Mpileup speedup#2

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jkbonfield wants to merge 242 commits intopd3:developfrom

jkbonfield:mpileup_speedup

Commits on Jun 13, 2015

Commits on Jun 29, 2015

Commits on Jul 6, 2015

update copyright dates for peakfit
mcshane
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Merge pull request #286 from samtools/feature/polysomy
mcshane
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Implements "bcftools view -G removes all format header lines"

winni2k
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mcshane
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The HMM structure becomes opaque for future flexibility

pd3
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mcshane
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RoH bugfix: Transition probabilities must scale to 1

pd3
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mcshane
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New bcftools roh --AF-dflt option; changed -a,-H defaults; fixed a bug in -e -

pd3
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mcshane
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Fix polysomy dependencies [minor]
jmarshall
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Merge pull request #287 from samtools/feature/roh
mcshane
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plot-vcfstats: Fix edge case in tstv_by_qual plot, see #229

pd3
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mcshane
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concat: new --compact-PS switch

pd3
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mcshane
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concat -d option to remove duplicates based on one of the collapse srings: <snps|indels|both|all|none>

pd3
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mcshane
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concat -l: Print warning and proceed if GT not present

pd3
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mcshane
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bcf_hdr_combine replaced by bcf_hdr_merge
mcshane
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More control duplicate lines removal with norm (REF still not treated well)

pd3
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mcshane
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Output missing FMT fields as "." rather than negative integer when querying FMT vectors, such as PL{0}

pd3
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mcshane
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Commits on Jul 7, 2015

Updated cnv command:

pd3
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mcshane
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cnv -O: Increase robustness by smoothing HMM lks before updating the mean

pd3
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mcshane
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cnv: Update to the modified HMM API

pd3
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mcshane
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cnv: Prior on CN2; changed the default -P to be more strict (0.5)

pd3
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mcshane
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Commits on Jul 17, 2015

Commits on Jul 28, 2015

merge: More informative error message when FILTER is undefined
mcshane
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Resolved assert when comparing long GT strings

pd3
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mcshane
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plugin: new --version switch
mcshane
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vcfplugin: header boilerplate mentioned the wrong file
mcshane
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Include ctype for toupper declaration in vcmp

pd3
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mcshane
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New fill-tags plugin to set INFO tags AN,AC,AC_Hom,AC_Het,AC_Hemi

pd3
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mcshane
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Fix bcftools_pluginCommand=plugin header annotation.

pd3
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mcshane
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New isec -n~BITMASK option

pd3
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mcshane
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New annotate -m option to mark sites present/absent in a file

pd3
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mcshane
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docs update
mcshane
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Merge branch 'develop' of github.com:samtools/bcftools into feature/cnv
mcshane
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Fix in -i/-e filtering in the convert command; query missing GT fields e.g. as GT="."

pd3
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mcshane
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bugfix in filtering expressions involving ALT=. sites

pd3
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mcshane
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Merge pull request #298 from samtools/feature/cnv
mcshane
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Merge branch 'develop' of github.com:samtools/bcftools into develop
mcshane
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rbuf_expand0 macro made analogous to hts_expand0

pd3
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mcshane
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Moved hts_bcf_wmode to be accesible by plugins

pd3
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mcshane
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norm: Replace IUPAC ambiguity codes in fasta ref with Ns

pd3
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mcshane
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norm: Set freed alleles to NULL to prevent multiple free()s

pd3
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mcshane
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stats: previously omitted ALT=. sites now count as SNPs in per-sample stats (HomRR counts)

pd3
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mcshane
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stats: output also indel nHET and nAA in PSI stats

pd3
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mcshane
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gtcheck: switch automatically to -G99 at ALT=. sites in absence of PLs

pd3
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mcshane
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gtcheck: more informative description of discordance per-site

pd3
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mcshane
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Support for -i/-e filtering in vcfstats

pd3
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mcshane
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remove install dependency on asciidoc
mcshane
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Merge pull request #295 from samtools/feature/fix.289
mcshane
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Merge pull request #299 from samtools/feature/stats
mcshane
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update man docs
mcshane
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Commits on Jul 29, 2015

call: new ploidy handling

pd3
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mcshane
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Commits on Aug 4, 2015

Merge pull request #300 from samtools/feature/concat
mcshane
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Commits on Aug 5, 2015

Commits on Aug 7, 2015

Check that opening chain and output files succeeded
jmarshall
committed

Commits on Sep 1, 2015

Commits on Sep 2, 2015

Commits on Sep 3, 2015

Add test for splitting and merging in one go

Jason Piper
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Jason Piper
committed

Commits on Sep 14, 2015

Commits on Sep 15, 2015

Commits on Sep 16, 2015

Commits on Sep 17, 2015

Update test VCF headers to v4.2

Jason Piper
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Jason Piper
committed

Commits on Sep 22, 2015

convert -H: Fixes issue #274; adds support for haploid and missing alleles
winni2k
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Commits on Sep 24, 2015

Merge pull request #321 from humanlongevity/develop
mcshane
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Commits on Sep 25, 2015

Fixed bug in trio calling introduced by bcc7b26e

pd3
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mcshane
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Commits on Sep 30, 2015

vcfindex: make index -s work even if length attribute is not present

pd3
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mcshane
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Bringing "call --gvcf" from experimental to main repo.

pd3
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mcshane
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Commits on Oct 12, 2015

add tests for trimming many alleles and dropping header+format
mcshane
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Commits on Oct 15, 2015

Commits on Oct 22, 2015

add test for consensus on empty vcf file
mcshane
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norm: Expand round buffer if needed. Fixes #336

pd3
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mcshane
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cnv: New -k option, fixed non-functional parsing of -dfloat,float

pd3
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mcshane
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CNV output include number of sites/hets in regions

pd3
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mcshane
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Reduce memory consumption in cnv plotting script

pd3
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mcshane
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Added cnv and polysomy commands to the docs

pd3
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mcshane
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Commits on Nov 6, 2015

Expanded docs to prevent errors reported in #346 and #239

pd3
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mcshane
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Support for --guess GL in vcf2sex

pd3
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mcshane
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Fixes in vcf2sex

pd3
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mcshane
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More informative error msg in fill-tags plugin

pd3
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mcshane
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Expanded plugin docs: explain "+pname" vs "plugin name"

pd3
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mcshane
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vcfmerge: Fix error message, correct chr name must be printed

pd3
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mcshane
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gtcheck: Use also sites without DP for GT checking; Plot discordance in the reverse order

pd3
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mcshane
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Distinguish between & and && in -i/-e FMT filtering

pd3
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mcshane
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Fix in filtering of missing values.

pd3
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mcshane
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Document requirement of compressed/indexed files when reading multiple VCFs simultaneously
mcshane
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document subset behaviour with regard to sample dependent tags
mcshane
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add some missing documentation
mcshane
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update man and html doc from the asciidoc
mcshane
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Commits on Nov 10, 2015

Commits on Nov 12, 2015

further fixes in vcf2sex

pd3
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mcshane
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plot-vcfstats: plotting of sample names fixed
dlaehnemann
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Commits on Nov 13, 2015

Merge pull request #352 from dlaehnemann/develop
mcshane
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Commits on Nov 16, 2015

Commits on Nov 18, 2015

Prevent empty PL fields on BCF output with "call -C alleles"

pd3
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mcshane
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Commits on Nov 19, 2015

add POS as a filter column
mcshane
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Commits on Nov 20, 2015

Merge pull request #354 from samtools/feature/filter_pos
mcshane
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Commits on Dec 6, 2015

Fix typo: annotate -x ^FORMAT/TAG did not work

pd3
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mcshane
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Commits on Dec 7, 2015

Commits on Dec 10, 2015

add --threads option for output compression threads

mcshane
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jmarshall
committed

Commits on Dec 15, 2015

Commits on Jan 11, 2016

Commits on Jan 14, 2016

reheader: support spaces in sample names

pd3
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mcshane
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annotate: add to FORMAT fields from a tab-delimited file

pd3
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mcshane
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The fill-tags plugin can add AF. Resolves #345

pd3
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mcshane
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roh: Viterbi training fixed, resolves #328

pd3
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mcshane
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Commits on Jan 15, 2016

concat: new --naive option for fast operations on large BCFs

pd3
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mcshane
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Merge pull request #359 from samtools/feature/naive_concat
mcshane
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Pass unchanged argc,argv to plugins with run() implemented.

pd3
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mcshane
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Commits on Jan 21, 2016

add --no-version option to suppress appending of version and command line to output headers
mcshane
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Commits on Jan 22, 2016

reheader: allow empty body with vcf.gz. Fixes #356

pd3
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mcshane
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Commits on Feb 1, 2016

Fix merging of Number=G format strings
jmarshall
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Commits on Feb 10, 2016

Commits on Feb 12, 2016

Commits on Feb 19, 2016

Commits on Feb 23, 2016

Commits on Mar 4, 2016

Commits on Mar 5, 2016

norm: should not crash on deletions in telomere N regions which cannot be extended to the left

pd3
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mcshane
committed

Commits on Mar 14, 2016

impute-info: do calculation with double; only convert to float on insert into VCF
mcshane
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Commits on Mar 15, 2016

getopt_long() returns int, not char
jmarshall
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Commits on Mar 16, 2016

Commits on Mar 17, 2016

GLs are log10 scaled, not ln scaled. Fixes #394

pd3
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mcshane
committed

Commits on Mar 31, 2016

Fix docs grammar [minor]
jmarshall
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Commits on Apr 18, 2016

Commits on Apr 22, 2016

Commits on Apr 29, 2016

filter: fix bug with uninitialised key
mcshane
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norm: informative error messages on fields with wrong Number=R,A values

pd3
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mcshane
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concat: `--naive` option now works for both bcf and vcf.gz

pd3
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mcshane
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Commits on Apr 30, 2016

reheader: allow multispace delimiters in `reheader -s` files

pd3
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mcshane
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Commits on May 3, 2016

mcall: trim all `Number=R` tags

pd3
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mcshane
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call: new `-F, --prior-freqs` option

pd3
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mcshane
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docs: fix up alphabetic order of commands in docs cnv>call
mcshane
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Commits on May 11, 2016

Use bcf_hdr_format() rather than deprecated bcf_hdr_fmt_text()
jmarshall
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Commits on May 12, 2016

Avoid angle brackets around option arguments
jmarshall
committed

Commits on May 16, 2016

Commits on May 17, 2016

Refactorings and warning preventions [minor]
jmarshall
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Commits on May 24, 2016

Commits on May 27, 2016

Avoid segfault when QUAL < 0
jmarshall
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Commits on Jun 2, 2016

consensus: handle variants which overlap region boundaries

pd3
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mcshane
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Commits on Jun 20, 2016

norm: strict checking of non-ACGTN bases in `norm -cwx`

pd3
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mcshane
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roh: fix nonfunctional --AF-dflt option

pd3
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mcshane
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call: re-enable numeric ploidy definitions via `--samples-file`

pd3
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mcshane
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Commits on Jun 21, 2016

cnv: add params estimated by -O to the summary cnv output

pd3
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mcshane
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call: add some extra info to the ploidy help message [minor]
mcshane
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plugin: decrease verbosity of plugin -l, old output via -lv and -lvv

pd3
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mcshane
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Commits on Jun 28, 2016

Commits on Jul 1, 2016

norm: avoid regression when ALT is a spanning deletion `*`
mcshane
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Commits on Jul 2, 2016

Commits on Jul 12, 2016

Make use of the pileup constructor/destructor interface.
jkbonfield
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Commits on Jul 13, 2016

Speed up of mpileup funcs.
jkbonfield
committed