:0	XC:i:82	MD:Z:19G62	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.57143597	163	17	2024	60	101M	=	2298	374	GTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATAT	@DAECIBEC@AGHEICGGIHJHGIEHAGHEDGICFLHILJCJ8FDE>KDD3;C?CJEDHFGEGFCF=F<>>EBIE@DECD?>DB9B<BAAGHIJGFFFFFE	X0:i:1	X1:i:0	MD:Z:17G83	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@G
+ERR229775.2494821	147	17	2024	60	101M	=	1749	-375	GTTACTGCCATTTTCACAGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATAT	CHFFGIFBHFHHHKIIHMHIGIIGEGHHGGJFFG>ECBHCJDADD;AE@;>C>HLEFCDH>IILJ@G6IJ<BHG?HIKGJI@E9F/G>GG:AEJACCEEB@	X0:i:1	X1:i:0	MD:Z:17G83	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.11251161	163	17	2065	60	101M	=	2333	368	GGAGCGACCGCGCAGGCTGCTGAGCGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGC	@<ADD;DC>3B"2=<"5?9=JGBBB'=:@;<FD<8CA47@<B@2@:F44/>DFC=?698AFCD4;74C@EBD7IBFHH8AD@G+-3<BBFFDF29CHDJD?	X0:i:1	X1:i:0	MD:Z:11A89	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.12020490	99	17	2089	60	101M	=	2330	341	CGCGTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAAC	B:G>HGHFHF>IIKJKIHKBKBLJLLLLJLLJKJJJKJJCHJKJLHMMBLHJJIGIJGI>HFCFGJKEHGFHIFMIJMIDMIIMIHGHADFFIHKIGHEDB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.18301321	163	17	2092	60	101M	=	2301	307	GTCACACGCAGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCT	AFEECE789<<EDAFA7C2=G<?@@@A7>',AD@GF@BG?>H<4F7GBIE=@>FCF;=;CEBFE>D=A=AAJGHKH;DDFKHG?C02BAIHG@@FEAA3=6	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.97978507	83	17	2135	60	101M	=	1893	-342	TCGACATGTCAGCGATTGTCACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGG	E=FGGHIGKINJBIJIJGMIJFMIJHIHJHHIGJLHJJIILFNNNLMLKLJKJGMMMLKKMLMKKJLLLLLJLLLJKKJILLKKJLKJJIEGGGHHHGHEB	X0:i:1	X1:i:0	MD:Z:85G15	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GG
+ERR229775.15256528	147	17	2147	60	2S99M	=	1898	-347	AGCGATTGTCACAGGCACTGCTGCTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATC	###E?E<9G=8IMIIFGED<9;(BABBB;8;99?ABIGDCHJD?<:;C7FBEE3EBHDG9@CCKGHH@??D@;HFG>1EEF=BCDAG<E>9631,D9DE@7	X0:i:1	X1:i:0	XC:i:99	MD:Z:20A52G25	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.75821297	145	17	2155	37	101M	*	0	0	ACAGGCACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATG	EFKFHHIIJIIH@IKGIJHHHFLLLJFGJKHJHEIIMJJKMLNKKIKKMJGELKLJKGHGLLKIJLKJKIJIKKIHHJFJJHHHHHGFGH<;DEFEIEEG@	X0:i:1	X1:i:0	MD:Z:65G35	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.105154648	83	17	2189	60	101M	=	1981	-308	CCCTCAAGAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATG	?BEHFGKILIHGFFGDFGEGFBHEGKHNLFJNLKKKLILKKIKKKLIFJCKJJJJLJKJJMLMJIIJJICLLJJIIJIIEHJGGJHIFHIIHDHFFFEFH?	X0:i:1	X1:i:0	MD:Z:31G69	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.52172354	83	17	2196	60	101M	=	1982	-314	GAGCTGGGCCTGGGGTCAACTTCCAGCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAGCTGGGCATGGTGGCTT	EHCBDDB?7=E=DBAKCDGLHHEIMICHKJHAKKKK>CDJIJIKMGFJKIFFJMLMHIIEMJKMDHIJKJKJJJIIJKIJJJHJHFHGFI<GG?EHEFFD?	X0:i:1	X1:i:0	MD:Z:24G76	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.5983641	99	17	2267	60	101M	=	2506	339	AATAATGGTGCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGC	BHFGIHHFHHFLIKKLJKKJJIKLIIILMKJIIILMJJJMJLLMKMLKJMLKKGMLHJIJDLKJNJJEJHFGHH>JGADHICGHJIJKDIIFIJCGEDGBD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EJ@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR229775.59500924	99	17	2276	60	101M	=	2490	314	GCTAGCTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAAT	&HIEGHLHGHFIHEKIHKJLJILJJLLKIIMJLLLJMJIHMKKJJMGFJJLCLIJNJKJLJGHGJ>G@@GJGHIHKHJJFIFKIKIKGIJIIIMHAEFGDD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.57143597	83	17	2298	60	101M	=	2024	-374	CACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACA	?EDFHFHFHHHEFJJFIHDEJFHHMEIF@KOJJJNJKMJMKL?JNMKLNKLMLMJJMJMMKJLCBLJILJLJLKIIKJII@JJF?JIFHEFKFJHIGGGFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.18301321	83	17	2301	60	2S99M	=	2092	-307	ACCTGTAATCCCAGCCCTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGCCCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAA	###GAB7.BC><:*5'=GG@A:?H@A8,@B77FE-EIEEEHBDBKJDH=IACICBGGLLJHH'%/HLJCHICICFADHA?E?>:B?I:FG=EI:@@=ADC?	X0:i:1	X1:i:0	XC:i:99	MD:Z:13A47A37	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ED
+ERR229775.39805220	83	17	2315	60	8S93M	=	2022	-385	TCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACA	#########DFBIFEJB?%?I@FFIMFFGFFFD;DLMJEJ>8FGMHGHBMKHFM=/GCJFJKEKJCFJD8JAHHIJJIIIDII@AEJFGHBGHHHHFEHC?	X0:i:1	X1:i:0	XC:i:93	MD:Z:93	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.12020490	147	17	2330	60	101M	=	2089	-341	CTAGGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACAACTAGCCAGGCGTGGT	EFKFGLHIEH<GJEHIMGJGGLHHKFGFJGGD?DEJEBFEGHFDGFFGAKFKKJIFIFCJDJJIJIGIIJHHIHC>GFHIIDDHHCIAJGBBHDB;=+EB@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.11251161	83	17	2333	60	101M	=	2065	-368	GGAGGATCGTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAAAAATACAAAAAACAACTAGCCAGGCGTGGTGGT	BA<CD67<BEJDIE>,>9DHC@BEKKIKCAAGKFEGIIHDCJHEG?IIFKJDEFFIMHKIDHDFFJJJIIICEEHJJIJJIJECIKJJILEI?FHFDGEEB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.80729707	99	17	2417	29	101M	=	2698	358	TAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGA	:EBE?HH<G>>CECHH;>?IDE<BJFEIHGFHKJHEMDCLGIFILKJJLGIIDCJ3GHGEGCKCFKDHIGGHEDF=ED25GCKDG?JDF=5CCDBFDAFEA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:29	NM:i:0	SM:i:29	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.94440410	99	17	2419	60	101M	=	2716	397	GCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGGAGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATC	?EEGGFH?FG@GHGIGEFHJDKLKIIJJIKGJLKMIJEJJIJLKMLNHLICCIJHEDDIHKFGKGFHHIGGICBD?BEGCCE>FLDGNIJIGHG@B?AGF@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.101859832	99	17	2474	60	101M	=	2762	388	AGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCGAAAAAGAAAG	?ECGDLGFKGCKHGKKIGKGHGIIIKJEILJKLJFJ@EHGH:CHJL?HJHIJHMLLIJIEFJKIIE=HB>HGJHJIBEH>GGJHJHHFMG;H?FCHB6>CA	X0:i:1	X1:i:0	MD:Z:90A10	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229775.59500924	147	17	2490	60	101M	=	2276	-314	AGGAGTTTGAGGCTGCTGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCGAAAAAGAAAGGAAGAAATAAAGAAAA	IEFKEGJJIMIIDJJIJGJHMHHIHIGHI?HHJLHJJJLKJMKGJMKJI?DJJKJJMKLJIIKHJFCGIFIFJ;KIIIHKJGGJIHHIGGCB@FCIEEEEB	X0:i:1	X1:i:0	MD:Z:74A26	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:D@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@CEC
+ERR229775.5983641	147	17	2506	60	101M	=	2267	-339	TGTGAGCTGTGATCGCATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCGAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAG	GDGGKHHJGGEIKAGHHKIKHKJHKMKEGNJJ?;LIKJJCJJNGJKLHKHCJHFFEK>GJJJJKFIJKIJHJIIIHHIHKJGGHGFHGGGBBEFCEFEEI@	X0:i:1	X1:i:0	MD:Z:58A42	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.52727770	163	17	2538	60	101M	=	2848	395	CCGGAGACAGAGTGAGTCACTGTCTCGAAAAAGAAAGGAAGAAATAAAGCAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTT	<B.B(07>@0=>12?7?C;8I=0;9>#AH@ECA9=9=0().D=:;CKBE'450120:7+@C<D>=E4C6E@CE5ACFI@D<@>9G=?;?E*=3<G=C7D?A	X0:i:1	X1:i:0	MD:Z:4T21A22A51	RG:Z:ERR229775	AM:i:37	NM:i:3	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@D@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.44852854	163	17	2547	60	101M	=	2817	370	GAGTGAGTCACTGTCTCGAAAAAGAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAG	AGEFEGBAEB@JGAHHJ>HEKKJJCHKKHFHGJKLIILLGJLLLJJMMJJIMMMJJMHKKEEJGKLJKMLMKJJILKGLHJKJIIMIIIMFFIGIGGKFGE	X0:i:1	X1:i:0	MD:Z:17A83	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.18618553	163	17	2570	60	101M	=	2828	358	GAAAGGAAGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCT	@>DGC8=FEC>CGDIEHCACFGFKKAFHKJ<HFEDHJIIF?IF8GJKKJI9FLJIJ@<FIHGMJKMLJJHJJIJLJKJHIJIKMGH?FJBBIEIF>BDDCJ	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@E
+ERR229775.83543817	99	17	2577	60	77M24S	=	2821	288	AGAAATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTC	4::A:>A>G8)>F<>ADDHDCGAJ<=JB,*EB797,>HHL@C95=/:EC=@@FC>GEJHC=479788BI96F0EKK#########################	X0:i:1	X1:i:0	XC:i:77	MD:Z:77	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.66162627	99	17	2602	60	101M	=	2766	264	AATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCT	?DFGEHGFHIHGJEKKGGJJLJKKJLLIIKMIFHMJJIIJLLKJJIJKHJKMKFAJLJKLJKGBHJIFKGHHLHIJMIIGF>BCGJGKDCJIJGGFKFIEH	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@J
+ERR229775.36854728	99	17	2628	60	99M2S	=	2910	357	CATCTAGCTTTGGCCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTAGGATGCAGCTGAGGGG	4GFEJG@EKG=@.BEGJ+AHFCFCGLGG<IMFFJJHC@IJGCJHLLMKKLMKEMB>D/E9CGADGFH?GDKGLFIAHDJ@BHGLEFDGEE=DDGIBFB###	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B@@@
+ERR229775.80729707	147	17	2698	29	23S78M	=	2417	-358	TGCTTCTGGGGCACAGGTCACACTCTCTTCCAGGTCTATGATTCAGCTGAGGGGTGCCACTCTTACCATCTAATCTGTGCGCTTATTTACTCTGCTTTAGT	########################HI<4*16J>9**D?/?:9**HC)F3A'6B3F/;1.(((>/2&-5=*;,3HA<':0+('/(;/*7.(7%;'.2C@481	XC:i:78	MD:Z:15G3G15C21C7C12	RG:Z:ERR229775	AM:i:29	NM:i:5	SM:i:29	MQ:i:29	XT:A:M	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.94440410	147	17	2716	60	101M	=	2419	-397	TGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGAC	DEFJHGD>7E>ADGG@:9HJBIEADHGGGIHJJFGA>A?99DE<KKIFDF?HIE?LHGFF@;E?>KGFCC=4<ICIFA;CA@=HIBF<><%DGG<HC=ED@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.73268968	99	17	2739	60	99M2S	=	3060	384	ACCATCTAATCTGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAG	BEEGGGLHJHGLIFJKKKLJIIJKLLMKMHKMKKJMJJLMMMMMLKJMMMMNJJKJIKKJLMMMMMMJNLLKKKMHLIAECG5*?FFD>;@BCCEDDF###	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.45483038	99	17	2750	60	101M	=	3055	353	TGTGCCCTTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTC	BFHGGFFLHHGIIJKLKKJKLJJIHIKKMLLLLLMFEKMMNLMJLLJJJKMIFCFLILKLLKMLNLICHBEJ3AFAEEKCBCDGFIF;?=CCHFFEEC83;	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.78014576	99	17	2757	60	91M10S	=	2948	291	TTATTTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTC	BFGGGHGFKHIIIHIJFKHIKJLILLKLJKKMLMJLFJLJJJLNMMMMLMMKLMKMLKLJBJJFGCGFFECGHFB@HFFF/7@67?9E@F###########	X0:i:1	X1:i:0	XC:i:91	MD:Z:91	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.101859832	147	17	2762	60	101M	=	2474	-388	TCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCA	<8=DBIGIHJGIDJIMHICF<G5>A?BGEFAG9FEGAAJ@CC?@DCFHAJ>>811?C;85FEHCBHA>@K8EE=3@<@EHB=;HI>FF?EB@FF=C5CBA@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.66162627	147	17	2766	60	101M	=	2602	-264	CTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGT	EHGCA-@LEEDGHEFLEMHB?B?@FGEIDG?CA?FC>AC<?GFCEHDI>D1??@;AEAGCGGAAJKGFHK<BKFEKIGHD+8@H@EGDIHD:;?@EICD@<	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.91036639	99	17	2776	60	101M	=	2967	291	GAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGGGTCTGAAACA	BHFEIJHJIHDGHJLJKGJJJIKKMJLLLKLMKKMJKLHLJCMMMG=HJIJGKGHIDGFFF;FCFFCBICBF;2>=IEB?LGCEFFHDCG#:3?EBFBGDF	X0:i:1	X1:i:0	MD:Z:90T10	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.44852854	83	17	2817	60	101M	=	2547	-370	GGGGACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGA	BCC?6ABEHFILIIJJGGG;IGIHMIHIHF?EH?HKHLKLKKMMLNMMJKKMMKMKLKKNLJKKKLMMLIKJLBKLJJLLLKBIIKJFKIIHHHIHKEEFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CBA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.83543817	147	17	2821	60	56S45M	=	2577	-288	TCTGCTTTGGTGAGGAAGAGGCCCCGGGTCCATGAAGGGGCCTTTCAGAGACGGGGGCCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGG	#########################################################7,,/?4:@2;'B6#'01'8,2'4&8.;H29?@:+&'-13CH;-1	X0:i:1	X1:i:0	XC:i:45	MD:Z:0A44	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.18618553	83	17	2828	60	101M	=	2570	-358	AGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAG	#B7@??990GHIIMFDEICAGH?FHCD<+@FEEHHIIIJILKKLKJKLNLJKKKMLMMJKIGBKIJJMMKK>GJLKJIKLLIHEJKJJIKEHGHE@EFDK?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.91229453	99	17	2831	60	101M	=	3084	353	AGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTC	?CGEEF?HBGFIGFKJJABI@JIIIKKJJLKJKLLABEHLJLLMKKILJJJJFKKHGFLI=DD?BGFEG>@BBFIJKIKGIHJIG@H<BF@@EEFBFADEA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.52727770	83	17	2848	60	15S86M	=	2538	-395	CCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGG	################H;EBD?5-8D6:,F><DFAGCIEA52<NKCIGKGLLLJLHE.GE<FDEHE=HIAGHKFLHDFGCFFC?@GIFGE>HHFKGEF:E7	X0:i:1	X1:i:0	XC:i:86	MD:Z:86	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.7004516	163	17	2878	60	101M	=	3107	329	ATGTGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTG	@EEFECDFD;:JG0C=?D;AGJ?GGGJEI<=JHHHHJKIKE>CFIKLGGE?HIH6?CAF>GBKBA9GIGB?EDFE@IHGFGHIGEFFJG:@FIC@EDB?6B	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.36854728	147	17	2910	60	25S76M	=	2628	-357	GGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCA	##########################HHKC9,>ABC?;DBGAH=8;;IEE<>2?HB@C>HCF7<;2G79===)C@5&=*B@86FEEHA@B9:<797DB3;@	X0:i:1	X1:i:0	XC:i:76	MD:Z:76	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.28172972	163	17	2918	60	101M	=	3194	376	GTGGCCCACAGCTCGGCCTGTCTTTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGGCCAGCAGCACCCACAGCAGCCA	BFECEDAFC@CGJH?GIIGGHIJIIGJHH<EKIGE=IFKIJLHKKGIJF=AHGFA>D;A;@=D@9BE>:D=BHI9;;A"99>><@>BCEEE=CFEFIBAC#	X0:i:1	X1:i:0	MD:Z:78T22	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.78014576	147	17	2948	60	101M	=	2757	-291	GCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGT	C@AB=GIC>BDHFFG@@??HHFHGEEIGHHHFBCFFIHHDJJEFMLHJKFEFHILEF>IHGGIIHJIHHI?EKIIHJJEJJHEJIDJHHIB@ED@EFEIDB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.19870548	163	17	2964	60	101M	=	3254	390	CACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCA	ADD<CEFEABBFG>ECGIGHJHBFH:F=:<9D??FIKJIGJHCHLGIHIEABDE@CGDDFFAFA?CDE@E9<DDGG>B?6>4B@@FAA6E6@5*>1=B>DB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.91036639	147	17	2967	60	101M	=	2776	-291	GGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAGCAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGAT	53AFE?BAHGJIHIBCCEDIGIF=GGGGHKCFKF@F=?CGLJGBKIIKGG?:IJJJJKLJKLKJLKKKIKHB@HICHBHKHFEHGFJHGFBCFE@CEIFEB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.11173812	99	17	3034	60	101M	=	3333	399	AGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATTTGTCACAGCAGGTAAGACTCTGCTTTCTGG	?CFKBHGHEHFGHEIGDHHILKLLLMIIKLJJKIJIKILMMM>JIMIHIMJFCDJLG0ADIHIGCGDEHHHEHIIKHKHGJIG8GKHKGNIMIIKGDFCEA	X0:i:1	X1:i:0	MD:Z:70C30	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@GF
+ERR229775.45483038	147	17	3055	60	52S49M	=	2750	-353	GCCCCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTGCCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCAT	#####################################################A54-7=90;?5::2<?DJI?@BCG?;HGFGIJFJFHG:=AEFEFCEE@	X0:i:1	X1:i:0	XC:i:49	MD:Z:49	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.73268968	147	17	3060	60	37S64M	=	2739	-384	GGGCGGGGAGGAGTTTGTGGTACAGTGGACAGCCCCTCCCCAGATGCCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACT	######################################D9599217"CCCFH:ELLJHAIGJIGJJLHKIJEKIKJHJEHIHGGIFGGJGBECCBFIEGDB	X0:i:1	X1:i:0	XC:i:64	MD:Z:0G8G54	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.91229453	147	17	3084	60	101M	=	2831	-353	GTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCAT	CGFGDKDHJIJGIMIGEHIFGIIJGGGOJIHFHJJH=EKFKKGGILDJJHCHCIFDECLKHLJFEHGFHIFBKIHKJJIHHDHGGDHEFGBECCCDDECE@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.70209647	99	17	3089	60	101M	=	3317	328	AGTTGACCAGACCATTTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAA	BEHGGIFFHIHGHHIJJIHKJIILLJLLGIMJKIMMMLLNLLLLJMMMJMHMMKMLKMM5GLHLMNLMKFKLKIOJGHHHJKLFFKKIH@E@GCFGECFGB	X0:i:1	X1:i:0	MD:Z:15C85	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@AEB
+ERR229775.91011602	163	17	3102	60	101M	=	3387	385	ATCTGTCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAAT	BEFIEFBFCB<GGHI@GHEDHJIKIJKIIIJJJJKILIKLIGHGJLFHJICHMBIKMHLLKMJHLKJJLLFJKKLHFHDDDJIFHKHHGLIE?C@GIFEE<	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.7004516	83	17	3107	60	101M	=	2878	-329	TCACAGCAGGTAAGACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCAC	EEGFKHHMIGLFMFHDKIJIIIKKDJJIJBCFGFKMJGKMIJKKG<FKIEJJMLJKKJLJJJKKJIEJLIJJHHGIILJLJJHGHKIKKIEIHHHHDHDG?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A@
+ERR229775.5896825	163	17	3144	60	101M	=	3415	371	CAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCC	@DECDC;CC?EGGCICHJIIIHGJHEIKHEJHIJ<FDHC;CIHCHLFLFIDJIGHIKJJJEDJEKCLKJJDJKIAFFHFFIHGCEGJI;>4>EAB?DH@DE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@FJ
+ERR229775.59323675	163	17	3154	60	101M	=	3389	335	TGGAATTCCTGTCCATCTGGCAGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTG	@B?ECD9@8@<GG>GCII88GHF<9:<?:??H=@IJGLCEIJJBKJKLICFIDFGHHFJCF9H?:FCIABGAEDDEGCI?7FFMIGDHIFHGJHFGDA:B@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.98041640	99	17	3175	60	96M5S	=	3494	373	AGGTGGGCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGGGGGGGGATC	?C@=A8EFGGGGIHE@JB>FIIILLLLHFJEHHJJHIJGKJGI?@BJJJJKDB>DKDJC<@EEBHFLGF?EIAGEHCCD@2ABEACFHDCC#9@?######	X0:i:1	X1:i:0	XC:i:96	MD:Z:91T3T0	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.28172972	83	17	3194	60	101M	=	2918	-376	TTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCA	BDFCHIEIJGKDHIJHIJIMHGG?IHIHJHKHJJGCGFKBMKMKJJLKLJJIIJFJMMMKMMMLMKFHLMKJJLLJIKIIKGDKLIKKIGHHKFGLDIHFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:ABA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@D
+ERR229775.453972	81	17	3215	37	2S99M	*	0	0	AGGCCGGGCACAGTGGCTCACGCCTGTAATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACAT	###>6FEBCCE@HGDIIHDG?GEIICHHF@FBBIGHDFFF1JMLLLJCIMLIHFLIHJIJFGE?KLJMMHCDKMLLKJLIIJEB@KJKIEGIGHFHBFEE?	X0:i:1	X1:i:0	XC:i:99	MD:Z:99	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.41226651	99	17	3242	60	101M	=	3478	336	TCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAA	BFEEGHHFGKGIIEKJKGJHIJIIIIIIEIJKJKJIMKLLMJJJKMMGKDCIJLKLGIJFIGHCBFDHFEIHBEBCKHHDHHI?GIJJGNIHHJGDGEGDD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IIK
+ERR229775.19870548	83	17	3254	60	101M	=	2964	-390	GGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGC	DEFIFHBEIIIDHFIGKHGIKCHIGKKOJILHMJKNHKGJIEKIMJMJDDJIJGAKKLKKLKKMKJJLLLCIKJIIJIJJJJHDEJIIIIGKHLHFGGEFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CCA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.43420834	99	17	3270	60	101M	=	3494	324	TGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCTGGCCAACATGGGGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGGGGCGCATGCCT	?ECHGGHFKIBJHJFGHKBJJIJKJMHKIKJMLLMIJKMKNKKJLI%@GMKHILH?EEHFAJJMMMDFBDIJJJGHGJDDHLDCG;HDA#77=<CB1=EC#	X0:i:1	X1:i:0	MD:Z:46T42T11	RG:Z:ERR229775	AM:i:37	NM:i:2	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.96667631	163	17	3288	60	101M	=	3497	309	GAGTTCAAGACCAGCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGG	@GEEFECHEC@FGHIGJEDDJHHHHHIK@<@KJFKKK@DIKHHLILMMMHEIJMMMMEKJHFMJIIJ@JFDEBEH@HIHHHHMIIIHKLIIJIIMHFKCFD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@HI
+ERR229775.98929975	163	17	3302	60	101M	=	3553	351	CCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATG	@BJECEAFG@BFGDB?IJIFJJI@EEKHIJGLKKLIIIILLLKEIHJEKJFFKCIIJ=EII;IEEEFEJFFGKJJGGIHHMIHMFIGGHKIIMIJHFECBB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.70209647	147	17	3317	60	101M	=	3089	-328	GAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACC	FA81FFGAGJIIIHFFKKKIHEHJJJIHKIMIGIJILCJILKKIDCLKJJELLJIIJEEKKILJJHDKJIJIKIKJKHIKJHIGGHJHHFCBEFEFEAGB@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.36971240	99	17	3328	60	101M	=	3603	375	TACTAAAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGA	BFEKGJJJFHBGIHKLLHJILKLMKILBJHJGIFJ<JKKIJLLJKKMJJILKMMMJJMKJJFHKJJNHKGFFGHHLIGK?LIIMFIKIGINIGGIHEGGEF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.11173812	147	17	3333	60	101M	=	3034	-399	AAAATACAAAAATTAGCCTGGCGTGGTGGCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTG	BB6EABHFFFFHKGEGA<GHF>FIJFJIJ=JJIG;EJEFBI<GAIF>KKJFE<JKHIECEEIKLJHGCGHH>:<IEG>GFD8/9:*E@EE3%DJ;D2BDD@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:IH@G@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.94803111	163	17	3384	60	101M	=	3606	322	CTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGA	BIEECCDHEBEGIBIGIGGHJIJHKIJKIHGLIJLJKKKLKKJKKJBIJIEJKJKKKIMJKHLEFIF@HFGDKGHIFLHHIHIHMIGBGJHGJIJHHGEFG	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.91011602	83	17	3387	60	101M	=	3102	-385	GGGAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTC	DDFFKHHFIMIHIJKGLIHIIHKIGJIDHIJKIJKNLLLNLKCKNKMJNKKMMJKKHNMJLIFAJJHIHIIHGLKIGJKKLIKKKJIHILGKFHHLEFDGB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:CBA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.59323675	83	17	3389	60	101M	=	3154	-335	GAAGCTGAGGGATGAGAACTGCTTGAACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTG	A5IGFFHGIIIJKINGEGIGI;KHE?1IHHJJKMJJHMKJBKNKMJMHGIMJIJLKJHKIE?GFFJKJEFEHKEIKIEGIFHC;AFHIGL@HHLGIGHDH?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.5896825	83	17	3415	60	101M	=	3144	-371	ACCTGGGAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCAT	@>>ADEB1CA>FB277FJIFJ;=B18+/A098D=55?==:<>(;0=7BBH@>BEHFCBBC99?JA6@G7.A;?:7:AJGJJJJIJJIGIIGGIFHGEEFE?	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.43002343	163	17	3466	29	43M58S	=	3687	321	CCTGGGCAACAGAGTAAGACTCTGTCTCAAAAAAAAAAAAATAACACCATTTTGGCTTCAGAATTCATATCCTCCTGCAAGGATATATACGCGAGAAATTA	58=>BB1BB6<HE:.-89(.:+5.A;G6F8EK)7;;I>59<A###########################################################	X0:i:145	XC:i:43	MD:Z:42C0	RG:Z:ERR229775	AM:i:0	NM:i:1	SM:i:0	MQ:i:37	XT:A:R	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.41226651	147	17	3478	60	101M	=	3242	-336	AGTAAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACA	G@CCGDAA:5;5E:@:FFFEAEEEKKKKJH@EFHIGFKMJJMMHLEDMKJGICIIII>IJHIGHHF:IFBBBHBFAG?G@HFCF;AGFDG>:AECFEEGAA	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@C
+ERR229775.43420834	147	17	3494	60	101M	=	3270	-324	AAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAAC	A9>D?@DFHHFFG9?577GHGD;IIGHGIGFKFFGDEBGACABDIB>I?G?HGKICIA9F<=>9>IGIIHJ@HIKCDDHGG<>GGCGCDJBBEFCFFEC<@	X0:i:1	X1:i:0	MD:Z:93G7	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:G@CICDGHJIEDB@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@BC@CCB@@@
+ERR229775.98041640	147	17	3494	60	46S55M	=	3175	-373	CCCGCCCCGCCACCCCAGCCTGGGCAACAGGGTAAGCCTCCGTCTAAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGA	###############################################?DHGJJJHE?HD9;D;0@HD?:J7>:5>8GI<GFCCAB??=DF81772CAA6:9	X0:i:1	X1:i:0	XC:i:55	MD:Z:55	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.96667631	83	17	3497	60	101M	=	3288	-309	AAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATA	BBCCDEEFFKKIJIJHIJHHKHHIHKJILGHFKGFGFGGDFGGJJIJKMIJJGJJIJJ?J?JJMKKJMJKKLJKHJIIIIIJJGJJKJIIGIHHHHFGFFB	X0:i:1	X1:i:0	MD:Z:90G10	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:NMNMNNMMKM@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.102280357	163	17	3516	60	101M	=	3772	356	TTTGGCTTCAGATTGCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTAT	BEEECEFFEBCHGGHDGGBCIIJJJJIIIJFKE?HIIIIJBK@EIKMK@IEJMKJKKJKKKHKMMKMJKLMLMMGCGGFIIIFIIKKKJAIJHHEGEBGFF	X0:i:1	X1:i:0	MD:Z:71G29	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:GJG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.78993145	99	17	3530	60	101M	=	3760	330	GCATATCCTCCTGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGT	BFHGGHGFKHELIJILKKKIIIIJJJBLAIJKMMJKMKLKJJJMKLLJKNMKMKMLNNNMMLEEDHGGIJJJJJI>IJHFGHJIHIIIINIGMIIGHFDED	X0:i:1	X1:i:0	MD:Z:57G43	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.98929975	83	17	3553	60	101M	=	3302	-351	TACGCGTGAAATTCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCT	A?>E?FIIFFJKKIFNGKIKJHIHIIEHJHLHDDDCCKJCGJJJKJJJJFFBLJKIFMKMJJJLJJJFLKIJIJJJJK@ILLIILIIFGKIKI?GHGKGEB	X0:i:1	X1:i:0	MD:Z:34G66	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.105205152	99	17	3562	60	93M8S	=	3856	394	AATTCAAGTCAATGACAAATCAGAAAAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTT	?D>?9HF>@ECDFDCDF<FGEEJHHJKCGLGFBA/D:;CDDJ?;?HFCEIJDIJCDFHACFCEDE@6C@>;HBDCIID9797+7.7B>6=HL#########	X0:i:1	X1:i:0	XC:i:93	MD:Z:25G67	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:AF@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.30258628	163	17	3583	60	101M	=	3859	349	AGAAAAAAAAACATATATATACGCAAAACAGTATCCTACTGTGTGTGTCGTTTGTTGTGGTTTCTACAGCTGTCCGTGTGATAATAATTCCTCTAGTTCAA	@@GCHH;6=>ECF=G4D==2BC*:=)6)'/-/4107;<BJ6::?DI@/*//0<8?<?BA$8:@5-+5E=9;+/364>+4+@=E7,CBC:;C;BLB?HDGGB	X0:i:1	X1:i:0	MD:Z:4G22C31T4G14T21	RG:Z:ERR229775	AM:i:25	NM:i:5	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:OOVRWWJELKO@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@IG
+ERR229775.15284212	99	17	3585	60	88M13S	=	3809	324	AAAAAAAAACATATATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAAT	?DEDDFFEIECHI;HHHAHI>HGLLGKIJGHFHCJIHEAGF:FJJDC8GIDFJBCFBHDGGH5GCFCBC=:AF/1826-7FJEIJHI##############	X0:i:1	X1:i:0	XC:i:88	MD:Z:2G85	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:MRSRRTRPQ@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.15906182	163	17	3598	60	101M	=	3862	364	TATATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTA	BFEEEE@<EBEIEFG@EGDDIJ>EKCDGA@>G@D?HJIIC;?=CD@JK?#;BJJ5DECBIABFDGHHCGFE?DJDGJGKDGI5BEIKHFFIKD-<EGDCCD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:ADBA@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@F
+ERR229775.36971240	147	17	3603	60	101M	=	3328	-375	ACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTC	><GG?GI=CLDHHKEHG@IGCFFIBFEIAHELJHLJEGHFJLK3IJJLJKFIKLAIJEFHCHIIFIHIHHJFFFIGJIEIIFFJGCICGGE>BH<FDEDD@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.94803111	83	17	3606	60	101M	=	3384	-322	CAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATA	?>EFEGMGIIKGIJJIJGJGJDJFJ?FMMKHNKIKKNNNLDMKLNLKKKLMCKKKNKKJLKJKKMKLKKMJMJMKKKKJLLIIIJJHJJKIHHGHJIGFFB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.15603458	163	17	3626	60	101M	=	3846	320	TGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTG	@EADDC9A@B@GH@GBCFB>>3CD?=;E@9>H;C;IJBIIIIIJIJHILHCBAF;=GI@BJDJE>>CFHKHIINE:BHIGH4E?EHJGG>AFMIFIEHAJ4	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@B@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.80842527	99	17	3639	60	101M	=	3844	305	GTGTTTTCGACAGCTGTCCGTGTTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTC	AGEFGHHG?JEIHJLJIKK@IJJJIJJMJJMJKMKMMMJMKKMKNNKKLJKLMKKLKLLKMKNLLKKKNLKKMKJJLLLLLJLILIPLJKILJIIGHFEJD	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.84503264	163	17	3670	60	101M	=	3903	331	TTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATC	AEFCIEFFEB<GGGIEHHFCIIGHIHIIHJ@LIHIIIJHHHJJIJIKLLJEJKKJLJIMMJIJEMIIIMMKMKMMKLLKJNKIILIJIIKLMIHJFHFEFE	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.71788763	99	17	3673	60	101M	=	3897	324	CTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTAC	BIFKGHIHHIIKIIEHIEJIIJJKKIMIMKLKJJMJJJMKKKKKMNKKKKKKNJMMMKKLKMMLMNMKNNMNLLMJKMLGLOKJPLLKIHLJGJGGGFJEB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.43002343	83	17	3687	37	101M	=	3466	-321	TATTCATTTTTAACTTCATAGTACCACATTCTTCCCGCTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCCCAAATCTACTCTCTGCCTCTGTG	DCCHB.BIBBBDC7>,CEHH?*;6936?956.-2%7)=C@3?BB.6C891FDGFJ?==>D@A:/DEB5@<E6)F?$5)CACGF;451D*,>4BDG@<FBC7	X0:i:1	X1:i:0	MD:Z:32A1A1A40A23	RG:Z:ERR229775	AM:i:0	NM:i:4	SM:i:37	MQ:i:29	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.101967836	163	17	3700	60	101M	=	3891	291	CTTCATAGTACCACATTCTACACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTC	@IEEFFBFEB@FGFGEHCDCHHGHHHIBDICHICGJKKKKILLHLJLLLKGHJLMLMHDJJKJLKKKMMKKNKINJOJOKKKLKMHHHEGA?CIGEHFFFF	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.60297548	99	17	3736	60	101M	=	3785	149	CCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTG	BEJFGJHHKIGGHJKGHJLKLLKHILILJJJKLIKMJKMLNLLILMMLNJJJKJFJJLJMNKKLNNJFLJKJBLKKIKIHMHJIIKIGFHMIIJGFHD>D@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:EG@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.78993145	147	17	3760	60	101M	=	3530	-330	AACCACAAATCTACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCG	1@DGHHHFIJE@:CKDGIJIFHJBFBFGIHJJEFCHGEKEIIHGJGFAIKDJJMLJJIILDKIKIKIHHJEBBAIHJJE?HHIGGCGHHGABEHDEGEH9A	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.102280357	83	17	3772	60	101M	=	3516	-356	ACTCTCTGCCTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTG	;EGFFHIFGIKIKGJIHGHJIDGIJHIJHIGGGHG>HLJJJNIJKKJMJNKLMKJLLJJJDCKKLKJAIGLJIJGIJJLKJLICJGJAIIIHKHHHIGHHB	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.60297548	147	17	3785	60	101M	=	3736	-149	GTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCT	@GFFFGJIJGIIHHKHJHHIHF@FIHIJLIHIFFJHJAGAIIHDGFDGAIEGHIAIKHIJIJKKIJKGKJD@IIAJKKEKJGDDJCG<JCCAE==DCGBD@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.15284212	147	17	3809	60	101M	=	3585	-324	TCATAGAAATAGAGTCCTGCAACACGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCT	HDEGLJJFHIKILCHCAAICE?A<3B>EE:,BJIGFGEFHFEBALJGJ?K4E;KILICFJELIFKJB>AHA<D><A6/DEH:ADH?GDFGB:@;4*CE@6@	X0:i:1	X1:i:0	MD:Z:101	RG:Z:ERR229775	AM:i:37	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.6931819	163	17	3836	37	101M	=	4080	344	GGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCG	BBFC<FBJE=BGGGHGHJEHJIFGAAIIHIGHFCKJIIIJJKJLGICGAIEIKFHFH=HFIHJBFGLJHIMJKOJHFHOJJNKKMFIHGGIMIJFHGFFE7	X0:i:1	X1:i:0	MD:Z:100A0	RG:Z:ERR229775	AM:i:0	NM:i:1	SM:i:37	MQ:i:7	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@EVN
+ERR229775.80842527	147	17	3844	60	101M	=	3639	-305	GTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTG	DGDFGIEIIHKIHIKAIIHIMHHHIHGHEFEHDFBJDAHAIJFFIJIMIJEILKKIJEC=KJJJJHDCFIIIKKJJJHHJJHIGJEGFJHB9E<<CACEGA	X0:i:1	X1:i:0	MD:Z:92A8	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.15603458	83	17	3846	60	101M	=	3626	-320	GTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCT	/D<EA?<7-=BIH?JHKILDE@JHDKHJIBEGHLDCJDFKHDJKIKCJHJKIIKKJIEMMKLJJJB?KKELLLJKIKKLKJIKGIHKHE>F@HFGEGGGC?	X0:i:1	X1:i:0	MD:Z:90A10	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.105205152	147	17	3856	60	101M	=	3562	-394	TCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTC	#BE=GGHILIIHKHHJGJHJDHEKD;+EBF?C>FFJ?<GDJF@>E?DCIFEIGB>=HGBDILKGIFB>FI=9*=<><'?;C69?8,6?DD253-72,D9>:	X0:i:1	X1:i:0	MD:Z:80A20	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.30258628	83	17	3859	60	27S74M	=	3583	-349	TCGTGGCCGTCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATAT	############################FLLJHF-.LGLKHKKHCIBLHBHDB?@@;7IH=9>7/5HIE+A@EHICFFIGIJ@AGI?>KHAGEFGHE:DE7	X0:i:1	X1:i:0	XC:i:74	MD:Z:74	RG:Z:ERR229775	AM:i:25	NM:i:0	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.15906182	83	17	3862	60	101M	=	3598	-364	TTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGG	FEFFGGJHCKHHKKGHILFE@:EBCFIIHLEHHIMHEEIFBEGJJJKIIBAIGJMMLMMJMIIJIJKJJJMGLAKAKFFEJIDGHIHCJK@GJJHJGGHEB	X0:i:1	X1:i:0	MD:Z:74A26	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:D@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.104583040	99	17	3884	37	84M17S	=	4097	298	CTCCCACAGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTA	?HFEEHFHBC7EGAHIHCHFDHL?HJ=FI48C>KFJL=EKCCJJJA<FDDJLBJ8FJJJHGJNJIIDICALJILDJ@-<<LDI##################	X0:i:1	X1:i:0	XC:i:84	MD:Z:52A31	RG:Z:ERR229775	AM:i:0	NM:i:1	SM:i:37	MQ:i:7	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
+ERR229775.101967836	83	17	3891	60	101M	=	3700	-291	AGTGTAGCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCT	HDEEGKIIHKHC8HHJIHGCDAHHGIGJHGGLDFGHKJHIGLKFCMBJIIMKKLKJJIFKLMHMJMMJIJLKJJLJJJMKLJHAHIGJJIDIHGGHGGCF?	X0:i:1	X1:i:0	MD:Z:45A55	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:C@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@A
+ERR229775.71788763	147	17	3897	60	101M	=	3673	-324	GCATGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCGCGCACCTGCTACACTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAG	FD@HEEBGIJIHFFFAIHGHGJHGHKGGGGGIHFBBEC@JAF@.MKJJHF8E>LKHJLJLLIIHJFKHIIGGKJHCG?EFBHIGDCF>F@CCDFEGEGFF@	X0:i:1	X1:i:0	MD:Z:39A61	RG:Z:ERR229775	AM:i:37	NM:i:1	SM:i:37	MQ:i:60	XT:A:U	BQ:Z:A@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@B
+ERR229775.84503264	83	17	3903	60	2S99M	=	3670	-331	GCCCCTGCTACCCTCCTTCTTAGGGCTGATATTCCGCGCCCCTGCTACCCTCCTTCTTATGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCT	###?DDA5-;91@B:HBJ<?ICFID><:89-=F65868-%4C9E5-=>9C+9C9H;AFC7GEBCCJJILKJHHAIHELLIJJD=C>IFEIIJIJHLEEGEB	X0:i:1	X1:i:0	XC:i:99	MD:Z:0A8A23A3A8A52	RG:Z:ERR229775	AM:i:25	NM:i:5	SM:i:25	MQ:i:60	XT:A:U	BQ:Z:@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
diff --git a/test/mpileup/mpileup.4.out b/test/mpileup/mpileup.4.out
new file mode 100644
index 000000000..217cc0e77
--- /dev/null
+++ b/test/mpileup/mpileup.4.out
@@ -0,0 +1,527 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##FORMAT=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
+##INFO=<ID=DPR,Number=R,Type=Integer,Description="Number of high-quality bases observed for each allele">
+##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	100	.	C	<*>	0	.	DP=18;DPR=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,189:9:0:0:9,0,0,0:9,0	0,9,108:3:0:0:3,0,0,0:3,0	0,15,134:5:0:0:5,0,0,0:5,0
+17	101	.	C	<*>	0	.	DP=18;DPR=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,182:9:0:0:9,0,0,0:9,0	0,9,99:3:0:0:3,0,0,0:3,0	0,15,132:5:0:0:5,0,0,0:5,0
+17	102	.	C	<*>	0	.	DP=18;DPR=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,188:9:0:0:9,0,0,0:9,0	0,9,111:3:0:0:3,0,0,0:3,0	0,15,139:5:0:0:5,0,0,0:5,0
+17	103	.	T	<*>	0	.	DP=18;DPR=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,189:8:0:0:8,0,0,0:8,0	0,9,108:3:0:0:3,0,0,0:3,0	0,15,147:5:0:0:5,0,0,0:5,0
+17	104	.	G	<*>	0	.	DP=18;DPR=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,178:8:0:0:8,0,0,0:8,0	0,6,89:2:0:0:2,0,0,0:2,0	0,15,133:5:0:0:5,0,0,0:5,0
+17	105	.	G	<*>	0	.	DP=19;DPR=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,170:9:0:0:9,0,0,0:9,0	0,9,97:3:0:0:3,0,0,0:3,0	0,15,125:5:0:0:5,0,0,0:5,0
+17	106	.	G	<*>	0	.	DP=19;DPR=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,30,190:10:0:0:10,0,0,0:10,0	0,6,85:2:0:0:2,0,0,0:2,0	0,15,124:5:0:0:5,0,0,0:5,0
+17	107	.	C	<*>	0	.	DP=19;DPR=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,192:9:0:0:9,0,0,0:9,0	0,9,108:3:0:0:3,0,0,0:3,0	0,15,136:5:0:0:5,0,0,0:5,0
+17	108	.	C	<*>	0	.	DP=19;DPR=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,190:9:0:0:9,0,0,0:9,0	0,9,108:3:0:0:3,0,0,0:3,0	0,15,135:5:0:0:5,0,0,0:5,0
+17	109	.	T	<*>	0	.	DP=19;DPR=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,195:9:0:0:9,0,0,0:9,0	0,9,110:3:0:0:3,0,0,0:3,0	0,15,150:5:0:0:5,0,0,0:5,0
+17	110	.	G	<*>	0	.	DP=19;DPR=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,194:9:0:0:9,0,0,0:9,0	0,9,104:3:0:0:3,0,0,0:3,0	0,15,136:5:0:0:5,0,0,0:5,0
+17	111	.	G	<*>	0	.	DP=19;DPR=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,30,167:10:0:0:10,0,0,0:10,0	0,6,88:2:0:0:2,0,0,0:2,0	0,12,118:4:0:0:4,0,0,0:4,0
+17	112	.	C	<*>	0	.	DP=19;DPR=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,191:9:0:0:9,0,0,0:9,0	0,9,95:3:0:0:3,0,0,0:3,0	0,15,135:5:0:0:5,0,0,0:5,0
+17	113	.	A	<*>	0	.	DP=19;DPR=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,176:9:0:0:9,0,0,0:9,0	0,6,87:2:0:0:2,0,0,0:2,0	0,15,139:5:0:0:5,0,0,0:5,0
+17	114	.	C	<*>	0	.	DP=19;DPR=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,182:9:0:0:9,0,0,0:9,0	0,9,103:3:0:0:3,0,0,0:3,0	0,15,133:5:0:0:5,0,0,0:5,0
+17	115	.	C	<*>	0	.	DP=21;DPR=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,30,189:10:0:0:10,0,0,0:10,0	0,6,89:2:0:0:2,0,0,0:2,0	0,18,147:6:0:0:6,0,0,0:6,0
+17	116	.	A	<*>	0	.	DP=21;DPR=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,183:9:0:0:9,0,0,0:9,0	0,6,90:2:0:0:2,0,0,0:2,0	0,21,175:7:0:0:6,1,0,0:7,0
+17	117	.	G	<*>	0	.	DP=21;DPR=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,183:9:0:0:9,0,0,0:9,0	0,6,85:2:0:0:2,0,0,0:2,0	0,21,177:7:0:0:6,1,0,0:7,0
+17	118	.	G	<*>	0	.	DP=20;DPR=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,175:9:0:0:9,0,0,0:9,0	0,3,60:1:0:0:1,0,0,0:1,0	0,21,162:7:0:0:6,1,0,0:7,0
+17	119	.	G	<*>	0	.	DP=19;DPR=17,0;I16=16,1,0,0,629,26439,0,0,958,55682,0,0,267,5553,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,175:8:0:0:8,0,0,0:8,0	0,6,73:2:0:0:2,0,0,0:2,0	0,21,160:7:0:0:6,1,0,0:7,0
+17	120	.	A	<*>	0	.	DP=19;DPR=17,0;I16=16,1,0,0,672,29188,0,0,958,55682,0,0,264,5518,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,175:8:0:0:8,0,0,0:8,0	0,6,83:2:0:0:2,0,0,0:2,0	0,21,171:7:0:0:6,1,0,0:7,0
+17	121	.	G	<*>	0	.	DP=19;DPR=17,0;I16=16,1,0,0,662,28460,0,0,958,55682,0,0,260,5454,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,181:8:0:0:8,0,0,0:8,0	0,6,80:2:0:0:2,0,0,0:2,0	0,21,168:7:0:0:6,1,0,0:7,0
+17	122	.	C	<*>	0	.	DP=20;DPR=18,0;I16=17,1,0,0,716,31224,0,0,1018,59282,0,0,256,5410,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,181:8:0:0:8,0,0,0:8,0	0,9,99:3:0:0:3,0,0,0:3,0	0,21,178:7:0:0:6,1,0,0:7,0
+17	123	.	T	<*>	0	.	DP=18;DPR=16,0;I16=15,1,0,0,661,29997,0,0,898,52082,0,0,255,5385,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,167:7:0:0:7,0,0,0:7,0	0,9,112:3:0:0:3,0,0,0:3,0	0,18,166:6:0:0:5,1,0,0:6,0
+17	124	.	T	<*>	0	.	DP=19;DPR=18,0;I16=17,1,0,0,626,24802,0,0,987,56523,0,0,279,6003,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,27,154:9:0:0:9,0,0,0:9,0	0,9,104:3:0:0:3,0,0,0:3,0	0,18,154:6:0:0:5,1,0,0:6,0
+17	125	.	A	<*>	0	.	DP=18;DPR=16,0;I16=15,1,0,0,611,25689,0,0,898,52082,0,0,254,5340,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,154:7:0:0:7,0,0,0:7,0	0,9,104:3:0:0:3,0,0,0:3,0	0,18,162:6:0:0:5,1,0,0:6,0
+17	126	.	A	<*>	0	.	DP=18;DPR=17,0;I16=16,1,0,0,648,27366,0,0,927,52923,0,0,279,5947,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,162:8:0:0:8,0,0,0:8,0	0,9,107:3:0:0:3,0,0,0:3,0	0,18,174:6:0:0:5,1,0,0:6,0
+17	127	.	C	<*>	0	.	DP=18;DPR=17,0;I16=16,1,0,0,646,26972,0,0,927,52923,0,0,279,5949,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,163:8:0:0:8,0,0,0:8,0	0,9,109:3:0:0:3,0,0,0:3,0	0,18,160:6:0:0:5,1,0,0:6,0
+17	128	.	A	<*>	0	.	DP=18;DPR=17,0;I16=16,1,0,0,673,28797,0,0,927,52923,0,0,279,5971,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,169:8:0:0:8,0,0,0:8,0	0,9,111:3:0:0:3,0,0,0:3,0	0,18,162:6:0:0:5,1,0,0:6,0
+17	129	.	A	<*>	0	.	DP=17;DPR=16,0;I16=15,1,0,0,645,27891,0,0,867,49323,0,0,280,6012,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,168:8:0:0:8,0,0,0:8,0	0,9,113:3:0:0:3,0,0,0:3,0	0,15,159:5:0:0:4,1,0,0:5,0
+17	130	.	A	<*>	0	.	DP=17;DPR=16,0;I16=15,1,0,0,641,27295,0,0,867,49323,0,0,281,6071,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,24,169:8:0:0:8,0,0,0:8,0	0,9,113:3:0:0:3,0,0,0:3,0	0,15,152:5:0:0:4,1,0,0:5,0
+17	131	.	C	<*>	0	.	DP=16;DPR=15,0;I16=14,1,0,0,606,25732,0,0,838,48482,0,0,256,5472,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,167:7:0:0:7,0,0,0:7,0	0,9,110:3:0:0:3,0,0,0:3,0	0,15,147:5:0:0:4,1,0,0:5,0
+17	132	.	A	<*>	0	.	DP=16;DPR=15,0;I16=14,1,0,0,627,27579,0,0,838,48482,0,0,256,5514,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,169:7:0:0:7,0,0,0:7,0	0,9,110:3:0:0:3,0,0,0:3,0	0,15,151:5:0:0:4,1,0,0:5,0
+17	133	.	T	<*>	0	.	DP=15;DPR=15,0;I16=13,2,0,0,584,22816,0,0,838,48482,0,0,282,6196,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,163:7:0:0:7,0,0,0:7,0	0,9,105:3:0:0:2,1,0,0:3,0	0,15,150:5:0:0:4,1,0,0:5,0
+17	134	.	C	<*>	0	.	DP=15;DPR=15,0;I16=13,2,0,0,607,24653,0,0,838,48482,0,0,283,6267,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,177:7:0:0:7,0,0,0:7,0	0,9,105:3:0:0:2,1,0,0:3,0	0,15,152:5:0:0:4,1,0,0:5,0
+17	135	.	T	<*>	0	.	DP=15;DPR=15,0;I16=13,2,0,0,600,24178,0,0,838,48482,0,0,284,6352,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,173:7:0:0:7,0,0,0:7,0	0,9,106:3:0:0:2,1,0,0:3,0	0,15,156:5:0:0:4,1,0,0:5,0
+17	136	.	G	<*>	0	.	DP=15;DPR=15,0;I16=13,2,0,0,574,22258,0,0,838,48482,0,0,286,6450,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,172:7:0:0:7,0,0,0:7,0	0,9,105:3:0:0:2,1,0,0:3,0	0,15,134:5:0:0:4,1,0,0:5,0
+17	137	.	T	<*>	0	.	DP=15;DPR=15,0;I16=13,2,0,0,563,21377,0,0,838,48482,0,0,289,6561,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,160:7:0:0:7,0,0,0:7,0	0,9,104:3:0:0:2,1,0,0:3,0	0,15,139:5:0:0:4,1,0,0:5,0
+17	138	.	C	<*>	0	.	DP=15;DPR=15,0;I16=13,2,0,0,584,23088,0,0,838,48482,0,0,291,6637,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,172:7:0:0:7,0,0,0:7,0	0,9,108:3:0:0:2,1,0,0:3,0	0,15,142:5:0:0:4,1,0,0:5,0
+17	139	.	C	<*>	0	.	DP=15;DPR=15,0;I16=13,2,0,0,554,20790,0,0,838,48482,0,0,292,6680,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,161:7:0:0:7,0,0,0:7,0	0,9,106:3:0:0:2,1,0,0:3,0	0,15,143:5:0:0:4,1,0,0:5,0
+17	140	.	A	<*>	0	.	DP=15;DPR=15,0;I16=13,2,0,0,583,22789,0,0,838,48482,0,0,292,6690,0,0;QS=3,0;MQSB=0.576923;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,21,163:7:0:0:7,0,0,0:7,0	0,9,107:3:0:0:2,1,0,0:3,0	0,15,153:5:0:0:4,1,0,0:5,0
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+17	583	.	T	<*>	0	.	DP=30;DPR=30,0;I16=16,14,0,0,1136,43996,0,0,1769,105241,0,0,539,11523,0,0;QS=3,0;MQSB=0.946202;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,24,238:8:0:0:4,4,0,0:8,0	0,15,163:5:0:0:4,1,0,0:5,0
+17	584	.	C	<*>	0	.	DP=31;DPR=29,0;I16=16,13,0,0,1051,39351,0,0,1709,101641,0,0,499,10619,0,0;QS=3,0;MQSB=0.960189;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,21,207:7:0:0:4,3,0,0:7,0	0,15,157:5:0:0:4,1,0,0:5,0
+17	585	.	A	<*>	0	.	DP=31;DPR=31,0;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,54,255:18:0:0:9,9,0,0:18,0	0,24,211:8:0:0:4,4,0,0:8,0	0,15,157:5:0:0:4,1,0,0:5,0
+17	586	.	T	<*>	0	.	DP=31;DPR=30,0;I16=16,14,0,0,1081,39839,0,0,1738,102482,0,0,546,11796,0,0;QS=3,0;MQSB=0.999136;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,24,212:8:0:0:4,4,0,0:8,0	0,15,156:5:0:0:4,1,0,0:5,0
+17	587	.	C	<*>	0	.	DP=31;DPR=30,0;I16=17,13,0,0,1070,39402,0,0,1769,105241,0,0,532,11350,0,0;QS=3,0;MQSB=0.963674;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,54,255:18:0:0:9,9,0,0:18,0	0,21,201:7:0:0:4,3,0,0:7,0	0,15,155:5:0:0:4,1,0,0:5,0
+17	588	.	A	<*>	0	.	DP=31;DPR=31,0;I16=17,14,0,0,1126,41642,0,0,1798,106082,0,0,562,12140,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,54,255:18:0:0:9,9,0,0:18,0	0,24,222:8:0:0:4,4,0,0:8,0	0,15,164:5:0:0:4,1,0,0:5,0
+17	589	.	A	<*>	0	.	DP=31;DPR=31,0;I16=17,14,0,0,1157,43973,0,0,1798,106082,0,0,568,12340,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,54,255:18:0:0:9,9,0,0:18,0	0,24,236:8:0:0:4,4,0,0:8,0	0,15,165:5:0:0:4,1,0,0:5,0
+17	590	.	C	<*>	0	.	DP=32;DPR=30,0;I16=16,14,0,0,1094,41302,0,0,1769,105241,0,0,549,11951,0,0;QS=3,0;MQSB=0.958545;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,54,255:18:0:0:9,9,0,0:18,0	0,18,192:6:0:0:3,3,0,0:6,0	0,18,175:6:0:0:4,2,0,0:6,0
+17	591	.	A	<*>	0	.	DP=31;DPR=31,0;I16=16,15,0,0,1165,44163,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQSB=0.999805;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,54,255:18:0:0:9,9,0,0:18,0	0,21,209:7:0:0:3,4,0,0:7,0	0,18,188:6:0:0:4,2,0,0:6,0
+17	592	.	A	<*>	0	.	DP=31;DPR=30,0;I16=15,15,0,0,1114,42144,0,0,1738,102482,0,0,571,12651,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,21,215:7:0:0:3,4,0,0:7,0	0,18,182:6:0:0:4,2,0,0:6,0
+17	593	.	C	<*>	0	.	DP=31;DPR=29,0;I16=15,14,0,0,1065,39889,0,0,1709,101641,0,0,550,12132,0,0;QS=3,0;MQSB=0.954405;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,18,191:6:0:0:3,3,0,0:6,0	0,18,174:6:0:0:4,2,0,0:6,0
+17	594	.	A	<*>	0	.	DP=33;DPR=32,0;I16=16,16,0,0,1163,42917,0,0,1858,109682,0,0,572,12672,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,21,205:7:0:0:3,4,0,0:7,0	0,24,212:8:0:0:5,3,0,0:8,0
+17	595	.	A	<*>	0	.	DP=33;DPR=33,0;I16=17,16,0,0,1130,39996,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,54,255:18:0:0:9,9,0,0:18,0	0,21,198:7:0:0:3,4,0,0:7,0	0,24,213:8:0:0:5,3,0,0:8,0
+17	596	.	A	<*>	0	.	DP=33;DPR=32,0;I16=16,16,0,0,1059,37039,0,0,1858,109682,0,0,590,12952,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,21,169:7:0:0:3,4,0,0:7,0	0,24,230:8:0:0:5,3,0,0:8,0
+17	597	.	C	<*>	0	.	DP=33;DPR=33,0;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,54,255:18:0:0:9,9,0,0:18,0	0,21,204:7:0:0:3,4,0,0:7,0	0,24,220:8:0:0:5,3,0,0:8,0
+17	598	.	T	<*>	0	.	DP=33;DPR=32,0;I16=16,16,0,0,1214,47104,0,0,1858,109682,0,0,593,13013,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,21,217:7:0:0:3,4,0,0:7,0	0,24,239:8:0:0:5,3,0,0:8,0
+17	599	.	T	<*>	0	.	DP=33;DPR=33,0;I16=16,17,0,0,1183,43669,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,21,197:7:0:0:3,4,0,0:7,0	0,27,247:9:0:0:5,4,0,0:9,0
+17	600	.	G	<*>	0	.	DP=32;DPR=32,0;I16=15,17,0,0,1174,44066,0,0,1858,109682,0,0,601,13145,0,0;QS=3,0;MQSB=0.999287;MQ0F=0	PL:DP:DV:SP:DP4:DPR	0,51,255:17:0:0:8,9,0,0:17,0	0,21,194:7:0:0:3,4,0,0:7,0	0,24,232:8:0:0:4,4,0,0:8,0
diff --git a/test/mpileup/mpileup.5.out b/test/mpileup/mpileup.5.out
new file mode 100644
index 000000000..5aa9d4aaa
--- /dev/null
+++ b/test/mpileup/mpileup.5.out
@@ -0,0 +1,529 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths">
+##FORMAT=<ID=ADF,Number=R,Type=Integer,Description="Allelic depths on the forward strand">
+##FORMAT=<ID=ADR,Number=R,Type=Integer,Description="Allelic depths on the reverse strand">
+##INFO=<ID=AD,Number=R,Type=Integer,Description="Total allelic depths">
+##INFO=<ID=ADF,Number=R,Type=Integer,Description="Total allelic depths on the forward strand">
+##INFO=<ID=ADR,Number=R,Type=Integer,Description="Total allelic depths on the reverse strand">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	100	.	C	<*>	0	.	DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,688,29762,0,0,958,55682,0,0,332,7446,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,189:9:0:9,0:0,0:9,0	0,9,108:3:0:3,0:0,0:3,0	0,15,134:5:0:5,0:0,0:5,0
+17	101	.	C	<*>	0	.	DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,650,27530,0,0,958,55682,0,0,331,7303,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,182:9:0:9,0:0,0:9,0	0,9,99:3:0:3,0:0,0:3,0	0,15,132:5:0:5,0:0,0:5,0
+17	102	.	C	<*>	0	.	DP=18;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,695,30453,0,0,958,55682,0,0,330,7178,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,188:9:0:9,0:0,0:9,0	0,9,111:3:0:3,0:0,0:3,0	0,15,139:5:0:5,0:0,0:5,0
+17	103	.	T	<*>	0	.	DP=18;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,692,31998,0,0,929,54841,0,0,323,7035,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,24,189:8:0:8,0:0,0:8,0	0,9,108:3:0:3,0:0,0:3,0	0,15,147:5:0:5,0:0,0:5,0
+17	104	.	G	<*>	0	.	DP=18;ADF=15,0;ADR=0,0;AD=15,0;I16=15,0,0,0,611,26723,0,0,900,54000,0,0,295,6259,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,24,178:8:0:8,0:0,0:8,0	0,6,89:2:0:2,0:0,0:2,0	0,15,133:5:0:5,0:0,0:5,0
+17	105	.	G	<*>	0	.	DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,604,23936,0,0,989,58441,0,0,317,6751,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,170:9:0:9,0:0,0:9,0	0,9,97:3:0:3,0:0,0:3,0	0,15,125:5:0:5,0:0,0:5,0
+17	106	.	G	<*>	0	.	DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,644,26574,0,0,989,58441,0,0,299,6093,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,30,190:10:0:10,0:0,0:10,0	0,6,85:2:0:2,0:0,0:2,0	0,15,124:5:0:5,0:0,0:5,0
+17	107	.	C	<*>	0	.	DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,694,30064,0,0,989,58441,0,0,313,6543,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,192:9:0:9,0:0,0:9,0	0,9,108:3:0:3,0:0,0:3,0	0,15,136:5:0:5,0:0,0:5,0
+17	108	.	C	<*>	0	.	DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,692,30148,0,0,989,58441,0,0,310,6420,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,190:9:0:9,0:0,0:9,0	0,9,108:3:0:3,0:0,0:3,0	0,15,135:5:0:5,0:0,0:5,0
+17	109	.	T	<*>	0	.	DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,741,34273,0,0,989,58441,0,0,307,6319,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,195:9:0:9,0:0,0:9,0	0,9,110:3:0:3,0:0,0:3,0	0,15,150:5:0:5,0:0,0:5,0
+17	110	.	G	<*>	0	.	DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,704,31276,0,0,989,58441,0,0,304,6240,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,194:9:0:9,0:0,0:9,0	0,9,104:3:0:3,0:0,0:3,0	0,15,136:5:0:5,0:0,0:5,0
+17	111	.	G	<*>	0	.	DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,584,24362,0,0,929,54841,0,0,272,5416,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,30,167:10:0:10,0:0,0:10,0	0,6,88:2:0:2,0:0,0:2,0	0,12,118:4:0:4,0:0,0:4,0
+17	112	.	C	<*>	0	.	DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,680,29854,0,0,989,58441,0,0,296,6052,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,191:9:0:9,0:0,0:9,0	0,9,95:3:0:3,0:0,0:3,0	0,15,135:5:0:5,0:0,0:5,0
+17	113	.	A	<*>	0	.	DP=19;ADF=16,0;ADR=0,0;AD=16,0;I16=16,0,0,0,645,28035,0,0,960,57600,0,0,266,5318,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,176:9:0:9,0:0,0:9,0	0,6,87:2:0:2,0:0,0:2,0	0,15,139:5:0:5,0:0,0:5,0
+17	114	.	C	<*>	0	.	DP=19;ADF=17,0;ADR=0,0;AD=17,0;I16=17,0,0,0,674,28788,0,0,989,58441,0,0,286,5856,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,182:9:0:9,0:0,0:9,0	0,9,103:3:0:3,0:0,0:3,0	0,15,133:5:0:5,0:0,0:5,0
+17	115	.	C	<*>	0	.	DP=21;ADF=18,0;ADR=0,0;AD=18,0;I16=18,0,0,0,708,30546,0,0,1049,62041,0,0,274,5490,0,0;QS=3,0;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,30,189:10:0:10,0:0,0:10,0	0,6,89:2:0:2,0:0,0:2,0	0,18,147:6:0:6,0:0,0:6,0
+17	116	.	A	<*>	0	.	DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,727,31755,0,0,1049,62041,0,0,253,5079,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,183:9:0:9,0:0,0:9,0	0,6,90:2:0:2,0:0,0:2,0	0,21,175:7:0:6,0:1,0:7,0
+17	117	.	G	<*>	0	.	DP=21;ADF=17,0;ADR=1,0;AD=18,0;I16=17,1,0,0,712,30478,0,0,1049,62041,0,0,249,5019,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,183:9:0:9,0:0,0:9,0	0,6,85:2:0:2,0:0,0:2,0	0,21,177:7:0:6,0:1,0:7,0
+17	118	.	G	<*>	0	.	DP=20;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,636,26574,0,0,958,55682,0,0,266,5426,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,27,175:9:0:9,0:0,0:9,0	0,3,60:1:0:1,0:0,0:1,0	0,21,162:7:0:6,0:1,0:7,0
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+17	120	.	A	<*>	0	.	DP=19;ADF=16,0;ADR=1,0;AD=17,0;I16=16,1,0,0,672,29188,0,0,958,55682,0,0,264,5518,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,24,175:8:0:8,0:0,0:8,0	0,6,83:2:0:2,0:0,0:2,0	0,21,171:7:0:6,0:1,0:7,0
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+17	584	.	C	<*>	0	.	DP=31;ADF=16,0;ADR=13,0;AD=29,0;I16=16,13,0,0,1051,39351,0,0,1709,101641,0,0,499,10619,0,0;QS=3,0;MQSB=0.960189;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,21,207:7:0:4,0:3,0:7,0	0,15,157:5:0:4,0:1,0:5,0
+17	585	.	A	<*>	0	.	DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1096,39866,0,0,1798,106082,0,0,549,11751,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,54,255:18:0:9,0:9,0:18,0	0,24,211:8:0:4,0:4,0:8,0	0,15,157:5:0:4,0:1,0:5,0
+17	586	.	T	<*>	0	.	DP=31;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1081,39839,0,0,1738,102482,0,0,546,11796,0,0;QS=3,0;MQSB=0.999136;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,24,212:8:0:4,0:4,0:8,0	0,15,156:5:0:4,0:1,0:5,0
+17	587	.	C	<*>	0	.	DP=31;ADF=17,0;ADR=13,0;AD=30,0;I16=17,13,0,0,1070,39402,0,0,1769,105241,0,0,532,11350,0,0;QS=3,0;MQSB=0.963674;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,54,255:18:0:9,0:9,0:18,0	0,21,201:7:0:4,0:3,0:7,0	0,15,155:5:0:4,0:1,0:5,0
+17	588	.	A	<*>	0	.	DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1126,41642,0,0,1798,106082,0,0,562,12140,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,54,255:18:0:9,0:9,0:18,0	0,24,222:8:0:4,0:4,0:8,0	0,15,164:5:0:4,0:1,0:5,0
+17	589	.	A	<*>	0	.	DP=31;ADF=17,0;ADR=14,0;AD=31,0;I16=17,14,0,0,1157,43973,0,0,1798,106082,0,0,568,12340,0,0;QS=3,0;MQSB=0.998229;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,54,255:18:0:9,0:9,0:18,0	0,24,236:8:0:4,0:4,0:8,0	0,15,165:5:0:4,0:1,0:5,0
+17	590	.	C	<*>	0	.	DP=32;ADF=16,0;ADR=14,0;AD=30,0;I16=16,14,0,0,1094,41302,0,0,1769,105241,0,0,549,11951,0,0;QS=3,0;MQSB=0.958545;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,54,255:18:0:9,0:9,0:18,0	0,18,192:6:0:3,0:3,0:6,0	0,18,175:6:0:4,0:2,0:6,0
+17	591	.	A	<*>	0	.	DP=31;ADF=16,0;ADR=15,0;AD=31,0;I16=16,15,0,0,1165,44163,0,0,1798,106082,0,0,579,12695,0,0;QS=3,0;MQSB=0.999805;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,54,255:18:0:9,0:9,0:18,0	0,21,209:7:0:3,0:4,0:7,0	0,18,188:6:0:4,0:2,0:6,0
+17	592	.	A	<*>	0	.	DP=31;ADF=15,0;ADR=15,0;AD=30,0;I16=15,15,0,0,1114,42144,0,0,1738,102482,0,0,571,12651,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,21,215:7:0:3,0:4,0:7,0	0,18,182:6:0:4,0:2,0:6,0
+17	593	.	C	<*>	0	.	DP=31;ADF=15,0;ADR=14,0;AD=29,0;I16=15,14,0,0,1065,39889,0,0,1709,101641,0,0,550,12132,0,0;QS=3,0;MQSB=0.954405;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,18,191:6:0:3,0:3,0:6,0	0,18,174:6:0:4,0:2,0:6,0
+17	594	.	A	<*>	0	.	DP=33;ADF=16,0;ADR=16,0;AD=32,0;I16=16,16,0,0,1163,42917,0,0,1858,109682,0,0,572,12672,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,21,205:7:0:3,0:4,0:7,0	0,24,212:8:0:5,0:3,0:8,0
+17	595	.	A	<*>	0	.	DP=33;ADF=17,0;ADR=16,0;AD=33,0;I16=17,16,0,0,1130,39996,0,0,1918,113282,0,0,589,12905,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,54,255:18:0:9,0:9,0:18,0	0,21,198:7:0:3,0:4,0:7,0	0,24,213:8:0:5,0:3,0:8,0
+17	596	.	A	<*>	0	.	DP=33;ADF=16,0;ADR=16,0;AD=32,0;I16=16,16,0,0,1059,37039,0,0,1858,109682,0,0,590,12952,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,21,169:7:0:3,0:4,0:7,0	0,24,230:8:0:5,0:3,0:8,0
+17	597	.	C	<*>	0	.	DP=33;ADF=17,0;ADR=16,0;AD=33,0;I16=17,16,0,0,1196,44890,0,0,1918,113282,0,0,592,12990,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,54,255:18:0:9,0:9,0:18,0	0,21,204:7:0:3,0:4,0:7,0	0,24,220:8:0:5,0:3,0:8,0
+17	598	.	T	<*>	0	.	DP=33;ADF=16,0;ADR=16,0;AD=32,0;I16=16,16,0,0,1214,47104,0,0,1858,109682,0,0,593,13013,0,0;QS=3,0;MQSB=1;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,21,217:7:0:3,0:4,0:7,0	0,24,239:8:0:5,0:3,0:8,0
+17	599	.	T	<*>	0	.	DP=33;ADF=16,0;ADR=17,0;AD=33,0;I16=16,17,0,0,1183,43669,0,0,1918,113282,0,0,599,13095,0,0;QS=3,0;MQSB=0.999838;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,21,197:7:0:3,0:4,0:7,0	0,27,247:9:0:5,0:4,0:9,0
+17	600	.	G	<*>	0	.	DP=32;ADF=15,0;ADR=17,0;AD=32,0;I16=15,17,0,0,1174,44066,0,0,1858,109682,0,0,601,13145,0,0;QS=3,0;MQSB=0.999287;MQ0F=0	PL:DP:SP:ADF:ADR:AD	0,51,255:17:0:8,0:9,0:17,0	0,21,194:7:0:3,0:4,0:7,0	0,24,232:8:0:4,0:4,0:8,0
diff --git a/test/mpileup/mpileup.ref.fa b/test/mpileup/mpileup.ref.fa
new file mode 100644
index 000000000..7c2ec2a88
--- /dev/null
+++ b/test/mpileup/mpileup.ref.fa
@@ -0,0 +1,71 @@
+>17 17:1-4200
+AAGCTTCTCACCCTGTTCCTGCATAGATAATTGCATGACAATTGCCTTGTCCCTGCTGAA
+TGTGCTCTGGGGTCTCTGGGGTCTCACCCACGACCAACTCCCTGGGCCTGGCACCAGGGA
+GCTTAACAAACATCTGTCCAGCGAATACCTGCATCCCTAGAAGTGAAGCCACCGCCCAAA
+GACACGCCCATGTCCAGCTTAACCTGCATCCCTAGAAGTGAAGGCACCGCCCAAAGACAC
+GCCCATGTCCAGCTTATTCTGCCCAGTTCCTCTCCAGAAAGGCTGCATGGTTGACACACA
+GTGCCTGCGACAAAGCTGAATGCTATCATTTAAAAACTCCTTGCTGGTTTGAGAGGCAGA
+AAATGATATCTCATAGTTGCTTTACTTTGCATATTTTAAAATTGTGACTTTCATGGCATA
+AATAATACTGGTTTATTACAGAAGCACTAGAAAATGCATGTGGACAAAAGTTGGGATTAG
+GAGAGAGAAATGAAGACATATGTCCACACAAAAACCTGTTCATTGCAGCTTTCTACCATC
+ACCAAAAATTGCAAACAACCACACGCCCTTCAACTGGGGAACTCATCAACAACAAACTTG
+TGGTTTACCCACACAATGGAAGACCACTTAGCAACAAAAAGGACCAAACTCCTGGTACAT
+GCAACTGACAGATGAATCTCAAACGCATTCCTCCGTGTGAAAGAAGCCGGACTCACAGGG
+CAACACACTATCTGACTGTTTCATGGGAAAGTCTGGAAACGGCAACACCATTGAGACAGA
+AAACAGGTGAGTGGTTGCCTGGGGCCAGGGAACTTTCTGGGGTCATATTCTCTGTGTTGA
+TTCTGGTGGTGGAAACAAGACTGTCCCAGCCTGGGTGATACAGCGAGACCCCATCTCTAC
+CAAAAAATTAAAAATTAGCTGGGCATGGTGGTGCATGCCTGTAGTCCCAGCTATTCACAG
+TGCTGAGGTGGGAAGATGCTTGAGCCCAGGAGTTCAAGGCTGCAATGAGCTATGATTGCG
+CCACTGCACTTTGGCCTGGACAACAGAGCAAAACCCTGTCTCTAAAAAAAGAAAAGAAAA
+GAAAAACTCACTGGATATGAATGATACAGGTTGAGGATCCATTATCTGAAATGCTTGGAC
+CAGATGTTTTGAATTTTGGATTTTTTCATATTTTGTAATCTTTGCAGTATATTTACCAGT
+TCAGCATCCCTAACTCAAAAATTCAAAAATCTGAAATCCCAAACGCGCCAATAAGCATTC
+CCTTTGAGCGTCATGTCGGTGCTTGGAATGTTTGGGGTTTTGGATTTACAGCTTTGGGAC
+GCTCAACCTGTACCTCAATAAACCTGATTTTAAAAAAGTTTGGGGGGATTCCCCTAAGCC
+CGCCACCCGGAGACAGCGGATTTCCTTAGTTACTTACTATGCTCCTTGGCCATTTCTCTA
+GGTATTGGTATATTGTGTCTGCTGTGAACTGTCCTTGGCCTGTTTGGTGACGGGTGAGGA
+GCAGGGACAGAAGGGTCCTGCGTGCCCTGCCTTCACAAGCCCCTGGAAGGAAAGTTGTTT
+TGGGATCTCTGCACCCTCAGCCTGGACAACTTGTGCCCATCTGGTGACCCCTCACTCAGC
+CACCAGACTTCCACGACAGGCTCCAGCCTCGGCACCTTCAGCCATGGACAGTTCCGCCAG
+CGTTGCCCTCTGTTCTGCTGTTTTCTCTACCAGAAGTGCCCTTCCCTCCTCACCTGACCA
+CTCTGGGGAAATCCCTCAGCACCCTCCCTGAGCATACCCTACTCTGGCACAAGCCCACCC
+TGCAAAGCCCCTGAGGCCCGCCCTGTGGCGTCTCTCCCTCCCTTGCTGTCAGGACAGTGG
+TCCTGGCCACCGGGGCTCACGGAGCCGCCCTGTGCCGTGTACCTCTGAGCCCTCTGCACA
+GTGCCTTCTGCTTGCCTGTGGCTTTGAGAAGAAACCCCTTCTGGTTATACATAAGACAGC
+CAGAGAAGGGAGTTGCCCAGGGTGGCACAGCACGTTGCTGCCAGTTACTGCCATTTTCAC
+GGGCATGAAATGGAGATAACAACAGGAGCGACCGCACAGGCTGCTGAGCGCGTCACACGC
+AGCCATCGCGCAGCTCAGGGATATTACGTGTAACTCGACATGTCAGCGATTGTCACAGGC
+ACTGCTACTCCTGGGGTTTTCCATCAAACCCTCAAGAGCTGGGCCTGGGGTCAACTTCCG
+GCCTGGGGAAACTGGGGCAAGTATCACCAGAGATGAGCTTTATAAAAATAATGGTGCTAG
+CTGGGCATGGTGGCTTGCACCTGTAATCCCAGCACTTTGGGAGGCCGAGCTAGGAGGATC
+GTTTGAGTCCAGCAGTTTGAGACCAGCCTGGCCAATACGGCAAAACCCAGTCTCTACAAA
+AAATACAAAAAACAACTAGCCAGGCGTGGTGGTGCACACCTGTAGTCCCAGCTACTCAGG
+AGGCTGAGGGGGAAGGACTGCTTGAGCCCAGGAGTTTGAGGCTGCTGTGAGCTGTGATCG
+CATCACTGCATTCCAGCCCGGTGACAGAGTGAGTCACTGTCTCAAAAAAGAAAGGAAGAA
+ATAAAGAAAACAAATAAAAATAATAGTGCAGACAAAAGGCCTTGACCCATCTAGCTTTGG
+CCCTCAGCATCAACCGCTAGATACGTCCCTCCCTTTCTTCTGGGGCACAGGTCACACTCT
+CTTCCAGGTCTAGGATGCAGCTGAGGGGTGCCCCTCTTACCATCTAATCTGTGCCCTTAT
+TTCCTCTGCTTTAGTGAGGAAGAGGCCCCTGGTCCATGAAGGGGCCTTTCAGAGACGGGG
+ACCCCTGAGGAGCCCCGAGCAGCAGCCGTCGTGTCTCACCCAGGGTGTCTGAAACAGATG
+TGGAGGTCTCGGGTGAGGCGTGGCTCAGATACAGGGAGTGGCCCACAGCTCGGCCTGTCT
+TTGAAAGGCCACGTGACCTGGCCCACGGCTGGCAGGTGGGACCCAGCTGCAGGGGTCCAG
+CAGCACCCACAGCAGCCACCTGTGGCAGGGAGGAGCTTGTGGTACAGTGGACAGGCCCTG
+CCCAGATGGCCCCCCGCCTGCCTGTGGAAGTTGACCAGACCATCTGTCACAGCAGGTAAG
+ACTCTGCTTTCTGGGCAACCCAGCAGGTGACCCTGGAATTCCTGTCCATCTGGCAGGTGG
+GCATTGAAACTGGTTTAAAAATGTCACACCATAGGCCGGGCACAGTGGCTCACGCCTGTA
+ATCCCAGCCCTTTGGGAGGCCAGGGTGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCA
+GCCTGGCCAACATGGTGAAACCCCGTCTACTAAAAATACAAAAATTAGCCTGGCGTGGTG
+GCGCATGCCTGTAATCCCAGCTACTTGGGAAGCTGAGGGATGAGAACTGCTTGAACCTGG
+GAGGCAGACGTTGCAGTGAGCTGAGATCACGCCACTGCACTCCAGCCTGGGCAACAGAGT
+AAGACTCTGTCTCAAAAAAAAAAAAATCACACCATTTTGGCTTCAGATTGCATATCCTCC
+TGCAAGGATATATACGCGTGAAATTCAAGTCAATGACAAATCAGAAGAAAAAACATATAT
+ATACGCAAACCAGTATCCTACTGTGTGTGTCGTTTGTTGTGTTTTCGACAGCTGTCCGTG
+TTATAATAATTCCTCTAGTTCAAATTTATTCATTTTTAACTTCATAGTACCACATTCTAC
+ACACTGCCCATGTCCCCTCAAGCTTCCCCTGGCTCCTGCAACCACAAATCTACTCTCTGC
+CTCTGTGGGTTGACCTATTCTGGACACGTCATAGAAATAGAGTCCTGCAACACGTGGCCG
+TCTGTGTCTGGCTTCTCTCGCTTAGCATCTTGTTTCCAAGGTCCTCCCACAGTGTAGCAT
+GCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAT
+GGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACACACCCGCT
+ACACTCCTTCTTAGGGCTGATATTCCACGCACCCGCTACACTCCTTCTTAGGGCTGATAT
+TCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCACCTGCTACACTCCTT
+CTTAGGGCTGATATTCCACGCACCTGCTACACTCCTTCTTAGGGCTGATATTCCACGCAC
diff --git a/test/mpileup/mpileup.ref.fa.fai b/test/mpileup/mpileup.ref.fa.fai
new file mode 100644
index 000000000..c2112667e
--- /dev/null
+++ b/test/mpileup/mpileup.ref.fa.fai
@@ -0,0 +1 @@
+17	4200	14	60	61
diff --git a/test/test.pl b/test/test.pl
index 981cc0b56..466ef0e07 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -249,6 +249,11 @@
 test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.1.out',fa=>'consensus2.fa',args=>'-H 1');
 test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.2.out',fa=>'consensus2.fa',args=>'-H 2');
 test_vcf_consensus($opts,in=>'empty',out=>'consensus.5.out',fa=>'consensus.fa',args=>'');
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.1.out',args=>q[-r17:100-150]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.2.out',args=>q[-t DP,DV -r17:100-600]); # test files from samtools mpileup test suite
+test_mpileup($opts,in=>[qw(1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-t DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.5.out',args=>q[-t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600]);
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};
@@ -922,3 +927,17 @@ sub test_naive_concat
     test_cmd($opts,exp=>$exp,out=>"concat.naive.vcf.out",cmd=>"$$opts{bin}/bcftools concat --naive $vcfs | $$opts{bin}/bcftools view -H");
 }
 
+sub test_mpileup
+{
+    my ($opts,%args) = @_;
+
+    for my $fmt ('bam','cram')
+    {
+        my @files = ();
+        for my $file (@{$args{in}}) { push @files, "$$opts{path}/mpileup/mpileup.$file.$fmt"; }
+        my $files = join(' ',@files);
+        my $grep_hdr = "grep -v ^##bcftools | grep -v ^##reference";
+        test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa $files 2>/dev/null | $grep_hdr");
+        test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa -Ob $files 2>/dev/null | $$opts{bin}/bcftools view  | $grep_hdr");
+    }
+}

From b20d1e7441d09238c1126b8a48f677ffb3170aed Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 26 Apr 2016 21:06:44 +0100
Subject: [PATCH 194/211] bring over mpileup documentation

---
 doc/bcftools.1    | 415 +++++++++++++++++++++++++++++++++++++++++++++-
 doc/bcftools.html | 219 +++++++++++++++++++++++-
 doc/bcftools.txt  | 193 +++++++++++++++++++++
 3 files changed, 818 insertions(+), 9 deletions(-)

diff --git a/doc/bcftools.1 b/doc/bcftools.1
index a85c9a1b1..16552f4b5 100644
--- a/doc/bcftools.1
+++ b/doc/bcftools.1
@@ -2,12 +2,12 @@
 .\"     Title: bcftools
 .\"    Author: [see the "AUTHORS" section]
 .\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
-.\"      Date: 2016-04-18 14:18 BST
+.\"      Date: 2016-04-26 21:06 BST
 .\"    Manual: \ \&
 .\"    Source: \ \&
 .\"  Language: English
 .\"
-.TH "BCFTOOLS" "1" "2016\-04\-18 14:18 BST" "\ \&" "\ \&"
+.TH "BCFTOOLS" "1" "2016\-04\-26 21:06 BST" "\ \&" "\ \&"
 .\" -----------------------------------------------------------------
 .\" * Define some portability stuff
 .\" -----------------------------------------------------------------
@@ -41,7 +41,7 @@ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatica
 BCFtools is designed to work on a stream\&. It regards an input file "\-" as the standard input (stdin) and outputs to the standard output (stdout)\&. Several commands can thus be combined with Unix pipes\&.
 .SS "VERSION"
 .sp
-This manual page was last updated \fB2016\-04\-18 14:18 BST\fR and refers to bcftools git version \fB1\&.3\-36\-g47e811c+\fR\&.
+This manual page was last updated \fB2016\-04\-26 21:06 BST\fR and refers to bcftools git version \fB1\&.3\&.1\-6\-g0848b12+\fR\&.
 .SS "BCF1"
 .sp
 The BCF1 format output by versions of samtools <= 0\&.1\&.19 is \fBnot\fR compatible with this version of bcftools\&. To read BCF1 files one can use the view command from old versions of bcftools packaged with samtools versions <= 0\&.1\&.19 to convert to VCF, which can then be read by this version of bcftools\&.
@@ -214,6 +214,19 @@ For a full list of available commands, run \fBbcftools\fR without arguments\&. F
 .IP \(bu 2.3
 .\}
 
+\fBmpileup\fR
+\&.\&. multi\-way pileup producing genotype likelihoods
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
 \fBnorm\fR
 \&.\&. normalize indels
 .RE
@@ -2147,6 +2160,402 @@ see
 see
 \fBCommon Options\fR
 .RE
+.SS "bcftools mpileup [\fIOPTIONS\fR] \-f \fIref\&.fa\fR \fIin\&.bam\fR [\fIin2\&.bam\fR [\&...]]"
+.sp
+Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files\&. This is based on the original \fBsamtools mpileup\fR command (with the \fB\-v\fR or \fB\-g\fR options) producing genotype likelihoods in VCF or BCF format, but not the textual pileup output\&. The \fBmpileup\fR command was transferred to bcftools in order to avoid errors resulting from use of incompatible versions of samtools and bcftools when using in the mpileup+bcftools call pipeline\&.
+.sp
+Individuals are identified from the SM tags in the @RG header lines\&. Multiple individuals can be pooled in one alignment file, also one individual can be separated into multiple files\&. If sample identifiers are absent, each input file is regarded as one sample\&.
+.sp
+Note that there are two orthogonal ways to specify locations in the input file; via \fB\-r\fR \fIregion\fR and \fB\-l\fR \fIpositions\fR\&. The former uses (and requires) an index to do random access while the latter streams through the file contents filtering out the specified regions, requiring no index\&. The two may be used in conjunction\&. For example a BED file containing locations of genes in chromosome 20 could be specified using \fB\-r 20 \-l chr20\&.bed\fR, meaning that the index is used to find chromosome 20 and then it is filtered for the regions listed in the BED file\&.
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBInput options\fR
+.RS 4
+.PP
+\fB\-6, \-\-illumina1\&.3+\fR
+.RS 4
+Assume the quality is in the Illumina 1\&.3+ encoding\&.
+.RE
+.PP
+\fB\-A, \-\-count\-orphans\fR
+.RS 4
+Do not skip anomalous read pairs in variant calling\&.
+.RE
+.PP
+\fB\-b, \-\-bam\-list\fR \fIFILE\fR
+.RS 4
+List of input alignment files, one file per line [null]
+.RE
+.PP
+\fB\-B, \-\-no\-BAQ\fR
+.RS 4
+Disable probabilistic realignment for the computation of base alignment quality (BAQ)\&. BAQ is the Phred\-scaled probability of a read base being misaligned\&. Applying this option greatly helps to reduce false SNPs caused by misalignments\&.
+.RE
+.PP
+\fB\-C, \-\-adjust\-MQ\fR \fIINT\fR
+.RS 4
+Coefficient for downgrading mapping quality for reads containing excessive mismatches\&. Given a read with a phred\-scaled probability q of being generated from the mapped posi\- tion, the new mapping quality is about sqrt((INT\-q)/INT)*INT\&. A zero value disables this functionality; if enabled, the recommended value for BWA is 50\&. [0]
+.RE
+.PP
+\fB\-d, \-\-max\-depth\fR \fIINT\fR
+.RS 4
+At a position, read maximally
+\fIINT\fR
+reads per input file\&. Note that bcftools has a minimum value of
+\fI8000/n\fR
+where
+\fIn\fR
+is the number of input files given to mpileup\&. This means the default is highly likely to be increased\&. Once above the cross\-sample minimum of 8000 the \-d parameter will have an effect\&. [250]
+.RE
+.PP
+\fB\-E, \-\-redo\-BAQ\fR
+.RS 4
+Recalculate BAQ on the fly, ignore existing BQ tags
+.RE
+.PP
+\fB\-f, \-\-fasta\-ref\fR \fIFILE\fR
+.RS 4
+The
+\fBfaidx\fR\-indexed reference file in the FASTA format\&. The file can be optionally compressed by
+\fBbgzip\fR
+[null]
+.RE
+.PP
+\fB\-G, \-\-exclude\-RG\fR \fIFILE\fR
+.RS 4
+Exclude reads from readgroups listed in FILE (one @RG\-ID per line)
+.RE
+.PP
+\fB\-l, \-\-positions\fR \fIFILE\fR
+.RS 4
+BED or position list file containing a list of regions or sites where output should be generated\&. Position list files contain two columns (chromosome and position) and start counting from 1\&. BED files contain at least 3 columns (chromosome, start and end position) and are 0\-based half\-open\&. While it is possible to mix both position\-list and BED coordinates in the same file, this is strongly ill advised due to the differing coordinate systems\&. [null]
+.RE
+.PP
+\fB\-q, \-min\-MQ\fR \fIINT\fR
+.RS 4
+Minimum mapping quality for an alignment to be used [0]
+.RE
+.PP
+\fB\-Q, \-\-min\-BQ\fR \fIINT\fR
+.RS 4
+Minimum base quality for a base to be considered [13]
+.RE
+.PP
+\fB\-r, \-\-region\fR \fISTR\fR
+.RS 4
+Only generate output in region\&. Requires the alignment files to be indexed\&. If used in conjunction with \-l then considers the intersection of the two requests [all sites]
+.RE
+.PP
+\fB\-R, \-\-ignore\-RG\fR
+.RS 4
+Ignore RG tags\&. Treat all reads in one alignment file as one sample\&.
+.RE
+.PP
+\fB\-\-rf, \-\-incl\-flags\fR \fISTR\fR|\fIINT\fR
+.RS 4
+Required flags: skip reads with mask bits unset [null]
+.RE
+.PP
+\fB\-\-ff, \-\-excl\-flags\fR \fISTR\fR|\fIINT\fR
+.RS 4
+Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
+.RE
+.PP
+\fB\-x, \-\-ignore\-overlaps\fR
+.RS 4
+Disable read\-pair overlap detection\&.
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBOutput options\fR
+.RS 4
+.PP
+\fB\-o, \-\-output\fR \fIFILE\fR
+.RS 4
+Write output to
+\fIFILE\fR, rather than the default of standard output\&. (The same short option is used for both
+\fB\-\-open\-prob\fR
+and
+\fB\-\-output\fR\&. If
+\fB\-o\fR\*(Aqs argument contains any non\-digit characters other than a leading + or \- sign, it is interpreted as
+\fB\-\-output\fR\&. Usually the filename extension will take care of this, but to write to an entirely numeric filename use
+\fB\-o \&./123\fR
+or
+\fB\-\-output 123\fR\&.)
+.RE
+.PP
+\fB\-O, \-\-output\-type\fR \fIb\fR|\fIu\fR|\fIz\fR|\fIv\fR
+.RS 4
+see
+\fBCommon Options\fR
+.RE
+.PP
+\fB\-t, \-\-output\-tags\fR \fILIST\fR
+.RS 4
+Comma\-separated list of FORMAT and INFO tags to output (case\-insensitive) [null]:
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBAD\fR
+\&.\&. Allelic depth, FORMAT
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBINFO/AD\fR
+\&.\&. Total allelic depth, INFO
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBADF\fR
+\&.\&. Allelic depths on the forward strand, FORMAT
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBINFO/ADF\fR
+\&.\&. Total allelic depths on the forward strand, INFO
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBADR\fR
+\&.\&. Allelic depths on the reverse strand, FORMAT
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBINFO/ADR\fR
+\&.\&. Total allelic depths on the reverse strand, INFO
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBDP\fR
+\&.\&. Number of high\-quality bases, FORMAT
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBSP\fR
+\&.\&. Phred\-scaled strand bias P\-value, FORMAT
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBDV\fR
+\&.\&. Deprecated in favor of AD; Number of high\-quality non\-reference bases, FORMAT
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBDPR\fR
+\&.\&. Deprecated in favor of AD; Number of high\-quality bases for each observed allele, FORMAT
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBINFO/DPR\fR
+\&.\&. Deprecated in favor of INFO/AD; Number of high\-quality bases for each observed allele, INFO
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+
+\fBDP4\fR
+\&.\&. Deprecated in favor of ADF and ADR; Number of high\-quality ref\-forward, ref\-reverse, alt\-forward and alt\-reverse bases, FORMAT
+.RE
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBOptions for SNP/INDEL genotype likelihood computation\fR
+.RS 4
+.PP
+\fB\-e, \-\-ext\-prob\fR \fIINT\fR
+.RS 4
+Phred\-scaled gap extension sequencing error probability\&. Reducing
+\fIINT\fR
+leads to longer indels [20]
+.RE
+.PP
+\fB\-F, \-\-gap\-frac\fR \fIFLOAT\fR
+.RS 4
+Minimum fraction of gapped reads [0\&.002]
+.RE
+.PP
+\fB\-h, \-\-tandem\-qual\fR \fIINT\fR
+.RS 4
+Coefficient for modeling homopolymer errors\&. Given an
+\fIl\fR\-long homopolymer run, the sequencing error of an indel of size s is modeled as
+\fIINT\fR*s/l [100]
+.RE
+.PP
+\fB\-I, \-\-skip\-indels\fR
+.RS 4
+Do not perform INDEL calling
+.RE
+.PP
+\fB\-L, \-\-max\-idepth\fR \fIINT\fR
+.RS 4
+Skip INDEL calling if the average per\-sample depth is above
+\fIINT\fR
+[250]
+.RE
+.PP
+\fB\-m, \-\-min\-ireads\fR \fIINT\fR
+.RS 4
+Minimum number gapped reads for indel candidates
+\fIINT\fR
+[1]
+.RE
+.PP
+\fB\-o, \-\-open\-prob\fR \fIINT\fR
+.RS 4
+Phred\-scaled gap open sequencing error probability\&. Reducing
+\fIINT\fR
+leads to more indel calls\&. (The same short option is used for both
+\fB\-\-open\-prob\fR
+and
+\fB\-\-output\fR\&. When \-o\(cqs argument contains only an optional + or \- sign followed by the digits 0 to 9, it is interpreted as
+\fB\-\-open\-prob\fR\&.) [40]
+.RE
+.PP
+\fB\-p, \-\-per\-sample\-mF\fR
+.RS 4
+Apply
+\fB\-m\fR
+and
+\fB\-F\fR
+thresholds per sample to increase sensitivity of calling\&. By default both options are applied to reads pooled from all samples\&.
+.RE
+.PP
+\fB\-P, \-\-platforms\fR \fISTR\fR
+.RS 4
+Comma\-delimited list of platforms (determined by
+\fB@RG\-PL\fR) from which indel candidates are obtained\&. It is recommended to collect indel candidates from sequencing technologies that have low indel error rate such as ILLUMINA [all]
+.RE
+.RE
+.sp
+.it 1 an-trap
+.nr an-no-space-flag 1
+.nr an-break-flag 1
+.br
+.ps +1
+\fBExamples:\fR
+.RS 4
+.sp
+Call SNPs and short INDELs, then mark low quality sites and sites with the read depth exceeding a limit\&. (The read depth should be adjusted to about twice the average read depth as higher read depths usually indicate problematic regions which are often enriched for artefacts\&.) One may consider to add \fB\-C50\fR to mpileup if mapping quality is overestimated for reads containing excessive mismatches\&. Applying this option usually helps for BWA\-backtrack alignments, but may not other aligners\&.
+.sp
+.if n \{\
+.RS 4
+.\}
+.nf
+    bcftools mpileup \-Ou \-f ref\&.fa aln\&.bam | \e
+    bcftools call \-Ou \-mv | \e
+    bcftools filter \-s LowQual \-e \*(Aq%QUAL<20 || DP>100\*(Aq > var\&.flt\&.vcf
+.fi
+.if n \{\
+.RE
+.\}
+.RE
 .SS "bcftools norm [\fIOPTIONS\fR] \fIfile\&.vcf\&.gz\fR"
 .sp
 Left\-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows\&. Left\-alignment and normalization will only be applied if the \fB\-\-fasta\-ref\fR option is supplied\&.
diff --git a/doc/bcftools.html b/doc/bcftools.html
index d089aec16..c7d181442 100644
--- a/doc/bcftools.html
+++ b/doc/bcftools.html
@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25197440"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
+<html xmlns="http://www.w3.org/1999/xhtml"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /><title>bcftools</title><link rel="stylesheet" type="text/css" href="docbook-xsl.css" /><meta name="generator" content="DocBook XSL Stylesheets V1.76.1" /></head><body><div xml:lang="en" class="refentry" title="bcftools" lang="en"><a id="idp25136800"></a><div class="titlepage"></div><div class="refnamediv"><h2>Name</h2><p>bcftools — utilities for variant calling and manipulating VCFs and BCFs.</p></div><div class="refsynopsisdiv" title="Synopsis"><a id="_synopsis"></a><h2>Synopsis</h2><p><span class="strong"><strong>bcftools</strong></span> [--version|--version-only] [--help] [<span class="emphasis"><em>COMMAND</em></span>] [<span class="emphasis"><em>OPTIONS</em></span>]</p></div><div class="refsect1" title="DESCRIPTION"><a id="_description"></a><h2>DESCRIPTION</h2><p>BCFtools  is  a set of utilities that manipulate variant calls in the Variant
 Call Format (VCF) and its binary counterpart BCF. All commands work
 transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.</p><p>Most commands accept VCF, bgzipped VCF and BCF with filetype detected
 automatically even when streaming from a pipe. Indexed VCF and BCF
@@ -8,7 +8,7 @@
 work in most, but not all situations. In general, whenever multiple VCFs are
 read simultaneously, they must be indexed and therefore also compressed.</p><p>BCFtools is designed to work on a stream. It regards an input file "-" as the
 standard input (stdin) and outputs to the standard output (stdout). Several
-commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2016-04-18 14:18 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.3-36-g47e811c+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
+commands can thus be  combined  with  Unix pipes.</p><div class="refsect2" title="VERSION"><a id="_version"></a><h3>VERSION</h3><p>This manual page was last updated <span class="strong"><strong>2016-04-26 21:06 BST</strong></span> and refers to bcftools git version <span class="strong"><strong>1.3.1-6-g0848b12+</strong></span>.</p></div><div class="refsect2" title="BCF1"><a id="_bcf1"></a><h3>BCF1</h3><p>The BCF1 format output by versions of samtools &lt;= 0.1.19 is <span class="strong"><strong>not</strong></span>
 compatible with this version of bcftools. To read BCF1 files one can use
 the view command from old versions of bcftools packaged with samtools
 versions &lt;= 0.1.19 to convert to VCF, which can then be read by
@@ -41,6 +41,8 @@
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#merge" title="bcftools merge [OPTIONS] A.vcf.gz B.vcf.gz […]">merge</a></strong></span>      ..  merge VCF/BCF files files from non-overlapping sample sets
 </li><li class="listitem">
+<span class="strong"><strong><a class="link" href="#mpileup" title="bcftools mpileup [OPTIONS] -f ref.fa in.bam [in2.bam […]]">mpileup</a></strong></span>  ..  multi-way pileup producing genotype likelihoods
+</li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#norm" title="bcftools norm [OPTIONS] file.vcf.gz">norm</a></strong></span>        ..  normalize indels
 </li><li class="listitem">
 <span class="strong"><strong><a class="link" href="#plugin" title="bcftools [plugin NAME|+NAME] [OPTIONS] FILE — [PLUGIN OPTIONS]">plugin</a></strong></span>    ..  run user-defined plugin
@@ -1230,7 +1232,212 @@
 <span class="strong"><strong>--threads</strong></span> <span class="emphasis"><em>INT</em></span>
 </span></dt><dd>
     see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
-</dd></dl></div></div><div class="refsect2" title="bcftools norm [OPTIONS] file.vcf.gz"><a id="norm"></a><h3>bcftools norm [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Left-align and normalize indels, check if REF alleles match the reference,
+</dd></dl></div></div><div class="refsect2" title="bcftools mpileup [OPTIONS] -f ref.fa in.bam [in2.bam […]]"><a id="mpileup"></a><h3>bcftools mpileup [<span class="emphasis"><em>OPTIONS</em></span>] <span class="strong"><strong>-f</strong></span> <span class="emphasis"><em>ref.fa</em></span> <span class="emphasis"><em>in.bam</em></span> [<span class="emphasis"><em>in2.bam</em></span> […]]</h3><p>Generate VCF or BCF containing genotype likelihoods for one or multiple
+alignment (BAM or CRAM) files. This is based on the original
+<span class="strong"><strong>samtools mpileup</strong></span> command (with the <span class="strong"><strong>-v</strong></span> or <span class="strong"><strong>-g</strong></span> options) producing
+genotype likelihoods in VCF or BCF format, but not the textual pileup
+output. The <span class="strong"><strong>mpileup</strong></span> command was transferred to bcftools in order to
+avoid errors resulting from use of incompatible versions of samtools
+and bcftools when using in the mpileup+bcftools call pipeline.</p><p>Individuals are identified from the SM tags in the @RG header lines.  Multiple
+individuals can be pooled in one alignment file, also one individual can be
+separated into multiple files.  If sample identifiers are absent, each input
+file is regarded as one sample.</p><p>Note that there are two orthogonal ways to specify locations in the
+input file; via <span class="strong"><strong>-r</strong></span> <span class="emphasis"><em>region</em></span> and <span class="strong"><strong>-l</strong></span> <span class="emphasis"><em>positions</em></span>.  The
+former uses (and requires) an index to do random access while the
+latter streams through the file contents filtering out the specified
+regions, requiring no index.  The two may be used in conjunction.  For
+example a BED file containing locations of genes in chromosome 20
+could be specified using <span class="strong"><strong>-r 20 -l chr20.bed</strong></span>, meaning that the
+index is used to find chromosome 20 and then it is filtered for the
+regions listed in the BED file.</p><div class="refsect3" title="Input options"><a id="_input_options"></a><h4>Input options</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-6, --illumina1.3+</strong></span>
+</span></dt><dd>
+    Assume the quality is in the Illumina 1.3+ encoding.
+</dd><dt><span class="term">
+<span class="strong"><strong>-A, --count-orphans</strong></span>
+</span></dt><dd>
+    Do not skip anomalous read pairs in variant calling.
+</dd><dt><span class="term">
+<span class="strong"><strong>-b, --bam-list</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    List of input alignment files, one file per line [null]
+</dd><dt><span class="term">
+<span class="strong"><strong>-B, --no-BAQ</strong></span>
+</span></dt><dd>
+    Disable probabilistic realignment for the computation of base alignment
+    quality (BAQ). BAQ is the Phred-scaled probability of a read base being
+    misaligned. Applying this option greatly helps to reduce false SNPs caused
+    by misalignments.
+</dd><dt><span class="term">
+<span class="strong"><strong>-C, --adjust-MQ</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Coefficient  for  downgrading mapping quality for reads containing
+    excessive mismatches. Given a read with a phred-scaled probability q of
+    being generated from the mapped posi- tion, the new mapping quality is
+    about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if
+    enabled, the recommended value for BWA is 50. [0]
+</dd><dt><span class="term">
+<span class="strong"><strong>-d, --max-depth</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    At a position, read maximally <span class="emphasis"><em>INT</em></span> reads per input file. Note that bcftools
+    has a minimum value of <span class="emphasis"><em>8000/n</em></span> where <span class="emphasis"><em>n</em></span> is the number of input files given
+    to mpileup.  This means the default is highly likely to be increased. Once
+    above the cross-sample minimum of 8000 the -d parameter will have an effect.
+    [250]
+</dd><dt><span class="term">
+<span class="strong"><strong>-E, --redo-BAQ</strong></span>
+</span></dt><dd>
+    Recalculate BAQ on the fly, ignore existing BQ tags
+</dd><dt><span class="term">
+<span class="strong"><strong>-f, --fasta-ref</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    The <span class="strong"><strong>faidx</strong></span>-indexed reference file in the FASTA format. The file can be
+    optionally compressed by <span class="strong"><strong>bgzip</strong></span> [null]
+</dd><dt><span class="term">
+<span class="strong"><strong>-G, --exclude-RG</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    Exclude reads from readgroups listed in FILE (one @RG-ID per line)
+</dd><dt><span class="term">
+<span class="strong"><strong>-l, --positions</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    BED or position list file containing a list of regions or sites where
+    output should be generated. Position list files contain two
+    columns (chromosome and position) and start counting from 1.  BED
+    files contain at least 3 columns (chromosome, start and end position)
+    and are 0-based half-open.
+    While it is possible to mix both position-list and BED coordinates in
+    the same file, this is strongly ill advised due to the differing
+    coordinate systems. [null]
+</dd><dt><span class="term">
+<span class="strong"><strong>-q, -min-MQ</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Minimum mapping quality for an alignment to be used [0]
+</dd><dt><span class="term">
+<span class="strong"><strong>-Q, --min-BQ</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Minimum base quality for a base to be considered [13]
+</dd><dt><span class="term">
+<span class="strong"><strong>-r, --region</strong></span> <span class="emphasis"><em>STR</em></span>
+</span></dt><dd>
+    Only generate output in region. Requires the alignment files to be
+    indexed.  If used in conjunction with -l then considers the intersection
+    of the two requests [all sites]
+</dd><dt><span class="term">
+<span class="strong"><strong>-R, --ignore-RG</strong></span>
+</span></dt><dd>
+    Ignore RG tags. Treat all reads in one alignment file as one sample.
+</dd><dt><span class="term">
+<span class="strong"><strong>--rf, --incl-flags</strong></span> <span class="emphasis"><em>STR</em></span>|<span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Required flags: skip reads with mask bits unset  [null]
+</dd><dt><span class="term">
+<span class="strong"><strong>--ff, --excl-flags</strong></span> <span class="emphasis"><em>STR</em></span>|<span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
+</dd><dt><span class="term">
+<span class="strong"><strong>-x, --ignore-overlaps</strong></span>
+</span></dt><dd>
+    Disable read-pair overlap detection.
+</dd></dl></div></div><div class="refsect3" title="Output options"><a id="_output_options"></a><h4>Output options</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-o, --output</strong></span> <span class="emphasis"><em>FILE</em></span>
+</span></dt><dd>
+    Write output to <span class="emphasis"><em>FILE</em></span>, rather than the default of standard output.
+    (The same short option is used for both <span class="strong"><strong>--open-prob</strong></span> and <span class="strong"><strong>--output</strong></span>.  If <span class="strong"><strong>-o</strong></span>'s
+    argument contains any non-digit characters other than a leading + or -
+    sign,  it  is  interpreted  as <span class="strong"><strong>--output</strong></span>.  Usually the filename extension
+    will take care of this, but to write to an entirely numeric filename use <span class="strong"><strong>-o
+    ./123</strong></span> or <span class="strong"><strong>--output 123</strong></span>.)
+</dd><dt><span class="term">
+<span class="strong"><strong>-O, --output-type</strong></span> <span class="emphasis"><em>b</em></span>|<span class="emphasis"><em>u</em></span>|<span class="emphasis"><em>z</em></span>|<span class="emphasis"><em>v</em></span>
+</span></dt><dd>
+    see <span class="strong"><strong><a class="link" href="#common_options" title="Common Options">Common Options</a></strong></span>
+</dd><dt><span class="term">
+<span class="strong"><strong>-t, --output-tags</strong></span> <span class="emphasis"><em>LIST</em></span>
+</span></dt><dd><p class="simpara">
+    Comma-separated list of FORMAT and INFO tags to output (case-insensitive) [null]:
+</p><div class="itemizedlist"><ul class="itemizedlist" type="disc"><li class="listitem">
+<span class="strong"><strong>AD</strong></span> .. Allelic depth, FORMAT
+</li><li class="listitem">
+<span class="strong"><strong>INFO/AD</strong></span> .. Total allelic depth, INFO
+</li><li class="listitem">
+<span class="strong"><strong>ADF</strong></span> .. Allelic depths on the forward strand, FORMAT
+</li><li class="listitem">
+<span class="strong"><strong>INFO/ADF</strong></span> .. Total allelic depths on the forward strand, INFO
+</li><li class="listitem">
+<span class="strong"><strong>ADR</strong></span> .. Allelic depths on the reverse strand, FORMAT
+</li><li class="listitem">
+<span class="strong"><strong>INFO/ADR</strong></span> .. Total allelic depths on the reverse strand, INFO
+</li><li class="listitem">
+<span class="strong"><strong>DP</strong></span> .. Number of high-quality bases, FORMAT
+</li><li class="listitem">
+<span class="strong"><strong>SP</strong></span> .. Phred-scaled strand bias P-value, FORMAT
+</li><li class="listitem">
+<span class="strong"><strong>DV</strong></span> .. Deprecated in favor of AD;
+              Number of high-quality non-reference bases, FORMAT
+</li><li class="listitem">
+<span class="strong"><strong>DPR</strong></span> .. Deprecated in favor of AD;
+               Number of high-quality bases for each observed allele, FORMAT
+</li><li class="listitem">
+<span class="strong"><strong>INFO/DPR</strong></span> .. Deprecated in favor of INFO/AD;
+                    Number of high-quality bases for each observed allele, INFO
+</li><li class="listitem">
+<span class="strong"><strong>DP4</strong></span> .. Deprecated in favor of ADF and ADR;
+               Number of high-quality ref-forward, ref-reverse,
+               alt-forward and alt-reverse bases, FORMAT
+</li></ul></div></dd></dl></div></div><div class="refsect3" title="Options for SNP/INDEL genotype likelihood computation"><a id="_options_for_snp_indel_genotype_likelihood_computation"></a><h4>Options for SNP/INDEL genotype likelihood computation</h4><div class="variablelist"><dl><dt><span class="term">
+<span class="strong"><strong>-e, --ext-prob</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Phred-scaled gap extension sequencing error probability. Reducing <span class="emphasis"><em>INT</em></span>
+    leads to longer indels [20]
+</dd><dt><span class="term">
+<span class="strong"><strong>-F, --gap-frac</strong></span> <span class="emphasis"><em>FLOAT</em></span>
+</span></dt><dd>
+    Minimum fraction of gapped reads [0.002]
+</dd><dt><span class="term">
+<span class="strong"><strong>-h, --tandem-qual</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Coefficient for modeling homopolymer errors. Given an <span class="emphasis"><em>l</em></span>-long homopolymer
+    run, the sequencing error of an indel of size s is modeled as <span class="emphasis"><em>INT</em></span>*s/l [100]
+</dd><dt><span class="term">
+<span class="strong"><strong>-I, --skip-indels</strong></span>
+</span></dt><dd>
+    Do not perform INDEL calling
+</dd><dt><span class="term">
+<span class="strong"><strong>-L, --max-idepth</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Skip INDEL calling if the average per-sample depth is above <span class="emphasis"><em>INT</em></span> [250]
+</dd><dt><span class="term">
+<span class="strong"><strong>-m, --min-ireads</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Minimum number gapped reads for indel candidates <span class="emphasis"><em>INT</em></span> [1]
+</dd><dt><span class="term">
+<span class="strong"><strong>-o, --open-prob</strong></span> <span class="emphasis"><em>INT</em></span>
+</span></dt><dd>
+    Phred-scaled gap open sequencing error probability. Reducing <span class="emphasis"><em>INT</em></span> leads
+    to more indel calls. (The same short option is used for both <span class="strong"><strong>--open-prob</strong></span>
+    and <span class="strong"><strong>--output</strong></span>.  When -o’s argument contains only an optional + or - sign
+    followed by the digits 0 to 9, it is interpreted  as <span class="strong"><strong>--open-prob</strong></span>.) [40]
+</dd><dt><span class="term">
+<span class="strong"><strong>-p, --per-sample-mF</strong></span>
+</span></dt><dd>
+    Apply <span class="strong"><strong>-m</strong></span> and <span class="strong"><strong>-F</strong></span> thresholds per sample to increase sensitivity of calling.
+    By default both options are applied to reads pooled from all samples.
+</dd><dt><span class="term">
+<span class="strong"><strong>-P, --platforms</strong></span> <span class="emphasis"><em>STR</em></span>
+</span></dt><dd>
+    Comma-delimited  list  of  platforms (determined by <span class="strong"><strong>@RG-PL</strong></span>) from which
+    indel candidates are obtained. It is recommended to collect indel
+    candidates from sequencing technologies that have low indel error rate
+    such as ILLUMINA [all]
+</dd></dl></div></div><div class="refsect3" title="Examples:"><a id="_examples_2"></a><h4>Examples:</h4><p>Call SNPs and short INDELs, then mark low quality sites and sites with the read
+depth exceeding a limit. (The read depth should be adjusted to about twice the
+average read depth as higher read depths usually indicate problematic regions
+which are often enriched for artefacts.) One may consider to add <span class="strong"><strong>-C50</strong></span> to
+mpileup if mapping quality is overestimated  for reads containing  excessive
+mismatches.  Applying this option usually helps for BWA-backtrack alignments,
+but may not other aligners.</p><pre class="screen">    bcftools mpileup -Ou -f ref.fa aln.bam | \
+    bcftools call -Ou -mv | \
+    bcftools filter -s LowQual -e '%QUAL&lt;20 || DP&gt;100' &gt; var.flt.vcf</pre></div></div><div class="refsect2" title="bcftools norm [OPTIONS] file.vcf.gz"><a id="norm"></a><h3>bcftools norm [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Left-align and normalize indels, check if REF alleles match the reference,
 split multiallelic sites into multiple rows; recover multiallelics from
 multiple rows. Left-alignment and normalization will only be applied if
 the <span class="strong"><strong><a class="link" href="#fasta_ref">--fasta-ref</a></strong></span> option is supplied.</p><div class="variablelist"><dl><dt><span class="term">
@@ -1413,7 +1620,7 @@
 <span class="strong"><strong>vcf2sex</strong></span>
 </span></dt><dd>
     determine sample sex by checking genotypes in haploid regions
-</dd></dl></div></div><div class="refsect3" title="Examples:"><a id="_examples_2"></a><h4>Examples:</h4><pre class="screen"># List options common to all plugins
+</dd></dl></div></div><div class="refsect3" title="Examples:"><a id="_examples_3"></a><h4>Examples:</h4><pre class="screen"># List options common to all plugins
 bcftools plugin
 
 # List available plugins
@@ -1601,7 +1808,7 @@
 %TGT            Translated genotype (e.g. C/A)
 %IUPACGT        Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
 %LINE           Prints the whole line
-%SAMPLE         Sample name</pre></div><div class="refsect3" title="Examples:"><a id="_examples_3"></a><h4>Examples:</h4><pre class="literallayout">bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz
+%SAMPLE         Sample name</pre></div><div class="refsect3" title="Examples:"><a id="_examples_4"></a><h4>Examples:</h4><pre class="literallayout">bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz
 bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz</pre></div></div><div class="refsect2" title="bcftools reheader [OPTIONS] file.vcf.gz"><a id="reheader"></a><h3>bcftools reheader [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span></h3><p>Modify header of VCF/BCF files, change sample names.</p><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-h, --header</strong></span> <span class="emphasis"><em>FILE</em></span>
 </span></dt><dd>
@@ -1797,7 +2004,7 @@
 </span></dt><dd>
     produce verbose per-site and per-sample output
 </dd></dl></div></div><div class="refsect2" title="bcftools view [OPTIONS] file.vcf.gz [REGION […]]"><a id="view"></a><h3>bcftools view [<span class="emphasis"><em>OPTIONS</em></span>] <span class="emphasis"><em>file.vcf.gz</em></span> [<span class="emphasis"><em>REGION</em></span> […]]</h3><p>View, subset and filter VCF or BCF files by position and filtering expression.
-Convert between VCF and BCF. Former <span class="strong"><strong>bcftools subset</strong></span>.</p><div class="refsect3" title="Output options"><a id="_output_options"></a><h4>Output options</h4><div class="variablelist"><dl><dt><span class="term">
+Convert between VCF and BCF. Former <span class="strong"><strong>bcftools subset</strong></span>.</p><div class="refsect3" title="Output options"><a id="_output_options_2"></a><h4>Output options</h4><div class="variablelist"><dl><dt><span class="term">
 <span class="strong"><strong>-G, --drop-genotypes</strong></span>
 </span></dt><dd>
     drop individual genotype information (after subsetting if <span class="strong"><strong>-s</strong></span> option is set)
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index ad0d9d170..a79e85e69 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -85,6 +85,7 @@ list of available options, run *bcftools* 'COMMAND' without arguments.
 - *<<index,index>>*      ..  index VCF/BCF
 - *<<isec,isec>>*        ..  intersections of VCF/BCF files
 - *<<merge,merge>>*      ..  merge VCF/BCF files files from non-overlapping sample sets
+- *<<mpileup,mpileup>>*  ..  multi-way pileup producing genotype likelihoods
 - *<<norm,norm>>*        ..  normalize indels
 - *<<plugin,plugin>>*    ..  run user-defined plugin
 - *<<polysomy,polysomy>>*   ..  detect contaminations and whole-chromosome aberrations
@@ -1282,6 +1283,198 @@ For "vertical" merge take a look at *<<norm,bcftools norm>>* instead.
     see *<<common_options,Common Options>>*
 
 
+[[mpileup]]
+=== bcftools mpileup ['OPTIONS'] *-f* 'ref.fa' 'in.bam' ['in2.bam' [...]]
+Generate VCF or BCF containing genotype likelihoods for one or multiple
+alignment (BAM or CRAM) files. This is based on the original 
+*samtools mpileup* command (with the *-v* or *-g* options) producing 
+genotype likelihoods in VCF or BCF format, but not the textual pileup
+output. The *mpileup* command was transferred to bcftools in order to
+avoid errors resulting from use of incompatible versions of samtools
+and bcftools when using in the mpileup+bcftools call pipeline.
+
+Individuals are identified from the SM tags in the @RG header lines.  Multiple
+individuals can be pooled in one alignment file, also one individual can be
+separated into multiple files.  If sample identifiers are absent, each input
+file is regarded as one sample.
+
+
+Note that there are two orthogonal ways to specify locations in the
+input file; via *-r* 'region' and *-l* 'positions'.  The
+former uses (and requires) an index to do random access while the
+latter streams through the file contents filtering out the specified
+regions, requiring no index.  The two may be used in conjunction.  For
+example a BED file containing locations of genes in chromosome 20
+could be specified using *-r 20 -l chr20.bed*, meaning that the
+index is used to find chromosome 20 and then it is filtered for the
+regions listed in the BED file.
+
+
+==== Input options
+
+*-6, --illumina1.3+*::
+    Assume the quality is in the Illumina 1.3+ encoding.
+
+*-A, --count-orphans*::
+    Do not skip anomalous read pairs in variant calling.
+
+*-b, --bam-list* 'FILE'::
+    List of input alignment files, one file per line [null]
+
+*-B, --no-BAQ*::
+    Disable probabilistic realignment for the computation of base alignment
+    quality (BAQ). BAQ is the Phred-scaled probability of a read base being
+    misaligned. Applying this option greatly helps to reduce false SNPs caused
+    by misalignments.
+
+*-C, --adjust-MQ* 'INT'::
+    Coefficient  for  downgrading mapping quality for reads containing
+    excessive mismatches. Given a read with a phred-scaled probability q of
+    being generated from the mapped posi- tion, the new mapping quality is
+    about sqrt((INT-q)/INT)*INT. A zero value disables this functionality; if
+    enabled, the recommended value for BWA is 50. [0]
+
+*-d, --max-depth* 'INT'::
+    At a position, read maximally 'INT' reads per input file. Note that bcftools
+    has a minimum value of '8000/n' where 'n' is the number of input files given
+    to mpileup.  This means the default is highly likely to be increased. Once
+    above the cross-sample minimum of 8000 the -d parameter will have an effect.
+    [250]
+
+*-E, --redo-BAQ*::
+    Recalculate BAQ on the fly, ignore existing BQ tags
+
+*-f, --fasta-ref* 'FILE'::
+    The *faidx*-indexed reference file in the FASTA format. The file can be
+    optionally compressed by *bgzip* [null]
+
+*-G, --exclude-RG* 'FILE'::
+    Exclude reads from readgroups listed in FILE (one @RG-ID per line)
+
+*-l, --positions* 'FILE'::
+    BED or position list file containing a list of regions or sites where
+    output should be generated. Position list files contain two
+    columns (chromosome and position) and start counting from 1.  BED
+    files contain at least 3 columns (chromosome, start and end position)
+    and are 0-based half-open.
+    While it is possible to mix both position-list and BED coordinates in
+    the same file, this is strongly ill advised due to the differing
+    coordinate systems. [null]
+
+*-q, -min-MQ* 'INT'::
+    Minimum mapping quality for an alignment to be used [0]
+
+*-Q, --min-BQ* 'INT'::
+    Minimum base quality for a base to be considered [13]
+
+*-r, --region* 'STR'::
+    Only generate output in region. Requires the alignment files to be
+    indexed.  If used in conjunction with -l then considers the intersection
+    of the two requests [all sites]
+
+*-R, --ignore-RG*::
+    Ignore RG tags. Treat all reads in one alignment file as one sample.
+
+*--rf, --incl-flags* 'STR'|'INT'::
+    Required flags: skip reads with mask bits unset  [null]
+
+*--ff, --excl-flags* 'STR'|'INT'::
+    Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
+
+*-x, --ignore-overlaps*::
+    Disable read-pair overlap detection.
+
+
+==== Output options
+
+*-o, --output* 'FILE'::
+    Write output to 'FILE', rather than the default of standard output.
+    (The same short option is used for both *--open-prob* and *--output*.  If *-o*'s
+    argument contains any non-digit characters other than a leading + or -
+    sign,  it  is  interpreted  as *--output*.  Usually the filename extension
+    will take care of this, but to write to an entirely numeric filename use *-o
+    ./123* or *--output 123*.)
+
+*-O, --output-type* 'b'|'u'|'z'|'v'::
+    see *<<common_options,Common Options>>*
+
+*-t, --output-tags* 'LIST'::
+    Comma-separated list of FORMAT and INFO tags to output (case-insensitive) [null]:
+
+    - *AD* .. Allelic depth, FORMAT
+    - *INFO/AD* .. Total allelic depth, INFO
+    - *ADF* .. Allelic depths on the forward strand, FORMAT
+    - *INFO/ADF* .. Total allelic depths on the forward strand, INFO
+    - *ADR* .. Allelic depths on the reverse strand, FORMAT
+    - *INFO/ADR* .. Total allelic depths on the reverse strand, INFO
+    - *DP* .. Number of high-quality bases, FORMAT
+    - *SP* .. Phred-scaled strand bias P-value, FORMAT
+
+    - *DV* .. Deprecated in favor of AD;
+              Number of high-quality non-reference bases, FORMAT
+    - *DPR* .. Deprecated in favor of AD;
+               Number of high-quality bases for each observed allele, FORMAT
+    - *INFO/DPR* .. Deprecated in favor of INFO/AD;
+                    Number of high-quality bases for each observed allele, INFO
+    - *DP4* .. Deprecated in favor of ADF and ADR;
+               Number of high-quality ref-forward, ref-reverse,
+               alt-forward and alt-reverse bases, FORMAT
+
+
+==== Options for SNP/INDEL genotype likelihood computation
+
+*-e, --ext-prob* 'INT'::
+    Phred-scaled gap extension sequencing error probability. Reducing 'INT'
+    leads to longer indels [20]
+
+*-F, --gap-frac* 'FLOAT'::
+    Minimum fraction of gapped reads [0.002]
+
+*-h, --tandem-qual* 'INT'::
+    Coefficient for modeling homopolymer errors. Given an 'l'-long homopolymer
+    run, the sequencing error of an indel of size s is modeled as 'INT'*s/l [100]
+
+*-I, --skip-indels*::
+    Do not perform INDEL calling
+
+*-L, --max-idepth* 'INT'::
+    Skip INDEL calling if the average per-sample depth is above 'INT' [250]
+
+*-m, --min-ireads* 'INT'::
+    Minimum number gapped reads for indel candidates 'INT' [1]
+
+*-o, --open-prob* 'INT'::
+    Phred-scaled gap open sequencing error probability. Reducing 'INT' leads
+    to more indel calls. (The same short option is used for both *--open-prob*
+    and *--output*.  When -o's argument contains only an optional + or - sign
+    followed by the digits 0 to 9, it is interpreted  as *--open-prob*.) [40]
+
+*-p, --per-sample-mF*::
+    Apply *-m* and *-F* thresholds per sample to increase sensitivity of calling.
+    By default both options are applied to reads pooled from all samples.
+
+*-P, --platforms* 'STR'::
+    Comma-delimited  list  of  platforms (determined by *@RG-PL*) from which
+    indel candidates are obtained. It is recommended to collect indel
+    candidates from sequencing technologies that have low indel error rate
+    such as ILLUMINA [all]
+
+==== Examples:
+
+Call SNPs and short INDELs, then mark low quality sites and sites with the read
+depth exceeding a limit. (The read depth should be adjusted to about twice the
+average read depth as higher read depths usually indicate problematic regions
+which are often enriched for artefacts.) One may consider to add *-C50* to
+mpileup if mapping quality is overestimated  for reads containing  excessive
+mismatches.  Applying this option usually helps for BWA-backtrack alignments,
+but may not other aligners.
+----
+    bcftools mpileup -Ou -f ref.fa aln.bam | \
+    bcftools call -Ou -mv | \
+    bcftools filter -s LowQual -e '%QUAL<20 || DP>100' > var.flt.vcf
+----
+
+
 [[norm]]
 === bcftools norm ['OPTIONS'] 'file.vcf.gz'
 Left-align and normalize indels, check if REF alleles match the reference,

From 6546afdc2d7084ffc3e4dfbe34f10d08bb2b031e Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 9 May 2016 10:07:37 +0100
Subject: [PATCH 195/211] mpileup: remove `printw()` which was only used in the
 text output

adds to @4e7c8fb86349761fed1b290357dbc792222ecdcb
---
 mpileup.c | 18 +-----------------
 1 file changed, 1 insertion(+), 17 deletions(-)

diff --git a/mpileup.c b/mpileup.c
index 4e0883fc0..75dcba21e 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -38,24 +38,8 @@ DEALINGS IN THE SOFTWARE.  */
 #include <htslib/kstring.h>
 #include <htslib/khash_str2int.h>
 #include <htslib/regidx.h>
-#include "bcftools.h"
-
-static inline int printw(int c, FILE *fp)
-{
-    char buf[16];
-    int l, x;
-    if (c == 0) return fputc('0', fp);
-    for (l = 0, x = c < 0? -c : c; x > 0; x /= 10) buf[l++] = x%10 + '0';
-    if (c < 0) buf[l++] = '-';
-    buf[l] = 0;
-    for (x = 0; x < l/2; ++x) {
-        int y = buf[x]; buf[x] = buf[l-1-x]; buf[l-1-x] = y;
-    }
-    fputs(buf, fp);
-    return 0;
-}
-
 #include <assert.h>
+#include "bcftools.h"
 #include "bam2bcf.h"
 #include "sample.h"
 

From acb1b9b6375d12b018fae8c640588716308d11c0 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 26 May 2016 13:56:14 +0100
Subject: [PATCH 196/211] remove deprecated options

* remove deprecated `-g`, `-v`, `-u`, `-D`, `-V`, `-S`
* remove `-R` short option to make way for `--regions-file` option later
---
 doc/bcftools.txt |  2 +-
 mpileup.c        | 26 +++++---------------------
 2 files changed, 6 insertions(+), 22 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index a79e85e69..fc26f6f1c 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1372,7 +1372,7 @@ regions listed in the BED file.
     indexed.  If used in conjunction with -l then considers the intersection
     of the two requests [all sites]
 
-*-R, --ignore-RG*::
+*--ignore-RG*::
     Ignore RG tags. Treat all reads in one alignment file as one sample.
 
 *--rf, --incl-flags* 'STR'|'INT'::
diff --git a/mpileup.c b/mpileup.c
index 75dcba21e..0f868e37a 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -652,7 +652,7 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
     fprintf(fp,
 "  -r, --region REG        region in which pileup is generated\n"
-"  -R, --ignore-RG         ignore RG tags (one BAM = one sample)\n"
+"      --ignore-RG         ignore RG tags (one BAM = one sample)\n"
 "  --rf, --incl-flags STR|INT  required flags: skip reads with mask bits unset [%s]\n", tmp_require);
     fprintf(fp,
 "  --ff, --excl-flags STR|INT  filter flags: skip reads with mask bits set\n"
@@ -717,6 +717,8 @@ int bam_mpileup(int argc, char *argv[])
         {"excl-flags", required_argument, NULL, 2},
         {"output", required_argument, NULL, 3},
         {"open-prob", required_argument, NULL, 4},
+        {"ignore-RG", no_argument, NULL, 5},
+        {"ignore-rg", no_argument, NULL, 5},
         {"illumina1.3+", no_argument, NULL, '6'},
         {"count-orphans", no_argument, NULL, 'A'},
         {"bam-list", required_argument, NULL, 'b'},
@@ -732,24 +734,13 @@ int bam_mpileup(int argc, char *argv[])
         {"exclude-rg", required_argument, NULL, 'G'},
         {"positions", required_argument, NULL, 'l'},
         {"region", required_argument, NULL, 'r'},
-        {"ignore-RG", no_argument, NULL, 'R'},
-        {"ignore-rg", no_argument, NULL, 'R'},
         {"min-MQ", required_argument, NULL, 'q'},
         {"min-mq", required_argument, NULL, 'q'},
         {"min-BQ", required_argument, NULL, 'Q'},
         {"min-bq", required_argument, NULL, 'Q'},
         {"ignore-overlaps", no_argument, NULL, 'x'},
-        {"BCF", no_argument, NULL, 'g'},
-        {"bcf", no_argument, NULL, 'g'},
-        {"VCF", no_argument, NULL, 'v'},
-        {"vcf", no_argument, NULL, 'v'},
         {"output-type", required_argument, NULL, 'O'},
-        {"output-BP", no_argument, NULL, 'O'},
-        {"output-bp", no_argument, NULL, 'O'},
-        {"output-MQ", no_argument, NULL, 's'},
-        {"output-mq", no_argument, NULL, 's'},
         {"output-tags", required_argument, NULL, 't'},
-        {"uncompressed", no_argument, NULL, 'u'},
         {"ext-prob", required_argument, NULL, 'e'},
         {"gap-frac", required_argument, NULL, 'F'},
         {"tandem-qual", required_argument, NULL, 'h'},
@@ -761,7 +752,7 @@ int bam_mpileup(int argc, char *argv[])
         {"platforms", required_argument, NULL, 'P'},
         {NULL, 0, NULL, 0}
     };
-    while ((c = getopt_long(argc, argv, "Agf:r:l:q:Q:uRC:BDSd:L:b:P:po:e:h:Im:F:EG:6O:sVvxt:",lopts,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "Af:r:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xt:",lopts,NULL)) >= 0) {
         switch (c) {
         case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
         case  1 :
@@ -774,6 +765,7 @@ int bam_mpileup(int argc, char *argv[])
             break;
         case  3 : mplp.output_fname = optarg; break;
         case  4 : mplp.openQ = atoi(optarg); break;
+        case  5 : mplp.flag |= MPLP_IGNORE_RG; break;
         case 'f':
             mplp.fai = fai_load(optarg);
             if (mplp.fai == NULL) return 1;
@@ -790,18 +782,10 @@ int bam_mpileup(int argc, char *argv[])
                   break;
         case 'P': mplp.pl_list = strdup(optarg); break;
         case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
-        case 'g': fprintf(stderr,"[warning] bcftools mpileup `-g` is functional, but deprecated. Please swith to -O in future.\n"); mplp.flag |= MPLP_BCF; break;
-        case 'v': fprintf(stderr,"[warning] bcftools mpileup `-v` is functional, but deprecated. Please swith to -O in future.\n"); mplp.flag |= MPLP_BCF | MPLP_VCF; break;
-        case 'u': fprintf(stderr,"[warning] bcftools mpileup `-u` is functional, but deprecated. Please swith to -O in future.\n"); mplp.flag |= MPLP_NO_COMP | MPLP_BCF; break;
         case 'B': mplp.flag &= ~MPLP_REALN; break;
-        case 'D': mplp.fmt_flag |= B2B_FMT_DP; fprintf(stderr, "[warning] bcftools mpileup option `-D` is functional, but deprecated. Please switch to `-t DP` in future.\n"); break;
-        case 'S': mplp.fmt_flag |= B2B_FMT_SP; fprintf(stderr, "[warning] bcftools mpileup option `-S` is functional, but deprecated. Please switch to `-t SP` in future.\n"); break;
-        case 'V': mplp.fmt_flag |= B2B_FMT_DV; fprintf(stderr, "[warning] bcftools mpileup option `-V` is functional, but deprecated. Please switch to `-t DV` in future.\n"); break;
         case 'I': mplp.flag |= MPLP_NO_INDEL; break;
         case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
         case '6': mplp.flag |= MPLP_ILLUMINA13; break;
-        case 'R': mplp.flag |= MPLP_IGNORE_RG; break;
-        case 's': error("The -s option is for text based mpileup output. Please use \"samtools mpileup -s\" instead.\n"); break;
         case 'O': 
             switch (optarg[0]) {
                 case 'b': mplp.output_type = FT_BCF_GZ; break;

From d1b8e8865bc8b06259d4a6c8fa4dee8668442b05 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 26 May 2016 14:41:51 +0100
Subject: [PATCH 197/211] mpileup: add `--gvcf` output mode

This commit brings over the `--gvcf` functionality from @pd3's branch,
consisting of relevant bits from pd3/bcftools@cf3219c3237dbd447bfa31be967f1605f531bfd6
and pd3/bcftools@ee8210d2f81af007c6b2ad47d699527c50d0a58e

Reference only blocks will be merged into gVCF blocks when the
minimum per-sample depth falls in the intervals defined by the
argument to the `-gvcf` option. Documentaion added to explain
the merging and a test added.
---
 Makefile                   |  4 +--
 doc/bcftools.txt           |  9 ++++++
 mpileup.c                  | 49 ++++++++++++++++++++++++++--
 test/mpileup/mpileup.6.out | 65 ++++++++++++++++++++++++++++++++++++++
 test/test.pl               |  1 +
 5 files changed, 123 insertions(+), 5 deletions(-)
 create mode 100644 test/mpileup/mpileup.6.out

diff --git a/Makefile b/Makefile
index 64f564fe6..ab12a7c87 100644
--- a/Makefile
+++ b/Makefile
@@ -168,7 +168,7 @@ convert.o: convert.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(htslib_vcfu
 tsv2vcf.o: tsv2vcf.c $(tsv2vcf_h)
 em.o: em.c $(htslib_vcf_h) kmin.h $(call_h)
 filter.o: filter.c $(HTSDIR)/htslib/khash_str2int.h $(filter_h) $(bcftools_h) $(htslib_hts_defs_h) $(htslib_vcfutils_h)
-gvcf.o: gvcf.c $(call_h)
+gvcf.o: gvcf.c gvcf.h $(call_h)
 kmin.o: kmin.c kmin.h
 mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h)
 prob1.o: prob1.c $(prob1_h)
@@ -177,7 +177,7 @@ ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)
 polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h
 peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
 consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h
-mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(bcftools_h) $(bam2bcf_h) $(sample_h)
+mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(bcftools_h) $(call_h) $(bam2bcf_h) $(sample_h)
 version.o: version.h version.c
 
 test/test-rbuf.o: test/test-rbuf.c rbuf.h
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index fc26f6f1c..3edbb4794 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1387,6 +1387,15 @@ regions listed in the BED file.
 
 ==== Output options
 
+*-g, --gvcf* 'INT'[,...]::
+    output gVCF blocks of homozygous REF calls, with depth (DP) ranges
+    specified by the list of integers. For example, passing '5,15' will
+    group sites into two types of gVCF blocks, the first with minimum
+    per-sample DP from the interval [5,15) and the latter with minimum
+    depth 15 or more. In this example, sites with minimum per-sample
+    depth less than 5 will be printed as separate records, outside of
+    gVCF blocks.
+
 *-o, --output* 'FILE'::
     Write output to 'FILE', rather than the default of standard output.
     (The same short option is used for both *--open-prob* and *--output*.  If *-o*'s
diff --git a/mpileup.c b/mpileup.c
index 0f868e37a..6dfbc35b4 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -42,6 +42,7 @@ DEALINGS IN THE SOFTWARE.  */
 #include "bcftools.h"
 #include "bam2bcf.h"
 #include "sample.h"
+#include "gvcf.h"
 
 #define MPLP_BCF        1
 #define MPLP_VCF        (1<<1)
@@ -66,6 +67,7 @@ typedef struct {
     faidx_t *fai;
     void *rghash;
     regidx_t *bed;
+    gvcf_t *gvcf;
     int argc;
     char **argv;
 } mplp_conf_t;
@@ -234,6 +236,31 @@ static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
     }
 }
 
+static void flush_bcf_records(mplp_conf_t *conf, htsFile *fp, bcf_hdr_t *hdr, bcf1_t *rec)
+{
+    if ( !conf->gvcf )
+    {
+        if ( rec ) bcf_write1(fp, hdr, rec);
+        return;
+    }
+
+    if ( !rec )
+    {
+        gvcf_write(conf->gvcf, fp, hdr, NULL, 0);
+        return;
+    }
+
+    int is_ref = 0;
+    if ( rec->n_allele==1 ) is_ref = 1;
+    else if ( rec->n_allele==2 )
+    {
+        // second allele is mpileup's X, not a variant
+        if ( rec->d.allele[1][0]=='<' && rec->d.allele[1][1]=='*' && rec->d.allele[1][2]=='>' ) is_ref = 1;
+    }
+    rec = gvcf_write(conf->gvcf, fp, hdr, rec, is_ref);
+    if ( rec ) bcf_write1(fp,hdr,rec);
+}
+
 /*
  * Performs pileup
  * @param conf configuration for this pileup
@@ -419,6 +446,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
     if ( conf->fmt_flag&B2B_INFO_ADR )
         bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
+    if ( conf->gvcf )
+        gvcf_update_header(conf->gvcf, bcf_hdr);
 
     for (i=0; i<sm->n; i++)
         bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
@@ -488,7 +517,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
         bcf_clear1(bcf_rec);
         bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
-        bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
+        flush_bcf_records(conf, bcf_fp, bcf_hdr, bcf_rec);
         // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
         if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0)
         {
@@ -498,10 +527,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
             if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
                 bcf_clear1(bcf_rec);
                 bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
-                bcf_write1(bcf_fp, bcf_hdr, bcf_rec);
+                flush_bcf_records(conf, bcf_fp, bcf_hdr, bcf_rec);
             }
         }
     }
+    flush_bcf_records(conf, bcf_fp, bcf_hdr, NULL);
 
     // clean up
     free(bc.tmp.s);
@@ -518,6 +548,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         free(bc.fmt_arr);
         free(bcr);
     }
+    if ( conf->gvcf ) gvcf_destroy(conf->gvcf);
     bam_smpl_destroy(sm); free(buf.s);
     for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
     free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
@@ -661,6 +692,8 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "  -x, --ignore-overlaps   disable read-pair overlap detection\n"
 "\n"
 "Output options:\n"
+"  -g, --gvcf INT[,...]    group non-variant sites into gVCF blocks according\n"
+"                          to minimum per-sample DP\n"
 "  -o, --output FILE       write output to FILE [standard output]\n"
 "  -O, --output-type TYPE  'b' compressed BCF; 'u' uncompressed BCF;\n"
 "                          'z' compressed VCF; 'v' uncompressed VCF [v]\n"
@@ -719,6 +752,7 @@ int bam_mpileup(int argc, char *argv[])
         {"open-prob", required_argument, NULL, 4},
         {"ignore-RG", no_argument, NULL, 5},
         {"ignore-rg", no_argument, NULL, 5},
+        {"gvcf", required_argument, NULL, 7},
         {"illumina1.3+", no_argument, NULL, '6'},
         {"count-orphans", no_argument, NULL, 'A'},
         {"bam-list", required_argument, NULL, 'b'},
@@ -752,7 +786,7 @@ int bam_mpileup(int argc, char *argv[])
         {"platforms", required_argument, NULL, 'P'},
         {NULL, 0, NULL, 0}
     };
-    while ((c = getopt_long(argc, argv, "Af:r:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xt:",lopts,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "Ag:f:r:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xt:",lopts,NULL)) >= 0) {
         switch (c) {
         case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
         case  1 :
@@ -766,6 +800,10 @@ int bam_mpileup(int argc, char *argv[])
         case  3 : mplp.output_fname = optarg; break;
         case  4 : mplp.openQ = atoi(optarg); break;
         case  5 : mplp.flag |= MPLP_IGNORE_RG; break;
+        case  7 :
+            mplp.gvcf = gvcf_init(optarg);
+            if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
+            break;
         case 'f':
             mplp.fai = fai_load(optarg);
             if (mplp.fai == NULL) return 1;
@@ -831,6 +869,11 @@ int bam_mpileup(int argc, char *argv[])
         }
     }
 
+    if ( mplp.gvcf && !(mplp.fmt_flag&B2B_FMT_DP) )
+    {
+        fprintf(stderr,"[warning] The -t DP option is required with --gvcf, switching on.\n");
+        mplp.fmt_flag |= B2B_FMT_DP;
+    }
     if ( mplp.flag&(MPLP_BCF|MPLP_VCF|MPLP_NO_COMP) )
     {
         if ( mplp.flag&MPLP_VCF )
diff --git a/test/mpileup/mpileup.6.out b/test/mpileup/mpileup.6.out
new file mode 100644
index 000000000..511652e48
--- /dev/null
+++ b/test/mpileup/mpileup.6.out
@@ -0,0 +1,65 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Number of high-quality bases">
+##FORMAT=<ID=DV,Number=1,Type=Integer,Description="Number of high-quality non-reference bases">
+##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
+##INFO=<ID=MinDP,Number=1,Type=Integer,Description="Minimum per-sample depth in this gVCF block">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100	HG00101	HG00102
+17	100	.	C	<*>	.	.	END=117;MinDP=2;QS=3,0	PL:DP	0,24,178:8	0,6,85:2	0,12,118:4
+17	118	.	G	<*>	.	.	MinDP=1;QS=3,0	PL:DP	0,27,175:9	0,3,60:1	0,21,162:7
+17	119	.	G	<*>	.	.	END=173;MinDP=2;QS=3,0	PL:DP	0,15,106:5	0,6,73:2	0,12,97:4
+17	174	.	G	<*>	.	.	END=188;MinDP=1;QS=3,0	PL:DP	0,15,111:5	0,3,27:1	0,15,138:5
+17	189	.	C	<*>	.	.	END=255;MinDP=2;QS=3,0	PL:DP	0,18,136:6	0,6,45:2	0,9,59:3
+17	256	.	A	<*>	.	.	END=258;MinDP=5;QS=3,0	PL:DP	0,33,247:11	0,15,110:5	0,18,155:6
+17	259	.	C	<*>	.	.	MinDP=4;QS=3,0	PL:DP	0,33,255:11	0,12,90:4	0,18,170:6
+17	260	.	T	<*>	.	.	END=265;MinDP=5;QS=3,0	PL:DP	0,33,254:11	0,15,98:5	0,15,122:5
+17	266	.	G	<*>	.	.	END=267;MinDP=4;QS=3,0	PL:DP	0,33,254:11	0,12,97:4	0,15,138:5
+17	268	.	T	<*>	.	.	MinDP=5;QS=3,0	PL:DP	0,33,238:11	0,15,110:5	0,15,156:5
+17	269	.	C	<*>	.	.	END=270;MinDP=4;QS=3,0	PL:DP	0,36,255:12	0,12,91:4	0,15,143:5
+17	271	.	T	<*>	.	.	MinDP=5;QS=3,0	PL:DP	0,36,255:12	0,15,113:5	0,15,152:5
+17	272	.	C	<*>	.	.	END=283;MinDP=4;QS=3,0	PL:DP	0,30,238:10	0,12,95:4	0,12,119:4
+17	284	.	T	<*>	.	.	END=301;MinDP=5;QS=3,0	PL:DP	0,30,231:10	0,18,119:6	0,15,126:5
+17	302	.	T	TA	0	.	INDEL;IDV=7;IMF=1;DP=25;I16=2,4,8,11,214,7674,793,33369,236,10564,993,55133,109,2229,377,8629;QS=0.511212,2.48879;VDB=0.27613;SGB=-4.22417;MQSB=0.0443614;MQ0F=0	PL:DP:DV	167,0,96:11:6	157,0,9:7:6	201,21,0:7:7
+17	303	.	G	<*>	.	.	END=354;MinDP=7;QS=3,0	PL:DP	0,27,225:9	0,21,183:7	0,21,185:7
+17	355	.	G	T,<*>	0	.	DP=28;I16=14,13,0,1,1001,37907,41,1681,1442,81174,60,3600,547,12487,25,625;QS=2.875,0.125,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.450096;BQB=1;MQ0F=0	PL:DP:DV	14,0,200,38,203,231:9:1	0,27,222,27,222,222:9:0	0,30,255,30,255,255:10:0
+17	356	.	G	<*>	.	.	END=374;MinDP=7;QS=3,0	PL:DP	0,27,228:9	0,21,187:7	0,27,251:9
+17	375	.	A	T,<*>	0	.	DP=31;I16=17,13,0,1,1138,43798,14,196,1676,96964,60,3600,547,12177,4,16;QS=2.9661,0.0338983,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.763662;BQB=1;MQ0F=0	PL:DP:DV	0,36,255,36,255,255:12:0	0,24,218,24,218,218:8:0	0,18,255,30,255,255:11:1
+17	376	.	G	<*>	.	.	END=404;MinDP=5;QS=3,0	PL:DP	0,33,255:11	0,15,131:5	0,30,255:10
+17	405	.	T	<*>	.	.	END=411;MinDP=3;QS=3,0	PL:DP	0,39,255:13	0,9,103:3	0,30,244:10
+17	412	.	C	T,<*>	0	.	DP=30;I16=17,12,1,0,1094,42458,14,196,1678,98882,60,3600,495,10659,25,625;QS=2.97455,0.0254545,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.991968;BQB=1;MQ0F=0	PL:DP:DV	0,30,255,42,255,255:15:1	0,12,124,12,124,124:4:0	0,33,255,33,255,255:11:0
+17	413	.	A	<*>	.	.	END=464;MinDP=2;QS=3,0	PL:DP	0,42,255:14	0,6,90:2	0,21,221:7
+17	465	.	C	<*>	.	.	END=511;MinDP=5;QS=3,0	PL:DP	0,51,255:17	0,15,131:5	0,24,221:8
+17	512	.	A	C,<*>	0	.	DP=33;I16=22,10,0,1,1121,40793,13,169,1866,110210,60,3600,628,14340,9,81;QS=2.97719,0.022807,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.981935;BQB=1;MQ0F=0	PL:DP:DV	0,39,255,51,255,255:18:1	0,21,183,21,183,183:7:0	0,24,231,24,231,231:8:0
+17	513	.	A	<*>	.	.	MinDP=6;QS=3,0	PL:DP	0,48,255:16	0,18,175:6	0,24,233:8
+17	514	.	A	T,<*>	0	.	DP=32;I16=20,9,0,1,1066,40004,16,256,1686,99410,60,3600,586,13500,11,121;QS=2.97075,0.0292505,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.980594;BQB=1;MQ0F=0	PL:DP:DV	0,31,255,45,255,255:16:1	0,18,171,18,171,171:6:0	0,24,235,24,235,235:8:0
+17	515	.	C	<*>	.	.	END=522;MinDP=5;QS=3,0	PL:DP	0,42,255:14	0,18,167:6	0,15,170:5
+17	523	.	T	G,<*>	0	.	DP=32;I16=23,8,1,0,1184,45708,15,225,1837,109369,60,3600,626,14446,25,625;QS=2.9794,0.0206044,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.872525;BQB=1;MQ0F=0	PL:DP:DV	0,44,255,57,255,255:20:1	0,21,191,21,191,191:7:0	0,15,166,15,166,166:5:0
+17	524	.	T	<*>	.	.	END=526;MinDP=4;QS=3,0	PL:DP	0,60,255:20	0,21,185:7	0,12,129:4
+17	527	.	A	<*>	.	.	END=548;MinDP=5;QS=3,0	PL:DP	0,48,255:16	0,18,169:6	0,15,150:5
+17	549	.	T	G,<*>	0	.	DP=32;I16=22,8,0,1,1101,40987,20,400,1746,103010,60,3600,530,11716,25,625;QS=2.96748,0.0325203,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.632337;BQB=1;MQ0F=0	PL:DP:DV	0,31,255,48,255,255:17:1	0,21,168,21,168,168:7:0	0,21,208,21,208,208:7:0
+17	550	.	T	<*>	.	.	END=558;MinDP=5;QS=3,0	PL:DP	0,45,255:15	0,15,139:5	0,18,177:6
+17	559	.	C	A,<*>	0	.	DP=27;I16=17,8,0,1,908,33726,14,196,1500,90000,29,841,448,9516,25,625;QS=2.92708,0.0729167,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.90038;BQB=1;MQ0F=0	PL:DP:DV	0,42,255,42,255,255:14:0	0,4,116,15,119,123:6:1	0,18,169,18,169,169:6:0
+17	560	.	C	<*>	.	.	END=564;MinDP=5;QS=3,0	PL:DP	0,42,255:14	0,15,121:5	0,21,179:7
+17	565	.	G	<*>	.	.	MinDP=4;QS=3,0	PL:DP	0,45,255:15	0,12,96:4	0,21,154:7
+17	566	.	C	<*>	.	.	END=573;MinDP=5;QS=3,0	PL:DP	0,45,255:15	0,15,155:5	0,18,167:6
+17	574	.	C	A,<*>	0	.	DP=31;I16=18,11,0,1,1088,41328,15,225,1740,104400,29,841,478,10422,25,625;QS=2.94071,0.0592885,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.929991;BQB=1;MQ0F=0	PL:DP:DV	0,48,255,48,255,255:16:0	0,9,170,21,173,177:8:1	0,18,173,18,173,173:6:0
+17	575	.	T	<*>	.	.	END=578;MinDP=5;QS=3,0	PL:DP	0,42,255:14	0,21,209:7	0,15,146:5
+17	579	.	G	<*>	.	.	MinDP=4;QS=3,0	PL:DP	0,48,255:16	0,24,224:8	0,12,145:4
+17	580	.	A	C,<*>	0	.	DP=30;I16=15,14,1,0,1060,39178,16,256,1709,101641,60,3600,510,11078,17,289;QS=2.97338,0.0266223,0;SGB=-0.556633;RPB=1;MQB=1;MQSB=0.946202;BQB=1;MQ0F=0	PL:DP:DV	0,34,255,48,255,255:17:1	0,24,221,24,221,221:8:0	0,15,155,15,155,155:5:0
+17	581	.	A	<*>	.	.	END=600;MinDP=5;QS=3,0	PL:DP	0,51,255:17	0,18,191:6	0,15,151:5
diff --git a/test/test.pl b/test/test.pl
index 466ef0e07..7d4c9ae50 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -254,6 +254,7 @@
 test_mpileup($opts,in=>[qw(1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-t DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.5.out',args=>q[-t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-t DP,DV -r17:100-600 --gvcf 0,2,5]);
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};

From 8091e198e1999558caf1921006c0509ec48c17ab Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 27 May 2016 10:21:34 +0100
Subject: [PATCH 198/211] mpileup: new `-s` and `-S` options to include only
 selected samples

pulling over of pd3/bcftools@cf5c354859cf7af542ba4cb936233a5ef8d2eb88
adding in `-S,--samples-file` option and exiting if no samples are
read from the file or list

TODO: add exclude logic with `^` prefix as in other bcftools commands

removed `config.h` from `sample.c` as leftover this is in samtools,
but not bcftools at the moment
---
 Makefile                   |  1 +
 doc/bcftools.txt           |  6 +++
 mpileup.c                  | 69 ++++++++++++++++++++++-------
 sample.c                   | 89 +++++++++++++++++---------------------
 sample.h                   |  3 +-
 test/mpileup/mpileup.7.out | 70 ++++++++++++++++++++++++++++++
 test/mplp.samples          |  2 +
 test/test.pl               |  3 ++
 8 files changed, 178 insertions(+), 65 deletions(-)
 create mode 100644 test/mpileup/mpileup.7.out
 create mode 100644 test/mplp.samples

diff --git a/Makefile b/Makefile
index ab12a7c87..d8e5ed880 100644
--- a/Makefile
+++ b/Makefile
@@ -178,6 +178,7 @@ polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_
 peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
 consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h
 mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(bcftools_h) $(call_h) $(bam2bcf_h) $(sample_h)
+sample.o: $(sample_h) $(htslib_hts_h) $(HTSDIR)/htslib/khash_str2int.h
 version.o: version.h version.c
 
 test/test-rbuf.o: test/test-rbuf.c rbuf.h
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 3edbb4794..6afea51b8 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1381,6 +1381,12 @@ regions listed in the BED file.
 *--ff, --excl-flags* 'STR'|'INT'::
     Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
 
+*-s, --samples* 'LIST'::
+    list of sample names. See *<<common_options,Common Options>>*
+
+*-S, --samples-file* 'FILE'::
+    file of sample names. See *<<common_options,Common Options>>*
+
 *-x, --ignore-overlaps*::
     Disable read-pair overlap detection.
 
diff --git a/mpileup.c b/mpileup.c
index 6dfbc35b4..93f0092eb 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -60,12 +60,12 @@ DEALINGS IN THE SOFTWARE.  */
 
 typedef struct {
     int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
-    int rflag_require, rflag_filter, output_type;
+    int rflag_require, rflag_filter, output_type, sample_is_file;
     int openQ, extQ, tandemQ, min_support; // for indels
     double min_frac; // for indels
-    char *reg, *pl_list, *fai_fname, *output_fname;
+    char *reg, *pl_list, *fai_fname, *output_fname, *samples_list;
     faidx_t *fai;
-    void *rghash;
+    void *rghash_exc;
     regidx_t *bed;
     gvcf_t *gvcf;
     int argc;
@@ -86,6 +86,7 @@ typedef struct {
     bam_hdr_t *h;
     mplp_ref_t *ref;
     const mplp_conf_t *conf;
+    void *rghash_inc;   // whitelist for readgroups on per-bam basis
 } mplp_aux_t;
 
 typedef struct {
@@ -158,6 +159,7 @@ static int mplp_func(void *data, bam1_t *b)
     int ret, skip = 0, ref_len;
     do {
         int has_ref;
+        skip = 0;
         ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
         if (ret < 0) break;
         // The 'B' cigar operation is not part of the specification, considering as obsolete.
@@ -172,9 +174,16 @@ static int mplp_func(void *data, bam1_t *b)
             skip = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],b->core.pos, bam_endpos(b)-1, NULL) ? 0 : 1;
             if (skip) continue;
         }
-        if (ma->conf->rghash) { // exclude read groups
+        if (ma->rghash_inc)
+        {
+            // skip unless read group is listed
+            uint8_t *rg = bam_aux_get(b, "RG");
+            if ( !rg ) { skip = 1; continue; }
+            if ( !khash_str2int_has_key(ma->rghash_inc, (const char*)(rg+1)) ) { skip = 1; continue; }
+        }
+        if (ma->conf->rghash_exc) { // exclude read groups
             uint8_t *rg = bam_aux_get(b, "RG");
-            skip = (rg && khash_str2int_get(ma->conf->rghash, (const char*)(rg+1), NULL)==0);
+            skip = (rg && khash_str2int_get(ma->conf->rghash_exc, (const char*)(rg+1), NULL)==0);
             if (skip) continue;
         }
         if (ma->conf->flag & MPLP_ILLUMINA13) {
@@ -278,7 +287,7 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
     bam_mplp_t iter;
     bam_hdr_t *h = NULL; /* header of first file in input list */
     char *ref;
-    void *rghash = NULL;
+    void *rghash_exc = NULL;
 
     bcf_callaux_t *bca = NULL;
     bcf_callret1_t *bcr = NULL;
@@ -303,6 +312,24 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         exit(EXIT_FAILURE);
     }
 
+    void *samples_inc = NULL;
+    if ( conf->samples_list )
+    {
+        int nsamples = 0;
+        char **samples = hts_readlist(conf->samples_list, conf->sample_is_file, &nsamples);
+        if (!samples) {
+            fprintf(stderr,"[%s] could not read the samples list %s\n", __func__, conf->samples_list);
+            exit(EXIT_FAILURE);
+        }
+        if ( nsamples ) samples_inc = khash_str2int_init();
+        for (i=0; i<nsamples; i++)
+        {
+            khash_str2int_inc(samples_inc, strdup(samples[i]));
+            free(samples[i]);
+        }
+        free(samples);
+    }
+
     // read the header of each file in the list and initialize data
     for (i = 0; i < n; ++i) {
         bam_hdr_t *h_tmp;
@@ -329,9 +356,10 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
             fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
             exit(EXIT_FAILURE);
         }
-        bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text);
+        if ( samples_inc ) data[i]->rghash_inc = khash_str2int_init();
+        bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text, samples_inc, data[i]->rghash_inc);
         // Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
-        rghash = bcf_call_add_rg(rghash, h_tmp->text, conf->pl_list);
+        rghash_exc = bcf_call_add_rg(rghash_exc, h_tmp->text, conf->pl_list);
         if (conf->reg) {
             hts_idx_t *idx = sam_index_load(data[i]->fp, fn[i]);
             if (idx == NULL) {
@@ -458,7 +486,6 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
     // Initialise the calling algorithm
     bca = bcf_call_init(-1., conf->min_baseQ);
     bcr = (bcf_callret1_t*) calloc(sm->n, sizeof(bcf_callret1_t));
-    bca->rghash = rghash;
     bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
     bca->min_frac = conf->min_frac;
     bca->min_support = conf->min_support;
@@ -519,7 +546,8 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
         flush_bcf_records(conf, bcf_fp, bcf_hdr, bcf_rec);
         // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
-        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, rghash) >= 0)
+        // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them
+        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, NULL) >= 0)
         {
             bcf_callaux_clean(bca, &bc);
             for (i = 0; i < gplp.n; ++i)
@@ -552,15 +580,17 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
     bam_smpl_destroy(sm); free(buf.s);
     for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
     free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
-    bcf_call_del_rghash(rghash);
+    bcf_call_del_rghash(rghash_exc);
     bam_mplp_destroy(iter);
     bam_hdr_destroy(h);
     for (i = 0; i < n; ++i) {
         sam_close(data[i]->fp);
         if (data[i]->iter) hts_itr_destroy(data[i]->iter);
+        if ( data[i]->rghash_inc ) khash_str2int_destroy_free(data[i]->rghash_inc);
         free(data[i]);
     }
     free(data); free(plp); free(n_plp);
+    if ( samples_inc ) khash_str2int_destroy_free(samples_inc);
     free(mp_ref.ref[0]);
     free(mp_ref.ref[1]);
     return ret;
@@ -689,6 +719,8 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "  --ff, --excl-flags STR|INT  filter flags: skip reads with mask bits set\n"
 "                                            [%s]\n", tmp_filter);
     fprintf(fp,
+"  -s, --samples LIST      comma separated list of samples to include\n"
+"  -S, --samples-file FILE file of samples to include\n"
 "  -x, --ignore-overlaps   disable read-pair overlap detection\n"
 "\n"
 "Output options:\n"
@@ -774,6 +806,8 @@ int bam_mpileup(int argc, char *argv[])
         {"min-bq", required_argument, NULL, 'Q'},
         {"ignore-overlaps", no_argument, NULL, 'x'},
         {"output-type", required_argument, NULL, 'O'},
+        {"samples", required_argument, NULL, 's'},
+        {"samples-file", required_argument, NULL, 'S'},
         {"output-tags", required_argument, NULL, 't'},
         {"ext-prob", required_argument, NULL, 'e'},
         {"gap-frac", required_argument, NULL, 'F'},
@@ -786,7 +820,7 @@ int bam_mpileup(int argc, char *argv[])
         {"platforms", required_argument, NULL, 'P'},
         {NULL, 0, NULL, 0}
     };
-    while ((c = getopt_long(argc, argv, "Ag:f:r:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xt:",lopts,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "Ag:f:r:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xt:s:S:",lopts,NULL)) >= 0) {
         switch (c) {
         case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
         case  1 :
@@ -824,6 +858,11 @@ int bam_mpileup(int argc, char *argv[])
         case 'I': mplp.flag |= MPLP_NO_INDEL; break;
         case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
         case '6': mplp.flag |= MPLP_ILLUMINA13; break;
+        case 's': mplp.samples_list = optarg; break;
+        case 'S':
+            mplp.samples_list = optarg;
+            mplp.sample_is_file = 1;
+            break;
         case 'O': 
             switch (optarg[0]) {
                 case 'b': mplp.output_type = FT_BCF_GZ; break;
@@ -854,11 +893,11 @@ int bam_mpileup(int argc, char *argv[])
         case 'G': {
                 FILE *fp_rg;
                 char buf[1024];
-                mplp.rghash = khash_str2int_init();
+                mplp.rghash_exc = khash_str2int_init();
                 if ((fp_rg = fopen(optarg, "r")) == NULL)
                     fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
                 while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
-                    khash_str2int_inc(mplp.rghash, strdup(buf));
+                    khash_str2int_inc(mplp.rghash_exc, strdup(buf));
                 fclose(fp_rg);
             }
             break;
@@ -907,7 +946,7 @@ int bam_mpileup(int argc, char *argv[])
     }
     else
         ret = mpileup(&mplp, argc - optind, argv + optind);
-    if (mplp.rghash) khash_str2int_destroy_free(mplp.rghash);
+    if (mplp.rghash_exc) khash_str2int_destroy_free(mplp.rghash_exc);
     free(mplp.reg); free(mplp.pl_list);
     if (mplp.fai) fai_destroy(mplp.fai);
     if (mplp.bed) regidx_destroy(mplp.bed);
diff --git a/sample.c b/sample.c
index e48cf3a39..06777ee45 100644
--- a/sample.c
+++ b/sample.c
@@ -1,7 +1,7 @@
 /*  sample.c -- group data by sample.
 
     Copyright (C) 2010, 2011 Broad Institute.
-    Copyright (C) 2013 Genome Research Ltd.
+    Copyright (C) 2013, 2016 Genome Research Ltd.
 
     Author: Heng Li <lh3@sanger.ac.uk>
 
@@ -23,67 +23,53 @@ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 DEALINGS IN THE SOFTWARE.  */
 
-#include <config.h>
-
 #include <stdlib.h>
 #include <string.h>
+#include <htslib/hts.h>
+#include <htslib/khash_str2int.h>
 #include "sample.h"
-#include "htslib/khash.h"
-KHASH_MAP_INIT_STR(sm, int)
 
 bam_sample_t *bam_smpl_init(void)
 {
     bam_sample_t *s;
     s = (bam_sample_t*) calloc(1, sizeof(bam_sample_t));
-    s->rg2smid = kh_init(sm);
-    s->sm2id = kh_init(sm);
+    s->rg2smid = khash_str2int_init();
+    s->sm2id = khash_str2int_init();
     return s;
 }
 
 void bam_smpl_destroy(bam_sample_t *sm)
 {
-    int i;
-    khint_t k;
-    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
-    if (sm == 0) return;
-    for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
+    if ( !sm ) return;
+    if ( sm->rg2smid ) khash_str2int_destroy_free(sm->rg2smid);
+    if ( sm->sm2id ) khash_str2int_destroy_free(sm->sm2id);
     free(sm->smpl);
-    for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
-        if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
-    kh_destroy(sm, (khash_t(sm)*) sm->rg2smid);
-    kh_destroy(sm, (khash_t(sm)*) sm->sm2id);
     free(sm);
 }
 
-static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
+static void add_pair(bam_sample_t *sm, void *sm2id, const char *readgroup, const char *sample)
 {
-    khint_t k_rg, k_sm;
-    int ret;
-    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
-    k_rg = kh_get(sm, rg2smid, key);
-    if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
-    k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
-    k_sm = kh_get(sm, sm2id, val);
-    if (k_sm == kh_end(sm2id)) { // absent
-        if (sm->n == sm->m) {
-            sm->m = sm->m? sm->m<<1 : 1;
-            sm->smpl = (char**) realloc(sm->smpl, sizeof(char*) * sm->m);
-        }
-        sm->smpl[sm->n] = strdup(val);
-        k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
-        kh_val(sm2id, k_sm) = sm->n++;
+    if ( khash_str2int_has_key(sm->rg2smid,readgroup) ) return;   // duplicated @RG-ID
+    
+    int ismpl;
+    if ( khash_str2int_get(sm2id, sample, &ismpl) < 0 )
+    {
+        // the sample encountered for the first time
+        ismpl = sm->n++;
+        hts_expand0(char*,sm->n,sm->m,sm->smpl);
+        sm->smpl[ismpl] = strdup(sample);
+        khash_str2int_set(sm2id, sm->smpl[ismpl], ismpl);
     }
-    kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
+    khash_str2int_set(sm->rg2smid, strdup(readgroup), ismpl);
 }
 
-int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt, void *white_list, void *white_hash)
 {
     const char *p = txt, *q, *r;
     kstring_t buf, first_sm;
     int n = 0;
-    khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
     if (txt == 0) {
-        add_pair(sm, sm2id, fn, fn);
+        add_pair(sm, sm->sm2id, fn, fn);
         return 0;
     }
     memset(&buf, 0, sizeof(kstring_t));
@@ -99,36 +85,41 @@ int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
             for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
             for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
             ioq = *u; ior = *v; *u = *v = '\0';
-            buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
-            add_pair(sm, sm2id, buf.s, r);
-            if ( !first_sm.s )
-                kputs(r,&first_sm);
+            if ( !white_list || khash_str2int_has_key(white_list,r) )
+            {
+                buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
+                add_pair(sm, sm->sm2id, buf.s, r);
+                if ( !first_sm.s )
+                    kputs(r,&first_sm);
+                if ( white_list ) khash_str2int_inc(white_hash,strdup(q));
+            }
             *u = ioq; *v = ior;
         } else break;
         p = q > r? q : r;
         ++n;
     }
-    if (n == 0) add_pair(sm, sm2id, fn, fn);
+    if (n == 0) add_pair(sm, sm->sm2id, fn, fn);
     // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
     //  use the tag instead.
     else if ( n==1 && first_sm.s )
-        add_pair(sm,sm2id,fn,first_sm.s);
+        add_pair(sm,sm->sm2id,fn,first_sm.s);
     if ( first_sm.s )
         free(first_sm.s);
 
-//  add_pair(sm, sm2id, fn, fn);
     free(buf.s);
     return 0;
 }
 
 int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
 {
-    khint_t k;
-    khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
-    if (rg) {
+    int ismpl;
+    if ( rg )
+    {
         str->l = 0;
         kputs(fn, str); kputc('/', str); kputs(rg, str);
-        k = kh_get(sm, rg2smid, str->s);
-    } else k = kh_get(sm, rg2smid, fn);
-    return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
+        if ( khash_str2int_get(sm->rg2smid, str->s, &ismpl) < 0 ) return -1;
+        return ismpl;
+    }
+    if ( khash_str2int_get(sm->rg2smid, fn, &ismpl) < 0 ) return -1;
+    return ismpl;
 }
diff --git a/sample.h b/sample.h
index 8e8efa5b7..f777a81f5 100644
--- a/sample.h
+++ b/sample.h
@@ -1,6 +1,7 @@
 /*  sample.h -- group data by sample.
 
     Copyright (C) 2010 Broad Institute.
+    Copyright (C) 2016 Genome Research Ltd.
 
     Author: Heng Li <lh3@sanger.ac.uk>
 
@@ -34,7 +35,7 @@ typedef struct {
 } bam_sample_t;
 
 bam_sample_t *bam_smpl_init(void);
-int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt);
+int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt, void *white_list, void *white_hash);
 int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str);
 void bam_smpl_destroy(bam_sample_t *sm);
 
diff --git a/test/mpileup/mpileup.7.out b/test/mpileup/mpileup.7.out
new file mode 100644
index 000000000..75e7fc96a
--- /dev/null
+++ b/test/mpileup/mpileup.7.out
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00101	HG00102
+17	100	.	C	<*>	0	.	DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0	PL	0,9,108	0,15,134
+17	101	.	C	<*>	0	.	DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0	PL	0,9,99	0,15,132
+17	102	.	C	<*>	0	.	DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0	PL	0,9,111	0,15,139
+17	103	.	T	<*>	0	.	DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0	PL	0,9,108	0,15,147
+17	104	.	G	<*>	0	.	DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0	PL	0,6,89	0,15,133
+17	105	.	G	<*>	0	.	DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0	PL	0,9,97	0,15,125
+17	106	.	G	<*>	0	.	DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0	PL	0,6,85	0,15,124
+17	107	.	C	<*>	0	.	DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0	PL	0,9,108	0,15,136
+17	108	.	C	<*>	0	.	DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0	PL	0,9,108	0,15,135
+17	109	.	T	<*>	0	.	DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0	PL	0,9,110	0,15,150
+17	110	.	G	<*>	0	.	DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0	PL	0,9,104	0,15,136
+17	111	.	G	<*>	0	.	DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0	PL	0,6,88	0,12,118
+17	112	.	C	<*>	0	.	DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0	PL	0,9,95	0,15,135
+17	113	.	A	<*>	0	.	DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0	PL	0,6,87	0,15,139
+17	114	.	C	<*>	0	.	DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0	PL	0,9,103	0,15,133
+17	115	.	C	<*>	0	.	DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0	PL	0,6,89	0,18,147
+17	116	.	A	<*>	0	.	DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,90	0,21,175
+17	117	.	G	<*>	0	.	DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,85	0,21,177
+17	118	.	G	<*>	0	.	DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,3,60	0,21,162
+17	119	.	G	<*>	0	.	DP=10;I16=8,1,0,0,321,14467,0,0,478,26882,0,0,125,2431,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,73	0,21,160
+17	120	.	A	<*>	0	.	DP=10;I16=8,1,0,0,361,17053,0,0,478,26882,0,0,123,2373,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,83	0,21,171
+17	121	.	G	<*>	0	.	DP=10;I16=8,1,0,0,347,15913,0,0,478,26882,0,0,121,2327,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,80	0,21,168
+17	122	.	C	<*>	0	.	DP=11;I16=9,1,0,0,396,18360,0,0,538,30482,0,0,119,2293,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,99	0,21,178
+17	123	.	T	<*>	0	.	DP=10;I16=8,1,0,0,387,19215,0,0,478,26882,0,0,119,2271,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,112	0,18,166
+17	124	.	T	<*>	0	.	DP=10;I16=8,1,0,0,350,15768,0,0,478,26882,0,0,119,2261,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,104	0,18,154
+17	125	.	A	<*>	0	.	DP=10;I16=8,1,0,0,358,16494,0,0,478,26882,0,0,118,2214,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,104	0,18,162
+17	126	.	A	<*>	0	.	DP=10;I16=8,1,0,0,373,17399,0,0,478,26882,0,0,117,2181,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,107	0,18,174
+17	127	.	C	<*>	0	.	DP=10;I16=8,1,0,0,366,16632,0,0,478,26882,0,0,116,2162,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,109	0,18,160
+17	128	.	A	<*>	0	.	DP=10;I16=8,1,0,0,378,17674,0,0,478,26882,0,0,115,2157,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,111	0,18,162
+17	129	.	A	<*>	0	.	DP=9;I16=7,1,0,0,354,17046,0,0,418,23282,0,0,115,2165,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,113	0,15,159
+17	130	.	A	<*>	0	.	DP=9;I16=7,1,0,0,349,16363,0,0,418,23282,0,0,115,2185,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,113	0,15,152
+17	131	.	C	<*>	0	.	DP=9;I16=7,1,0,0,330,14822,0,0,418,23282,0,0,115,2217,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,110	0,15,147
+17	132	.	A	<*>	0	.	DP=9;I16=7,1,0,0,348,16432,0,0,418,23282,0,0,115,2261,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,110	0,15,151
+17	133	.	T	<*>	0	.	DP=8;I16=6,2,0,0,315,12451,0,0,418,23282,0,0,141,2941,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,105	0,15,150
+17	134	.	C	<*>	0	.	DP=8;I16=6,2,0,0,314,12374,0,0,418,23282,0,0,142,3006,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,105	0,15,152
+17	135	.	T	<*>	0	.	DP=8;I16=6,2,0,0,314,12470,0,0,418,23282,0,0,143,3081,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,106	0,15,156
+17	136	.	G	<*>	0	.	DP=8;I16=6,2,0,0,291,10787,0,0,418,23282,0,0,145,3165,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,105	0,15,134
+17	137	.	T	<*>	0	.	DP=8;I16=6,2,0,0,300,11444,0,0,418,23282,0,0,148,3258,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,104	0,15,139
+17	138	.	C	<*>	0	.	DP=8;I16=6,2,0,0,300,11542,0,0,418,23282,0,0,150,3312,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,108	0,15,142
+17	139	.	C	<*>	0	.	DP=8;I16=6,2,0,0,291,10833,0,0,418,23282,0,0,152,3378,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,106	0,15,143
+17	140	.	A	<*>	0	.	DP=8;I16=6,2,0,0,314,12410,0,0,418,23282,0,0,153,3405,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,107	0,15,153
+17	141	.	G	<*>	0	.	DP=8;I16=6,2,0,0,295,11151,0,0,418,23282,0,0,153,3391,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,108	0,15,142
+17	142	.	C	<*>	0	.	DP=8;I16=6,2,0,0,264,9036,0,0,418,23282,0,0,153,3385,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,97	0,15,129
+17	143	.	G	<*>	0	.	DP=8;I16=5,2,0,0,218,7170,0,0,358,19682,0,0,146,3338,0,0;QS=2,0;MQSB=0.7;MQ0F=0	PL	0,9,95	0,12,97
+17	144	.	A	<*>	0	.	DP=8;I16=6,2,0,0,287,10705,0,0,418,23282,0,0,153,3397,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,105	0,15,129
+17	145	.	A	<*>	0	.	DP=8;I16=6,2,0,0,294,11200,0,0,418,23282,0,0,153,3415,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,106	0,15,138
+17	146	.	T	<*>	0	.	DP=8;I16=6,2,0,0,281,10419,0,0,418,23282,0,0,153,3441,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,103	0,15,128
+17	147	.	A	<*>	0	.	DP=8;I16=6,2,0,0,286,10442,0,0,418,23282,0,0,153,3475,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,99	0,15,140
+17	148	.	C	<*>	0	.	DP=8;I16=6,2,0,0,301,11401,0,0,418,23282,0,0,152,3466,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,106	0,15,146
+17	149	.	C	<*>	0	.	DP=8;I16=6,2,0,0,293,10907,0,0,418,23282,0,0,150,3414,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,109	0,15,140
+17	150	.	T	<*>	0	.	DP=7;I16=5,2,0,0,277,11093,0,0,389,22441,0,0,149,3369,0,0;QS=2,0;MQSB=0.5;MQ0F=0	PL	0,6,84	0,15,152
diff --git a/test/mplp.samples b/test/mplp.samples
new file mode 100644
index 000000000..1a9b396e6
--- /dev/null
+++ b/test/mplp.samples
@@ -0,0 +1,2 @@
+HG00101
+HG00102
diff --git a/test/test.pl b/test/test.pl
index 7d4c9ae50..84b38a40c 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -255,6 +255,8 @@
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-t DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.5.out',args=>q[-t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-t DP,DV -r17:100-600 --gvcf 0,2,5]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -s HG00101,HG00102]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -S {PATH}/mplp.samples]);
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};
@@ -932,6 +934,7 @@ sub test_mpileup
 {
     my ($opts,%args) = @_;
 
+    $args{args} =~ s/{PATH}/$$opts{path}/g;
     for my $fmt ('bam','cram')
     {
         my @files = ();

From d2f30681b5ed24dece42b09c9cb7a3b46bda4d1a Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Tue, 31 May 2016 14:42:37 +0100
Subject: [PATCH 199/211] mpileup: switch `--output-tags` option to
 `--annotate`

switch `-t/--output-tags` option to `-a/--annotate` to make room for
the `-t/--targets` option

available annotations are now listed on request with `-a ?` rather than
cluttering up the help output.
---
 doc/bcftools.txt | 48 +++++++++++++++++++++---------------------
 mpileup.c        | 54 +++++++++++++++++++++++++++++++++++-------------
 test/test.pl     |  8 +++----
 3 files changed, 69 insertions(+), 41 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 6afea51b8..35949ec97 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1393,6 +1393,31 @@ regions listed in the BED file.
 
 ==== Output options
 
+*-a, --annotate* 'LIST'::
+    Comma-separated list of FORMAT and INFO tags to output. (case-insensitive,
+    the "FORMAT/" prefix is optional, and use "?" to list available annotations
+    on the command line) [null]:
+
+    *FORMAT/AD* .. Allelic depth (Number=R,Type=Integer)
+    *FORMAT/ADF* .. Allelic depths on the forward strand (Number=R,Type=Integer)
+    *FORMAT/ADR* .. Allelic depths on the reverse strand (Number=R,Type=Integer)
+    *FORMAT/DP* .. Number of high-quality bases (Number=1,Type=Integer)
+    *FORMAT/SP* .. Phred-scaled strand bias P-value (Number=1,Type=Integer)
+
+    *INFO/AD* .. Total allelic depth (Number=R,Type=Integer)
+    *INFO/ADF* .. Total allelic depths on the forward strand (Number=R,Type=Integer)
+    *INFO/ADR* .. Total allelic depths on the reverse strand (Number=R,Type=Integer)
+
+    *FORMAT/DV* .. Deprecated in favor of FORMAT/AD;
+            Number of high-quality non-reference bases, (Number=1,Type=Integer)
+    *FORMAT/DP4* .. Deprecated in favor of FORMAT/ADF and FORMAT/ADR;
+            Number of high-quality ref-forward, ref-reverse,
+            alt-forward and alt-reverse bases (Number=4,Type=Integer)
+    *FORMAT/DPR* .. Deprecated in favor of FORMAT/AD;
+            Number of high-quality bases for each observed allele (Number=R,Type=Integer)
+    *INFO/DPR* .. Deprecated in favor of INFO/AD;
+            Number of high-quality bases for each observed allele (Number=R,Type=Integer)
+
 *-g, --gvcf* 'INT'[,...]::
     output gVCF blocks of homozygous REF calls, with depth (DP) ranges
     specified by the list of integers. For example, passing '5,15' will
@@ -1413,29 +1438,6 @@ regions listed in the BED file.
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
-*-t, --output-tags* 'LIST'::
-    Comma-separated list of FORMAT and INFO tags to output (case-insensitive) [null]:
-
-    - *AD* .. Allelic depth, FORMAT
-    - *INFO/AD* .. Total allelic depth, INFO
-    - *ADF* .. Allelic depths on the forward strand, FORMAT
-    - *INFO/ADF* .. Total allelic depths on the forward strand, INFO
-    - *ADR* .. Allelic depths on the reverse strand, FORMAT
-    - *INFO/ADR* .. Total allelic depths on the reverse strand, INFO
-    - *DP* .. Number of high-quality bases, FORMAT
-    - *SP* .. Phred-scaled strand bias P-value, FORMAT
-
-    - *DV* .. Deprecated in favor of AD;
-              Number of high-quality non-reference bases, FORMAT
-    - *DPR* .. Deprecated in favor of AD;
-               Number of high-quality bases for each observed allele, FORMAT
-    - *INFO/DPR* .. Deprecated in favor of INFO/AD;
-                    Number of high-quality bases for each observed allele, INFO
-    - *DP4* .. Deprecated in favor of ADF and ADR;
-               Number of high-quality ref-forward, ref-reverse,
-               alt-forward and alt-reverse bases, FORMAT
-
-
 ==== Options for SNP/INDEL genotype likelihood computation
 
 *-e, --ext-prob* 'INT'::
diff --git a/mpileup.c b/mpileup.c
index 93f0092eb..b2d5d449b 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -660,15 +660,15 @@ int parse_format_flag(const char *str)
     char **tags = hts_readlist(str, 0, &n_tags);
     for(i=0; i<n_tags; i++)
     {
-        if ( !strcasecmp(tags[i],"DP") ) flag |= B2B_FMT_DP;
-        else if ( !strcasecmp(tags[i],"DV") ) { flag |= B2B_FMT_DV; fprintf(stderr, "[warning] tag DV functional, but deprecated. Please switch to `AD` in future.\n"); }
-        else if ( !strcasecmp(tags[i],"SP") ) flag |= B2B_FMT_SP;
-        else if ( !strcasecmp(tags[i],"DP4") ) { flag |= B2B_FMT_DP4; fprintf(stderr, "[warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future.\n"); }
-        else if ( !strcasecmp(tags[i],"DPR") ) { flag |= B2B_FMT_DPR; fprintf(stderr, "[warning] tag DPR functional, but deprecated. Please switch to `AD` in future.\n"); }
+        if ( !strcasecmp(tags[i],"DP") || !strcasecmp(tags[i],"FORMAT/DP") || !strcasecmp(tags[i],"FMT/DP") ) flag |= B2B_FMT_DP;
+        else if ( !strcasecmp(tags[i],"DV") || !strcasecmp(tags[i],"FORMAT/DV") || !strcasecmp(tags[i],"FMT/DV") ) { flag |= B2B_FMT_DV; fprintf(stderr, "[warning] tag DV functional, but deprecated. Please switch to `AD` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"SP") || !strcasecmp(tags[i],"FORMAT/SP") || !strcasecmp(tags[i],"FMT/SP") ) flag |= B2B_FMT_SP;
+        else if ( !strcasecmp(tags[i],"DP4") || !strcasecmp(tags[i],"FORMAT/DP4") || !strcasecmp(tags[i],"FMT/DP4") ) { flag |= B2B_FMT_DP4; fprintf(stderr, "[warning] tag DP4 functional, but deprecated. Please switch to `ADF` and `ADR` in future.\n"); }
+        else if ( !strcasecmp(tags[i],"DPR") || !strcasecmp(tags[i],"FORMAT/DPR") || !strcasecmp(tags[i],"FMT/DPR") ) { flag |= B2B_FMT_DPR; fprintf(stderr, "[warning] tag DPR functional, but deprecated. Please switch to `AD` in future.\n"); }
         else if ( !strcasecmp(tags[i],"INFO/DPR") ) { flag |= B2B_INFO_DPR; fprintf(stderr, "[warning] tag INFO/DPR functional, but deprecated. Please switch to `INFO/AD` in future.\n"); }
-        else if ( !strcasecmp(tags[i],"AD") ) flag |= B2B_FMT_AD;
-        else if ( !strcasecmp(tags[i],"ADF") ) flag |= B2B_FMT_ADF;
-        else if ( !strcasecmp(tags[i],"ADR") ) flag |= B2B_FMT_ADR;
+        else if ( !strcasecmp(tags[i],"AD") || !strcasecmp(tags[i],"FORMAT/AD") || !strcasecmp(tags[i],"FMT/AD") ) flag |= B2B_FMT_AD;
+        else if ( !strcasecmp(tags[i],"ADF") || !strcasecmp(tags[i],"FORMAT/ADF") || !strcasecmp(tags[i],"FMT/ADF") ) flag |= B2B_FMT_ADF;
+        else if ( !strcasecmp(tags[i],"ADR") || !strcasecmp(tags[i],"FORMAT/ADR") || !strcasecmp(tags[i],"FMT/ADR") ) flag |= B2B_FMT_ADR;
         else if ( !strcasecmp(tags[i],"INFO/AD") ) flag |= B2B_INFO_AD;
         else if ( !strcasecmp(tags[i],"INFO/ADF") ) flag |= B2B_INFO_ADF;
         else if ( !strcasecmp(tags[i],"INFO/ADR") ) flag |= B2B_INFO_ADR;
@@ -683,6 +683,26 @@ int parse_format_flag(const char *str)
     return flag;
 }
 
+static void list_annotations(FILE *fp)
+{
+    fprintf(fp,
+"\n"
+"FORMAT annotation tags available (\"FORMAT/\" prefix is optional):\n"
+"\n"
+"  FORMAT/AD  .. Allelic depth (Number=R,Type=Integer)\n"
+"  FORMAT/ADF .. Allelic depths on the forward strand (Number=R,Type=Integer)\n"
+"  FORMAT/ADR .. Allelic depths on the reverse strand (Number=R,Type=Integer)\n"
+"  FORMAT/DP  .. Number of high-quality bases (Number=1,Type=Integer)\n"
+"  FORMAT/SP  .. Phred-scaled strand bias P-value (Number=1,Type=Integer)\n"
+"\n"
+"INFO annotation tags available:\n"
+"\n"
+"  INFO/AD  .. Total allelic depth (Number=R,Type=Integer)\n"
+"  INFO/ADF .. Total allelic depths on the forward strand (Number=R,Type=Integer)\n"
+"  INFO/ADR .. Total allelic depths on the reverse strand (Number=R,Type=Integer)\n"
+"\n");
+}
+
 static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 {
     char *tmp_require = bam_flag2str(mplp->rflag_require);
@@ -724,13 +744,12 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "  -x, --ignore-overlaps   disable read-pair overlap detection\n"
 "\n"
 "Output options:\n"
+"  -a, --annotate LIST     optional tags to output; '?' to list []\n"
 "  -g, --gvcf INT[,...]    group non-variant sites into gVCF blocks according\n"
 "                          to minimum per-sample DP\n"
 "  -o, --output FILE       write output to FILE [standard output]\n"
 "  -O, --output-type TYPE  'b' compressed BCF; 'u' uncompressed BCF;\n"
 "                          'z' compressed VCF; 'v' uncompressed VCF [v]\n"
-"  -t, --output-tags LIST  optional tags to output:\n"
-"               DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR []\n"
 "\n"
 "SNP/INDEL genotype likelihoods options:\n"
 "  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
@@ -749,7 +768,8 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "  -p, --per-sample-mF     apply -m and -F per-sample for increased sensitivity\n"
 "  -P, --platforms STR     comma separated list of platforms for indels [all]\n"
 "\n"
-"Notes: Assuming diploid individuals.\n");
+"Notes: Assuming diploid individuals.\n"
+"\n");
 
     free(tmp_require);
     free(tmp_filter);
@@ -808,7 +828,7 @@ int bam_mpileup(int argc, char *argv[])
         {"output-type", required_argument, NULL, 'O'},
         {"samples", required_argument, NULL, 's'},
         {"samples-file", required_argument, NULL, 'S'},
-        {"output-tags", required_argument, NULL, 't'},
+        {"annotate", required_argument, NULL, 'a'},
         {"ext-prob", required_argument, NULL, 'e'},
         {"gap-frac", required_argument, NULL, 'F'},
         {"tandem-qual", required_argument, NULL, 'h'},
@@ -820,7 +840,7 @@ int bam_mpileup(int argc, char *argv[])
         {"platforms", required_argument, NULL, 'P'},
         {NULL, 0, NULL, 0}
     };
-    while ((c = getopt_long(argc, argv, "Ag:f:r:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xt:s:S:",lopts,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "Ag:f:r:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:",lopts,NULL)) >= 0) {
         switch (c) {
         case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
         case  1 :
@@ -901,7 +921,13 @@ int bam_mpileup(int argc, char *argv[])
                 fclose(fp_rg);
             }
             break;
-        case 't': mplp.fmt_flag |= parse_format_flag(optarg); break;
+        case 'a':
+            if (optarg[0]=='?') {
+                list_annotations(stderr);
+                return 1;
+            }
+            mplp.fmt_flag |= parse_format_flag(optarg);
+        break;
         default:
             fprintf(stderr,"Invalid option: '%c'\n", c);
             return 1;
diff --git a/test/test.pl b/test/test.pl
index 84b38a40c..f34d563f1 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -250,11 +250,11 @@
 test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.2.out',fa=>'consensus2.fa',args=>'-H 2');
 test_vcf_consensus($opts,in=>'empty',out=>'consensus.5.out',fa=>'consensus.fa',args=>'');
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.1.out',args=>q[-r17:100-150]);
-test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.2.out',args=>q[-t DP,DV -r17:100-600]); # test files from samtools mpileup test suite
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.2.out',args=>q[-a DP,DV -r17:100-600]); # test files from samtools mpileup test suite
 test_mpileup($opts,in=>[qw(1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite
-test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-t DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
-test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.5.out',args=>q[-t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600]);
-test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-t DP,DV -r17:100-600 --gvcf 0,2,5]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.5.out',args=>q[-a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-a DP,DV -r17:100-600 --gvcf 0,2,5]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -s HG00101,HG00102]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -S {PATH}/mplp.samples]);
 

From c153e8b8a15aaaaf03c6752d55d8378ff08f358e Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 13 Jun 2016 16:52:39 +0100
Subject: [PATCH 200/211] regidx: import regidx api from htslib into bcftools

This is meant as a temporary change while we extend the
regidx api, but allow bcftools code to use these changes
before they appear in some form in htslib.

This commit does not add new features, just copies over
`regidx.[ch]` and rejiggers the linking to use these
local bcftools copies.

the `*_c` are removed due to relying on `hts_internal.h`
(see fc9aeb6f77668afed412119701c5c58b0fca8091)
---
 Makefile    |   6 +-
 consensus.c |   2 +-
 ploidy.c    |   2 +-
 ploidy.h    |   2 +-
 regidx.c    | 338 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 regidx.h    | 154 ++++++++++++++++++++++++
 6 files changed, 498 insertions(+), 6 deletions(-)
 create mode 100644 regidx.c
 create mode 100644 regidx.h

diff --git a/Makefile b/Makefile
index d8e5ed880..abae700b7 100644
--- a/Makefile
+++ b/Makefile
@@ -135,7 +135,7 @@ call_h = call.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) vcmp.h
 convert_h = convert.h $(htslib_vcf_h)
 tsv2vcf_h = tsv2vcf.h $(htslib_vcf_h)
 filter_h = filter.h $(htslib_vcf_h)
-ploidy_h = ploidy.h $(htslib_regidx_h)
+ploidy_h = ploidy.h regidx.h
 prob1_h = prob1.h $(htslib_vcf_h) $(call_h)
 roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kstring.h $(HTSDIR)/htslib/kseq.h $(bcftools_h)
 cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
@@ -173,10 +173,10 @@ kmin.o: kmin.c kmin.h
 mcall.o: mcall.c $(HTSDIR)/htslib/kfunc.h $(call_h)
 prob1.o: prob1.c $(prob1_h)
 vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h
-ploidy.o: ploidy.c $(htslib_regidx_h) $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h)
+ploidy.o: ploidy.c regidx.h $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h)
 polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h
 peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
-consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) $(HTSDIR)/htslib/regidx.h
+consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) regidx.h
 mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(bcftools_h) $(call_h) $(bam2bcf_h) $(sample_h)
 sample.o: $(sample_h) $(htslib_hts_h) $(HTSDIR)/htslib/khash_str2int.h
 version.o: version.h version.c
diff --git a/consensus.c b/consensus.c
index 79b4a5f91..5e37b05de 100644
--- a/consensus.c
+++ b/consensus.c
@@ -35,8 +35,8 @@
 #include <htslib/kstring.h>
 #include <htslib/synced_bcf_reader.h>
 #include <htslib/kseq.h>
-#include <htslib/regidx.h>
 #include "bcftools.h"
+#include "regidx.h"
 #include "rbuf.h"
 
 typedef struct
diff --git a/ploidy.c b/ploidy.c
index 719e1753c..6b54850db 100644
--- a/ploidy.c
+++ b/ploidy.c
@@ -22,11 +22,11 @@
     THE SOFTWARE.
 */
 
-#include <htslib/regidx.h>
 #include <htslib/khash_str2int.h>
 #include <htslib/kseq.h>
 #include <htslib/hts.h>
 #include "bcftools.h"
+#include "regidx.h"
 #include "ploidy.h"
 
 struct _ploidy_t
diff --git a/ploidy.h b/ploidy.h
index 6deef737f..1e7d2f78f 100644
--- a/ploidy.h
+++ b/ploidy.h
@@ -55,7 +55,7 @@
 #ifndef __PLOIDY_H__
 #define __PLOIDY_H__
 
-#include <htslib/regidx.h>
+#include "regidx.h"
 
 typedef struct _ploidy_t ploidy_t;
 
diff --git a/regidx.c b/regidx.c
new file mode 100644
index 000000000..db9086e0a
--- /dev/null
+++ b/regidx.c
@@ -0,0 +1,338 @@
+/* 
+    Copyright (C) 2014 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+#include <htslib/hts.h>
+#include <htslib/kstring.h>
+#include <htslib/kseq.h>
+#include <htslib/khash_str2int.h>
+#include "regidx.h"
+
+#define LIDX_SHIFT 13   // number of insignificant index bits
+
+// List of regions for one chromosome
+typedef struct
+{
+    int *idx, nidx;
+    int nregs, mregs;   // n:used, m:alloced
+    reg_t *regs;
+    void *payload;
+}
+reglist_t;
+
+// Container of all sequences
+struct _regidx_t
+{
+    int nseq, mseq;     // n:used, m:alloced
+    reglist_t *seq;     // regions for each sequence
+    void *seq2regs;     // hash for fast lookup from chr name to regions
+    char **seq_names;
+    regidx_free_f free;     // function to free any data allocated by regidx_parse_f
+    regidx_parse_f parse;   // parse one input line
+    void *usr;              // user data to pass to regidx_parse_f
+
+    // temporary data for index initialization
+    kstring_t str;
+    int rid_prev, start_prev, end_prev;
+    int payload_size;
+    void *payload;
+};
+
+int regidx_seq_nregs(regidx_t *idx, const char *seq)
+{
+    int iseq;
+    if ( khash_str2int_get(idx->seq2regs, seq, &iseq)!=0 ) return 0; // no such sequence
+    return idx->seq[iseq].nregs;
+}
+
+int regidx_nregs(regidx_t *idx)
+{
+    int i, nregs = 0;
+    for (i=0; i<idx->nseq; i++) nregs += idx->seq[i].nregs;
+    return nregs;
+}
+
+char **regidx_seq_names(regidx_t *idx, int *n)
+{
+    *n = idx->nseq;
+    return idx->seq_names;
+}
+
+int _regidx_build_index(regidx_t *idx)
+{
+    int iseq;
+    for (iseq=0; iseq<idx->nseq; iseq++)
+    {
+        reglist_t *list = &idx->seq[iseq];
+        int j,k, imax = 0;   // max index bin
+        for (j=0; j<list->nregs; j++)
+        {
+            int ibeg = list->regs[j].start >> LIDX_SHIFT;
+            int iend = list->regs[j].end >> LIDX_SHIFT;
+            if ( imax < iend + 1 )
+            {
+                int old_imax = imax; 
+                imax = iend + 1;
+                kroundup32(imax);
+                list->idx = (int*) realloc(list->idx, imax*sizeof(int));
+                for (k=old_imax; k<imax; k++) list->idx[k] = -1;
+            }
+            if ( ibeg==iend )
+            {
+                if ( list->idx[ibeg]<0 ) list->idx[ibeg] = j;
+            }
+            else
+            {
+                for (k=ibeg; k<=iend; k++)
+                    if ( list->idx[k]<0 ) list->idx[k] = j;
+            }
+            list->nidx = iend + 1;
+        }
+    }
+    return 0;
+}
+
+int regidx_insert(regidx_t *idx, char *line)
+{
+    if ( !line )
+        return _regidx_build_index(idx);
+
+    char *chr_from, *chr_to;
+    reg_t reg;
+    int ret = idx->parse(line,&chr_from,&chr_to,&reg,idx->payload,idx->usr);
+    if ( ret==-2 ) return -1;   // error
+    if ( ret==-1 ) return 0;    // skip the line
+
+    int rid;
+    idx->str.l = 0;
+    kputsn(chr_from, chr_to-chr_from+1, &idx->str);
+    if ( khash_str2int_get(idx->seq2regs, idx->str.s, &rid)!=0 )
+    {
+        idx->nseq++;
+        int m_prev = idx->mseq;
+        hts_expand0(reglist_t,idx->nseq,idx->mseq,idx->seq);
+        hts_expand0(char*,idx->nseq,m_prev,idx->seq_names);
+        idx->seq_names[idx->nseq-1] = strdup(idx->str.s);
+        rid = khash_str2int_inc(idx->seq2regs, idx->seq_names[idx->nseq-1]);
+    }
+
+    reglist_t *list = &idx->seq[rid];
+    list->nregs++;
+    int m_prev = list->mregs;
+    hts_expand(reg_t,list->nregs,list->mregs,list->regs);
+    list->regs[list->nregs-1] = reg;
+    if ( idx->payload_size )
+    {
+        if ( m_prev < list->mregs ) list->payload = realloc(list->payload,idx->payload_size*list->mregs);
+        memcpy(list->payload + idx->payload_size*(list->nregs-1), idx->payload, idx->payload_size);
+    }
+
+    if ( idx->rid_prev==rid )
+    {
+        if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 
+        { 
+            fprintf(stderr,"The regions are not sorted: %s:%d-%d is before %s:%d-%d\n", 
+                idx->str.s,idx->start_prev+1,idx->end_prev+1,idx->str.s,reg.start+1,reg.end+1); 
+            return -1;
+        }
+    }
+    idx->rid_prev = rid;
+    idx->start_prev = reg.start;
+    idx->end_prev = reg.end;
+    return 0;
+}
+
+regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f free_f, size_t payload_size, void *usr_dat)
+{
+    if ( !parser )
+    {
+        if ( !fname ) parser = regidx_parse_tab;
+        else
+        {
+            int len = strlen(fname);
+            if ( len>=7 && !strcasecmp(".bed.gz",fname+len-7) )
+                parser = regidx_parse_bed;
+            else if ( len>=8 && !strcasecmp(".bed.bgz",fname+len-8) )
+                parser = regidx_parse_bed;
+            else if ( len>=4 && !strcasecmp(".bed",fname+len-4) )
+                parser = regidx_parse_bed;
+            else
+                parser = regidx_parse_tab;
+        }
+    }
+
+    regidx_t *idx = (regidx_t*) calloc(1,sizeof(regidx_t));
+    idx->free  = free_f;
+    idx->parse = parser;
+    idx->usr   = usr_dat;
+    idx->seq2regs = khash_str2int_init();
+    idx->rid_prev   = -1;
+    idx->start_prev = -1;
+    idx->end_prev   = -1;
+    idx->payload_size = payload_size;
+    if ( payload_size ) idx->payload = malloc(payload_size);
+
+    if ( !fname ) return idx;
+    
+    kstring_t str = {0,0,0};
+
+    htsFile *fp = hts_open(fname,"r");
+    if ( !fp ) goto error;
+
+    while ( hts_getline(fp, KS_SEP_LINE, &str) > 0 )
+    {
+        if ( regidx_insert(idx, str.s) ) goto error;
+    }
+    regidx_insert(idx, NULL);
+    
+    free(str.s);
+    hts_close(fp);
+    return idx;
+
+error:
+    free(str.s);
+    if ( fp ) hts_close(fp);
+    regidx_destroy(idx);
+    return NULL;
+}
+
+void regidx_destroy(regidx_t *idx)
+{
+    int i, j;
+    for (i=0; i<idx->nseq; i++)
+    {
+        reglist_t *list = &idx->seq[i];
+        if ( idx->free )
+        {
+            for (j=0; j<list->nregs; j++)
+                idx->free(list->payload + idx->payload_size*j);
+        }
+        free(list->payload);
+        free(list->regs);
+        free(list->idx);
+    }
+    free(idx->seq_names);
+    free(idx->seq);
+    free(idx->str.s);
+    free(idx->payload);
+    khash_str2int_destroy_free(idx->seq2regs);
+    free(idx);
+}
+
+int regidx_overlap(regidx_t *idx, const char *chr, uint32_t from, uint32_t to, regitr_t *itr)
+{
+    if ( itr ) itr->i = itr->n = 0;
+
+    int iseq;
+    if ( khash_str2int_get(idx->seq2regs, chr, &iseq)!=0 ) return 0; // no such sequence
+
+    reglist_t *list = &idx->seq[iseq];
+    if ( !list->nregs ) return 0;
+
+    int i, ibeg = from>>LIDX_SHIFT; 
+    int ireg = ibeg < list->nidx ? list->idx[ibeg] : list->idx[ list->nidx - 1 ];
+    if ( ireg < 0 )
+    {
+        // linear search; if slow, replace with binary search
+        if ( ibeg > list->nidx ) ibeg = list->nidx;
+        for (i=ibeg - 1; i>=0; i--)
+            if ( list->idx[i] >=0 ) break;
+        ireg = i>=0 ? list->idx[i] : 0;
+    }
+    for (i=ireg; i<list->nregs; i++)
+    {
+        if ( list->regs[i].start > to ) return 0;   // no match
+        if ( list->regs[i].end >= from && list->regs[i].start <= to ) break; // found
+    }
+
+    if ( i>=list->nregs ) return 0;   // no match
+
+    if ( !itr ) return 1;
+
+    itr->i = 0;
+    itr->n = list->nregs - i;
+    itr->reg = &idx->seq[iseq].regs[i];
+    if ( idx->payload_size )
+        itr->payload = idx->seq[iseq].payload + i*idx->payload_size;
+    else
+        itr->payload = NULL;
+
+    return 1;
+}
+
+int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    ss = se+1;
+    reg->start = hts_parse_decimal(ss, &se, 0);
+    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    ss = se+1;
+    reg->end = hts_parse_decimal(ss, &se, 0) - 1;
+    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+    
+    return 0;
+}
+
+int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
+    
+    char *se = ss;
+    while ( *se && !isspace(*se) ) se++;
+    if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    ss = se+1;
+    reg->start = hts_parse_decimal(ss, &se, 0) - 1;
+    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+
+    if ( !se[0] || !se[1] )
+        reg->end = reg->start;
+    else
+    {
+        ss = se+1;
+        reg->end = hts_parse_decimal(ss, &se, 0);
+        if ( ss==se ) reg->end = reg->start;
+        else reg->end--;
+    }
+    
+    return 0;
+}
+
diff --git a/regidx.h b/regidx.h
new file mode 100644
index 000000000..79e82b77d
--- /dev/null
+++ b/regidx.h
@@ -0,0 +1,154 @@
+/* 
+    Copyright (C) 2014 Genome Research Ltd.
+
+    Author: Petr Danecek <pd3@sanger.ac.uk>
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+    
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+    
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+    AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+    OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+    THE SOFTWARE.
+*/
+
+/*
+    Regions indexing with an optional payload. Inspired by samtools/bedidx.c.
+    This code is intended as future replacement of bcf_sr_regions_t.
+
+    Example of usage:
+
+        // Init the parser and print regions. In this example the payload is a
+        // pointer to a string. For the description of parse_custom and
+        // free_custom functions, see regidx_parse_f and regidx_free_f below,
+        // and for working example see test/test-regidx.c.
+        regidx_t *idx = regidx_init(in_fname,parse_custom,free_custom,sizeof(char*),NULL);
+
+        // Query overlap with chr:from-to
+        regitr_t itr;
+        if ( regidx_overlap(idx, chr,from,to, &itr) ) printf("There is an overlap!\n");
+
+        while ( REGITR_OVERLAP(itr,from,to) )
+        {
+            printf("[%d,%d] overlaps with [%d,%d], payload=%s\n", from,to, 
+                REGITR_START(itr), REGITR_END(itr), REGITR_PAYLOAD(itr,char*));
+            itr.i++;
+        }
+
+        regidx_destroy(regs);
+*/
+
+#ifndef HTSLIB_REGIDX_H
+#define HTSLIB_REGIDX_H
+
+#include <stdio.h>
+#include <inttypes.h>
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+typedef struct _regidx_t regidx_t;
+typedef struct
+{
+    uint32_t start, end;
+}
+reg_t;
+typedef struct
+{
+    int i, n;
+    reg_t *reg;
+    void *payload;
+}
+regitr_t;
+
+#define REGITR_START(itr) (itr).reg[(itr).i].start
+#define REGITR_END(itr)   (itr).reg[(itr).i].end
+#define REGITR_PAYLOAD(itr,type_t) ((type_t*)(itr).payload)[(itr).i]
+#define REGITR_OVERLAP(itr,from,to) (itr.i < itr.n && REGITR_START(itr)<=to && REGITR_END(itr)>=from )
+
+/*
+ *  regidx_parse_f - Function to parse one input line, such as regidx_parse_bed
+ *  or regidx_parse_tab below. The function is expected to set `chr_from` and
+ *  `chr_to` to point to first and last character of chromosome name and set
+ *  coordinates `reg->start` and `reg->end` (0-based, inclusive). If
+ *  regidx_init() was called with non-zero payload_size, the `payload` points
+ *  to a memory location of the payload_size and `usr` is data passed to
+ *  regidx_init(). Any memory allocated by the function will be freed by
+ *  regidx_free_f on regidx_destroy().
+ *
+ *  Return value: 0 on success, -1 to skip a record, -2 on fatal error.
+ */
+typedef int  (*regidx_parse_f)(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr);
+typedef void (*regidx_free_f)(void *payload);
+
+int regidx_parse_bed(const char*,char**,char**,reg_t*,void*,void*);   // CHROM,FROM,TO (0-based,right-open)
+int regidx_parse_tab(const char*,char**,char**,reg_t*,void*,void*);   // CHROM,POS (1-based, inclusive)
+
+/*
+ *  regidx_init() - creates new index
+ *  @param fname:  input file name or NULL if regions will be added one-by-one via regidx_insert()
+ *  @param parsef: regidx_parse_bed, regidx_parse_tab or see description of regidx_parse_f. If NULL,
+ *                 the format will be autodected, currently either regidx_parse_tab (the default) or
+ *                 regidx_parse_bed (file must be named 'bed' or 'bed.gz') will be used. Note that
+ *                 the exact autodetection algorithm will change.
+ *  @param freef:  NULL or see description of regidx_parse_f
+ *  @param payload_size: 0 with regidx_parse_bed, regidx_parse_tab or see regidx_parse_f
+ *  @param usr:    optional user data passed to regidx_parse_f
+ *
+ *  Returns index on success or NULL on error.
+ */
+regidx_t *regidx_init(const char *fname, regidx_parse_f parsef, regidx_free_f freef, size_t payload_size, void *usr);
+
+/*
+ *  regidx_destroy() - free memory allocated by regidx_init
+ */
+void regidx_destroy(regidx_t *idx);
+
+/*
+ *  regidx_overlap() - check overlap of the location chr:from-to with regions
+ *  @param start,end:   0-based start, end coordinate (inclusive)
+ *  @param itr:         pointer to iterator, can be NULL if not needed
+ *
+ *  Returns 0 if there is no overlap or 1 if overlap is found. The overlapping
+ *  regions can be iterated as shown in the example above.
+ */
+int regidx_overlap(regidx_t *idx, const char *chr, uint32_t start, uint32_t end, regitr_t *itr);
+
+/*
+ *  regidx_insert() - add a new region. 
+ *
+ *  After last region has been added, call regidx_insert(idx,NULL) to
+ *  build the index.
+ *
+ *  Returns 0 on success or -1 on error.
+ */
+int regidx_insert(regidx_t *idx, char *line);
+
+/*
+ *  regidx_seq_names() - return list of all sequence names
+ */
+char **regidx_seq_names(regidx_t *idx, int *n);
+
+/*
+ *  regidx_seq_nregs() - number of regions
+ *  regidx_nregs()  - total number of regions
+ */
+int regidx_seq_nregs(regidx_t *idx, const char *seq);
+int regidx_nregs(regidx_t *idx);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif

From d766590e0ef46e483a93adbee5427ff2ebe21c8e Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Fri, 17 Jun 2016 13:19:46 +0100
Subject: [PATCH 201/211] regidx: extend regidx API

* added functions to loop over all regions
* lazy index build in case random access is not required
* support for chromosome names only, beg-end coordinates not mandatory
* set cap at maximum coordinate at 2147483647, hts_itr does not support larger
* tab and reg parsers will throw on finding a `0` to catch user
  error of using 0-based rather than 1-based coords
---
 Makefile  |   5 +-
 mpileup.c |   2 +-
 regidx.c  | 223 ++++++++++++++++++++++++++++++++++++++++++------------
 regidx.h  |  53 +++++++++++--
 4 files changed, 223 insertions(+), 60 deletions(-)

diff --git a/Makefile b/Makefile
index abae700b7..1d923e995 100644
--- a/Makefile
+++ b/Makefile
@@ -45,7 +45,7 @@ OBJS     = main.o vcfindex.o tabix.o \
            vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o \
            vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o \
            vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
-           vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o version.o \
+           vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o regidx.o version.o \
            mpileup.o bam2bcf.o bam2bcf_indel.o sample.o \
            ccall.o em.o prob1.o kmin.o # the original samtools calling
 
@@ -176,8 +176,9 @@ vcmp.o: vcmp.c $(htslib_hts_h) vcmp.h
 ploidy.o: ploidy.c regidx.h $(HTSDIR)/htslib/khash_str2int.h $(HTSDIR)/htslib/kseq.h $(htslib_hts_h) $(bcftools_h) $(ploidy_h)
 polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_h) peakfit.h
 peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
+regidx.o: regidx.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) regidx.h
 consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) regidx.h
-mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) $(htslib_regidx_h) $(bcftools_h) $(call_h) $(bam2bcf_h) $(sample_h)
+mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) regidx.h $(bcftools_h) $(call_h) $(bam2bcf_h) $(sample_h)
 sample.o: $(sample_h) $(htslib_hts_h) $(HTSDIR)/htslib/khash_str2int.h
 version.o: version.h version.c
 
diff --git a/mpileup.c b/mpileup.c
index b2d5d449b..dbd0d68aa 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -37,8 +37,8 @@ DEALINGS IN THE SOFTWARE.  */
 #include <htslib/faidx.h>
 #include <htslib/kstring.h>
 #include <htslib/khash_str2int.h>
-#include <htslib/regidx.h>
 #include <assert.h>
+#include "regidx.h"
 #include "bcftools.h"
 #include "bam2bcf.h"
 #include "sample.h"
diff --git a/regidx.c b/regidx.c
index db9086e0a..a3f3a57e0 100644
--- a/regidx.c
+++ b/regidx.c
@@ -1,5 +1,5 @@
 /* 
-    Copyright (C) 2014 Genome Research Ltd.
+    Copyright (C) 2014-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -28,6 +28,7 @@
 #include <htslib/khash_str2int.h>
 #include "regidx.h"
 
+#define MAX_COOR 2147483647     // CSI and hts_itr_query limit
 #define LIDX_SHIFT 13   // number of insignificant index bits
 
 // List of regions for one chromosome
@@ -53,7 +54,8 @@ struct _regidx_t
 
     // temporary data for index initialization
     kstring_t str;
-    int rid_prev, start_prev, end_prev;
+    int rid_prev;
+    uint32_t start_prev, end_prev;
     int payload_size;
     void *payload;
 };
@@ -78,50 +80,68 @@ char **regidx_seq_names(regidx_t *idx, int *n)
     return idx->seq_names;
 }
 
-int _regidx_build_index(regidx_t *idx)
+int _regidx_build_index(regidx_t *idx, reglist_t *list)
 {
-    int iseq;
-    for (iseq=0; iseq<idx->nseq; iseq++)
+    int j,k, imax = 0;   // max index bin
+    for (j=0; j<list->nregs; j++)
     {
-        reglist_t *list = &idx->seq[iseq];
-        int j,k, imax = 0;   // max index bin
-        for (j=0; j<list->nregs; j++)
+        int ibeg = list->regs[j].start >> LIDX_SHIFT;
+        int iend = list->regs[j].end >> LIDX_SHIFT;
+        if ( imax < iend + 1 )
         {
-            int ibeg = list->regs[j].start >> LIDX_SHIFT;
-            int iend = list->regs[j].end >> LIDX_SHIFT;
-            if ( imax < iend + 1 )
-            {
-                int old_imax = imax; 
-                imax = iend + 1;
-                kroundup32(imax);
-                list->idx = (int*) realloc(list->idx, imax*sizeof(int));
-                for (k=old_imax; k<imax; k++) list->idx[k] = -1;
-            }
-            if ( ibeg==iend )
-            {
-                if ( list->idx[ibeg]<0 ) list->idx[ibeg] = j;
-            }
-            else
-            {
-                for (k=ibeg; k<=iend; k++)
-                    if ( list->idx[k]<0 ) list->idx[k] = j;
-            }
-            list->nidx = iend + 1;
+            int old_imax = imax; 
+            imax = iend + 1;
+            kroundup32(imax);
+            list->idx = (int*) realloc(list->idx, imax*sizeof(int));
+            for (k=old_imax; k<imax; k++) list->idx[k] = -1;
+        }
+        if ( ibeg==iend )
+        {
+            if ( list->idx[ibeg]<0 ) list->idx[ibeg] = j;
+        }
+        else
+        {
+            for (k=ibeg; k<=iend; k++)
+                if ( list->idx[k]<0 ) list->idx[k] = j;
+        }
+        list->nidx = iend + 1;
+    }
+    return 0;
+}
+
+int regidx_insert_list(regidx_t *idx, char *line, char delim)
+{
+    kstring_t tmp = {0,0,0};
+    char *ss = line;
+    while ( *ss )
+    {
+        char *se = ss;
+        while ( *se && *se!=delim ) se++;
+        tmp.l = 0;
+        kputsn(ss, se-ss, &tmp);
+        if ( regidx_insert(idx,tmp.s) < 0 )
+        {
+            free(tmp.s);
+            return -1;
         }
+        if ( !*se ) break;
+        ss = se+1;
     }
+    free(tmp.s);
     return 0;
 }
 
 int regidx_insert(regidx_t *idx, char *line)
 {
-    if ( !line )
-        return _regidx_build_index(idx);
+    if ( !line ) return 0;
 
     char *chr_from, *chr_to;
     reg_t reg;
     int ret = idx->parse(line,&chr_from,&chr_to,&reg,idx->payload,idx->usr);
     if ( ret==-2 ) return -1;   // error
     if ( ret==-1 ) return 0;    // skip the line
+    if ( reg.start > MAX_COOR - 1 ) reg.start = MAX_COOR - 1;
+    if ( reg.end   > MAX_COOR - 1 ) reg.end   = MAX_COOR - 1;
 
     int rid;
     idx->str.l = 0;
@@ -151,7 +171,7 @@ int regidx_insert(regidx_t *idx, char *line)
     {
         if ( idx->start_prev > reg.start || (idx->start_prev==reg.start && idx->end_prev>reg.end) ) 
         { 
-            fprintf(stderr,"The regions are not sorted: %s:%d-%d is before %s:%d-%d\n", 
+            fprintf(stderr,"The regions are not sorted: %s:%u-%u is before %s:%u-%u\n", 
                 idx->str.s,idx->start_prev+1,idx->end_prev+1,idx->str.s,reg.start+1,reg.end+1); 
             return -1;
         }
@@ -187,8 +207,8 @@ regidx_t *regidx_init(const char *fname, regidx_parse_f parser, regidx_free_f fr
     idx->usr   = usr_dat;
     idx->seq2regs = khash_str2int_init();
     idx->rid_prev   = -1;
-    idx->start_prev = -1;
-    idx->end_prev   = -1;
+    idx->start_prev = 0;
+    idx->end_prev   = 0;
     idx->payload_size = payload_size;
     if ( payload_size ) idx->payload = malloc(payload_size);
 
@@ -249,29 +269,42 @@ int regidx_overlap(regidx_t *idx, const char *chr, uint32_t from, uint32_t to, r
     reglist_t *list = &idx->seq[iseq];
     if ( !list->nregs ) return 0;
 
-    int i, ibeg = from>>LIDX_SHIFT; 
-    int ireg = ibeg < list->nidx ? list->idx[ibeg] : list->idx[ list->nidx - 1 ];
-    if ( ireg < 0 )
+    int i;
+    if ( list->nregs==1 )
     {
-        // linear search; if slow, replace with binary search
-        if ( ibeg > list->nidx ) ibeg = list->nidx;
-        for (i=ibeg - 1; i>=0; i--)
-            if ( list->idx[i] >=0 ) break;
-        ireg = i>=0 ? list->idx[i] : 0;
+        // one region only, the index was not built to save memory
+        if ( idx->seq[iseq].regs[0].start > to ) return 0; // no match
+        if ( idx->seq[iseq].regs[0].end < from ) return 0;
+        i = 0;
     }
-    for (i=ireg; i<list->nregs; i++)
+    else
     {
-        if ( list->regs[i].start > to ) return 0;   // no match
-        if ( list->regs[i].end >= from && list->regs[i].start <= to ) break; // found
-    }
+        if ( !list->idx ) _regidx_build_index(idx, list);
 
-    if ( i>=list->nregs ) return 0;   // no match
+        int ibeg = from>>LIDX_SHIFT; 
+        int ireg = ibeg < list->nidx ? list->idx[ibeg] : list->idx[ list->nidx - 1 ];
+        if ( ireg < 0 )
+        {
+            // linear search; if slow, replace with binary search
+            if ( ibeg > list->nidx ) ibeg = list->nidx;
+            for (i=ibeg - 1; i>=0; i--)
+                if ( list->idx[i] >=0 ) break;
+            ireg = i>=0 ? list->idx[i] : 0;
+        }
+        for (i=ireg; i<list->nregs; i++)
+        {
+            if ( list->regs[i].start > to ) return 0;   // no match
+            if ( list->regs[i].end >= from ) break; // found
+        }
 
+        if ( i>=list->nregs ) return 0;   // no match
+    }
     if ( !itr ) return 1;
 
     itr->i = 0;
     itr->n = list->nregs - i;
     itr->reg = &idx->seq[iseq].regs[i];
+    itr->seq = iseq;
     if ( idx->payload_size )
         itr->payload = idx->seq[iseq].payload + i*idx->payload_size;
     else
@@ -289,11 +322,18 @@ int regidx_parse_bed(const char *line, char **chr_beg, char **chr_end, reg_t *re
     
     char *se = ss;
     while ( *se && !isspace(*se) ) se++;
-    if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
 
     *chr_beg = ss;
     *chr_end = se-1;
 
+    if ( !*se )
+    {
+        // just the chromosome name
+        reg->start = 0;
+        reg->end   = MAX_COOR - 1;
+        return 0;
+    }
+
     ss = se+1;
     reg->start = hts_parse_decimal(ss, &se, 0);
     if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
@@ -314,14 +354,23 @@ int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, reg_t *re
     
     char *se = ss;
     while ( *se && !isspace(*se) ) se++;
-    if ( !*se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
 
     *chr_beg = ss;
     *chr_end = se-1;
 
+    if ( !*se )
+    {
+        // just the chromosome name
+        reg->start = 0;
+        reg->end   = MAX_COOR - 1;
+        return 0;
+    }
+
     ss = se+1;
-    reg->start = hts_parse_decimal(ss, &se, 0) - 1;
-    if ( ss==se ) { fprintf(stderr,"Could not parse bed line: %s\n", line); return -2; }
+    reg->start = hts_parse_decimal(ss, &se, 0);
+    if ( ss==se ) { fprintf(stderr,"Could not parse tab line: %s\n", line); return -2; }
+    if ( reg->start==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
+    reg->start--;
 
     if ( !se[0] || !se[1] )
         reg->end = reg->start;
@@ -330,9 +379,83 @@ int regidx_parse_tab(const char *line, char **chr_beg, char **chr_end, reg_t *re
         ss = se+1;
         reg->end = hts_parse_decimal(ss, &se, 0);
         if ( ss==se ) reg->end = reg->start;
+        else if ( reg->end==0 ) { fprintf(stderr,"Could not parse tab line, expected 1-based coordinate: %s\n", line); return -2; }
         else reg->end--;
     }
+    return 0;
+}
+
+int regidx_parse_reg(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr)
+{
+    char *ss = (char*) line;
+    while ( *ss && isspace(*ss) ) ss++;
+    if ( !*ss ) return -1;      // skip blank lines
+    if ( *ss=='#' ) return -1;  // skip comments
     
+    char *se = ss;
+    while ( *se && *se!=':' ) se++;
+
+    *chr_beg = ss;
+    *chr_end = se-1;
+
+    if ( !*se )
+    {
+        reg->start = 0;
+        reg->end   = MAX_COOR - 1;
+        return 0;
+    }
+
+    ss = se+1;
+    reg->start = hts_parse_decimal(ss, &se, 0);
+    if ( ss==se ) { fprintf(stderr,"Could not parse reg line: %s\n", line); return -2; }
+    if ( reg->start==0 ) { fprintf(stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; }
+    reg->start--;
+
+    if ( !se[0] || !se[1] )
+        reg->end = se[0]=='-' ? MAX_COOR - 1 : reg->start;
+    else
+    {
+        ss = se+1;
+        reg->end = hts_parse_decimal(ss, &se, 0);
+        if ( ss==se ) reg->end = reg->start;
+        else if ( reg->end==0 ) { fprintf(stderr,"Could not parse reg line, expected 1-based coordinate: %s\n", line); return -2; }
+        else reg->end--;
+    }
     return 0;
 }
 
+int regidx_loop(regidx_t *idx, regitr_t *itr)
+{
+    if ( !itr->reg )
+    {
+        if ( !idx->nseq ) return 0;
+        itr->i = itr->n = 0;
+        itr->seq = -1;
+    }
+
+    itr->i++;
+
+    if ( itr->i >= itr->n )
+    {
+        itr->seq++;
+        if ( itr->seq >= idx->nseq ) return 0;
+
+        reglist_t *list = &idx->seq[itr->seq];
+        itr->reg = &list->regs[0];
+        itr->i   = 0;
+        itr->n   = list->nregs;
+    }
+
+    if ( idx->payload_size )
+        itr->payload = idx->seq[itr->seq].payload + itr->i*idx->payload_size;
+    else
+        itr->payload = NULL;
+
+    return 1;
+}
+
+const char *regitr_seqname(regidx_t *idx, regitr_t *itr)
+{
+    return (const char*)idx->seq_names[itr->seq];
+}
+
diff --git a/regidx.h b/regidx.h
index 79e82b77d..18cd98a35 100644
--- a/regidx.h
+++ b/regidx.h
@@ -1,5 +1,5 @@
 /* 
-    Copyright (C) 2014 Genome Research Ltd.
+    Copyright (C) 2014-2016 Genome Research Ltd.
 
     Author: Petr Danecek <pd3@sanger.ac.uk>
 
@@ -23,7 +23,7 @@
 */
 
 /*
-    Regions indexing with an optional payload. Inspired by samtools/bedidx.c.
+    Region indexing with an optional payload. Inspired by samtools/bedidx.c.
     This code is intended as future replacement of bcf_sr_regions_t.
 
     Example of usage:
@@ -46,6 +46,28 @@
         }
 
         regidx_destroy(regs);
+
+
+    Another example, loop over all regions:
+        
+        regidx_t *idx = regidx_init(in_fname,NULL,NULL,0,NULL);
+        regitr_t itr;
+        REGITR_INIT(itr);
+        while ( regidx_loop(idx,&itr) )
+            printf("chr=%s  beg=%d  end=%d\n", regitr_seqname(&itr),REGITR_START(itr),REGITR_END(itr));
+        regidx_destroy(regs);
+
+
+    A note about memory requirements: All regions are stored in memory. When
+    the whole uint32_t range is indexed (beg=0,end=UINT32_MAX), the index takes
+    up to 2.1MB of memory per sequence (50MB in total for 24 sequences). 
+    Howeveer, in typical usage the memory requirements are 10x lower, for
+    example 200k human exons require 0.2MB per sequence (5MB in total). With
+    only one region per per sequence (e.g. whole chromosomes), the index is not
+    build and the required memory is neglibible. The index is created only when
+    regidx_overlap() is called, therefore in the regidx_loop() mode the memory
+    is always small.
+
 */
 
 #ifndef HTSLIB_REGIDX_H
@@ -69,6 +91,7 @@ typedef struct
     int i, n;
     reg_t *reg;
     void *payload;
+    int seq;
 }
 regitr_t;
 
@@ -76,6 +99,8 @@ regitr_t;
 #define REGITR_END(itr)   (itr).reg[(itr).i].end
 #define REGITR_PAYLOAD(itr,type_t) ((type_t*)(itr).payload)[(itr).i]
 #define REGITR_OVERLAP(itr,from,to) (itr.i < itr.n && REGITR_START(itr)<=to && REGITR_END(itr)>=from )
+#define REGITR_INIT(itr)  (itr).reg = 0
+
 
 /*
  *  regidx_parse_f - Function to parse one input line, such as regidx_parse_bed
@@ -92,8 +117,14 @@ regitr_t;
 typedef int  (*regidx_parse_f)(const char *line, char **chr_beg, char **chr_end, reg_t *reg, void *payload, void *usr);
 typedef void (*regidx_free_f)(void *payload);
 
-int regidx_parse_bed(const char*,char**,char**,reg_t*,void*,void*);   // CHROM,FROM,TO (0-based,right-open)
-int regidx_parse_tab(const char*,char**,char**,reg_t*,void*,void*);   // CHROM,POS (1-based, inclusive)
+/*
+ *  A note about the parsers: 
+ *      - leading spaces are ignored
+ *      - lines starting with "#" are ignored
+ */
+int regidx_parse_bed(const char*,char**,char**,reg_t*,void*,void*);   // CHROM or whitespace-separated CHROM,FROM,TO (0-based,right-open)
+int regidx_parse_tab(const char*,char**,char**,reg_t*,void*,void*);   // CHROM or whitespace-separated CHROM,POS (1-based, inclusive)
+int regidx_parse_reg(const char*,char**,char**,reg_t*,void*,void*);   // CHROM, CHROM:POS, CHROM:FROM-TO, CHROM:FROM- (1-based, inclusive)
 
 /*
  *  regidx_init() - creates new index
@@ -125,15 +156,23 @@ void regidx_destroy(regidx_t *idx);
  */
 int regidx_overlap(regidx_t *idx, const char *chr, uint32_t start, uint32_t end, regitr_t *itr);
 
+/*
+ *  regidx_loop() - loop over all regions
+ *  Returns 0 when done or 1 when itr is set to next region
+ */
+int regidx_loop(regidx_t *idx, regitr_t *itr);
+
+/*  Current sequence name */
+const char *regitr_seqname(regidx_t *idx, regitr_t *itr);
+
 /*
  *  regidx_insert() - add a new region. 
- *
- *  After last region has been added, call regidx_insert(idx,NULL) to
- *  build the index.
+ *  regidx_insert_list() - add new regions from a list
  *
  *  Returns 0 on success or -1 on error.
  */
 int regidx_insert(regidx_t *idx, char *line);
+int regidx_insert_list(regidx_t *idx, char *line, char delim);
 
 /*
  *  regidx_seq_names() - return list of all sequence names

From d4a7db37512b2dac3318f1aa35be7b30dd2150e2 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Mon, 20 Jun 2016 09:58:26 +0100
Subject: [PATCH 202/211] mpileup: support multiple regions

* `-r/--region` replaced by `-r/--regions` which will accept a comma separated
  list of regions as in other bcftools commands. `--region` still accepted
* `-R/--regions-file` option added to read regions from a file

This commit lifts over work originally done in pd3/bcftools@cfd7cf9092ffddc1ec0441a3c463bc2ac7084bad

Note: when more than one region is given, all indices are stored in memory,
which can be a problem when running on many bams. An alternative would be
to cache pre-filled `hts_itr`'s for each region.

Resolves #369
---
 bam2bcf.h        |   5 +-
 bam2bcf_indel.c  |  70 ++----
 doc/bcftools.txt |  12 +-
 mpileup.c        | 589 ++++++++++++++++++++++++++++-------------------
 test/test.pl     |   1 +
 5 files changed, 377 insertions(+), 300 deletions(-)

diff --git a/bam2bcf.h b/bam2bcf.h
index 54e5faaaa..f81f9cf02 100644
--- a/bam2bcf.h
+++ b/bam2bcf.h
@@ -1,7 +1,7 @@
 /*  bam2bcf.h -- variant calling.
 
     Copyright (C) 2010-2012 Broad Institute.
-    Copyright (C) 2012-2014 Genome Research Ltd.
+    Copyright (C) 2012-2014,2016 Genome Research Ltd.
 
     Author: Heng Li <lh3@sanger.ac.uk>
 
@@ -128,8 +128,7 @@ extern "C" {
     int bcf_call_combine(int n, const bcf_callret1_t *calls, bcf_callaux_t *bca, int ref_base /*4-bit*/, bcf_call_t *call);
     int bcf_call2bcf(bcf_call_t *bc, bcf1_t *b, bcf_callret1_t *bcr, int fmt_flag,
                      const bcf_callaux_t *bca, const char *ref);
-    int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
-                          const void *rghash);
+    int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref);
     void bcf_callaux_clean(bcf_callaux_t *bca, bcf_call_t *call);
 
 #ifdef __cplusplus
diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 95cc5b076..9065949af 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -1,7 +1,7 @@
 /*  bam2bcf_indel.c -- indel caller.
 
     Copyright (C) 2010, 2011 Broad Institute.
-    Copyright (C) 2012-2014 Genome Research Ltd.
+    Copyright (C) 2012-2014,2016 Genome Research Ltd.
 
     Author: Heng Li <lh3@sanger.ac.uk>
 
@@ -26,26 +26,24 @@ DEALINGS IN THE SOFTWARE.  */
 #include <assert.h>
 #include <ctype.h>
 #include <string.h>
-#include "htslib/hts.h"
-#include "htslib/sam.h"
+#include <htslib/hts.h>
+#include <htslib/sam.h>
+#include <htslib/khash_str2int.h>
 #include "bam2bcf.h"
-#include "htslib/khash.h"
-KHASH_SET_INIT_STR(rg)
 
-#include "htslib/ksort.h"
+#include <htslib/ksort.h>
 KSORT_INIT_GENERIC(uint32_t)
 
 #define MINUS_CONST 0x10000000
 #define INDEL_WINDOW_SIZE 50
 
-void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
+void *bcf_call_add_rg(void *hash, const char *hdtext, const char *list)
 {
     const char *s, *p, *q, *r, *t;
-    khash_t(rg) *hash;
-    if (list == 0 || hdtext == 0) return _hash;
-    if (_hash == 0) _hash = kh_init(rg);
-    hash = (khash_t(rg)*)_hash;
-    if ((s = strstr(hdtext, "@RG\t")) == 0) return hash;
+
+    if (list == 0 || hdtext == 0) return hash;
+    if ( !hash ) hash = khash_str2int_init();
+    if ((s = strstr(hdtext, "@RG\t")) == 0) return hash;    // @RG lines not present
     do {
         t = strstr(s + 4, "@RG\t"); // the next @RG
         if ((p = strstr(s, "\tID:")) != 0) p += 4;
@@ -60,13 +58,10 @@ void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
             x = (char*) calloc((lp > lq? lp : lq) + 1, 1);
             for (r = q; *r && *r != '\t' && *r != '\n'; ++r) x[r-q] = *r;
             if (strstr(list, x)) { // insert ID to the hash table
-                khint_t k;
-                int ret;
                 for (r = p; *r && *r != '\t' && *r != '\n'; ++r) x[r-p] = *r;
                 x[r-p] = 0;
-                k = kh_get(rg, hash, x);
-                if (k == kh_end(hash)) k = kh_put(rg, hash, x, &ret);
-                else free(x);
+                if ( khash_str2int_has_key(hash,x) ) free(x);
+                else khash_str2int_set(hash,x,1);
             } else free(x);
         }
         s = t;
@@ -74,15 +69,9 @@ void *bcf_call_add_rg(void *_hash, const char *hdtext, const char *list)
     return hash;
 }
 
-void bcf_call_del_rghash(void *_hash)
+void bcf_call_del_rghash(void *hash)
 {
-    khint_t k;
-    khash_t(rg) *hash = (khash_t(rg)*)_hash;
-    if (hash == 0) return;
-    for (k = kh_begin(hash); k < kh_end(hash); ++k)
-        if (kh_exist(hash, k))
-            free((char*)kh_key(hash, k));
-    kh_destroy(rg, hash);
+    khash_str2int_destroy_free(hash);
 }
 
 static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
@@ -144,30 +133,13 @@ static inline int est_indelreg(int pos, const char *ref, int l, char *ins4)
             - 8: estimated sequence quality                     .. (aux>>8)&0xff
             - 8: indel quality                                  .. aux&0xff
  */
-int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref,
-                      const void *rghash)
+int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_callaux_t *bca, const char *ref)
 {
     int i, s, j, k, t, n_types, *types, max_rd_len, left, right, max_ins, *score1, *score2, max_ref2;
     int N, K, l_run, ref_type, n_alt;
     char *inscns = 0, *ref2, *query, **ref_sample;
-    khash_t(rg) *hash = (khash_t(rg)*)rghash;
     if (ref == 0 || bca == 0) return -1;
-    // mark filtered reads
-    if (rghash) {
-        N = 0;
-        for (s = N = 0; s < n; ++s) {
-            for (i = 0; i < n_plp[s]; ++i) {
-                bam_pileup1_t *p = plp[s] + i;
-                const uint8_t *rg = bam_aux_get(p->b, "RG");
-                p->aux = 1; // filtered by default
-                if (rg) {
-                    khint_t k = kh_get(rg, hash, (const char*)(rg + 1));
-                    if (k != kh_end(hash)) p->aux = 0, ++N; // not filtered
-                }
-            }
-        }
-        if (N == 0) return -1; // no reads left
-    }
+
     // determine if there is a gap
     for (s = N = 0; s < n; ++s) {
         for (i = 0; i < n_plp[s]; ++i)
@@ -187,12 +159,10 @@ int bcf_call_gap_prep(int n, int *n_plp, bam_pileup1_t **plp, int pos, bcf_calla
             int na = 0, nt = 0;
             for (i = 0; i < n_plp[s]; ++i) {
                 const bam_pileup1_t *p = plp[s] + i;
-                if (rghash == 0 || p->aux == 0) {
-                    ++nt;
-                    if (p->indel != 0) {
-                        ++na;
-                        aux[m++] = MINUS_CONST + p->indel;
-                    }
+                ++nt;
+                if (p->indel != 0) {
+                    ++na;
+                    aux[m++] = MINUS_CONST + p->indel;
                 }
                 j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b));
                 if (j > max_rd_len) max_rd_len = j;
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 35949ec97..1e966ae9d 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1367,10 +1367,14 @@ regions listed in the BED file.
 *-Q, --min-BQ* 'INT'::
     Minimum base quality for a base to be considered [13]
 
-*-r, --region* 'STR'::
-    Only generate output in region. Requires the alignment files to be
-    indexed.  If used in conjunction with -l then considers the intersection
-    of the two requests [all sites]
+*-r, --regions* 'CHR'|'CHR:POS'|'CHR:FROM-TO'|'CHR:FROM-'[,...]::
+    Only generate mpileup output in given regions. Requires the alignment files
+    to be indexed.  If used in conjunction with -l then considers the intersection;
+    see *<<common_options,Common Options>>*
+
+*-R, --regions-file* 'FILE'::
+    As for *-r, --regions*, but regions read from FILE;
+    see *<<common_options,Common Options>>*
 
 *--ignore-RG*::
     Ignore RG tags. Treat all reads in one alignment file as one sample.
diff --git a/mpileup.c b/mpileup.c
index dbd0d68aa..cfccde46b 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -58,16 +58,39 @@ DEALINGS IN THE SOFTWARE.  */
 #define MPLP_PER_SAMPLE (1<<11)
 #define MPLP_SMART_OVERLAPS (1<<12)
 
+typedef struct _mplp_aux_t mplp_aux_t;
+typedef struct _mplp_pileup_t mplp_pileup_t;
+
+// Data shared by all bam files
 typedef struct {
     int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
     int rflag_require, rflag_filter, output_type, sample_is_file;
     int openQ, extQ, tandemQ, min_support; // for indels
     double min_frac; // for indels
-    char *reg, *pl_list, *fai_fname, *output_fname, *samples_list;
+    char *reg_fname, *pl_list, *fai_fname, *output_fname, *samples_list;
+    int reg_is_file;
     faidx_t *fai;
-    void *rghash_exc;
-    regidx_t *bed;
+    regidx_t *bed, *reg;    // bed: skipping regions, reg: index-jump to regions
     gvcf_t *gvcf;
+
+    // auxiliary structures for calling
+    bcf_callaux_t *bca;
+    bcf_callret1_t *bcr;
+    bcf_call_t bc;
+    bam_mplp_t iter;
+    mplp_aux_t **mplp_data;
+    int nfiles;
+    char **files;
+    mplp_pileup_t *gplp;
+    int *n_plp;
+    const bam_pileup1_t **plp;
+    bam_sample_t *smpl;
+    kstring_t buf;
+    bcf1_t *bcf_rec;
+    htsFile *bcf_fp;
+    bcf_hdr_t *bcf_hdr;
+    void *rghash_exc;   // shared by all bams
+
     int argc;
     char **argv;
 } mplp_conf_t;
@@ -80,20 +103,24 @@ typedef struct {
 
 #define MPLP_REF_INIT {{NULL,NULL},{-1,-1},{0,0}}
 
-typedef struct {
+// Data specific to each bam file
+struct _mplp_aux_t {
     samFile *fp;
     hts_itr_t *iter;
     bam_hdr_t *h;
     mplp_ref_t *ref;
     const mplp_conf_t *conf;
-    void *rghash_inc;   // whitelist for readgroups on per-bam basis
-} mplp_aux_t;
+    void *rghash_inc;   // whitelist for readgroups on per-bam basis, precedes blacklist
+    void *rghash_exc;   // blacklist of readgroups 
+    hts_idx_t *idx;     // maintained only with more than one -r regions
+};
 
-typedef struct {
+// Data passed to htslib/mpileup
+struct _mplp_pileup_t {
     int n;
     int *n_plp, *m_plp;
     bam_pileup1_t **plp;
-} mplp_pileup_t;
+};
 
 static int mplp_get_ref(mplp_aux_t *ma, int tid,  char **ref, int *ref_len) {
     mplp_ref_t *r = ma->ref;
@@ -156,35 +183,34 @@ static int mplp_func(void *data, bam1_t *b)
 {
     char *ref;
     mplp_aux_t *ma = (mplp_aux_t*)data;
-    int ret, skip = 0, ref_len;
-    do {
+    int ret, ref_len;
+    while (1)
+    {
         int has_ref;
-        skip = 0;
         ret = ma->iter? sam_itr_next(ma->fp, ma->iter, b) : sam_read1(ma->fp, ma->h, b);
         if (ret < 0) break;
         // The 'B' cigar operation is not part of the specification, considering as obsolete.
         //  bam_remove_B(b);
-        if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) { // exclude unmapped reads
-            skip = 1;
-            continue;
-        }
-        if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) { skip = 1; continue; }
-        if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) { skip = 1; continue; }
-        if (ma->conf->bed) { // test overlap
-            skip = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],b->core.pos, bam_endpos(b)-1, NULL) ? 0 : 1;
-            if (skip) continue;
+        if (b->core.tid < 0 || (b->core.flag&BAM_FUNMAP)) continue; // exclude unmapped reads
+        if (ma->conf->rflag_require && !(ma->conf->rflag_require&b->core.flag)) continue;
+        if (ma->conf->rflag_filter && ma->conf->rflag_filter&b->core.flag) continue;
+        if (ma->conf->bed)
+        {
+            // test overlap
+            if ( !regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],b->core.pos, bam_endpos(b)-1, NULL) ) continue;
         }
         if (ma->rghash_inc)
         {
             // skip unless read group is listed
             uint8_t *rg = bam_aux_get(b, "RG");
-            if ( !rg ) { skip = 1; continue; }
-            if ( !khash_str2int_has_key(ma->rghash_inc, (const char*)(rg+1)) ) { skip = 1; continue; }
+            if ( !rg ) continue;
+            if ( !khash_str2int_has_key(ma->rghash_inc, (const char*)(rg+1)) ) continue;
         }
-        if (ma->conf->rghash_exc) { // exclude read groups
+        if ( ma->rghash_exc )
+        {
+            // exclude read groups
             uint8_t *rg = bam_aux_get(b, "RG");
-            skip = (rg && khash_str2int_get(ma->conf->rghash_exc, (const char*)(rg+1), NULL)==0);
-            if (skip) continue;
+            if ( rg && khash_str2int_has_key(ma->rghash_exc, (const char*)(rg+1)) ) continue;
         }
         if (ma->conf->flag & MPLP_ILLUMINA13) {
             int i;
@@ -198,23 +224,23 @@ static int mplp_func(void *data, bam1_t *b)
             if (has_ref && ref_len <= b->core.pos) { // exclude reads outside of the reference sequence
                 fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n",
                         __func__, b->core.pos, ref_len, b->core.tid);
-                skip = 1;
                 continue;
             }
         } else {
             has_ref = 0;
         }
 
-        skip = 0;
         if (has_ref && (ma->conf->flag&MPLP_REALN)) sam_prob_realn(b, ref, ref_len, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3);
         if (has_ref && ma->conf->capQ_thres > 10) {
             int q = sam_cap_mapq(b, ref, ref_len, ma->conf->capQ_thres);
-            if (q < 0) skip = 1;
+            if (q < 0) continue;    // skip
             else if (b->core.qual > q) b->core.qual = q;
         }
-        if (b->core.qual < ma->conf->min_mq) skip = 1;
-        else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) skip = 1;
-    } while (skip);
+        if (b->core.qual < ma->conf->min_mq) continue;
+        else if ((ma->conf->flag&MPLP_NO_ORPHAN) && (b->core.flag&BAM_FPAIRED) && !(b->core.flag&BAM_FPROPER_PAIR)) continue;
+
+        return ret;
+    };
     return ret;
 }
 
@@ -270,48 +296,70 @@ static void flush_bcf_records(mplp_conf_t *conf, htsFile *fp, bcf_hdr_t *hdr, bc
     if ( rec ) bcf_write1(fp,hdr,rec);
 }
 
-/*
- * Performs pileup
- * @param conf configuration for this pileup
- * @param n number of files specified in fn
- * @param fn filenames
- */
-static int mpileup(mplp_conf_t *conf, int n, char **fn)
+static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end)
 {
-    extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
-    extern void bcf_call_del_rghash(void *rghash);
-    mplp_aux_t **data;
-    int i, tid, pos, *n_plp, beg0 = 0, end0 = INT_MAX, ref_len, max_depth, max_indel_depth;
-    const bam_pileup1_t **plp;
-    mplp_ref_t mp_ref = MPLP_REF_INIT;
-    bam_mplp_t iter;
-    bam_hdr_t *h = NULL; /* header of first file in input list */
+    bam_hdr_t *hdr = conf->mplp_data[0]->h; // header of first file in input list
+
+    int ret, i, tid, pos, ref_len;
     char *ref;
-    void *rghash_exc = NULL;
 
-    bcf_callaux_t *bca = NULL;
-    bcf_callret1_t *bcr = NULL;
-    bcf_call_t bc;
-    htsFile *bcf_fp = NULL;
-    bcf_hdr_t *bcf_hdr = NULL;
+    while ( (ret=bam_mplp_auto(conf->iter, &tid, &pos, conf->n_plp, conf->plp)) > 0) 
+    {
+        if ( end && (pos<beg || pos>end) ) continue;
+        if (conf->bed && tid >= 0 && !regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL)) continue;
+        mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len);
 
-    bam_sample_t *sm = NULL;
-    kstring_t buf;
-    mplp_pileup_t gplp;
+        int total_depth, _ref0, ref16;
+        for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i];
+        group_smpl(conf->gplp, conf->smpl, &conf->buf, conf->nfiles, conf->files, conf->n_plp, conf->plp, conf->flag & MPLP_IGNORE_RG);
+        _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
+        ref16 = seq_nt16_table[_ref0];
+        bcf_callaux_clean(conf->bca, &conf->bc);
+        for (i = 0; i < conf->gplp->n; ++i)
+            bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], ref16, conf->bca, conf->bcr + i);
+        conf->bc.tid = tid; conf->bc.pos = pos;
+        bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, ref16, &conf->bc);
+        bcf_clear1(conf->bcf_rec);
+        bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, 0, 0);
+        flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
+
+        // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
+        // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them
+        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < conf->max_indel_depth 
+            && bcf_call_gap_prep(conf->gplp->n, conf->gplp->n_plp, conf->gplp->plp, pos, conf->bca, ref) >= 0)
+        {
+            bcf_callaux_clean(conf->bca, &conf->bc);
+            for (i = 0; i < conf->gplp->n; ++i)
+                bcf_call_glfgen(conf->gplp->n_plp[i], conf->gplp->plp[i], -1, conf->bca, conf->bcr + i);
+            if (bcf_call_combine(conf->gplp->n, conf->bcr, conf->bca, -1, &conf->bc) >= 0) 
+            {
+                bcf_clear1(conf->bcf_rec);
+                bcf_call2bcf(&conf->bc, conf->bcf_rec, conf->bcr, conf->fmt_flag, conf->bca, ref);
+                flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, conf->bcf_rec);
+            }
+        }
+    }
+    return 0;
+}
 
-    memset(&gplp, 0, sizeof(mplp_pileup_t));
-    memset(&buf, 0, sizeof(kstring_t));
-    memset(&bc, 0, sizeof(bcf_call_t));
-    data = (mplp_aux_t**) calloc(n, sizeof(mplp_aux_t*));
-    plp = (const bam_pileup1_t**) calloc(n, sizeof(bam_pileup1_t*));
-    n_plp = (int*) calloc(n, sizeof(int));
-    sm = bam_smpl_init();
+static int mpileup(mplp_conf_t *conf)
+{
+    extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
+    extern void bcf_call_del_rghash(void *rghash);
 
-    if (n == 0) {
+    if (conf->nfiles == 0) {
         fprintf(stderr,"[%s] no input file/data given\n", __func__);
         exit(EXIT_FAILURE);
     }
 
+    mplp_ref_t mp_ref = MPLP_REF_INIT;
+    conf->gplp = (mplp_pileup_t *) calloc(1,sizeof(mplp_pileup_t));
+    conf->mplp_data = (mplp_aux_t**) calloc(conf->nfiles, sizeof(mplp_aux_t*));
+    conf->plp = (const bam_pileup1_t**) calloc(conf->nfiles, sizeof(bam_pileup1_t*));
+    conf->n_plp = (int*) calloc(conf->nfiles, sizeof(int));
+    conf->smpl = bam_smpl_init();
+
+    int i;
     void *samples_inc = NULL;
     if ( conf->samples_list )
     {
@@ -330,270 +378,313 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn)
         free(samples);
     }
 
+    // Allow to run mpileup on multiple regions in one go. This comes at cost: the bai index
+    // must be kept in the memory for the whole time which can be a problem with many bams.
+    // Therefore if none or only one region is requested, we initialize the bam iterator as
+    // before and free the index. Only when multiple regions are queried, we keep the index.
+    regitr_t reg_itr;
+    REGITR_INIT(reg_itr);
+    int nregs = 0;
+    if ( conf->reg_fname )
+    {
+        if ( conf->reg_is_file )
+        {
+            conf->reg = regidx_init(conf->reg_fname,NULL,NULL,0,NULL);
+            if ( !conf->reg ) {
+                fprintf(stderr,"Could not parse the regions: %s\n", conf->reg_fname);
+                exit(EXIT_FAILURE);
+            }
+        }
+        else
+        {
+            conf->reg = regidx_init(NULL,regidx_parse_reg,NULL,sizeof(char*),NULL);
+            if ( regidx_insert_list(conf->reg,conf->reg_fname,',') !=0 ) {
+                fprintf(stderr,"Could not parse the regions: %s\n", conf->reg_fname);
+                exit(EXIT_FAILURE);
+            }
+        }
+        nregs = regidx_nregs(conf->reg);
+        regidx_loop(conf->reg,&reg_itr);    // position the region iterator at the first region
+    }
+
     // read the header of each file in the list and initialize data
-    for (i = 0; i < n; ++i) {
+    // beware: mpileup has always assumed that tid's are consistent in the headers, add sanity check at least!
+    bam_hdr_t *hdr = NULL;      // header of first file in input list
+    for (i = 0; i < conf->nfiles; ++i) {
         bam_hdr_t *h_tmp;
-        data[i] = (mplp_aux_t*) calloc(1, sizeof(mplp_aux_t));
-        data[i]->fp = sam_open(fn[i], "rb");
-        if ( !data[i]->fp )
+        conf->mplp_data[i] = (mplp_aux_t*) calloc(1, sizeof(mplp_aux_t));
+        conf->mplp_data[i]->fp = sam_open(conf->files[i], "rb");
+        if ( !conf->mplp_data[i]->fp )
         {
-            fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, fn[i], strerror(errno));
+            fprintf(stderr, "[%s] failed to open %s: %s\n", __func__, conf->files[i], strerror(errno));
             exit(EXIT_FAILURE);
         }
-        if (hts_set_opt(data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
+        if (hts_set_opt(conf->mplp_data[i]->fp, CRAM_OPT_DECODE_MD, 0)) {
             fprintf(stderr, "Failed to set CRAM_OPT_DECODE_MD value\n");
             exit(EXIT_FAILURE);
         }
-        if (conf->fai_fname && hts_set_fai_filename(data[i]->fp, conf->fai_fname) != 0) {
+        if (conf->fai_fname && hts_set_fai_filename(conf->mplp_data[i]->fp, conf->fai_fname) != 0) {
             fprintf(stderr, "[%s] failed to process %s: %s\n",
                     __func__, conf->fai_fname, strerror(errno));
             exit(EXIT_FAILURE);
         }
-        data[i]->conf = conf;
-        data[i]->ref = &mp_ref;
-        h_tmp = sam_hdr_read(data[i]->fp);
+        conf->mplp_data[i]->conf = conf;
+        conf->mplp_data[i]->ref = &mp_ref;
+        h_tmp = sam_hdr_read(conf->mplp_data[i]->fp);
         if ( !h_tmp ) {
-            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, fn[i]);
+            fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, conf->files[i]);
             exit(EXIT_FAILURE);
         }
-        if ( samples_inc ) data[i]->rghash_inc = khash_str2int_init();
-        bam_smpl_add(sm, fn[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text, samples_inc, data[i]->rghash_inc);
+        conf->mplp_data[i]->h = i? hdr : h_tmp; // for i==0, "h" has not been set yet
+        conf->mplp_data[i]->rghash_exc = conf->rghash_exc;
+        if ( samples_inc ) conf->mplp_data[i]->rghash_inc = khash_str2int_init();
+        bam_smpl_add(conf->smpl, conf->files[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text, samples_inc, conf->mplp_data[i]->rghash_inc);
         // Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
-        rghash_exc = bcf_call_add_rg(rghash_exc, h_tmp->text, conf->pl_list);
+        conf->mplp_data[i]->rghash_exc = bcf_call_add_rg(conf->mplp_data[i]->rghash_exc, h_tmp->text, conf->pl_list);
         if (conf->reg) {
-            hts_idx_t *idx = sam_index_load(data[i]->fp, fn[i]);
+            hts_idx_t *idx = sam_index_load(conf->mplp_data[i]->fp, conf->files[i]);
             if (idx == NULL) {
-                fprintf(stderr, "[%s] fail to load index for %s\n", __func__, fn[i]);
+                fprintf(stderr, "[%s] fail to load index for %s\n", __func__, conf->files[i]);
                 exit(EXIT_FAILURE);
             }
-            if ( (data[i]->iter=sam_itr_querys(idx, h_tmp, conf->reg)) == 0) {
-                fprintf(stderr, "[E::%s] fail to parse region '%s' with %s\n", __func__, conf->reg, fn[i]);
+            conf->buf.l = 0;
+            ksprintf(&conf->buf,"%s:%u-%u",regitr_seqname(conf->reg,&reg_itr),REGITR_START(reg_itr)+1,REGITR_END(reg_itr)+1);
+            conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, conf->buf.s);
+            if ( !conf->mplp_data[i]->iter ) 
+            {
+                conf->mplp_data[i]->iter = sam_itr_querys(idx, conf->mplp_data[i]->h, regitr_seqname(conf->reg,&reg_itr));
+                if ( conf->mplp_data[i]->iter ) {
+                    fprintf(stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s);
+                    exit(EXIT_FAILURE);
+                }
+                fprintf(stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,regitr_seqname(conf->reg,&reg_itr),conf->files[i]);
                 exit(EXIT_FAILURE);
             }
-            if (i == 0) beg0 = data[i]->iter->beg, end0 = data[i]->iter->end;
-            hts_idx_destroy(idx);
+            if ( nregs==1 ) // no need to keep the index in memory
+               hts_idx_destroy(idx);
+            else
+                conf->mplp_data[i]->idx = idx;
         }
-        else
-            data[i]->iter = NULL;
 
-        if (i == 0) h = data[i]->h = h_tmp; // save the header of the first file
+        if (i == 0) hdr = h_tmp; /* save the header of first file in list */
         else {
             // FIXME: check consistency between h and h_tmp
             bam_hdr_destroy(h_tmp);
 
             // we store only the first file's header; it's (alleged to be)
             // compatible with the i-th file's target_name lookup needs
-            data[i]->h = h;
+            conf->mplp_data[i]->h = hdr;
         }
     }
     // allocate data storage proportionate to number of samples being studied sm->n
-    gplp.n = sm->n;
-    gplp.n_plp = (int*) calloc(sm->n, sizeof(int));
-    gplp.m_plp = (int*) calloc(sm->n, sizeof(int));
-    gplp.plp = (bam_pileup1_t**) calloc(sm->n, sizeof(bam_pileup1_t*));
+    conf->gplp->n = conf->smpl->n;
+    conf->gplp->n_plp = (int*) calloc(conf->smpl->n, sizeof(int));
+    conf->gplp->m_plp = (int*) calloc(conf->smpl->n, sizeof(int));
+    conf->gplp->plp = (bam_pileup1_t**) calloc(conf->smpl->n, sizeof(bam_pileup1_t*));  
 
-    fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, sm->n, n);
+    fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, conf->smpl->n, conf->nfiles);
     // write the VCF header
-    bcf_fp = hts_open(conf->output_fname?conf->output_fname:"-", hts_bcf_wmode(conf->output_type));
-    if (bcf_fp == NULL) {
+    conf->bcf_fp = hts_open(conf->output_fname?conf->output_fname:"-", hts_bcf_wmode(conf->output_type));
+    if (conf->bcf_fp == NULL) {
         fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
         exit(EXIT_FAILURE);
     }
 
     // BCF header creation
-    bcf_hdr = bcf_hdr_init("w");
-    kstring_t str = {0,0,NULL};
+    conf->bcf_hdr = bcf_hdr_init("w");
+    conf->buf.l = 0;
 
-    ksprintf(&str, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
-    bcf_hdr_append(bcf_hdr, str.s);
+    ksprintf(&conf->buf, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
+    bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
 
-    str.l = 0;
-    ksprintf(&str, "##bcftoolsCommand=mpileup");
-    for (i=1; i<conf->argc; i++) ksprintf(&str, " %s", conf->argv[i]);
-    kputc('\n', &str);
-    bcf_hdr_append(bcf_hdr, str.s);
+    conf->buf.l = 0;
+    ksprintf(&conf->buf, "##bcftoolsCommand=mpileup");
+    for (i=1; i<conf->argc; i++) ksprintf(&conf->buf, " %s", conf->argv[i]);
+    kputc('\n', &conf->buf);
+    bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
 
     if (conf->fai_fname)
     {
-        str.l = 0;
-        ksprintf(&str, "##reference=file://%s\n", conf->fai_fname);
-        bcf_hdr_append(bcf_hdr, str.s);
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##reference=file://%s\n", conf->fai_fname);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
     }
 
     // Translate BAM @SQ tags to BCF ##contig tags
     // todo: use/write new BAM header manipulation routines, fill also UR, M5
-    for (i=0; i<h->n_targets; i++)
+    for (i=0; i<hdr->n_targets; i++)
     {
-        str.l = 0;
-        ksprintf(&str, "##contig=<ID=%s,length=%d>", h->target_name[i], h->target_len[i]);
-        bcf_hdr_append(bcf_hdr, str.s);
-    }
-    free(str.s);
-    bcf_hdr_append(bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##contig=<ID=%s,length=%d>", hdr->target_name[i], hdr->target_len[i]);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    }
+    conf->buf.l = 0;
+
+    bcf_hdr_append(conf->bcf_hdr,"##ALT=<ID=*,Description=\"Represents allele(s) other than observed.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=INDEL,Number=0,Type=Flag,Description=\"Indicates that the variant is an INDEL.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=IDV,Number=1,Type=Integer,Description=\"Maximum number of reads supporting an indel\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=IMF,Number=1,Type=Float,Description=\"Maximum fraction of reads supporting an indel\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=DP,Number=1,Type=Integer,Description=\"Raw read depth\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=VDB,Number=1,Type=Float,Description=\"Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)\",Version=\"3\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSB,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)\">");
 #if CDF_MWU_TESTS
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=RPB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Read Position Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=BQB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Base Quality Bias [CDF] (bigger is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQSB2,Number=1,Type=Float,Description=\"Mann-Whitney U test of Mapping Quality vs Strand Bias [CDF] (bigger is better)\">");
 #endif
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
-    bcf_hdr_append(bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
-    bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=SGB,Number=1,Type=Float,Description=\"Segregation based metric.\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=MQ0F,Number=1,Type=Float,Description=\"Fraction of MQ0 reads (smaller is better)\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=I16,Number=16,Type=Float,Description=\"Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h\">");
+    bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=QS,Number=R,Type=Float,Description=\"Auxiliary tag used for calling\">");
+    bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=PL,Number=G,Type=Integer,Description=\"List of Phred-scaled genotype likelihoods\">");
     if ( conf->fmt_flag&B2B_FMT_DP )
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DP,Number=1,Type=Integer,Description=\"Number of high-quality bases\">");
     if ( conf->fmt_flag&B2B_FMT_DV )
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DV,Number=1,Type=Integer,Description=\"Number of high-quality non-reference bases\">");
     if ( conf->fmt_flag&B2B_FMT_DPR )
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
     if ( conf->fmt_flag&B2B_INFO_DPR )
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=DPR,Number=R,Type=Integer,Description=\"Number of high-quality bases observed for each allele\">");
     if ( conf->fmt_flag&B2B_FMT_DP4 )
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=DP4,Number=4,Type=Integer,Description=\"Number of high-quality ref-fwd, ref-reverse, alt-fwd and alt-reverse bases\">");
     if ( conf->fmt_flag&B2B_FMT_SP )
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=SP,Number=1,Type=Integer,Description=\"Phred-scaled strand bias P-value\">");
     if ( conf->fmt_flag&B2B_FMT_AD )
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=AD,Number=R,Type=Integer,Description=\"Allelic depths\">");
     if ( conf->fmt_flag&B2B_FMT_ADF )
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=ADF,Number=R,Type=Integer,Description=\"Allelic depths on the forward strand\">");
     if ( conf->fmt_flag&B2B_FMT_ADR )
-        bcf_hdr_append(bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
+        bcf_hdr_append(conf->bcf_hdr,"##FORMAT=<ID=ADR,Number=R,Type=Integer,Description=\"Allelic depths on the reverse strand\">");
     if ( conf->fmt_flag&B2B_INFO_AD )
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=AD,Number=R,Type=Integer,Description=\"Total allelic depths\">");
     if ( conf->fmt_flag&B2B_INFO_ADF )
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=ADF,Number=R,Type=Integer,Description=\"Total allelic depths on the forward strand\">");
     if ( conf->fmt_flag&B2B_INFO_ADR )
-        bcf_hdr_append(bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
+        bcf_hdr_append(conf->bcf_hdr,"##INFO=<ID=ADR,Number=R,Type=Integer,Description=\"Total allelic depths on the reverse strand\">");
     if ( conf->gvcf )
-        gvcf_update_header(conf->gvcf, bcf_hdr);
-
-    for (i=0; i<sm->n; i++)
-        bcf_hdr_add_sample(bcf_hdr, sm->smpl[i]);
-    bcf_hdr_add_sample(bcf_hdr, NULL);
-    bcf_hdr_write(bcf_fp, bcf_hdr);
-    // End of BCF header creation
-
-    // Initialise the calling algorithm
-    bca = bcf_call_init(-1., conf->min_baseQ);
-    bcr = (bcf_callret1_t*) calloc(sm->n, sizeof(bcf_callret1_t));
-    bca->openQ = conf->openQ, bca->extQ = conf->extQ, bca->tandemQ = conf->tandemQ;
-    bca->min_frac = conf->min_frac;
-    bca->min_support = conf->min_support;
-    bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
-
-    bc.bcf_hdr = bcf_hdr;
-    bc.n = sm->n;
-    bc.PL = (int32_t*) malloc(15 * sm->n * sizeof(*bc.PL));
+        gvcf_update_header(conf->gvcf, conf->bcf_hdr);
+
+    for (i=0; i<conf->smpl->n; i++)
+        bcf_hdr_add_sample(conf->bcf_hdr, conf->smpl->smpl[i]);
+    bcf_hdr_add_sample(conf->bcf_hdr, NULL);
+    bcf_hdr_write(conf->bcf_fp, conf->bcf_hdr);
+
+    conf->bca = bcf_call_init(-1., conf->min_baseQ);
+    conf->bcr = (bcf_callret1_t*) calloc(conf->smpl->n, sizeof(bcf_callret1_t));
+    conf->bca->openQ = conf->openQ, conf->bca->extQ = conf->extQ, conf->bca->tandemQ = conf->tandemQ;
+    conf->bca->min_frac = conf->min_frac;
+    conf->bca->min_support = conf->min_support;
+    conf->bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
+
+    conf->bc.bcf_hdr = conf->bcf_hdr;
+    conf->bc.n = conf->smpl->n;
+    conf->bc.PL = (int32_t*) malloc(15 * conf->smpl->n * sizeof(*conf->bc.PL));
     if (conf->fmt_flag)
     {
         assert( sizeof(float)==sizeof(int32_t) );
-        bc.DP4 = (int32_t*) malloc(sm->n * sizeof(int32_t) * 4);
-        bc.fmt_arr = (uint8_t*) malloc(sm->n * sizeof(float)); // all fmt_flag fields
+        conf->bc.DP4 = (int32_t*) malloc(conf->smpl->n * sizeof(int32_t) * 4);
+        conf->bc.fmt_arr = (uint8_t*) malloc(conf->smpl->n * sizeof(float)); // all fmt_flag fields, float and int32
         if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
         {
             // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
-            bc.ADR = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
-            bc.ADF = (int32_t*) malloc((sm->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
-            for (i=0; i<sm->n; i++)
+            conf->bc.ADR = (int32_t*) malloc((conf->smpl->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            conf->bc.ADF = (int32_t*) malloc((conf->smpl->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            for (i=0; i<conf->smpl->n; i++)
             {
-                bcr[i].ADR = bc.ADR + (i+1)*B2B_MAX_ALLELES;
-                bcr[i].ADF = bc.ADF + (i+1)*B2B_MAX_ALLELES;
+                conf->bcr[i].ADR = conf->bc.ADR + (i+1)*B2B_MAX_ALLELES;
+                conf->bcr[i].ADF = conf->bc.ADF + (i+1)*B2B_MAX_ALLELES;
             }
         }
     }
 
-    // init pileup
-    iter = bam_mplp_init(n, mplp_func, (void**)data);
-    if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(iter);
-    max_depth = conf->max_depth;
-    if (max_depth * sm->n > 1<<20)
+    // init mpileup
+    conf->iter = bam_mplp_init(conf->nfiles, mplp_func, (void**)conf->mplp_data);
+    if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(conf->iter);
+    if ( conf->max_depth * conf->smpl->n > 1<<20)
         fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
-    if (max_depth * sm->n < 8000) {
-        max_depth = 8000 / sm->n;
-        fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, max_depth);
+    if ( conf->max_depth * conf->smpl->n < 8000) {
+        conf->max_depth = 8000 / conf->smpl->n;
+        fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, conf->max_depth);
     }
-    max_indel_depth = conf->max_indel_depth * sm->n;
-    bam_mplp_set_maxcnt(iter, max_depth);
-    bcf1_t *bcf_rec = bcf_init1();
-    int ret;
-    // begin pileup
-    while ( (ret=bam_mplp_auto(iter, &tid, &pos, n_plp, plp)) > 0) {
-        if (conf->reg && (pos < beg0 || pos >= end0)) continue; // out of the region requested
-        if (conf->bed && tid >= 0 && !regidx_overlap(conf->bed, h->target_name[tid], pos, pos, NULL)) continue;
-        mplp_get_ref(data[0], tid, &ref, &ref_len);
-        //printf("tid=%d len=%d ref=%p/%s\n", tid, ref_len, ref, ref);
-        int total_depth, _ref0, ref16;
-        for (i = total_depth = 0; i < n; ++i) total_depth += n_plp[i];
-        group_smpl(&gplp, sm, &buf, n, fn, n_plp, plp, conf->flag & MPLP_IGNORE_RG);
-        _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
-        ref16 = seq_nt16_table[_ref0];
-        bcf_callaux_clean(bca, &bc);
-        for (i = 0; i < gplp.n; ++i)
-            bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], ref16, bca, bcr + i);
-        bc.tid = tid; bc.pos = pos;
-        bcf_call_combine(gplp.n, bcr, bca, ref16, &bc);
-        bcf_clear1(bcf_rec);
-        bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, 0, 0);
-        flush_bcf_records(conf, bcf_fp, bcf_hdr, bcf_rec);
-        // call indels; todo: subsampling with total_depth>max_indel_depth instead of ignoring?
-        // check me: rghash in bcf_call_gap_prep() should have no effect, reads mplp_func already excludes them
-        if (!(conf->flag&MPLP_NO_INDEL) && total_depth < max_indel_depth && bcf_call_gap_prep(gplp.n, gplp.n_plp, gplp.plp, pos, bca, ref, NULL) >= 0)
+    bam_mplp_set_maxcnt(conf->iter, conf->max_depth);
+    conf->max_indel_depth = conf->max_indel_depth * conf->smpl->n;
+    conf->bcf_rec = bcf_init1();
+
+    // Run mpileup for multiple regions
+    if ( nregs )
+    {
+        int ireg = 0;
+        do 
         {
-            bcf_callaux_clean(bca, &bc);
-            for (i = 0; i < gplp.n; ++i)
-                bcf_call_glfgen(gplp.n_plp[i], gplp.plp[i], -1, bca, bcr + i);
-            if (bcf_call_combine(gplp.n, bcr, bca, -1, &bc) >= 0) {
-                bcf_clear1(bcf_rec);
-                bcf_call2bcf(&bc, bcf_rec, bcr, conf->fmt_flag, bca, ref);
-                flush_bcf_records(conf, bcf_fp, bcf_hdr, bcf_rec);
+            // first region is already positioned
+            if ( ireg++ > 0 )
+            {
+                conf->buf.l = 0;
+                ksprintf(&conf->buf,"%s:%u-%u",regitr_seqname(conf->reg,&reg_itr),REGITR_START(reg_itr),REGITR_END(reg_itr));
+
+                for (i=0; i<conf->nfiles; i++) 
+                {
+                    hts_itr_destroy(conf->mplp_data[i]->iter);
+                    conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, conf->buf.s);
+                    if ( !conf->mplp_data[i]->iter ) 
+                    {
+                        conf->mplp_data[i]->iter = sam_itr_querys(conf->mplp_data[i]->idx, conf->mplp_data[i]->h, regitr_seqname(conf->reg,&reg_itr));
+                        if ( conf->mplp_data[i]->iter ) {
+                            fprintf(stderr,"[E::%s] fail to parse region '%s'\n", __func__, conf->buf.s);
+                            exit(EXIT_FAILURE);
+                        }
+                        fprintf(stderr,"[E::%s] the sequence \"%s\" not found: %s\n",__func__,regitr_seqname(conf->reg,&reg_itr),conf->files[i]);
+                        exit(EXIT_FAILURE);
+                    }
+                    bam_mplp_reset(conf->iter);
+                }
             }
+            mpileup_reg(conf,REGITR_START(reg_itr),REGITR_END(reg_itr));
         }
+        while ( regidx_loop(conf->reg,&reg_itr) );
     }
-    flush_bcf_records(conf, bcf_fp, bcf_hdr, NULL);
+    else
+        mpileup_reg(conf,0,0);
+
+    flush_bcf_records(conf, conf->bcf_fp, conf->bcf_hdr, NULL);
 
     // clean up
-    free(bc.tmp.s);
-    bcf_destroy1(bcf_rec);
-    if (bcf_fp)
+    free(conf->bc.tmp.s);
+    bcf_destroy1(conf->bcf_rec);
+    if (conf->bcf_fp)
     {
-        hts_close(bcf_fp);
-        bcf_hdr_destroy(bcf_hdr);
-        bcf_call_destroy(bca);
-        free(bc.PL);
-        free(bc.DP4);
-        free(bc.ADR);
-        free(bc.ADF);
-        free(bc.fmt_arr);
-        free(bcr);
+        hts_close(conf->bcf_fp);
+        bcf_hdr_destroy(conf->bcf_hdr);
+        bcf_call_destroy(conf->bca);
+        free(conf->bc.PL);
+        free(conf->bc.DP4);
+        free(conf->bc.ADR);
+        free(conf->bc.ADF);
+        free(conf->bc.fmt_arr);
+        free(conf->bcr);
     }
     if ( conf->gvcf ) gvcf_destroy(conf->gvcf);
-    bam_smpl_destroy(sm); free(buf.s);
-    for (i = 0; i < gplp.n; ++i) free(gplp.plp[i]);
-    free(gplp.plp); free(gplp.n_plp); free(gplp.m_plp);
-    bcf_call_del_rghash(rghash_exc);
-    bam_mplp_destroy(iter);
-    bam_hdr_destroy(h);
-    for (i = 0; i < n; ++i) {
-        sam_close(data[i]->fp);
-        if (data[i]->iter) hts_itr_destroy(data[i]->iter);
-        if ( data[i]->rghash_inc ) khash_str2int_destroy_free(data[i]->rghash_inc);
-        free(data[i]);
+    bam_smpl_destroy(conf->smpl); free(conf->buf.s);
+    for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]);
+    free(conf->gplp->plp); free(conf->gplp->n_plp); free(conf->gplp->m_plp); free(conf->gplp);
+    bam_mplp_destroy(conf->iter);
+    bam_hdr_destroy(hdr);
+    for (i = 0; i < conf->nfiles; ++i) {
+        if ( nregs>1 ) hts_idx_destroy(conf->mplp_data[i]->idx);
+        sam_close(conf->mplp_data[i]->fp);
+        if ( conf->mplp_data[i]->iter) hts_itr_destroy(conf->mplp_data[i]->iter);
+        if ( conf->mplp_data[i]->rghash_inc ) khash_str2int_destroy_free(conf->mplp_data[i]->rghash_inc);
+        free(conf->mplp_data[i]);
     }
-    free(data); free(plp); free(n_plp);
+    free(conf->mplp_data); free(conf->plp); free(conf->n_plp);
     if ( samples_inc ) khash_str2int_destroy_free(samples_inc);
     free(mp_ref.ref[0]);
     free(mp_ref.ref[1]);
-    return ret;
+    return 0;
 }
 
 #define MAX_PATH_LEN 1024
@@ -732,7 +823,8 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
     fprintf(fp,
 "  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
     fprintf(fp,
-"  -r, --region REG        region in which pileup is generated\n"
+"  -r, --regions REG[,...] comma separated list of regions in which pileup is generated\n"
+"  -R, --regions-file FILE restrict to regions listed in a file\n"
 "      --ignore-RG         ignore RG tags (one BAM = one sample)\n"
 "  --rf, --incl-flags STR|INT  required flags: skip reads with mask bits unset [%s]\n", tmp_require);
     fprintf(fp,
@@ -820,6 +912,8 @@ int bam_mpileup(int argc, char *argv[])
         {"exclude-rg", required_argument, NULL, 'G'},
         {"positions", required_argument, NULL, 'l'},
         {"region", required_argument, NULL, 'r'},
+        {"regions", required_argument, NULL, 'r'},
+        {"regions-file", required_argument, NULL, 'R'},
         {"min-MQ", required_argument, NULL, 'q'},
         {"min-mq", required_argument, NULL, 'q'},
         {"min-BQ", required_argument, NULL, 'Q'},
@@ -840,7 +934,7 @@ int bam_mpileup(int argc, char *argv[])
         {"platforms", required_argument, NULL, 'P'},
         {NULL, 0, NULL, 0}
     };
-    while ((c = getopt_long(argc, argv, "Ag:f:r:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:",lopts,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "Ag:f:r:R:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:",lopts,NULL)) >= 0) {
         switch (c) {
         case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
         case  1 :
@@ -864,7 +958,8 @@ int bam_mpileup(int argc, char *argv[])
             mplp.fai_fname = optarg;
             break;
         case 'd': mplp.max_depth = atoi(optarg); break;
-        case 'r': mplp.reg = strdup(optarg); break;
+        case 'r': mplp.reg_fname = strdup(optarg); break;
+        case 'R': mplp.reg_fname = strdup(optarg); mplp.reg_is_file = 1; break;
         case 'l':
                   // In the original version the whole BAM was streamed which is inefficient
                   //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
@@ -964,17 +1059,25 @@ int bam_mpileup(int argc, char *argv[])
         return 1;
     }
     int ret;
-    if (file_list) {
+    if (file_list) 
+    {
         if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
-        ret = mpileup(&mplp,nfiles,fn);
+        mplp.files  = fn;
+        mplp.nfiles = nfiles;
+        ret = mpileup(&mplp);
         for (c=0; c<nfiles; c++) free(fn[c]);
         free(fn);
     }
     else
-        ret = mpileup(&mplp, argc - optind, argv + optind);
+    {
+        mplp.nfiles = argc - optind;
+        mplp.files  = argv + optind;
+        ret = mpileup(&mplp);
+    }
     if (mplp.rghash_exc) khash_str2int_destroy_free(mplp.rghash_exc);
-    free(mplp.reg); free(mplp.pl_list);
+    free(mplp.reg_fname); free(mplp.pl_list);
     if (mplp.fai) fai_destroy(mplp.fai);
     if (mplp.bed) regidx_destroy(mplp.bed);
+    if (mplp.reg) regidx_destroy(mplp.reg);
     return ret;
 }
diff --git a/test/test.pl b/test/test.pl
index f34d563f1..b6ea2304d 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -255,6 +255,7 @@
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.5.out',args=>q[-a DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -r17:100-600]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-a DP,DV -r17:100-600 --gvcf 0,2,5]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -s HG00101,HG00102]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -S {PATH}/mplp.samples]);
 

From ceb0a20edc0b7c0384d3c9a1330a9f1704f9176f Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 22 Jun 2016 10:38:52 +0100
Subject: [PATCH 203/211] mpileup: in read_file_list(), check for URL syntax or
 extant files

see samtools/samtools@91283dd2093f7ce7a2e1bda34db72f12df2aa7ae
---
 mpileup.c    |  9 ++++++++-
 test/test.pl | 28 +++++++++++++++++++++++++++-
 2 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/mpileup.c b/mpileup.c
index cfccde46b..f76f12e57 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -687,6 +687,13 @@ static int mpileup(mplp_conf_t *conf)
     return 0;
 }
 
+static int is_url(const char *s)
+{
+    static const char uri_scheme_chars[] =
+        "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+.-";
+    return s[strspn(s, uri_scheme_chars)] == ':';
+}
+
 #define MAX_PATH_LEN 1024
 int read_file_list(const char *file_list,int *n,char **argv[])
 {
@@ -716,7 +723,7 @@ int read_file_list(const char *file_list,int *n,char **argv[])
 
         // check sanity of the file list
         buf[len] = 0;
-        if (stat(buf, &sb) != 0)
+        if (! (is_url(buf) || stat(buf, &sb) == 0))
         {
             // no such file, check if it is safe to print its name
             int i, safe_to_print = 1;
diff --git a/test/test.pl b/test/test.pl
index b6ea2304d..5304e1575 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -30,6 +30,7 @@
 use lib "$FindBin::Bin";
 use Getopt::Long;
 use File::Temp qw/ tempfile tempdir /;
+use Cwd qw/ abs_path /;
 
 my $opts = parse_params();
 
@@ -249,7 +250,7 @@
 test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.1.out',fa=>'consensus2.fa',args=>'-H 1');
 test_vcf_consensus($opts,in=>'consensus2',out=>'consensus2.2.out',fa=>'consensus2.fa',args=>'-H 2');
 test_vcf_consensus($opts,in=>'empty',out=>'consensus.5.out',fa=>'consensus.fa',args=>'');
-test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.1.out',args=>q[-r17:100-150]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.1.out',args=>q[-r17:100-150],test_list=>1);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.2.out',args=>q[-a DP,DV -r17:100-600]); # test files from samtools mpileup test suite
 test_mpileup($opts,in=>[qw(1)],out=>'mpileup/mpileup.3.out',args=>q[-B --ff 0x14 -r17:1050-1060]); # test file converted to vcf from samtools mpileup test suite
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.4.out',args=>q[-a DP,DPR,DV,DP4,INFO/DPR,SP -r17:100-600]); #test files from samtools mpileup test suite
@@ -935,6 +936,26 @@ sub test_mpileup
 {
     my ($opts,%args) = @_;
 
+    if ($args{test_list})
+    {
+        # make a local copy, create bams, index the bams and the reference
+        open(my $fh1,'>',"$$opts{tmp}/mpileup.bam.list") or error("$$opts{tmp}/mpileup.bam.list: $!");
+        open(my $fh2,'>',"$$opts{tmp}/mpileup.cram.list") or error("$$opts{tmp}/mpileup.cram.list: $!");
+        open(my $fh3,'>',"$$opts{tmp}/mpileup.bam.urllist") or error("$$opts{tmp}/mpileup.bam.urllist: $!");
+        open(my $fh4,'>',"$$opts{tmp}/mpileup.cram.urllist") or error("$$opts{tmp}/mpileup.cram.urllist: $!");
+        for my $file (@{$args{in}})
+        {
+            print $fh1 "$$opts{path}/mpileup/mpileup.$file.bam\n";
+            print $fh2 "$$opts{path}/mpileup/mpileup.$file.cram\n";
+            print $fh3 "file://", abs_path("$$opts{path}/mpileup/mpileup.$file.bam"), "\n";
+            print $fh4 "file://", abs_path("$$opts{path}/mpileup/mpileup.$file.cram"), "\n";
+        }
+        close($fh1);
+        close($fh2);
+        close($fh3);
+        close($fh4);
+	}
+
     $args{args} =~ s/{PATH}/$$opts{path}/g;
     for my $fmt ('bam','cram')
     {
@@ -944,5 +965,10 @@ sub test_mpileup
         my $grep_hdr = "grep -v ^##bcftools | grep -v ^##reference";
         test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa $files 2>/dev/null | $grep_hdr");
         test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa -Ob $files 2>/dev/null | $$opts{bin}/bcftools view  | $grep_hdr");
+        if ($args{test_list})
+        {
+            test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa -b $$opts{tmp}/mpileup.$fmt.list 2>/dev/null | $grep_hdr");
+            test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa -Ob -b $$opts{tmp}/mpileup.$fmt.urllist 2>/dev/null | $$opts{bin}/bcftools view  | $grep_hdr");
+        }
     }
 }

From 46479b6a01b8d17b54eea35e2cf954e4a6596435 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Wed, 22 Jun 2016 11:47:53 +0100
Subject: [PATCH 204/211] mpileup: add `--no-version` and `--threads` options
 as for other bcftools commands

the point of `--no-version` is to remove invocation specify metadata in the header
lines for pipeline systems that are tracking this separately. we are outputting
the `##reference` line though in mpileup. could drop this as well when
`--no-version` used. seems silly to add a separate option.
---
 doc/bcftools.txt |  6 ++++++
 mpileup.c        | 28 ++++++++++++++++++++--------
 test/test.pl     |  2 +-
 3 files changed, 27 insertions(+), 9 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 1e966ae9d..d0e67b8e4 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1431,6 +1431,9 @@ regions listed in the BED file.
     depth less than 5 will be printed as separate records, outside of
     gVCF blocks.
 
+*--no-version*::
+    see *<<common_options,Common Options>>*
+
 *-o, --output* 'FILE'::
     Write output to 'FILE', rather than the default of standard output.
     (The same short option is used for both *--open-prob* and *--output*.  If *-o*'s
@@ -1442,6 +1445,9 @@ regions listed in the BED file.
 *-O, --output-type* 'b'|'u'|'z'|'v'::
     see *<<common_options,Common Options>>*
 
+*--threads* 'INT'::
+    see *<<common_options,Common Options>>*
+
 ==== Options for SNP/INDEL genotype likelihood computation
 
 *-e, --ext-prob* 'INT'::
diff --git a/mpileup.c b/mpileup.c
index f76f12e57..68c7d1ff8 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -68,7 +68,7 @@ typedef struct {
     int openQ, extQ, tandemQ, min_support; // for indels
     double min_frac; // for indels
     char *reg_fname, *pl_list, *fai_fname, *output_fname, *samples_list;
-    int reg_is_file;
+    int reg_is_file, record_cmd_line, n_threads;
     faidx_t *fai;
     regidx_t *bed, *reg;    // bed: skipping regions, reg: index-jump to regions
     gvcf_t *gvcf;
@@ -489,19 +489,23 @@ static int mpileup(mplp_conf_t *conf)
         fprintf(stderr, "[%s] failed to write to %s: %s\n", __func__, conf->output_fname? conf->output_fname : "standard output", strerror(errno));
         exit(EXIT_FAILURE);
     }
+    if ( conf->n_threads ) hts_set_threads(conf->bcf_fp, conf->n_threads);
 
     // BCF header creation
     conf->bcf_hdr = bcf_hdr_init("w");
     conf->buf.l = 0;
 
-    ksprintf(&conf->buf, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
-    bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    if (conf->record_cmd_line)
+    {
+        ksprintf(&conf->buf, "##bcftoolsVersion=%s+htslib-%s\n",bcftools_version(),hts_version());
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
 
-    conf->buf.l = 0;
-    ksprintf(&conf->buf, "##bcftoolsCommand=mpileup");
-    for (i=1; i<conf->argc; i++) ksprintf(&conf->buf, " %s", conf->argv[i]);
-    kputc('\n', &conf->buf);
-    bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+        conf->buf.l = 0;
+        ksprintf(&conf->buf, "##bcftoolsCommand=mpileup");
+        for (i=1; i<conf->argc; i++) ksprintf(&conf->buf, " %s", conf->argv[i]);
+        kputc('\n', &conf->buf);
+        bcf_hdr_append(conf->bcf_hdr, conf->buf.s);
+    }
 
     if (conf->fai_fname)
     {
@@ -846,9 +850,11 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "  -a, --annotate LIST     optional tags to output; '?' to list []\n"
 "  -g, --gvcf INT[,...]    group non-variant sites into gVCF blocks according\n"
 "                          to minimum per-sample DP\n"
+"      --no-version        do not append version and command line to the header\n"
 "  -o, --output FILE       write output to FILE [standard output]\n"
 "  -O, --output-type TYPE  'b' compressed BCF; 'u' uncompressed BCF;\n"
 "                          'z' compressed VCF; 'v' uncompressed VCF [v]\n"
+"      --threads INT       number of extra output compression threads [0]\n"
 "\n"
 "SNP/INDEL genotype likelihoods options:\n"
 "  -e, --ext-prob INT      Phred-scaled gap extension seq error probability [%d]\n", mplp->extQ);
@@ -892,6 +898,8 @@ int bam_mpileup(int argc, char *argv[])
     mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
     mplp.output_fname = NULL;
     mplp.output_type = FT_VCF;
+    mplp.record_cmd_line = 1;
+    mplp.n_threads = 0;
 
     static const struct option lopts[] =
     {
@@ -904,6 +912,8 @@ int bam_mpileup(int argc, char *argv[])
         {"ignore-RG", no_argument, NULL, 5},
         {"ignore-rg", no_argument, NULL, 5},
         {"gvcf", required_argument, NULL, 7},
+        {"no-version", no_argument, NULL, 8},
+        {"threads",required_argument,NULL,9},
         {"illumina1.3+", no_argument, NULL, '6'},
         {"count-orphans", no_argument, NULL, 'A'},
         {"bam-list", required_argument, NULL, 'b'},
@@ -964,6 +974,8 @@ int bam_mpileup(int argc, char *argv[])
             if (mplp.fai == NULL) return 1;
             mplp.fai_fname = optarg;
             break;
+        case  8 : mplp.record_cmd_line = 0; break;
+        case  9 : mplp.n_threads = strtol(optarg, 0, 0); break;
         case 'd': mplp.max_depth = atoi(optarg); break;
         case 'r': mplp.reg_fname = strdup(optarg); break;
         case 'R': mplp.reg_fname = strdup(optarg); mplp.reg_is_file = 1; break;
diff --git a/test/test.pl b/test/test.pl
index 5304e1575..542d72c3b 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -967,7 +967,7 @@ sub test_mpileup
         test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa -Ob $files 2>/dev/null | $$opts{bin}/bcftools view  | $grep_hdr");
         if ($args{test_list})
         {
-            test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa -b $$opts{tmp}/mpileup.$fmt.list 2>/dev/null | $grep_hdr");
+            test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa -b $$opts{tmp}/mpileup.$fmt.list --no-version 2>/dev/null | grep -v ^##reference");
             test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools mpileup $args{args} -f $$opts{path}/mpileup/mpileup.ref.fa -Ob -b $$opts{tmp}/mpileup.$fmt.urllist 2>/dev/null | $$opts{bin}/bcftools view  | $grep_hdr");
         }
     }

From c5520606270ce31d602822225ca9b7a2f11f0116 Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 23 Jun 2016 08:59:42 +0100
Subject: [PATCH 205/211] mpileup: enable `-g` short `--gvcf` option that was
 missed

---
 mpileup.c | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/mpileup.c b/mpileup.c
index 68c7d1ff8..057ba42cf 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -911,7 +911,7 @@ int bam_mpileup(int argc, char *argv[])
         {"open-prob", required_argument, NULL, 4},
         {"ignore-RG", no_argument, NULL, 5},
         {"ignore-rg", no_argument, NULL, 5},
-        {"gvcf", required_argument, NULL, 7},
+        {"gvcf", required_argument, NULL, 'g'},
         {"no-version", no_argument, NULL, 8},
         {"threads",required_argument,NULL,9},
         {"illumina1.3+", no_argument, NULL, '6'},
@@ -965,7 +965,7 @@ int bam_mpileup(int argc, char *argv[])
         case  3 : mplp.output_fname = optarg; break;
         case  4 : mplp.openQ = atoi(optarg); break;
         case  5 : mplp.flag |= MPLP_IGNORE_RG; break;
-        case  7 :
+        case 'g':
             mplp.gvcf = gvcf_init(optarg);
             if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
             break;

From 2607f11bdc2df8daaa637d639c67f14a27867208 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 23 Jun 2016 11:00:13 +0100
Subject: [PATCH 206/211] mpileup: exclude samples when prefixed with ^

---
 mpileup.c                  | 24 ++++++++-----
 sample.c                   | 14 ++++++--
 sample.h                   |  2 +-
 test/mpileup/mpileup.8.out | 70 ++++++++++++++++++++++++++++++++++++++
 test/test.pl               |  2 ++
 5 files changed, 99 insertions(+), 13 deletions(-)
 create mode 100644 test/mpileup/mpileup.8.out

diff --git a/mpileup.c b/mpileup.c
index 057ba42cf..31e5433f7 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -359,20 +359,26 @@ static int mpileup(mplp_conf_t *conf)
     conf->n_plp = (int*) calloc(conf->nfiles, sizeof(int));
     conf->smpl = bam_smpl_init();
 
-    int i;
-    void *samples_inc = NULL;
+    int i, samples_logic = 1;   // 1: include, 0: exclude
+    void *samples_list = NULL;  // hash of sample names to include or exclude
     if ( conf->samples_list )
     {
         int nsamples = 0;
-        char **samples = hts_readlist(conf->samples_list, conf->sample_is_file, &nsamples);
+        char *list = conf->samples_list;
+        if ( list[0]=='^' )
+        {
+            list++;
+            samples_logic = 0;
+        }
+        char **samples = hts_readlist(list, conf->sample_is_file, &nsamples);
         if (!samples) {
-            fprintf(stderr,"[%s] could not read the samples list %s\n", __func__, conf->samples_list);
+            fprintf(stderr,"[%s] could not read the samples list %s\n", __func__, list);
             exit(EXIT_FAILURE);
         }
-        if ( nsamples ) samples_inc = khash_str2int_init();
+        if ( nsamples ) samples_list = khash_str2int_init();
         for (i=0; i<nsamples; i++)
         {
-            khash_str2int_inc(samples_inc, strdup(samples[i]));
+            khash_str2int_inc(samples_list, strdup(samples[i]));
             free(samples[i]);
         }
         free(samples);
@@ -437,8 +443,8 @@ static int mpileup(mplp_conf_t *conf)
         }
         conf->mplp_data[i]->h = i? hdr : h_tmp; // for i==0, "h" has not been set yet
         conf->mplp_data[i]->rghash_exc = conf->rghash_exc;
-        if ( samples_inc ) conf->mplp_data[i]->rghash_inc = khash_str2int_init();
-        bam_smpl_add(conf->smpl, conf->files[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text, samples_inc, conf->mplp_data[i]->rghash_inc);
+        if ( samples_list ) conf->mplp_data[i]->rghash_inc = khash_str2int_init();
+        bam_smpl_add(conf->smpl, conf->files[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text, samples_list, samples_logic, conf->mplp_data[i]->rghash_inc);
         // Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
         conf->mplp_data[i]->rghash_exc = bcf_call_add_rg(conf->mplp_data[i]->rghash_exc, h_tmp->text, conf->pl_list);
         if (conf->reg) {
@@ -685,7 +691,7 @@ static int mpileup(mplp_conf_t *conf)
         free(conf->mplp_data[i]);
     }
     free(conf->mplp_data); free(conf->plp); free(conf->n_plp);
-    if ( samples_inc ) khash_str2int_destroy_free(samples_inc);
+    if ( samples_list ) khash_str2int_destroy_free(samples_list);
     free(mp_ref.ref[0]);
     free(mp_ref.ref[1]);
     return 0;
diff --git a/sample.c b/sample.c
index 06777ee45..40361a2cb 100644
--- a/sample.c
+++ b/sample.c
@@ -63,7 +63,7 @@ static void add_pair(bam_sample_t *sm, void *sm2id, const char *readgroup, const
     khash_str2int_set(sm->rg2smid, strdup(readgroup), ismpl);
 }
 
-int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt, void *white_list, void *white_hash)
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt, void *sample_list, int sample_logic, void *white_hash)
 {
     const char *p = txt, *q, *r;
     kstring_t buf, first_sm;
@@ -85,13 +85,21 @@ int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt, void *white_
             for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
             for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
             ioq = *u; ior = *v; *u = *v = '\0';
-            if ( !white_list || khash_str2int_has_key(white_list,r) )
+
+            // r now points to a null terminated sample name
+            int accept_rg = 1;
+            if ( sample_list )
+            {
+                accept_rg = khash_str2int_has_key(sample_list,r);
+                if ( sample_logic==0 ) accept_rg = accept_rg ? 0 : 1;
+            }
+            if ( accept_rg )
             {
                 buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
                 add_pair(sm, sm->sm2id, buf.s, r);
                 if ( !first_sm.s )
                     kputs(r,&first_sm);
-                if ( white_list ) khash_str2int_inc(white_hash,strdup(q));
+                if ( sample_list ) khash_str2int_inc(white_hash,strdup(q));
             }
             *u = ioq; *v = ior;
         } else break;
diff --git a/sample.h b/sample.h
index f777a81f5..4828c32f2 100644
--- a/sample.h
+++ b/sample.h
@@ -35,7 +35,7 @@ typedef struct {
 } bam_sample_t;
 
 bam_sample_t *bam_smpl_init(void);
-int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt, void *white_list, void *white_hash);
+int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt, void *sample_list, int sample_logic, void *white_hash);
 int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str);
 void bam_smpl_destroy(bam_sample_t *sm);
 
diff --git a/test/mpileup/mpileup.8.out b/test/mpileup/mpileup.8.out
new file mode 100644
index 000000000..c13653928
--- /dev/null
+++ b/test/mpileup/mpileup.8.out
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	HG00100
+17	100	.	C	<*>	0	.	DP=9;I16=9,0,0,0,350,14094,0,0,509,29641,0,0,159,3427,0,0;QS=1,0;MQ0F=0	PL	0,27,189
+17	101	.	C	<*>	0	.	DP=9;I16=9,0,0,0,331,12701,0,0,509,29641,0,0,159,3349,0,0;QS=1,0;MQ0F=0	PL	0,27,182
+17	102	.	C	<*>	0	.	DP=9;I16=9,0,0,0,349,13977,0,0,509,29641,0,0,159,3283,0,0;QS=1,0;MQ0F=0	PL	0,27,188
+17	103	.	T	<*>	0	.	DP=9;I16=8,0,0,0,338,14304,0,0,480,28800,0,0,153,3193,0,0;QS=1,0;MQ0F=0	PL	0,24,189
+17	104	.	G	<*>	0	.	DP=9;I16=8,0,0,0,310,12224,0,0,480,28800,0,0,152,3138,0,0;QS=1,0;MQ0F=0	PL	0,24,178
+17	105	.	G	<*>	0	.	DP=10;I16=9,0,0,0,306,10992,0,0,540,32400,0,0,151,3093,0,0;QS=1,0;MQ0F=0	PL	0,27,170
+17	106	.	G	<*>	0	.	DP=10;I16=10,0,0,0,371,14379,0,0,569,33241,0,0,160,3140,0,0;QS=1,0;MQ0F=0	PL	0,30,190
+17	107	.	C	<*>	0	.	DP=10;I16=9,0,0,0,364,14858,0,0,540,32400,0,0,151,3037,0,0;QS=1,0;MQ0F=0	PL	0,27,192
+17	108	.	C	<*>	0	.	DP=10;I16=9,0,0,0,358,14384,0,0,540,32400,0,0,151,3027,0,0;QS=1,0;MQ0F=0	PL	0,27,190
+17	109	.	T	<*>	0	.	DP=10;I16=9,0,0,0,367,15083,0,0,540,32400,0,0,151,3029,0,0;QS=1,0;MQ0F=0	PL	0,27,195
+17	110	.	G	<*>	0	.	DP=10;I16=9,0,0,0,369,15193,0,0,540,32400,0,0,151,3043,0,0;QS=1,0;MQ0F=0	PL	0,27,194
+17	111	.	G	<*>	0	.	DP=10;I16=10,0,0,0,316,10760,0,0,569,33241,0,0,165,3265,0,0;QS=1,0;MQ0F=0	PL	0,30,167
+17	112	.	C	<*>	0	.	DP=10;I16=9,0,0,0,362,14690,0,0,540,32400,0,0,151,3107,0,0;QS=1,0;MQ0F=0	PL	0,27,191
+17	113	.	A	<*>	0	.	DP=10;I16=9,0,0,0,334,12490,0,0,540,32400,0,0,150,3106,0,0;QS=1,0;MQ0F=0	PL	0,27,176
+17	114	.	C	<*>	0	.	DP=10;I16=9,0,0,0,347,13441,0,0,540,32400,0,0,149,3115,0,0;QS=1,0;MQ0F=0	PL	0,27,182
+17	115	.	C	<*>	0	.	DP=10;I16=10,0,0,0,367,14165,0,0,569,33241,0,0,166,3458,0,0;QS=1,0;MQ0F=0	PL	0,30,189
+17	116	.	A	<*>	0	.	DP=10;I16=9,0,0,0,351,13723,0,0,540,32400,0,0,146,3114,0,0;QS=1,0;MQ0F=0	PL	0,27,183
+17	117	.	G	<*>	0	.	DP=10;I16=9,0,0,0,342,13166,0,0,540,32400,0,0,144,3106,0,0;QS=1,0;MQ0F=0	PL	0,27,183
+17	118	.	G	<*>	0	.	DP=9;I16=9,0,0,0,317,11785,0,0,509,29641,0,0,164,3550,0,0;QS=1,0;MQ0F=0	PL	0,27,175
+17	119	.	G	<*>	0	.	DP=9;I16=8,0,0,0,308,11972,0,0,480,28800,0,0,142,3122,0,0;QS=1,0;MQ0F=0	PL	0,24,175
+17	120	.	A	<*>	0	.	DP=9;I16=8,0,0,0,311,12135,0,0,480,28800,0,0,141,3145,0,0;QS=1,0;MQ0F=0	PL	0,24,175
+17	121	.	G	<*>	0	.	DP=9;I16=8,0,0,0,315,12547,0,0,480,28800,0,0,139,3127,0,0;QS=1,0;MQ0F=0	PL	0,24,181
+17	122	.	C	<*>	0	.	DP=9;I16=8,0,0,0,320,12864,0,0,480,28800,0,0,137,3117,0,0;QS=1,0;MQ0F=0	PL	0,24,181
+17	123	.	T	<*>	0	.	DP=8;I16=7,0,0,0,274,10782,0,0,420,25200,0,0,136,3114,0,0;QS=1,0;MQ0F=0	PL	0,21,167
+17	124	.	T	<*>	0	.	DP=9;I16=9,0,0,0,276,9034,0,0,509,29641,0,0,160,3742,0,0;QS=1,0;MQ0F=0	PL	0,27,154
+17	125	.	A	<*>	0	.	DP=8;I16=7,0,0,0,253,9195,0,0,420,25200,0,0,136,3126,0,0;QS=1,0;MQ0F=0	PL	0,21,154
+17	126	.	A	<*>	0	.	DP=8;I16=8,0,0,0,275,9967,0,0,449,26041,0,0,162,3766,0,0;QS=1,0;MQ0F=0	PL	0,24,162
+17	127	.	C	<*>	0	.	DP=8;I16=8,0,0,0,280,10340,0,0,449,26041,0,0,163,3787,0,0;QS=1,0;MQ0F=0	PL	0,24,163
+17	128	.	A	<*>	0	.	DP=8;I16=8,0,0,0,295,11123,0,0,449,26041,0,0,164,3814,0,0;QS=1,0;MQ0F=0	PL	0,24,169
+17	129	.	A	<*>	0	.	DP=8;I16=8,0,0,0,291,10845,0,0,449,26041,0,0,165,3847,0,0;QS=1,0;MQ0F=0	PL	0,24,168
+17	130	.	A	<*>	0	.	DP=8;I16=8,0,0,0,292,10932,0,0,449,26041,0,0,166,3886,0,0;QS=1,0;MQ0F=0	PL	0,24,169
+17	131	.	C	<*>	0	.	DP=7;I16=7,0,0,0,276,10910,0,0,420,25200,0,0,141,3255,0,0;QS=1,0;MQ0F=0	PL	0,21,167
+17	132	.	A	<*>	0	.	DP=7;I16=7,0,0,0,279,11147,0,0,420,25200,0,0,141,3253,0,0;QS=1,0;MQ0F=0	PL	0,21,169
+17	133	.	T	<*>	0	.	DP=7;I16=7,0,0,0,269,10365,0,0,420,25200,0,0,141,3255,0,0;QS=1,0;MQ0F=0	PL	0,21,163
+17	134	.	C	<*>	0	.	DP=7;I16=7,0,0,0,293,12279,0,0,420,25200,0,0,141,3261,0,0;QS=1,0;MQ0F=0	PL	0,21,177
+17	135	.	T	<*>	0	.	DP=7;I16=7,0,0,0,286,11708,0,0,420,25200,0,0,141,3271,0,0;QS=1,0;MQ0F=0	PL	0,21,173
+17	136	.	G	<*>	0	.	DP=7;I16=7,0,0,0,283,11471,0,0,420,25200,0,0,141,3285,0,0;QS=1,0;MQ0F=0	PL	0,21,172
+17	137	.	T	<*>	0	.	DP=7;I16=7,0,0,0,263,9933,0,0,420,25200,0,0,141,3303,0,0;QS=1,0;MQ0F=0	PL	0,21,160
+17	138	.	C	<*>	0	.	DP=7;I16=7,0,0,0,284,11546,0,0,420,25200,0,0,141,3325,0,0;QS=1,0;MQ0F=0	PL	0,21,172
+17	139	.	C	<*>	0	.	DP=7;I16=7,0,0,0,263,9957,0,0,420,25200,0,0,140,3302,0,0;QS=1,0;MQ0F=0	PL	0,21,161
+17	140	.	A	<*>	0	.	DP=7;I16=7,0,0,0,269,10379,0,0,420,25200,0,0,139,3285,0,0;QS=1,0;MQ0F=0	PL	0,21,163
+17	141	.	G	<*>	0	.	DP=6;I16=6,0,0,0,239,9599,0,0,360,21600,0,0,139,3273,0,0;QS=1,0;MQ0F=0	PL	0,18,158
+17	142	.	C	<*>	0	.	DP=6;I16=6,0,0,0,239,9557,0,0,360,21600,0,0,139,3265,0,0;QS=1,0;MQ0F=0	PL	0,18,157
+17	143	.	G	<*>	0	.	DP=6;I16=6,0,0,0,197,6487,0,0,360,21600,0,0,139,3261,0,0;QS=1,0;MQ0F=0	PL	0,18,128
+17	144	.	A	<*>	0	.	DP=6;I16=6,0,0,0,232,9020,0,0,360,21600,0,0,138,3212,0,0;QS=1,0;MQ0F=0	PL	0,18,152
+17	145	.	A	<*>	0	.	DP=6;I16=6,0,0,0,233,9089,0,0,360,21600,0,0,137,3169,0,0;QS=1,0;MQ0F=0	PL	0,18,153
+17	146	.	T	<*>	0	.	DP=6;I16=6,0,0,0,233,9065,0,0,360,21600,0,0,136,3132,0,0;QS=1,0;MQ0F=0	PL	0,18,152
+17	147	.	A	<*>	0	.	DP=6;I16=6,0,0,0,229,8771,0,0,360,21600,0,0,135,3101,0,0;QS=1,0;MQ0F=0	PL	0,18,150
+17	148	.	C	<*>	0	.	DP=6;I16=6,0,0,0,240,9618,0,0,360,21600,0,0,134,3076,0,0;QS=1,0;MQ0F=0	PL	0,18,157
+17	149	.	C	<*>	0	.	DP=6;I16=6,0,0,0,219,8419,0,0,360,21600,0,0,133,3057,0,0;QS=1,0;MQ0F=0	PL	0,18,148
+17	150	.	T	<*>	0	.	DP=6;I16=6,0,0,0,234,9158,0,0,360,21600,0,0,131,2993,0,0;QS=1,0;MQ0F=0	PL	0,18,153
diff --git a/test/test.pl b/test/test.pl
index 542d72c3b..577d1e57e 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -259,6 +259,8 @@
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.6.out',args=>q[-a DP,DV -r17:100-200,17:201-300,17:301-400,17:401-500,17:501-600 --gvcf 0,2,5]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -s HG00101,HG00102]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -S {PATH}/mplp.samples]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -s ^HG00101,HG00102]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -S ^{PATH}/mplp.samples]);
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};

From 51e31af88085104472ec74bebb70f40f281b93ae Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 23 Jun 2016 12:05:43 +0100
Subject: [PATCH 207/211] mpileup: -l replaced with -t,-T to match other
 bcftools commands

---
 doc/bcftools.txt | 25 +++++++++++--------------
 mpileup.c        | 45 +++++++++++++++++++++++++++++++++++++++------
 test/test.pl     |  1 +
 3 files changed, 51 insertions(+), 20 deletions(-)

diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index d0e67b8e4..2b87151de 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1298,16 +1298,17 @@ individuals can be pooled in one alignment file, also one individual can be
 separated into multiple files.  If sample identifiers are absent, each input
 file is regarded as one sample.
 
-
 Note that there are two orthogonal ways to specify locations in the
-input file; via *-r* 'region' and *-l* 'positions'.  The
+input file; via *-r* 'region' and *-t* 'positions'.  The
 former uses (and requires) an index to do random access while the
 latter streams through the file contents filtering out the specified
 regions, requiring no index.  The two may be used in conjunction.  For
 example a BED file containing locations of genes in chromosome 20
-could be specified using *-r 20 -l chr20.bed*, meaning that the
+could be specified using *-r 20 -t chr20.bed*, meaning that the
 index is used to find chromosome 20 and then it is filtered for the
-regions listed in the BED file.
+regions listed in the BED file. Also note that the *-r* option can be much
+slower than *-t* with many regions and can require more memory when
+multiple regions and many alignment files are processed.
 
 
 ==== Input options
@@ -1351,16 +1352,6 @@ regions listed in the BED file.
 *-G, --exclude-RG* 'FILE'::
     Exclude reads from readgroups listed in FILE (one @RG-ID per line)
 
-*-l, --positions* 'FILE'::
-    BED or position list file containing a list of regions or sites where
-    output should be generated. Position list files contain two
-    columns (chromosome and position) and start counting from 1.  BED
-    files contain at least 3 columns (chromosome, start and end position)
-    and are 0-based half-open.
-    While it is possible to mix both position-list and BED coordinates in
-    the same file, this is strongly ill advised due to the differing
-    coordinate systems. [null]
-
 *-q, -min-MQ* 'INT'::
     Minimum mapping quality for an alignment to be used [0]
 
@@ -1391,6 +1382,12 @@ regions listed in the BED file.
 *-S, --samples-file* 'FILE'::
     file of sample names. See *<<common_options,Common Options>>*
 
+*-t, --targets* 'LIST'::
+    see *<<common_options,Common Options>>*
+
+*-T, --targets-file* 'FILE'::
+    see *<<common_options,Common Options>>*
+
 *-x, --ignore-overlaps*::
     Disable read-pair overlap detection.
 
diff --git a/mpileup.c b/mpileup.c
index 31e5433f7..bc2f7d12a 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -71,6 +71,7 @@ typedef struct {
     int reg_is_file, record_cmd_line, n_threads;
     faidx_t *fai;
     regidx_t *bed, *reg;    // bed: skipping regions, reg: index-jump to regions
+    int bed_logic;          // 1: include region, 0: exclude region
     gvcf_t *gvcf;
 
     // auxiliary structures for calling
@@ -197,7 +198,20 @@ static int mplp_func(void *data, bam1_t *b)
         if (ma->conf->bed)
         {
             // test overlap
-            if ( !regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],b->core.pos, bam_endpos(b)-1, NULL) ) continue;
+            regitr_t itr;
+            int beg = b->core.pos, end = bam_endpos(b)-1;
+            int overlap = regidx_overlap(ma->conf->bed, ma->h->target_name[b->core.tid],beg,end, &itr);
+            if ( !ma->conf->bed_logic && !overlap )
+            {
+                // exclude only reads which are fully contained in the region
+                while ( REGITR_OVERLAP(itr,beg,end) )
+                {
+                    if ( beg < REGITR_START(itr) ) { overlap = 1; break; }
+                    if ( end > REGITR_END(itr) ) { overlap = 1; break; }
+                    itr.i++;
+                }
+            }
+            if ( !overlap ) continue;
         }
         if (ma->rghash_inc)
         {
@@ -306,7 +320,12 @@ static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end)
     while ( (ret=bam_mplp_auto(conf->iter, &tid, &pos, conf->n_plp, conf->plp)) > 0) 
     {
         if ( end && (pos<beg || pos>end) ) continue;
-        if (conf->bed && tid >= 0 && !regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL)) continue;
+        if ( conf->bed && tid >= 0 )
+        {
+            int overlap = regidx_overlap(conf->bed, hdr->target_name[tid], pos, pos, NULL);
+            if ( !conf->bed_logic ) overlap = overlap ? 0 : 1;
+            if ( !overlap ) continue;
+        }
         mplp_get_ref(conf->mplp_data[0], tid, &ref, &ref_len);
 
         int total_depth, _ref0, ref16;
@@ -835,7 +854,6 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
 "  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs\n"
 "  -f, --fasta-ref FILE    faidx indexed reference sequence file\n"
 "  -G, --exclude-RG FILE   exclude read groups listed in FILE\n"
-"  -l, --positions FILE    skip unlisted positions (chr pos) or regions (BED)\n"
 "  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
     fprintf(fp,
 "  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
@@ -850,6 +868,8 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
     fprintf(fp,
 "  -s, --samples LIST      comma separated list of samples to include\n"
 "  -S, --samples-file FILE file of samples to include\n"
+"  -t, --targets REG[,...] similar to -r but streams rather than index-jumps\n"
+"  -T, --targets-file FILE similar to -R but streams rather than index-jumps\n"
 "  -x, --ignore-overlaps   disable read-pair overlap detection\n"
 "\n"
 "Output options:\n"
@@ -933,10 +953,11 @@ int bam_mpileup(int argc, char *argv[])
         {"fasta-ref", required_argument, NULL, 'f'},
         {"exclude-RG", required_argument, NULL, 'G'},
         {"exclude-rg", required_argument, NULL, 'G'},
-        {"positions", required_argument, NULL, 'l'},
         {"region", required_argument, NULL, 'r'},
         {"regions", required_argument, NULL, 'r'},
         {"regions-file", required_argument, NULL, 'R'},
+        {"targets", required_argument, NULL, 't'},
+        {"targets-file", required_argument, NULL, 'T'},
         {"min-MQ", required_argument, NULL, 'q'},
         {"min-mq", required_argument, NULL, 'q'},
         {"min-BQ", required_argument, NULL, 'Q'},
@@ -957,7 +978,7 @@ int bam_mpileup(int argc, char *argv[])
         {"platforms", required_argument, NULL, 'P'},
         {NULL, 0, NULL, 0}
     };
-    while ((c = getopt_long(argc, argv, "Ag:f:r:R:l:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:",lopts,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "Ag:f:r:R:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:t:T:",lopts,NULL)) >= 0) {
         switch (c) {
         case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
         case  1 :
@@ -985,10 +1006,22 @@ int bam_mpileup(int argc, char *argv[])
         case 'd': mplp.max_depth = atoi(optarg); break;
         case 'r': mplp.reg_fname = strdup(optarg); break;
         case 'R': mplp.reg_fname = strdup(optarg); mplp.reg_is_file = 1; break;
-        case 'l':
+        case 't':
                   // In the original version the whole BAM was streamed which is inefficient
                   //  with few BED intervals and big BAMs. Todo: devise a heuristic to determine
                   //  best strategy, that is streaming or jumping.
+                  if ( optarg[0]=='^' ) optarg++;
+                  else mplp.bed_logic = 1;
+                  mplp.bed = regidx_init(NULL,regidx_parse_reg,NULL,0,NULL);
+                  if ( regidx_insert_list(mplp.bed,optarg,',') !=0 )
+                  {
+                      fprintf(stderr,"Could not parse the targets: %s\n", optarg);
+                      exit(EXIT_FAILURE);
+                  }
+                  break;
+        case 'T':
+                  if ( optarg[0]=='^' ) optarg++;
+                  else mplp.bed_logic = 1;
                   mplp.bed = regidx_init(optarg,NULL,NULL,0,NULL);
                   if (!mplp.bed) { fprintf(stderr, "bcftools mpileup: Could not read file \"%s\"", optarg); return 1; }
                   break;
diff --git a/test/test.pl b/test/test.pl
index 577d1e57e..9c807d30e 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -261,6 +261,7 @@
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -S {PATH}/mplp.samples]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -s ^HG00101,HG00102]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -S ^{PATH}/mplp.samples]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-t17:100-150 -S ^{PATH}/mplp.samples]);
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};

From 7f4929c3d16fc41540ba70e16ca64072e3c6211c Mon Sep 17 00:00:00 2001
From: Shane McCarthy <sm15@sanger.ac.uk>
Date: Thu, 30 Jun 2016 09:14:36 +0100
Subject: [PATCH 208/211] rename sample.* to bam_sample.*

---
 Makefile                 | 8 ++++----
 sample.c => bam_sample.c | 4 ++--
 sample.h => bam_sample.h | 2 +-
 mpileup.c                | 2 +-
 4 files changed, 8 insertions(+), 8 deletions(-)
 rename sample.c => bam_sample.c (98%)
 rename sample.h => bam_sample.h (97%)

diff --git a/Makefile b/Makefile
index 1d923e995..75cc3b85b 100644
--- a/Makefile
+++ b/Makefile
@@ -46,7 +46,7 @@ OBJS     = main.o vcfindex.o tabix.o \
            vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o \
            vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o \
            vcfcnv.o HMM.o vcfplugin.o consensus.o ploidy.o regidx.o version.o \
-           mpileup.o bam2bcf.o bam2bcf_indel.o sample.o \
+           mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o \
            ccall.o em.o prob1.o kmin.o # the original samtools calling
 
 EXTRA_CPPFLAGS = -I. -I$(HTSDIR) -DPLUGINPATH=\"$(pluginpath)\"
@@ -141,7 +141,7 @@ roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kst
 cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
 bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
 sam_h = sam.h $(htslib_sam_h) $(bam_h)
-sample_h = sample.h $(htslib_kstring_h)
+bam_sample_h = bam_sample.h $(htslib_kstring_h)
 
 main.o: main.c $(htslib_hts_h) version.h $(bcftools_h)
 vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
@@ -178,8 +178,8 @@ polysomy.o: polysomy.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(bcftools_
 peakfit.o: peakfit.c peakfit.h $(htslib_hts_h) $(HTSDIR)/htslib/kstring.h
 regidx.o: regidx.c $(htslib_hts_h) $(htslib_kstring_h) $(htslib_kseq_h) $(htslib_khash_str2int_h) regidx.h
 consensus.o: consensus.c $(htslib_hts_h) $(HTSDIR)/htslib/kseq.h rbuf.h $(bcftools_h) regidx.h
-mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) regidx.h $(bcftools_h) $(call_h) $(bam2bcf_h) $(sample_h)
-sample.o: $(sample_h) $(htslib_hts_h) $(HTSDIR)/htslib/khash_str2int.h
+mpileup.o: mpileup.c $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) regidx.h $(bcftools_h) $(call_h) $(bam2bcf_h) $(bam_sample_h)
+bam_sample.o: $(bam_sample_h) $(htslib_hts_h) $(HTSDIR)/htslib/khash_str2int.h
 version.o: version.h version.c
 
 test/test-rbuf.o: test/test-rbuf.c rbuf.h
diff --git a/sample.c b/bam_sample.c
similarity index 98%
rename from sample.c
rename to bam_sample.c
index 40361a2cb..c5d0c0c21 100644
--- a/sample.c
+++ b/bam_sample.c
@@ -1,4 +1,4 @@
-/*  sample.c -- group data by sample.
+/*  bam_sample.c -- group data by sample.
 
     Copyright (C) 2010, 2011 Broad Institute.
     Copyright (C) 2013, 2016 Genome Research Ltd.
@@ -27,7 +27,7 @@ DEALINGS IN THE SOFTWARE.  */
 #include <string.h>
 #include <htslib/hts.h>
 #include <htslib/khash_str2int.h>
-#include "sample.h"
+#include "bam_sample.h"
 
 bam_sample_t *bam_smpl_init(void)
 {
diff --git a/sample.h b/bam_sample.h
similarity index 97%
rename from sample.h
rename to bam_sample.h
index 4828c32f2..16bbfb4bd 100644
--- a/sample.h
+++ b/bam_sample.h
@@ -1,4 +1,4 @@
-/*  sample.h -- group data by sample.
+/*  bam_sample.h -- group data by sample.
 
     Copyright (C) 2010 Broad Institute.
     Copyright (C) 2016 Genome Research Ltd.
diff --git a/mpileup.c b/mpileup.c
index bc2f7d12a..d0c1c97db 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -41,7 +41,7 @@ DEALINGS IN THE SOFTWARE.  */
 #include "regidx.h"
 #include "bcftools.h"
 #include "bam2bcf.h"
-#include "sample.h"
+#include "bam_sample.h"
 #include "gvcf.h"
 
 #define MPLP_BCF        1

From 5562f0594ddf2af2b8a5faeece0ad627dc06bee9 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 24 Jun 2016 21:18:21 +0100
Subject: [PATCH 209/211] mpileup: changes -G/--exclude-RG to -G/--read-groups

* prefix with ^ to negate the selection
* assign/rename samples by providing second field:
    RG_ID_1  SAMPLE_A
    RG_ID_2  SAMPLE_A
    RG_ID_3  SAMPLE_B
* on read group name conflict give the alignment file,
  asterisk for all reads in the file:
    RG_ID_1  FILE_1.bam  SAMPLE_A
    RG_ID_2  FILE_2.bam  SAMPLE_A
    *        FILE_3.bam  SAMPLE_C

Resolves 4th item in
https://github.com/samtools/bcftools/pull/414#issuecomment-222139272
and https://github.com/samtools/samtools/issues/324.
---
 Makefile                    |   2 +-
 bam2bcf_indel.c             |  37 ----
 bam_sample.c                | 333 +++++++++++++++++++++++++++++-------
 bam_sample.h                |  32 ++--
 doc/bcftools.txt            |  22 ++-
 mpileup.c                   | 189 ++++++++------------
 test/mpileup/mpileup.10.out |  70 ++++++++
 test/mpileup/mpileup.9.out  |  70 ++++++++
 test/mplp.10.samples        |   5 +
 test/mplp.9.samples         |   2 +
 test/test.pl                |   3 +-
 11 files changed, 524 insertions(+), 241 deletions(-)
 create mode 100644 test/mpileup/mpileup.10.out
 create mode 100644 test/mpileup/mpileup.9.out
 create mode 100644 test/mplp.10.samples
 create mode 100644 test/mplp.9.samples

diff --git a/Makefile b/Makefile
index 75cc3b85b..341f729ac 100644
--- a/Makefile
+++ b/Makefile
@@ -141,7 +141,7 @@ roh_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kst
 cnv_h = HMM.h $(htslib_vcf_h) $(htslib_synced_bcf_reader_h)
 bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
 sam_h = sam.h $(htslib_sam_h) $(bam_h)
-bam_sample_h = bam_sample.h $(htslib_kstring_h)
+bam_sample_h = bam_sample.h $(htslib_sam_h)
 
 main.o: main.c $(htslib_hts_h) version.h $(bcftools_h)
 vcfannotate.o: vcfannotate.c $(htslib_vcf_h) $(htslib_synced_bcf_reader_h) $(HTSDIR)/htslib/kseq.h $(bcftools_h) vcmp.h $(filter_h)
diff --git a/bam2bcf_indel.c b/bam2bcf_indel.c
index 9065949af..eda81afa8 100644
--- a/bam2bcf_indel.c
+++ b/bam2bcf_indel.c
@@ -37,43 +37,6 @@ KSORT_INIT_GENERIC(uint32_t)
 #define MINUS_CONST 0x10000000
 #define INDEL_WINDOW_SIZE 50
 
-void *bcf_call_add_rg(void *hash, const char *hdtext, const char *list)
-{
-    const char *s, *p, *q, *r, *t;
-
-    if (list == 0 || hdtext == 0) return hash;
-    if ( !hash ) hash = khash_str2int_init();
-    if ((s = strstr(hdtext, "@RG\t")) == 0) return hash;    // @RG lines not present
-    do {
-        t = strstr(s + 4, "@RG\t"); // the next @RG
-        if ((p = strstr(s, "\tID:")) != 0) p += 4;
-        if ((q = strstr(s, "\tPL:")) != 0) q += 4;
-        if (p && q && (t == 0 || (p < t && q < t))) { // ID and PL are both present
-            int lp, lq;
-            char *x;
-            for (r = p; *r && *r != '\t' && *r != '\n'; ++r) { }
-            lp = r - p;
-            for (r = q; *r && *r != '\t' && *r != '\n'; ++r) { }
-            lq = r - q;
-            x = (char*) calloc((lp > lq? lp : lq) + 1, 1);
-            for (r = q; *r && *r != '\t' && *r != '\n'; ++r) x[r-q] = *r;
-            if (strstr(list, x)) { // insert ID to the hash table
-                for (r = p; *r && *r != '\t' && *r != '\n'; ++r) x[r-p] = *r;
-                x[r-p] = 0;
-                if ( khash_str2int_has_key(hash,x) ) free(x);
-                else khash_str2int_set(hash,x,1);
-            } else free(x);
-        }
-        s = t;
-    } while (s);
-    return hash;
-}
-
-void bcf_call_del_rghash(void *hash)
-{
-    khash_str2int_destroy_free(hash);
-}
-
 static int tpos2qpos(const bam1_core_t *c, const uint32_t *cigar, int32_t tpos, int is_left, int32_t *_tpos)
 {
     int k, x = c->pos, y = 0, last_y = 0;
diff --git a/bam_sample.c b/bam_sample.c
index c5d0c0c21..a8f22bd16 100644
--- a/bam_sample.c
+++ b/bam_sample.c
@@ -25,109 +25,316 @@ DEALINGS IN THE SOFTWARE.  */
 
 #include <stdlib.h>
 #include <string.h>
+#include <ctype.h>
 #include <htslib/hts.h>
+#include <htslib/kstring.h>
 #include <htslib/khash_str2int.h>
+#include <khash_str2str.h>
 #include "bam_sample.h"
 
-bam_sample_t *bam_smpl_init(void)
+
+typedef struct
+{
+    char *fname;
+    void *rg2idx;       // hash: read group name to BCF output sample index. Maintained by bsmpl_add_readgroup
+    int default_idx;    // default BCF output sample index
+}
+file_t;
+
+struct _bam_smpl_t
 {
-    bam_sample_t *s;
-    s = (bam_sample_t*) calloc(1, sizeof(bam_sample_t));
-    s->rg2smid = khash_str2int_init();
-    s->sm2id = khash_str2int_init();
-    return s;
+    kstring_t tmp;
+    file_t *files;
+    int ignore_rg, nsmpl, nfiles;
+    char **smpl;        // list of BCF output sample names. Maintained by bsmpl_add_readgroup
+    void *sample_list;  // hash: BAM input sample name to BCF output sample name. This is the -s/-S list
+    int sample_logic;   // the -s/-S logic, 1: include, 0: exclude
+    void *rg_list;      // hash: BAM/rg_id to sample name or */rg_id for global ids. This is the -G list
+    int rg_logic;       // the -G logic, 1: include, 0: exclude
+    void *name2idx;     // hash: BCF output sample name to BCF output sample index. Maintained by bsmpl_add_readgroup
+};
+
+bam_smpl_t *bam_smpl_init(void)
+{
+    bam_smpl_t *bsmpl;
+    bsmpl = (bam_smpl_t*) calloc(1, sizeof(bam_smpl_t));
+    bsmpl->name2idx = khash_str2int_init();
+    return bsmpl;
 }
 
-void bam_smpl_destroy(bam_sample_t *sm)
+void bam_smpl_destroy(bam_smpl_t *bsmpl)
 {
-    if ( !sm ) return;
-    if ( sm->rg2smid ) khash_str2int_destroy_free(sm->rg2smid);
-    if ( sm->sm2id ) khash_str2int_destroy_free(sm->sm2id);
-    free(sm->smpl);
-    free(sm);
+    if ( !bsmpl ) return;
+    if ( bsmpl->name2idx ) khash_str2int_destroy_free(bsmpl->name2idx);
+    if ( bsmpl->sample_list ) khash_str2str_destroy_free_all(bsmpl->sample_list);
+    if ( bsmpl->rg_list ) khash_str2str_destroy_free_all(bsmpl->rg_list);
+    int i;
+    for (i=0; i<bsmpl->nfiles; i++)
+    {
+        file_t *file = &bsmpl->files[i];
+        if ( file->rg2idx ) khash_str2int_destroy_free(file->rg2idx);
+        free(file->fname);
+    }
+    free(bsmpl->smpl);
+    free(bsmpl->files);
+    free(bsmpl->tmp.s);
+    free(bsmpl);
 }
 
-static void add_pair(bam_sample_t *sm, void *sm2id, const char *readgroup, const char *sample)
+void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl)
+{
+    bsmpl->ignore_rg = 1;
+}
+
+static void bsmpl_add_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char *smpl_name)
 {
-    if ( khash_str2int_has_key(sm->rg2smid,readgroup) ) return;   // duplicated @RG-ID
-    
     int ismpl;
-    if ( khash_str2int_get(sm2id, sample, &ismpl) < 0 )
+    if ( khash_str2int_get(bsmpl->name2idx,smpl_name,&ismpl) < 0 )
     {
-        // the sample encountered for the first time
-        ismpl = sm->n++;
-        hts_expand0(char*,sm->n,sm->m,sm->smpl);
-        sm->smpl[ismpl] = strdup(sample);
-        khash_str2int_set(sm2id, sm->smpl[ismpl], ismpl);
+        // new sample
+        bsmpl->nsmpl++;
+        bsmpl->smpl = (char**) realloc(bsmpl->smpl,sizeof(char*)*bsmpl->nsmpl);
+        bsmpl->smpl[bsmpl->nsmpl-1] = strdup(smpl_name);
+        ismpl = khash_str2int_inc(bsmpl->name2idx,bsmpl->smpl[bsmpl->nsmpl-1]);
     }
-    khash_str2int_set(sm->rg2smid, strdup(readgroup), ismpl);
+    if ( !strcmp("*",rg_id) )
+    {
+        // all read groups in the bam treated as the same sample
+        file->default_idx = ismpl;
+        return;
+    }
+    if ( !file->rg2idx ) file->rg2idx = khash_str2int_init();
+    if ( khash_str2int_has_key(file->rg2idx,rg_id) ) return;    // duplicate @RG:ID
+    khash_str2int_set(file->rg2idx, strdup(rg_id), ismpl);
 }
+int bsmpl_keep_readgroup(bam_smpl_t *bsmpl, file_t *file, const char *rg_id, const char **smpl_name)
+{
+    char *rg_smpl = khash_str2str_get(bsmpl->rg_list,rg_id);    // unique read group present in one bam only
+    if ( !rg_smpl )
+    {
+        // read group specific to this bam
+        bsmpl->tmp.l = 0;
+        ksprintf(&bsmpl->tmp,"%s\t%s",rg_id,file->fname);
+        rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s);
+    }
+    if ( !rg_smpl )
+    {
+        // any read group in this file?
+        bsmpl->tmp.l = 0;
+        ksprintf(&bsmpl->tmp,"*\t%s",file->fname);
+        rg_smpl = khash_str2str_get(bsmpl->rg_list,bsmpl->tmp.s);
+    }
+    if ( !rg_smpl && bsmpl->rg_logic ) return 0;
+    if ( rg_smpl && !bsmpl->rg_logic ) return 0;
 
-int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt, void *sample_list, int sample_logic, void *white_hash)
+    if ( rg_smpl && rg_smpl[0]!='\t' ) *smpl_name = rg_smpl;
+    return 1;
+}
+
+int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname)
 {
-    const char *p = txt, *q, *r;
-    kstring_t buf, first_sm;
-    int n = 0;
-    if (txt == 0) {
-        add_pair(sm, sm->sm2id, fn, fn);
-        return 0;
+    bsmpl->nfiles++;
+    bsmpl->files = (file_t*) realloc(bsmpl->files,bsmpl->nfiles*sizeof(file_t));
+    file_t *file = &bsmpl->files[bsmpl->nfiles-1];
+    memset(file,0,sizeof(file_t));
+    file->fname  = strdup(fname);
+    file->default_idx = -1;
+
+    if ( bsmpl->ignore_rg || !bam_hdr )
+    {
+        bsmpl_add_readgroup(bsmpl,file,"*",file->fname);    // --ignore-RG set or no BAM header
+        return bsmpl->nfiles-1;
     }
-    memset(&buf, 0, sizeof(kstring_t));
-    memset(&first_sm, 0, sizeof(kstring_t));
-    while ((q = strstr(p, "@RG")) != 0) {
+
+    int has_rg = 0;
+    const char *p = bam_hdr, *q, *r;
+    while ((q = strstr(p, "@RG")) != 0) 
+    {
         p = q + 3;
         r = q = 0;
         if ((q = strstr(p, "\tID:")) != 0) q += 4;
         if ((r = strstr(p, "\tSM:")) != 0) r += 4;
-        if (r && q) {
+        if (r && q)
+        {
             char *u, *v;
             int ioq, ior;
             for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
             for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
             ioq = *u; ior = *v; *u = *v = '\0';
 
-            // r now points to a null terminated sample name
+            // q now points to a null terminated read group id
+            // r points to a null terminated sample name
             int accept_rg = 1;
-            if ( sample_list )
+            if ( bsmpl->sample_list )
+            {
+                // restrict samples based on the -s/-S options
+                char *name = khash_str2str_get(bsmpl->sample_list,r);
+                if ( bsmpl->sample_logic==0 )
+                    accept_rg = name ? 0 : 1;
+                else if ( !name )
+                    accept_rg = 0;
+                else
+                    r = name;
+            }
+            if ( accept_rg && bsmpl->rg_list )
             {
-                accept_rg = khash_str2int_has_key(sample_list,r);
-                if ( sample_logic==0 ) accept_rg = accept_rg ? 0 : 1;
+                // restrict readgroups based on the -G option, possibly renaming the sample
+                accept_rg = bsmpl_keep_readgroup(bsmpl,file,q,&r);
             }
             if ( accept_rg )
             {
-                buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
-                add_pair(sm, sm->sm2id, buf.s, r);
-                if ( !first_sm.s )
-                    kputs(r,&first_sm);
-                if ( sample_list ) khash_str2int_inc(white_hash,strdup(q));
+                bsmpl_add_readgroup(bsmpl,file,q,r);
+                has_rg = 1;
             }
+
             *u = ioq; *v = ior;
-        } else break;
+        }
+        else
+            break;
         p = q > r? q : r;
-        ++n;
     }
-    if (n == 0) add_pair(sm, sm->sm2id, fn, fn);
-    // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
-    //  use the tag instead.
-    else if ( n==1 && first_sm.s )
-        add_pair(sm,sm->sm2id,fn,first_sm.s);
-    if ( first_sm.s )
-        free(first_sm.s);
-
-    free(buf.s);
-    return 0;
+    if ( !has_rg )
+    {
+        free(file->fname);
+        bsmpl->nfiles--;
+        return -1;
+    }
+    return bsmpl->nfiles-1;
 }
 
-int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
+const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl)
 {
-    int ismpl;
-    if ( rg )
+    *nsmpl = bsmpl->nsmpl;
+    return (const char**)bsmpl->smpl;
+}
+
+int bam_smpl_get_sample_id(bam_smpl_t *bsmpl, int bam_id, bam1_t *bam_rec)
+{
+    file_t *file = &bsmpl->files[bam_id];
+    if ( file->default_idx >= 0 ) return file->default_idx;
+
+    char *aux_rg = (char*) bam_aux_get(bam_rec, "RG");
+    if ( !aux_rg ) return -1;
+
+    int rg_id;
+    if ( khash_str2int_get(file->rg2idx, aux_rg+1, &rg_id)==0 ) return rg_id;
+    return -1;
+}
+
+int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file)
+{
+    if ( list[0]!='^' ) bsmpl->sample_logic = 1;
+    else list++;
+
+    int i, nsamples = 0;
+    char **samples = hts_readlist(list, is_file, &nsamples);
+    if ( !nsamples ) return 0;
+
+    kstring_t ori = {0,0,0};
+    kstring_t ren = {0,0,0};
+
+    bsmpl->sample_list = khash_str2str_init();
+    for (i=0; i<nsamples; i++)
+    {
+        char *ptr = samples[i];
+        ori.l = ren.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &ori);
+            escaped = 0;
+            ptr++;
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &ren);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        khash_str2str_set(bsmpl->sample_list,strdup(ori.s),strdup(ren.l?ren.s:ori.s));
+        free(samples[i]);
+    }
+    free(samples);
+    free(ori.s);
+    free(ren.s);
+    return nsamples;
+}
+
+int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file)
+{
+    if ( list[0]!='^' ) bsmpl->rg_logic = 1;
+    else list++;
+
+    int i, nrows  = 0;
+    char **rows = hts_readlist(list, is_file, &nrows);
+    if ( !nrows ) return 0;
+
+    kstring_t fld1 = {0,0,0};
+    kstring_t fld2 = {0,0,0};
+    kstring_t fld3 = {0,0,0};
+
+    bsmpl->rg_list = khash_str2str_init();
+    for (i=0; i<nrows; i++)
     {
-        str->l = 0;
-        kputs(fn, str); kputc('/', str); kputs(rg, str);
-        if ( khash_str2int_get(sm->rg2smid, str->s, &ismpl) < 0 ) return -1;
-        return ismpl;
+        char *ptr = rows[i];
+        fld1.l = fld2.l = fld3.l = 0;
+        int escaped = 0;
+        while ( *ptr )
+        {
+            if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+            if ( isspace(*ptr) && !escaped ) break;
+            kputc(*ptr, &fld1);
+            escaped = 0;
+            ptr++;
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &fld2);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        if ( *ptr )
+        {
+            while ( *ptr && isspace(*ptr) ) ptr++;
+            while ( *ptr )
+            {
+                if ( *ptr=='\\' && !escaped ) { escaped = 1; ptr++; continue; }
+                if ( isspace(*ptr) && !escaped ) break;
+                kputc(*ptr, &fld3);
+                escaped = 0;
+                ptr++;
+            }
+        }
+        if ( fld3.l )
+        {
+            // ID FILE SAMPLE
+            kputc('\t',&fld1);
+            kputs(fld2.s,&fld1);
+            fld2.l = 0;
+            kputs(fld3.s,&fld2);
+        }
+        khash_str2str_set(bsmpl->rg_list,strdup(fld1.s),strdup(fld2.l?fld2.s:"\t"));
+        free(rows[i]);
     }
-    if ( khash_str2int_get(sm->rg2smid, fn, &ismpl) < 0 ) return -1;
-    return ismpl;
+    free(rows);
+    free(fld1.s);
+    free(fld2.s);
+    free(fld3.s);
+    return nrows;
 }
+
+
diff --git a/bam_sample.h b/bam_sample.h
index 16bbfb4bd..ea493d35d 100644
--- a/bam_sample.h
+++ b/bam_sample.h
@@ -26,17 +26,25 @@ DEALINGS IN THE SOFTWARE.  */
 #ifndef BAM_SAMPLE_H
 #define BAM_SAMPLE_H
 
-#include "htslib/kstring.h"
-
-typedef struct {
-    int n, m;
-    char **smpl;
-    void *rg2smid, *sm2id;
-} bam_sample_t;
-
-bam_sample_t *bam_smpl_init(void);
-int bam_smpl_add(bam_sample_t *sm, const char *abs, const char *txt, void *sample_list, int sample_logic, void *white_hash);
-int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str);
-void bam_smpl_destroy(bam_sample_t *sm);
+#include <htslib/sam.h>
+
+typedef struct _bam_smpl_t bam_smpl_t;
+
+bam_smpl_t *bam_smpl_init(void);
+
+int bam_smpl_add_samples(bam_smpl_t *bsmpl, char *list, int is_file);
+int bam_smpl_add_readgroups(bam_smpl_t *bsmpl, char *list, int is_file);
+void bam_smpl_ignore_readgroups(bam_smpl_t* bsmpl);
+
+// The above should be called only before bams are added. Returns the BAM id
+// to be passed to bam_smpl_get_sample_id() later. It is safe to assume
+// sequential numbering, starting from 0.
+//
+int bam_smpl_add_bam(bam_smpl_t *bsmpl, char *bam_hdr, const char *fname);
+
+const char **bam_smpl_get_samples(bam_smpl_t *bsmpl, int *nsmpl);
+int bam_smpl_get_sample_id(bam_smpl_t *bsmpl, int bam_id, bam1_t *bam_rec);
+
+void bam_smpl_destroy(bam_smpl_t *bsmpl);
 
 #endif
diff --git a/doc/bcftools.txt b/doc/bcftools.txt
index 2b87151de..b7ae585ed 100644
--- a/doc/bcftools.txt
+++ b/doc/bcftools.txt
@@ -1349,8 +1349,15 @@ multiple regions and many alignment files are processed.
     The *faidx*-indexed reference file in the FASTA format. The file can be
     optionally compressed by *bgzip* [null]
 
-*-G, --exclude-RG* 'FILE'::
-    Exclude reads from readgroups listed in FILE (one @RG-ID per line)
+*-G, --read-groups* [&#94;]'FILE'::
+    list of read groups to include or exclude if prefixed with "&#94;".
+    One read group per line.  This file can also be used to assign new sample
+    names to read groups by giving the new sample name as a second
+    white-space-separated field, like this: "read_group_id new_sample_name".
+    If the read group name is not unique, also the bam file name can
+    be included: "read_group_id file_name sample_name".  If all
+    reads from the alignment file should be treated as a single sample, the
+    asterisk symbol can be used: "* file_name sample_name". 
 
 *-q, -min-MQ* 'INT'::
     Minimum mapping quality for an alignment to be used [0]
@@ -1376,11 +1383,16 @@ multiple regions and many alignment files are processed.
 *--ff, --excl-flags* 'STR'|'INT'::
     Filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP]
 
-*-s, --samples* 'LIST'::
+*-s, --samples* [&#94;]'LIST'::
     list of sample names. See *<<common_options,Common Options>>*
 
-*-S, --samples-file* 'FILE'::
-    file of sample names. See *<<common_options,Common Options>>*
+*-S, --samples-file* [&#94;]'FILE'::
+    file of sample names to include or exclude if prefixed with "&#94;".
+    One sample per line. This file can also be used to rename samples by giving
+    the new sample name as a second white-space-separated column, like this:
+    "old_name new_name".  If a sample name contains spaces, the spaces can be
+    escaped using the backslash character, for example "Not\ a\ good\ sample\
+    name".
 
 *-t, --targets* 'LIST'::
     see *<<common_options,Common Options>>*
diff --git a/mpileup.c b/mpileup.c
index d0c1c97db..8c2d4e147 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -64,10 +64,10 @@ typedef struct _mplp_pileup_t mplp_pileup_t;
 // Data shared by all bam files
 typedef struct {
     int min_mq, flag, min_baseQ, capQ_thres, max_depth, max_indel_depth, fmt_flag;
-    int rflag_require, rflag_filter, output_type, sample_is_file;
+    int rflag_require, rflag_filter, output_type;
     int openQ, extQ, tandemQ, min_support; // for indels
     double min_frac; // for indels
-    char *reg_fname, *pl_list, *fai_fname, *output_fname, *samples_list;
+    char *reg_fname, *pl_list, *fai_fname, *output_fname;
     int reg_is_file, record_cmd_line, n_threads;
     faidx_t *fai;
     regidx_t *bed, *reg;    // bed: skipping regions, reg: index-jump to regions
@@ -85,13 +85,11 @@ typedef struct {
     mplp_pileup_t *gplp;
     int *n_plp;
     const bam_pileup1_t **plp;
-    bam_sample_t *smpl;
+    bam_smpl_t *bsmpl;
     kstring_t buf;
     bcf1_t *bcf_rec;
     htsFile *bcf_fp;
     bcf_hdr_t *bcf_hdr;
-    void *rghash_exc;   // shared by all bams
-
     int argc;
     char **argv;
 } mplp_conf_t;
@@ -111,8 +109,7 @@ struct _mplp_aux_t {
     bam_hdr_t *h;
     mplp_ref_t *ref;
     const mplp_conf_t *conf;
-    void *rghash_inc;   // whitelist for readgroups on per-bam basis, precedes blacklist
-    void *rghash_exc;   // blacklist of readgroups 
+    int bam_id;
     hts_idx_t *idx;     // maintained only with more than one -r regions
 };
 
@@ -213,19 +210,7 @@ static int mplp_func(void *data, bam1_t *b)
             }
             if ( !overlap ) continue;
         }
-        if (ma->rghash_inc)
-        {
-            // skip unless read group is listed
-            uint8_t *rg = bam_aux_get(b, "RG");
-            if ( !rg ) continue;
-            if ( !khash_str2int_has_key(ma->rghash_inc, (const char*)(rg+1)) ) continue;
-        }
-        if ( ma->rghash_exc )
-        {
-            // exclude read groups
-            uint8_t *rg = bam_aux_get(b, "RG");
-            if ( rg && khash_str2int_has_key(ma->rghash_exc, (const char*)(rg+1)) ) continue;
-        }
+        if ( bam_smpl_get_sample_id(ma->conf->bsmpl,ma->bam_id,b)<0 ) continue;
         if (ma->conf->flag & MPLP_ILLUMINA13) {
             int i;
             uint8_t *qual = bam_get_qual(b);
@@ -258,25 +243,18 @@ static int mplp_func(void *data, bam1_t *b)
     return ret;
 }
 
-static void group_smpl(mplp_pileup_t *m, bam_sample_t *sm, kstring_t *buf,
-                       int n, char *const*fn, int *n_plp, const bam_pileup1_t **plp, int ignore_rg)
+static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t **plp)
 {
     int i, j;
     memset(m->n_plp, 0, m->n * sizeof(int));
-    for (i = 0; i < n; ++i) {
-        for (j = 0; j < n_plp[i]; ++j) {
+    for (i = 0; i < n; ++i) // iterate over all bams
+    {
+        for (j = 0; j < n_plp[i]; ++j)  // iterate over all reads available at this position
+        {
             const bam_pileup1_t *p = plp[i] + j;
-            uint8_t *q;
-            int id = -1;
-            q = ignore_rg? NULL : bam_aux_get(p->b, "RG");
-            if (q) id = bam_smpl_rg2smid(sm, fn[i], (char*)q+1, buf);
-            if (id < 0) id = bam_smpl_rg2smid(sm, fn[i], 0, buf);
-            if (id < 0 || id >= m->n) {
-                assert(q); // otherwise a bug
-                fprintf(stderr, "[%s] Read group %s used in file %s but absent from the header or an alignment missing read group.\n", __func__, (char*)q+1, fn[i]);
-                exit(EXIT_FAILURE);
-            }
-            if (m->n_plp[id] == m->m_plp[id]) {
+            int id = bam_smpl_get_sample_id(bsmpl,i,p->b);
+            if (m->n_plp[id] == m->m_plp[id]) 
+            {
                 m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
                 m->plp[id] = (bam_pileup1_t*) realloc(m->plp[id], sizeof(bam_pileup1_t) * m->m_plp[id]);
             }
@@ -330,7 +308,7 @@ static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end)
 
         int total_depth, _ref0, ref16;
         for (i = total_depth = 0; i < conf->nfiles; ++i) total_depth += conf->n_plp[i];
-        group_smpl(conf->gplp, conf->smpl, &conf->buf, conf->nfiles, conf->files, conf->n_plp, conf->plp, conf->flag & MPLP_IGNORE_RG);
+        group_smpl(conf->gplp, conf->bsmpl, conf->nfiles, conf->n_plp, conf->plp);
         _ref0 = (ref && pos < ref_len)? ref[pos] : 'N';
         ref16 = seq_nt16_table[_ref0];
         bcf_callaux_clean(conf->bca, &conf->bc);
@@ -363,9 +341,6 @@ static int mpileup_reg(mplp_conf_t *conf, uint32_t beg, uint32_t end)
 
 static int mpileup(mplp_conf_t *conf)
 {
-    extern void *bcf_call_add_rg(void *rghash, const char *hdtext, const char *list);
-    extern void bcf_call_del_rghash(void *rghash);
-
     if (conf->nfiles == 0) {
         fprintf(stderr,"[%s] no input file/data given\n", __func__);
         exit(EXIT_FAILURE);
@@ -376,32 +351,6 @@ static int mpileup(mplp_conf_t *conf)
     conf->mplp_data = (mplp_aux_t**) calloc(conf->nfiles, sizeof(mplp_aux_t*));
     conf->plp = (const bam_pileup1_t**) calloc(conf->nfiles, sizeof(bam_pileup1_t*));
     conf->n_plp = (int*) calloc(conf->nfiles, sizeof(int));
-    conf->smpl = bam_smpl_init();
-
-    int i, samples_logic = 1;   // 1: include, 0: exclude
-    void *samples_list = NULL;  // hash of sample names to include or exclude
-    if ( conf->samples_list )
-    {
-        int nsamples = 0;
-        char *list = conf->samples_list;
-        if ( list[0]=='^' )
-        {
-            list++;
-            samples_logic = 0;
-        }
-        char **samples = hts_readlist(list, conf->sample_is_file, &nsamples);
-        if (!samples) {
-            fprintf(stderr,"[%s] could not read the samples list %s\n", __func__, list);
-            exit(EXIT_FAILURE);
-        }
-        if ( nsamples ) samples_list = khash_str2int_init();
-        for (i=0; i<nsamples; i++)
-        {
-            khash_str2int_inc(samples_list, strdup(samples[i]));
-            free(samples[i]);
-        }
-        free(samples);
-    }
 
     // Allow to run mpileup on multiple regions in one go. This comes at cost: the bai index
     // must be kept in the memory for the whole time which can be a problem with many bams.
@@ -435,6 +384,7 @@ static int mpileup(mplp_conf_t *conf)
     // read the header of each file in the list and initialize data
     // beware: mpileup has always assumed that tid's are consistent in the headers, add sanity check at least!
     bam_hdr_t *hdr = NULL;      // header of first file in input list
+    int i;
     for (i = 0; i < conf->nfiles; ++i) {
         bam_hdr_t *h_tmp;
         conf->mplp_data[i] = (mplp_aux_t*) calloc(1, sizeof(mplp_aux_t));
@@ -460,12 +410,20 @@ static int mpileup(mplp_conf_t *conf)
             fprintf(stderr,"[%s] fail to read the header of %s\n", __func__, conf->files[i]);
             exit(EXIT_FAILURE);
         }
-        conf->mplp_data[i]->h = i? hdr : h_tmp; // for i==0, "h" has not been set yet
-        conf->mplp_data[i]->rghash_exc = conf->rghash_exc;
-        if ( samples_list ) conf->mplp_data[i]->rghash_inc = khash_str2int_init();
-        bam_smpl_add(conf->smpl, conf->files[i], (conf->flag&MPLP_IGNORE_RG)? 0 : h_tmp->text, samples_list, samples_logic, conf->mplp_data[i]->rghash_inc);
-        // Collect read group IDs with PL (platform) listed in pl_list (note: fragile, strstr search)
-        conf->mplp_data[i]->rghash_exc = bcf_call_add_rg(conf->mplp_data[i]->rghash_exc, h_tmp->text, conf->pl_list);
+        conf->mplp_data[i]->h = i ? hdr : h_tmp; // for j==0, "h" has not been set yet
+        conf->mplp_data[i]->bam_id = bam_smpl_add_bam(conf->bsmpl,h_tmp->text,conf->files[i]);
+        if ( conf->mplp_data[i]->bam_id<0 )
+        {
+            // no usable readgroups in this bam, it can be skipped
+            sam_close(conf->mplp_data[i]->fp);
+            free(conf->mplp_data[i]);
+            bam_hdr_destroy(h_tmp);
+            free(conf->files[i]);
+            if ( i+1<conf->nfiles ) memmove(&conf->files[i],&conf->files[i+1],sizeof(*conf->files)*(conf->nfiles-i-1));
+            conf->nfiles--;
+            i--;
+            continue;
+        }
         if (conf->reg) {
             hts_idx_t *idx = sam_index_load(conf->mplp_data[i]->fp, conf->files[i]);
             if (idx == NULL) {
@@ -491,7 +449,7 @@ static int mpileup(mplp_conf_t *conf)
                 conf->mplp_data[i]->idx = idx;
         }
 
-        if (i == 0) hdr = h_tmp; /* save the header of first file in list */
+        if ( !hdr ) hdr = h_tmp; /* save the header of first file in list */
         else {
             // FIXME: check consistency between h and h_tmp
             bam_hdr_destroy(h_tmp);
@@ -502,12 +460,12 @@ static int mpileup(mplp_conf_t *conf)
         }
     }
     // allocate data storage proportionate to number of samples being studied sm->n
-    conf->gplp->n = conf->smpl->n;
-    conf->gplp->n_plp = (int*) calloc(conf->smpl->n, sizeof(int));
-    conf->gplp->m_plp = (int*) calloc(conf->smpl->n, sizeof(int));
-    conf->gplp->plp = (bam_pileup1_t**) calloc(conf->smpl->n, sizeof(bam_pileup1_t*));  
+    bam_smpl_get_samples(conf->bsmpl, &conf->gplp->n);
+    conf->gplp->n_plp = (int*) calloc(conf->gplp->n, sizeof(int));
+    conf->gplp->m_plp = (int*) calloc(conf->gplp->n, sizeof(int));
+    conf->gplp->plp = (bam_pileup1_t**) calloc(conf->gplp->n, sizeof(bam_pileup1_t*));  
 
-    fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, conf->smpl->n, conf->nfiles);
+    fprintf(stderr, "[%s] %d samples in %d input files\n", __func__, conf->gplp->n, conf->nfiles);
     // write the VCF header
     conf->bcf_fp = hts_open(conf->output_fname?conf->output_fname:"-", hts_bcf_wmode(conf->output_type));
     if (conf->bcf_fp == NULL) {
@@ -597,32 +555,33 @@ static int mpileup(mplp_conf_t *conf)
     if ( conf->gvcf )
         gvcf_update_header(conf->gvcf, conf->bcf_hdr);
 
-    for (i=0; i<conf->smpl->n; i++)
-        bcf_hdr_add_sample(conf->bcf_hdr, conf->smpl->smpl[i]);
-    bcf_hdr_add_sample(conf->bcf_hdr, NULL);
+    int nsmpl;
+    const char **smpl = bam_smpl_get_samples(conf->bsmpl, &nsmpl);
+    for (i=0; i<nsmpl; i++)
+        bcf_hdr_add_sample(conf->bcf_hdr, smpl[i]);
     bcf_hdr_write(conf->bcf_fp, conf->bcf_hdr);
 
     conf->bca = bcf_call_init(-1., conf->min_baseQ);
-    conf->bcr = (bcf_callret1_t*) calloc(conf->smpl->n, sizeof(bcf_callret1_t));
+    conf->bcr = (bcf_callret1_t*) calloc(nsmpl, sizeof(bcf_callret1_t));
     conf->bca->openQ = conf->openQ, conf->bca->extQ = conf->extQ, conf->bca->tandemQ = conf->tandemQ;
     conf->bca->min_frac = conf->min_frac;
     conf->bca->min_support = conf->min_support;
     conf->bca->per_sample_flt = conf->flag & MPLP_PER_SAMPLE;
 
     conf->bc.bcf_hdr = conf->bcf_hdr;
-    conf->bc.n = conf->smpl->n;
-    conf->bc.PL = (int32_t*) malloc(15 * conf->smpl->n * sizeof(*conf->bc.PL));
+    conf->bc.n  = nsmpl;
+    conf->bc.PL = (int32_t*) malloc(15 * nsmpl * sizeof(*conf->bc.PL));
     if (conf->fmt_flag)
     {
         assert( sizeof(float)==sizeof(int32_t) );
-        conf->bc.DP4 = (int32_t*) malloc(conf->smpl->n * sizeof(int32_t) * 4);
-        conf->bc.fmt_arr = (uint8_t*) malloc(conf->smpl->n * sizeof(float)); // all fmt_flag fields, float and int32
+        conf->bc.DP4 = (int32_t*) malloc(nsmpl * sizeof(int32_t) * 4);
+        conf->bc.fmt_arr = (uint8_t*) malloc(nsmpl * sizeof(float)); // all fmt_flag fields, float and int32
         if ( conf->fmt_flag&(B2B_INFO_DPR|B2B_FMT_DPR|B2B_INFO_AD|B2B_INFO_ADF|B2B_INFO_ADR|B2B_FMT_AD|B2B_FMT_ADF|B2B_FMT_ADR) )
         {
             // first B2B_MAX_ALLELES fields for total numbers, the rest per-sample
-            conf->bc.ADR = (int32_t*) malloc((conf->smpl->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
-            conf->bc.ADF = (int32_t*) malloc((conf->smpl->n+1)*B2B_MAX_ALLELES*sizeof(int32_t));
-            for (i=0; i<conf->smpl->n; i++)
+            conf->bc.ADR = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            conf->bc.ADF = (int32_t*) malloc((nsmpl+1)*B2B_MAX_ALLELES*sizeof(int32_t));
+            for (i=0; i<nsmpl; i++)
             {
                 conf->bcr[i].ADR = conf->bc.ADR + (i+1)*B2B_MAX_ALLELES;
                 conf->bcr[i].ADF = conf->bc.ADF + (i+1)*B2B_MAX_ALLELES;
@@ -633,14 +592,14 @@ static int mpileup(mplp_conf_t *conf)
     // init mpileup
     conf->iter = bam_mplp_init(conf->nfiles, mplp_func, (void**)conf->mplp_data);
     if ( conf->flag & MPLP_SMART_OVERLAPS ) bam_mplp_init_overlaps(conf->iter);
-    if ( conf->max_depth * conf->smpl->n > 1<<20)
+    if ( conf->max_depth * nsmpl > 1<<20)
         fprintf(stderr, "(%s) Max depth is above 1M. Potential memory hog!\n", __func__);
-    if ( conf->max_depth * conf->smpl->n < 8000) {
-        conf->max_depth = 8000 / conf->smpl->n;
+    if ( conf->max_depth * nsmpl < 8000) {
+        conf->max_depth = 8000 / nsmpl;
         fprintf(stderr, "<%s> Set max per-file depth to %d\n", __func__, conf->max_depth);
     }
     bam_mplp_set_maxcnt(conf->iter, conf->max_depth);
-    conf->max_indel_depth = conf->max_indel_depth * conf->smpl->n;
+    conf->max_indel_depth = conf->max_indel_depth * nsmpl;
     conf->bcf_rec = bcf_init1();
 
     // Run mpileup for multiple regions
@@ -697,7 +656,7 @@ static int mpileup(mplp_conf_t *conf)
         free(conf->bcr);
     }
     if ( conf->gvcf ) gvcf_destroy(conf->gvcf);
-    bam_smpl_destroy(conf->smpl); free(conf->buf.s);
+    free(conf->buf.s);
     for (i = 0; i < conf->gplp->n; ++i) free(conf->gplp->plp[i]);
     free(conf->gplp->plp); free(conf->gplp->n_plp); free(conf->gplp->m_plp); free(conf->gplp);
     bam_mplp_destroy(conf->iter);
@@ -706,11 +665,9 @@ static int mpileup(mplp_conf_t *conf)
         if ( nregs>1 ) hts_idx_destroy(conf->mplp_data[i]->idx);
         sam_close(conf->mplp_data[i]->fp);
         if ( conf->mplp_data[i]->iter) hts_itr_destroy(conf->mplp_data[i]->iter);
-        if ( conf->mplp_data[i]->rghash_inc ) khash_str2int_destroy_free(conf->mplp_data[i]->rghash_inc);
         free(conf->mplp_data[i]);
     }
     free(conf->mplp_data); free(conf->plp); free(conf->n_plp);
-    if ( samples_list ) khash_str2int_destroy_free(samples_list);
     free(mp_ref.ref[0]);
     free(mp_ref.ref[1]);
     return 0;
@@ -853,7 +810,7 @@ static void print_usage(FILE *fp, const mplp_conf_t *mplp)
     fprintf(fp,
 "  -E, --redo-BAQ          recalculate BAQ on the fly, ignore existing BQs\n"
 "  -f, --fasta-ref FILE    faidx indexed reference sequence file\n"
-"  -G, --exclude-RG FILE   exclude read groups listed in FILE\n"
+"  -G, --read-groups FILE  select or exclude read groups listed in the file\n"
 "  -q, --min-MQ INT        skip alignments with mapQ smaller than INT [%d]\n", mplp->min_mq);
     fprintf(fp,
 "  -Q, --min-BQ INT        skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp->min_baseQ);
@@ -926,6 +883,7 @@ int bam_mpileup(int argc, char *argv[])
     mplp.output_type = FT_VCF;
     mplp.record_cmd_line = 1;
     mplp.n_threads = 0;
+    mplp.bsmpl = bam_smpl_init();
 
     static const struct option lopts[] =
     {
@@ -951,8 +909,7 @@ int bam_mpileup(int argc, char *argv[])
         {"redo-BAQ", no_argument, NULL, 'E'},
         {"redo-baq", no_argument, NULL, 'E'},
         {"fasta-ref", required_argument, NULL, 'f'},
-        {"exclude-RG", required_argument, NULL, 'G'},
-        {"exclude-rg", required_argument, NULL, 'G'},
+        {"read-groups", required_argument, NULL, 'G'},
         {"region", required_argument, NULL, 'r'},
         {"regions", required_argument, NULL, 'r'},
         {"regions-file", required_argument, NULL, 'R'},
@@ -991,7 +948,7 @@ int bam_mpileup(int argc, char *argv[])
             break;
         case  3 : mplp.output_fname = optarg; break;
         case  4 : mplp.openQ = atoi(optarg); break;
-        case  5 : mplp.flag |= MPLP_IGNORE_RG; break;
+        case  5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break;
         case 'g':
             mplp.gvcf = gvcf_init(optarg);
             if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
@@ -1031,11 +988,8 @@ int bam_mpileup(int argc, char *argv[])
         case 'I': mplp.flag |= MPLP_NO_INDEL; break;
         case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
         case '6': mplp.flag |= MPLP_ILLUMINA13; break;
-        case 's': mplp.samples_list = optarg; break;
-        case 'S':
-            mplp.samples_list = optarg;
-            mplp.sample_is_file = 1;
-            break;
+        case 's': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,0)<0 ) error("Could not read samples: %s\n",optarg); break;
+        case 'S': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,1)<0 ) error("Could not read samples: %s\n",optarg); break;
         case 'O': 
             switch (optarg[0]) {
                 case 'b': mplp.output_type = FT_BCF_GZ; break;
@@ -1063,17 +1017,7 @@ int bam_mpileup(int argc, char *argv[])
         case 'F': mplp.min_frac = atof(optarg); break;
         case 'm': mplp.min_support = atoi(optarg); break;
         case 'L': mplp.max_indel_depth = atoi(optarg); break;
-        case 'G': {
-                FILE *fp_rg;
-                char buf[1024];
-                mplp.rghash_exc = khash_str2int_init();
-                if ((fp_rg = fopen(optarg, "r")) == NULL)
-                    fprintf(stderr, "(%s) Fail to open file %s. Continue anyway.\n", __func__, optarg);
-                while (!feof(fp_rg) && fscanf(fp_rg, "%s", buf) > 0) // this is not a good style, but forgive me...
-                    khash_str2int_inc(mplp.rghash_exc, strdup(buf));
-                fclose(fp_rg);
-            }
-            break;
+        case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break;
         case 'a':
             if (optarg[0]=='?') {
                 list_annotations(stderr);
@@ -1116,26 +1060,27 @@ int bam_mpileup(int argc, char *argv[])
         print_usage(stderr, &mplp);
         return 1;
     }
-    int ret;
+    int ret,i;
     if (file_list) 
     {
         if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
         mplp.files  = fn;
         mplp.nfiles = nfiles;
-        ret = mpileup(&mplp);
-        for (c=0; c<nfiles; c++) free(fn[c]);
-        free(fn);
     }
     else
     {
         mplp.nfiles = argc - optind;
-        mplp.files  = argv + optind;
-        ret = mpileup(&mplp);
+        mplp.files  = (char**) malloc(mplp.nfiles*sizeof(char*));
+        for (i=0; i<mplp.nfiles; i++) mplp.files[i] = strdup(argv[optind+i]);
     }
-    if (mplp.rghash_exc) khash_str2int_destroy_free(mplp.rghash_exc);
+    ret = mpileup(&mplp);
+
+    for (i=0; i<mplp.nfiles; i++) free(mplp.files[i]);
+    free(mplp.files);
     free(mplp.reg_fname); free(mplp.pl_list);
     if (mplp.fai) fai_destroy(mplp.fai);
     if (mplp.bed) regidx_destroy(mplp.bed);
     if (mplp.reg) regidx_destroy(mplp.reg);
+    bam_smpl_destroy(mplp.bsmpl);
     return ret;
 }
diff --git a/test/mpileup/mpileup.10.out b/test/mpileup/mpileup.10.out
new file mode 100644
index 000000000..1436904c2
--- /dev/null
+++ b/test/mpileup/mpileup.10.out
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE1b	HG00100	SAMPLE1a	SAMPLE2	SAMPLE3
+17	100	.	C	<*>	0	.	DP=16;I16=15,0,0,0,609,26637,0,0,838,48482,0,0,310,7132,0,0;QS=5,0;MQ0F=0	PL	0,3,19	0,6,78	0,12,128	0,9,108	0,15,134
+17	101	.	C	<*>	0	.	DP=16;I16=15,0,0,0,587,25433,0,0,838,48482,0,0,309,7011,0,0;QS=5,0;MQ0F=0	PL	0,3,22	0,6,79	0,12,123	0,9,99	0,15,132
+17	102	.	C	<*>	0	.	DP=16;I16=15,0,0,0,621,27715,0,0,838,48482,0,0,308,6904,0,0;QS=5,0;MQ0F=0	PL	0,3,20	0,6,78	0,12,129	0,9,111	0,15,139
+17	103	.	T	<*>	0	.	DP=16;I16=14,0,0,0,612,28790,0,0,809,47641,0,0,301,6775,0,0;QS=4,0;MQ0F=0	PL	0,0,0	0,6,79	0,12,131	0,9,108	0,15,147
+17	104	.	G	<*>	0	.	DP=16;I16=13,0,0,0,546,24526,0,0,780,46800,0,0,273,6009,0,0;QS=4,0;MQ0F=0	PL	0,0,0	0,6,78	0,12,123	0,6,89	0,15,133
+17	105	.	G	<*>	0	.	DP=17;I16=15,0,0,0,542,21886,0,0,869,51241,0,0,295,6507,0,0;QS=5,0;MQ0F=0	PL	0,3,26	0,6,77	0,12,106	0,9,97	0,15,125
+17	106	.	G	<*>	0	.	DP=17;I16=15,0,0,0,570,23834,0,0,869,51241,0,0,277,5851,0,0;QS=5,0;MQ0F=0	PL	0,6,43	0,6,75	0,12,130	0,6,85	0,15,124
+17	107	.	C	<*>	0	.	DP=17;I16=15,0,0,0,614,26864,0,0,869,51241,0,0,291,6299,0,0;QS=5,0;MQ0F=0	PL	0,3,30	0,6,77	0,12,130	0,9,108	0,15,136
+17	108	.	C	<*>	0	.	DP=17;I16=15,0,0,0,615,27183,0,0,869,51241,0,0,288,6170,0,0;QS=5,0;MQ0F=0	PL	0,3,30	0,6,78	0,12,128	0,9,108	0,15,135
+17	109	.	T	<*>	0	.	DP=17;I16=15,0,0,0,664,31304,0,0,869,51241,0,0,285,6059,0,0;QS=5,0;MQ0F=0	PL	0,3,33	0,6,77	0,12,133	0,9,110	0,15,150
+17	110	.	G	<*>	0	.	DP=17;I16=15,0,0,0,624,28074,0,0,869,51241,0,0,282,5966,0,0;QS=5,0;MQ0F=0	PL	0,3,35	0,6,78	0,12,130	0,9,104	0,15,136
+17	111	.	G	<*>	0	.	DP=17;I16=14,0,0,0,514,21894,0,0,809,47641,0,0,250,5124,0,0;QS=5,0;MQ0F=0	PL	0,6,45	0,6,75	0,12,92	0,6,88	0,12,118
+17	112	.	C	<*>	0	.	DP=17;I16=15,0,0,0,600,26654,0,0,869,51241,0,0,274,5738,0,0;QS=5,0;MQ0F=0	PL	0,3,30	0,6,77	0,12,129	0,9,95	0,15,135
+17	113	.	A	<*>	0	.	DP=17;I16=14,0,0,0,575,25583,0,0,840,50400,0,0,244,4978,0,0;QS=5,0;MQ0F=0	PL	0,3,30	0,6,71	0,12,120	0,6,87	0,15,139
+17	114	.	C	<*>	0	.	DP=17;I16=15,0,0,0,595,25667,0,0,869,51241,0,0,264,5486,0,0;QS=5,0;MQ0F=0	PL	0,3,33	0,6,75	0,12,118	0,9,103	0,15,133
+17	115	.	C	<*>	0	.	DP=19;I16=16,0,0,0,635,27881,0,0,929,54841,0,0,252,5086,0,0;QS=5,0;MQ0F=0	PL	0,6,43	0,6,80	0,12,123	0,6,89	0,18,147
+17	116	.	A	<*>	0	.	DP=19;I16=15,1,0,0,653,29009,0,0,929,54841,0,0,231,4637,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,37	0,6,75	0,12,121	0,6,90	0,21,175
+17	117	.	G	<*>	0	.	DP=19;I16=15,1,0,0,642,27956,0,0,929,54841,0,0,227,4535,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,37	0,6,77	0,12,117	0,6,85	0,21,177
+17	118	.	G	<*>	0	.	DP=19;I16=15,1,0,0,599,25205,0,0,898,52082,0,0,243,4897,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,6,43	0,6,77	0,12,116	0,3,60	0,21,162
+17	119	.	G	<*>	0	.	DP=18;I16=15,1,0,0,591,24995,0,0,898,52082,0,0,243,4977,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,38	0,6,78	0,12,114	0,6,73	0,21,160
+17	120	.	A	<*>	0	.	DP=18;I16=15,1,0,0,634,27744,0,0,898,52082,0,0,239,4893,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,41	0,6,75	0,12,116	0,6,83	0,21,171
+17	121	.	G	<*>	0	.	DP=18;I16=15,1,0,0,631,27499,0,0,898,52082,0,0,235,4829,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,39	0,6,80	0,12,121	0,6,80	0,21,168
+17	122	.	C	<*>	0	.	DP=19;I16=16,1,0,0,675,29543,0,0,958,55682,0,0,231,4785,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,40	0,6,78	0,12,119	0,9,99	0,21,178
+17	123	.	T	<*>	0	.	DP=17;I16=14,1,0,0,624,28628,0,0,838,48482,0,0,230,4760,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,39	0,6,75	0,9,98	0,9,112	0,18,166
+17	124	.	T	<*>	0	.	DP=17;I16=15,1,0,0,567,23061,0,0,867,49323,0,0,254,5378,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,6,33	0,6,70	0,9,89	0,9,104	0,18,154
+17	125	.	A	<*>	0	.	DP=16;I16=13,1,0,0,544,23440,0,0,778,44882,0,0,228,4714,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,38	0,6,72	0,6,63	0,9,104	0,18,162
+17	126	.	A	<*>	0	.	DP=16;I16=14,1,0,0,577,24833,0,0,807,45723,0,0,252,5318,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,6,50	0,6,72	0,6,67	0,9,107	0,18,174
+17	127	.	C	<*>	0	.	DP=16;I16=14,1,0,0,573,24303,0,0,807,45723,0,0,251,5315,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,6,46	0,6,69	0,6,75	0,9,109	0,18,160
+17	128	.	A	<*>	0	.	DP=16;I16=14,1,0,0,601,26205,0,0,807,45723,0,0,250,5330,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,6,59	0,6,74	0,6,72	0,9,111	0,18,162
+17	129	.	A	<*>	0	.	DP=15;I16=13,1,0,0,576,25510,0,0,747,42123,0,0,250,5362,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,6,59	0,6,72	0,6,73	0,9,113	0,15,159
+17	130	.	A	<*>	0	.	DP=15;I16=13,1,0,0,570,24774,0,0,747,42123,0,0,250,5410,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,6,60	0,6,76	0,6,68	0,9,113	0,15,152
+17	131	.	C	<*>	0	.	DP=14;I16=12,1,0,0,530,22844,0,0,718,41282,0,0,224,4798,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,38	0,6,77	0,6,71	0,9,110	0,15,147
+17	132	.	A	<*>	0	.	DP=14;I16=12,1,0,0,552,24766,0,0,718,41282,0,0,223,4825,0,0;QS=5,0;MQSB=1;MQ0F=0	PL	0,3,42	0,6,73	0,6,75	0,9,110	0,15,151
+17	133	.	T	<*>	0	.	DP=13;I16=11,2,0,0,512,20224,0,0,718,41282,0,0,248,5490,0,0;QS=5,0;MQSB=0.590909;MQ0F=0	PL	0,3,38	0,6,74	0,6,71	0,9,105	0,15,150
+17	134	.	C	<*>	0	.	DP=13;I16=11,2,0,0,526,21368,0,0,718,41282,0,0,248,5542,0,0;QS=5,0;MQSB=0.590909;MQ0F=0	PL	0,3,41	0,6,79	0,6,77	0,9,105	0,15,152
+17	135	.	T	<*>	0	.	DP=13;I16=11,2,0,0,523,21213,0,0,718,41282,0,0,248,5606,0,0;QS=5,0;MQSB=0.590909;MQ0F=0	PL	0,3,40	0,6,78	0,6,77	0,9,106	0,15,156
+17	136	.	G	<*>	0	.	DP=13;I16=11,2,0,0,495,19137,0,0,718,41282,0,0,249,5681,0,0;QS=5,0;MQSB=0.590909;MQ0F=0	PL	0,3,39	0,6,79	0,6,71	0,9,105	0,15,134
+17	137	.	T	<*>	0	.	DP=13;I16=11,2,0,0,494,18984,0,0,718,41282,0,0,251,5767,0,0;QS=5,0;MQSB=0.590909;MQ0F=0	PL	0,3,39	0,6,73	0,6,69	0,9,104	0,15,139
+17	138	.	C	<*>	0	.	DP=13;I16=11,2,0,0,504,19886,0,0,718,41282,0,0,252,5816,0,0;QS=5,0;MQSB=0.590909;MQ0F=0	PL	0,3,40	0,6,79	0,6,71	0,9,108	0,15,142
+17	139	.	C	<*>	0	.	DP=13;I16=11,2,0,0,479,17977,0,0,718,41282,0,0,252,5830,0,0;QS=5,0;MQSB=0.590909;MQ0F=0	PL	0,3,37	0,6,76	0,6,62	0,9,106	0,15,143
+17	140	.	A	<*>	0	.	DP=13;I16=11,2,0,0,509,20051,0,0,718,41282,0,0,251,5809,0,0;QS=5,0;MQSB=0.590909;MQ0F=0	PL	0,3,39	0,6,73	0,6,70	0,9,107	0,15,153
+17	141	.	G	<*>	0	.	DP=12;I16=10,2,0,0,452,17388,0,0,658,37682,0,0,250,5750,0,0;QS=5,0;MQSB=0.6;MQ0F=0	PL	0,3,36	0,6,79	0,3,34	0,9,108	0,15,142
+17	142	.	C	<*>	0	.	DP=12;I16=10,2,0,0,426,15624,0,0,658,37682,0,0,249,5701,0,0;QS=5,0;MQSB=0.6;MQ0F=0	PL	0,3,39	0,6,78	0,3,37	0,9,97	0,15,129
+17	143	.	G	<*>	0	.	DP=12;I16=9,2,0,0,353,11735,0,0,598,34082,0,0,241,5613,0,0;QS=5,0;MQSB=0.611111;MQ0F=0	PL	0,3,33	0,6,60	0,3,36	0,9,95	0,12,97
+17	144	.	A	<*>	0	.	DP=12;I16=10,2,0,0,443,16837,0,0,658,37682,0,0,246,5584,0,0;QS=5,0;MQSB=0.6;MQ0F=0	PL	0,3,33	0,6,75	0,3,41	0,9,105	0,15,129
+17	145	.	A	<*>	0	.	DP=12;I16=10,2,0,0,451,17401,0,0,658,37682,0,0,244,5518,0,0;QS=5,0;MQSB=0.6;MQ0F=0	PL	0,3,42	0,6,74	0,3,34	0,9,106	0,15,138
+17	146	.	T	<*>	0	.	DP=12;I16=10,2,0,0,439,16671,0,0,658,37682,0,0,242,5464,0,0;QS=5,0;MQSB=0.6;MQ0F=0	PL	0,3,37	0,6,73	0,3,41	0,9,103	0,15,128
+17	147	.	A	<*>	0	.	DP=12;I16=10,2,0,0,444,16692,0,0,658,37682,0,0,240,5422,0,0;QS=5,0;MQSB=0.6;MQ0F=0	PL	0,3,40	0,6,70	0,3,41	0,9,99	0,15,140
+17	148	.	C	<*>	0	.	DP=12;I16=10,2,0,0,465,18131,0,0,658,37682,0,0,237,5341,0,0;QS=5,0;MQSB=0.6;MQ0F=0	PL	0,3,39	0,6,77	0,3,41	0,9,106	0,15,146
+17	149	.	C	<*>	0	.	DP=12;I16=10,2,0,0,433,16205,0,0,658,37682,0,0,233,5221,0,0;QS=5,0;MQSB=0.6;MQ0F=0	PL	0,3,38	0,6,77	0,3,18	0,9,109	0,15,140
+17	150	.	T	<*>	0	.	DP=11;I16=9,2,0,0,436,17434,0,0,629,36841,0,0,230,5112,0,0;QS=5,0;MQSB=0.5;MQ0F=0	PL	0,3,36	0,6,76	0,3,40	0,6,84	0,15,152
diff --git a/test/mpileup/mpileup.9.out b/test/mpileup/mpileup.9.out
new file mode 100644
index 000000000..56efb518b
--- /dev/null
+++ b/test/mpileup/mpileup.9.out
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=17,length=4200>
+##ALT=<ID=*,Description="Represents allele(s) other than observed.">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of reads supporting an indel">
+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of reads supporting an indel">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">
+##INFO=<ID=RPB,Number=1,Type=Float,Description="Mann-Whitney U test of Read Position Bias (bigger is better)">
+##INFO=<ID=MQB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality Bias (bigger is better)">
+##INFO=<ID=BQB,Number=1,Type=Float,Description="Mann-Whitney U test of Base Quality Bias (bigger is better)">
+##INFO=<ID=MQSB,Number=1,Type=Float,Description="Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better)">
+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">
+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">
+##INFO=<ID=I16,Number=16,Type=Float,Description="Auxiliary tag used for calling, see description of bcf_callret1_t in bam2bcf.h">
+##INFO=<ID=QS,Number=R,Type=Float,Description="Auxiliary tag used for calling">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	SAMPLE1	SAMPLE2
+17	100	.	C	<*>	0	.	DP=9;I16=8,0,0,0,338,15668,0,0,449,26041,0,0,173,4019,0,0;QS=2,0;MQ0F=0	PL	0,9,108	0,15,134
+17	101	.	C	<*>	0	.	DP=9;I16=8,0,0,0,319,14829,0,0,449,26041,0,0,172,3954,0,0;QS=2,0;MQ0F=0	PL	0,9,99	0,15,132
+17	102	.	C	<*>	0	.	DP=9;I16=8,0,0,0,346,16476,0,0,449,26041,0,0,171,3895,0,0;QS=2,0;MQ0F=0	PL	0,9,111	0,15,139
+17	103	.	T	<*>	0	.	DP=9;I16=8,0,0,0,354,17694,0,0,449,26041,0,0,170,3842,0,0;QS=2,0;MQ0F=0	PL	0,9,108	0,15,147
+17	104	.	G	<*>	0	.	DP=9;I16=7,0,0,0,301,14499,0,0,420,25200,0,0,143,3121,0,0;QS=2,0;MQ0F=0	PL	0,6,89	0,15,133
+17	105	.	G	<*>	0	.	DP=9;I16=8,0,0,0,298,12944,0,0,449,26041,0,0,166,3658,0,0;QS=2,0;MQ0F=0	PL	0,9,97	0,15,125
+17	106	.	G	<*>	0	.	DP=9;I16=7,0,0,0,273,12195,0,0,420,25200,0,0,139,2953,0,0;QS=2,0;MQ0F=0	PL	0,6,85	0,15,124
+17	107	.	C	<*>	0	.	DP=9;I16=8,0,0,0,330,15206,0,0,449,26041,0,0,162,3506,0,0;QS=2,0;MQ0F=0	PL	0,9,108	0,15,136
+17	108	.	C	<*>	0	.	DP=9;I16=8,0,0,0,334,15764,0,0,449,26041,0,0,159,3393,0,0;QS=2,0;MQ0F=0	PL	0,9,108	0,15,135
+17	109	.	T	<*>	0	.	DP=9;I16=8,0,0,0,374,19190,0,0,449,26041,0,0,156,3290,0,0;QS=2,0;MQ0F=0	PL	0,9,110	0,15,150
+17	110	.	G	<*>	0	.	DP=9;I16=8,0,0,0,335,16083,0,0,449,26041,0,0,153,3197,0,0;QS=2,0;MQ0F=0	PL	0,9,104	0,15,136
+17	111	.	G	<*>	0	.	DP=9;I16=6,0,0,0,268,13602,0,0,360,21600,0,0,107,2151,0,0;QS=2,0;MQ0F=0	PL	0,6,88	0,12,118
+17	112	.	C	<*>	0	.	DP=9;I16=8,0,0,0,318,15164,0,0,449,26041,0,0,145,2945,0,0;QS=2,0;MQ0F=0	PL	0,9,95	0,15,135
+17	113	.	A	<*>	0	.	DP=9;I16=7,0,0,0,311,15545,0,0,420,25200,0,0,116,2212,0,0;QS=2,0;MQ0F=0	PL	0,6,87	0,15,139
+17	114	.	C	<*>	0	.	DP=9;I16=8,0,0,0,327,15347,0,0,449,26041,0,0,137,2741,0,0;QS=2,0;MQ0F=0	PL	0,9,103	0,15,133
+17	115	.	C	<*>	0	.	DP=11;I16=8,0,0,0,341,16381,0,0,480,28800,0,0,108,2032,0,0;QS=2,0;MQ0F=0	PL	0,6,89	0,18,147
+17	116	.	A	<*>	0	.	DP=11;I16=8,1,0,0,376,18032,0,0,509,29641,0,0,107,1965,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,90	0,21,175
+17	117	.	G	<*>	0	.	DP=11;I16=8,1,0,0,370,17312,0,0,509,29641,0,0,105,1913,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,85	0,21,177
+17	118	.	G	<*>	0	.	DP=11;I16=7,1,0,0,319,14789,0,0,449,26041,0,0,102,1876,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,3,60	0,21,162
+17	119	.	G	<*>	0	.	DP=10;I16=8,1,0,0,321,14467,0,0,478,26882,0,0,125,2431,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,73	0,21,160
+17	120	.	A	<*>	0	.	DP=10;I16=8,1,0,0,361,17053,0,0,478,26882,0,0,123,2373,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,83	0,21,171
+17	121	.	G	<*>	0	.	DP=10;I16=8,1,0,0,347,15913,0,0,478,26882,0,0,121,2327,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,6,80	0,21,168
+17	122	.	C	<*>	0	.	DP=11;I16=9,1,0,0,396,18360,0,0,538,30482,0,0,119,2293,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,99	0,21,178
+17	123	.	T	<*>	0	.	DP=10;I16=8,1,0,0,387,19215,0,0,478,26882,0,0,119,2271,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,112	0,18,166
+17	124	.	T	<*>	0	.	DP=10;I16=8,1,0,0,350,15768,0,0,478,26882,0,0,119,2261,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,104	0,18,154
+17	125	.	A	<*>	0	.	DP=10;I16=8,1,0,0,358,16494,0,0,478,26882,0,0,118,2214,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,104	0,18,162
+17	126	.	A	<*>	0	.	DP=10;I16=8,1,0,0,373,17399,0,0,478,26882,0,0,117,2181,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,107	0,18,174
+17	127	.	C	<*>	0	.	DP=10;I16=8,1,0,0,366,16632,0,0,478,26882,0,0,116,2162,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,109	0,18,160
+17	128	.	A	<*>	0	.	DP=10;I16=8,1,0,0,378,17674,0,0,478,26882,0,0,115,2157,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,111	0,18,162
+17	129	.	A	<*>	0	.	DP=9;I16=7,1,0,0,354,17046,0,0,418,23282,0,0,115,2165,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,113	0,15,159
+17	130	.	A	<*>	0	.	DP=9;I16=7,1,0,0,349,16363,0,0,418,23282,0,0,115,2185,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,113	0,15,152
+17	131	.	C	<*>	0	.	DP=9;I16=7,1,0,0,330,14822,0,0,418,23282,0,0,115,2217,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,110	0,15,147
+17	132	.	A	<*>	0	.	DP=9;I16=7,1,0,0,348,16432,0,0,418,23282,0,0,115,2261,0,0;QS=2,0;MQSB=1;MQ0F=0	PL	0,9,110	0,15,151
+17	133	.	T	<*>	0	.	DP=8;I16=6,2,0,0,315,12451,0,0,418,23282,0,0,141,2941,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,105	0,15,150
+17	134	.	C	<*>	0	.	DP=8;I16=6,2,0,0,314,12374,0,0,418,23282,0,0,142,3006,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,105	0,15,152
+17	135	.	T	<*>	0	.	DP=8;I16=6,2,0,0,314,12470,0,0,418,23282,0,0,143,3081,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,106	0,15,156
+17	136	.	G	<*>	0	.	DP=8;I16=6,2,0,0,291,10787,0,0,418,23282,0,0,145,3165,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,105	0,15,134
+17	137	.	T	<*>	0	.	DP=8;I16=6,2,0,0,300,11444,0,0,418,23282,0,0,148,3258,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,104	0,15,139
+17	138	.	C	<*>	0	.	DP=8;I16=6,2,0,0,300,11542,0,0,418,23282,0,0,150,3312,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,108	0,15,142
+17	139	.	C	<*>	0	.	DP=8;I16=6,2,0,0,291,10833,0,0,418,23282,0,0,152,3378,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,106	0,15,143
+17	140	.	A	<*>	0	.	DP=8;I16=6,2,0,0,314,12410,0,0,418,23282,0,0,153,3405,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,107	0,15,153
+17	141	.	G	<*>	0	.	DP=8;I16=6,2,0,0,295,11151,0,0,418,23282,0,0,153,3391,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,108	0,15,142
+17	142	.	C	<*>	0	.	DP=8;I16=6,2,0,0,264,9036,0,0,418,23282,0,0,153,3385,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,97	0,15,129
+17	143	.	G	<*>	0	.	DP=8;I16=5,2,0,0,218,7170,0,0,358,19682,0,0,146,3338,0,0;QS=2,0;MQSB=0.7;MQ0F=0	PL	0,9,95	0,12,97
+17	144	.	A	<*>	0	.	DP=8;I16=6,2,0,0,287,10705,0,0,418,23282,0,0,153,3397,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,105	0,15,129
+17	145	.	A	<*>	0	.	DP=8;I16=6,2,0,0,294,11200,0,0,418,23282,0,0,153,3415,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,106	0,15,138
+17	146	.	T	<*>	0	.	DP=8;I16=6,2,0,0,281,10419,0,0,418,23282,0,0,153,3441,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,103	0,15,128
+17	147	.	A	<*>	0	.	DP=8;I16=6,2,0,0,286,10442,0,0,418,23282,0,0,153,3475,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,99	0,15,140
+17	148	.	C	<*>	0	.	DP=8;I16=6,2,0,0,301,11401,0,0,418,23282,0,0,152,3466,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,106	0,15,146
+17	149	.	C	<*>	0	.	DP=8;I16=6,2,0,0,293,10907,0,0,418,23282,0,0,150,3414,0,0;QS=2,0;MQSB=0.666667;MQ0F=0	PL	0,9,109	0,15,140
+17	150	.	T	<*>	0	.	DP=7;I16=5,2,0,0,277,11093,0,0,389,22441,0,0,149,3369,0,0;QS=2,0;MQSB=0.5;MQ0F=0	PL	0,6,84	0,15,152
diff --git a/test/mplp.10.samples b/test/mplp.10.samples
new file mode 100644
index 000000000..5d8cc1377
--- /dev/null
+++ b/test/mplp.10.samples
@@ -0,0 +1,5 @@
+ERR162872
+ERR162875   SAMPLE1a
+ERR013140   SAMPLE1b
+ERR229776   SAMPLE2
+ERR229775   SAMPLE3
diff --git a/test/mplp.9.samples b/test/mplp.9.samples
new file mode 100644
index 000000000..af6b516fe
--- /dev/null
+++ b/test/mplp.9.samples
@@ -0,0 +1,2 @@
+HG00101 SAMPLE1
+HG00102 SAMPLE2
diff --git a/test/test.pl b/test/test.pl
index 9c807d30e..4779cd271 100755
--- a/test/test.pl
+++ b/test/test.pl
@@ -261,7 +261,8 @@
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.7.out',args=>q[-r17:100-150 -S {PATH}/mplp.samples]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -s ^HG00101,HG00102]);
 test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-r17:100-150 -S ^{PATH}/mplp.samples]);
-test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.8.out',args=>q[-t17:100-150 -S ^{PATH}/mplp.samples]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.9.out',args=>q[-t17:100-150 -S {PATH}/mplp.9.samples]);
+test_mpileup($opts,in=>[qw(1 2 3)],out=>'mpileup/mpileup.10.out',args=>q[-t17:100-150 -G {PATH}/mplp.10.samples]);
 
 print "\nNumber of tests:\n";
 printf "    total   .. %d\n", $$opts{nok}+$$opts{nfailed};

From 251fe2afc26422e39b164a373ce93f22551f8261 Mon Sep 17 00:00:00 2001
From: James Bonfield <jkb@sanger.ac.uk>
Date: Tue, 12 Jul 2016 17:52:50 +0100
Subject: [PATCH 210/211] Make use of the pileup constructor/destructor
 interface.

Our first foray into exploiting this is to cache the
bam_smpl_get_sample_id return value.  We compute this once in the
constructor (the first time we see a new bam1_t) instead of for every
pileup location in group_smpl.

TO DO: Group_smpl itself could now become distributed perhaps.  Rather
than an N*M loop clustering all sample IDs together, each new bam
could be added to sample struct on first appearance and removed when
it goes out of sight.

The slight caveat preventing this from being implemented immediately
is that the constructor/destructors are called for every BAM
overlapping the region rather than every filtered base that ultimately
ends up in a pileup.  Indeed sometimes we get constructors for
reads entirely filtered out.
---
 mpileup.c | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/mpileup.c b/mpileup.c
index 8c2d4e147..01db650d8 100644
--- a/mpileup.c
+++ b/mpileup.c
@@ -243,6 +243,18 @@ static int mplp_func(void *data, bam1_t *b)
     return ret;
 }
 
+// Called once per new bam added to the pileup.
+// We cache sample information here so we don't have to keep recomputing this
+// on each and every pileup column.
+//
+// Cd is an arbitrary block of data we can write into, which ends up in
+// the pileup structures.  We stash the sample ID there.
+static int pileup_constructor(void *data, const bam1_t *b, bam_pileup_cd *cd) {
+    mplp_aux_t *ma = (mplp_aux_t *)data;
+    cd->i = bam_smpl_get_sample_id(ma->conf->bsmpl, ma->bam_id, (bam1_t *)b);
+    return 0;
+}
+
 static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, const bam_pileup1_t **plp)
 {
     int i, j;
@@ -252,7 +264,7 @@ static void group_smpl(mplp_pileup_t *m, bam_smpl_t *bsmpl, int n, int *n_plp, c
         for (j = 0; j < n_plp[i]; ++j)  // iterate over all reads available at this position
         {
             const bam_pileup1_t *p = plp[i] + j;
-            int id = bam_smpl_get_sample_id(bsmpl,i,p->b);
+            int id = p->cd.i;
             if (m->n_plp[id] == m->m_plp[id]) 
             {
                 m->m_plp[id] = m->m_plp[id]? m->m_plp[id]<<1 : 8;
@@ -601,6 +613,7 @@ static int mpileup(mplp_conf_t *conf)
     bam_mplp_set_maxcnt(conf->iter, conf->max_depth);
     conf->max_indel_depth = conf->max_indel_depth * nsmpl;
     conf->bcf_rec = bcf_init1();
+    bam_mplp_constructor(conf->iter, pileup_constructor);
 
     // Run mpileup for multiple regions
     if ( nregs )

From c333e8b45838109ebd206a1ef95a07901ccb86cc Mon Sep 17 00:00:00 2001
From: James Bonfield <jkb@sanger.ac.uk>
Date: Wed, 13 Jul 2016 11:34:10 +0100
Subject: [PATCH 211/211] Speed up of mpileup funcs.

Mann Whitney test now uses a precomputed table instead of continually
calculating the same values many times over.

calc_mwu_bias now has short-cuts to compute the result faster when one
or both of a[] and b[] hold zero values.
---
 bam2bcf.c |   32 +-
 mw.h      | 1917 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 1941 insertions(+), 8 deletions(-)
 create mode 100644 mw.h

diff --git a/bam2bcf.c b/bam2bcf.c
index 8bb799ebd..b4fb7f1ef 100644
--- a/bam2bcf.c
+++ b/bam2bcf.c
@@ -350,11 +350,22 @@ double calc_chisq_bias(int *a, int *b, int n)
     return prob;
 }
 
+static double mann_whitney_1947_(int n, int m, int U)
+{
+     if (U<0) return 0;
+     if (n==0||m==0) return U==0 ? 1 : 0;
+    return (double)n/(n+m)*mann_whitney_1947_(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947_(n,m-1,U);
+}
+
 double mann_whitney_1947(int n, int m, int U)
 {
-    if (U<0) return 0;
-    if (n==0||m==0) return U==0 ? 1 : 0;
-    return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U);
+    #include "mw.h"
+
+    assert(n >= 2 && m >= 2);
+
+    return (n < 8 && m < 8 && U < 50)
+        ? mw[n-2][m-2][U]
+        : mann_whitney_1947_(n,m,U);
 }
 
 double mann_whitney_1947_cdf(int n, int m, int U)
@@ -416,11 +427,16 @@ double calc_mwu_bias(int *a, int *b, int n)
     double U = 0, ties = 0;
     for (i=0; i<n; i++)
     {
-        na += a[i];
-        U  += a[i] * (nb + b[i]*0.5);
-        nb += b[i];
-        if ( a[i] && b[i] )
-        {
+        if (!a[i]) {
+            if (!b[i]) continue;
+            nb += b[i];
+        } else if (!b[i]) {
+            na += a[i];
+            U  += a[i] * nb;
+        } else {
+            na += a[i];
+            U  += a[i] * (nb + b[i]*0.5);
+            nb += b[i];
             double tie = a[i] + b[i];
             ties += (tie*tie-1)*tie;
         }
diff --git a/mw.h b/mw.h
new file mode 100644
index 000000000..b41a028cb
--- /dev/null
+++ b/mw.h
@@ -0,0 +1,1917 @@
+// Code to build this table is below
+#ifdef BUILD_MW
+#include <stdio.h>
+
+double mann_whitney_1947(int n, int m, int U)
+{
+    if (U<0) return 0;
+    if (n==0||m==0) return U==0 ? 1 : 0;
+    return (double)n/(n+m)*mann_whitney_1947(n-1,m,U-m) + (double)m/(n+m)*mann_whitney_1947(n,m-1,U);
+}
+
+int main(void) {
+    int i, j, k;
+    printf("static double mw[6][6][50] = // [2-7][2-7][0-49]\n{\n");
+    for (i = 2; i < 8; i++) {
+	printf("    {\n");
+	for (j = 2; j < 8; j++) {
+	    printf("        {\n");
+	    for (k = 0; k < 50; k++) {
+		printf("            %.17f,\n", mann_whitney_1947(i,j,k));
+	    }
+	    printf("        },\n");
+	}
+	printf("    },\n");
+    }
+    printf("};\n");
+    return 0;
+}
+#endif
+
+static double mw[6][6][50] = // [2-7][2-7][0-49]
+{
+    {
+        {
+            0.16666666666666666,
+            0.16666666666666666,
+            0.33333333333333331,
+            0.16666666666666666,
+            0.16666666666666666,
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+            0.00000000000000000,
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+            0.00000000000000000,
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+            0.00000000000000000,
+            0.00000000000000000,
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+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
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+            0.00000000000000000,
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+            0.00000000000000000,
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+            0.00000000000000000,
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+            0.00000000000000000,
+            0.00000000000000000,
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+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
+            0.09999999999999999,
+            0.09999999999999999,
+            0.19999999999999998,
+            0.20000000000000001,
+            0.20000000000000001,
+            0.10000000000000001,
+            0.10000000000000001,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
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+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+            0.00000000000000000,
+        },
+        {
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+            0.00000000000000000,
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+            0.00000000000000000,
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+            0.00000000000000000,
+        },
+        {
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+            0.09523809523809523,
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+            0.09523809523809523,
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+        },
+        {
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+            0.10714285714285714,
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+            0.10714285714285715,
+            0.10714285714285715,
+            0.07142857142857144,
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+            0.00000000000000000,
+        },
+        {
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+            0.05555555555555555,
+            0.08333333333333334,
+            0.08333333333333333,
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+            0.11111111111111113,
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+        },
+    },
+    {
+        {
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+        },
+        {
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+        },
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