Fix vcf-merge when using COLLAPSE_NONE

test/merge.10.a.vcf

@@ -0,0 +1,9 @@
+##fileformat=VCFv4.1
+##contig=<ID=1,assembly=b37,length=249250621>
+##reference=file:///ref.fa
+##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=GT,Number=1,Type=String,Description="Genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
+1	10	.	C	G	.	.	AN=4;AC=2	GT	0/1
+1	12	.	T	A	.	.	AN=4;AC=2	GT	0/1

test/merge.10.b.vcf

@@ -0,0 +1,8 @@
+##fileformat=VCFv4.1
+##contig=<ID=1,assembly=b37,length=249250621>
+##reference=file:///ref.fa
+##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=GT,Number=1,Type=String,Description="Genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	B
+1	10	.	CGT	CGA,AGT	.	.	AN=4;AC=1	GT	1/2

test/merge.10.none.out

@@ -0,0 +1,11 @@
+##fileformat=VCFv4.1
+##FILTER=<ID=PASS,Description="All filters passed">
+##contig=<ID=1,assembly=b37,length=249250621>
+##reference=file:///ref.fa
+##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=GT,Number=1,Type=String,Description="Genotypes">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A	B
+1	10	.	C	G	.	.	AN=2;AC=1	GT	0/1	./.
+1	10	.	CGT	CGA,AGT	.	.	AN=2;AC=1,1	GT	./.	1/2
+1	12	.	T	A	.	.	AN=2;AC=1	GT	0/1	./.

test/test.pl

@@ -97,6 +97,7 @@
 test_vcf_merge($opts,in=>['merge.8.a','merge.8.b'],out=>'merge.8.out',args=>'-i AN:sum,AC:sum');
 test_vcf_merge($opts,in=>['merge.9.a','merge.9.b'],out=>'merge.9.1.out',args=>'');
 test_vcf_merge($opts,in=>['merge.9.a','merge.9.b'],out=>'merge.9.2.out',args=>'-i AN:sum,AC:sum');
+test_vcf_merge($opts,in=>['merge.10.a','merge.10.b'],out=>'merge.10.none.out',args=>'-m none');
 # test_vcf_merge_big($opts,in=>'merge_big.1',out=>'merge_big.1.1',nsmpl=>79000,nfiles=>79,nalts=>486,args=>'');   # commented out for speed
 test_vcf_query($opts,in=>'query.string',out=>'query.string.1.out',args=>q[-f '%CHROM\\t%POS\\t%CLNREVSTAT\\n' -i'CLNREVSTAT="criteria_provided,_conflicting_interpretations"']);
 test_vcf_query($opts,in=>'query.string',out=>'query.string.1.out',args=>q[-f '%CHROM\\t%POS\\t%CLNREVSTAT\\n' -i'CLNREVSTAT="criteria_provided" || CLNREVSTAT="_conflicting_interpretations"']);

vcfmerge.c

@@ -149,7 +149,7 @@ typedef struct
     maux_t *maux;
     regidx_t *regs;    // apply regions only after the blocks are expanded
     regitr_t *regs_itr;
-    int header_only, collapse, output_type, force_samples, merge_by_id, do_gvcf, filter_logic, missing_to_ref, no_index;
+    int header_only, collapse, output_type, force_samples, merge_by_id, do_gvcf, filter_logic, missing_to_ref, no_index, non_normalize_alleles;
     char *header_fname, *output_fname, *regions_list, *info_rules, *file_list;
     faidx_t *gvcf_fai;
     info_rule_t *rules;
@@ -973,7 +973,7 @@ void merge_chrom2qual(args_t *args, bcf1_t *out)
     for (i=0; i<ma->nals; i++)
         if ( i==0 || al_idxs[i] ) ma->out_als[k++] = strdup(ma->als[i]);
     assert( k==ma->nout_als );
-    normalize_alleles(ma->out_als, ma->nout_als);
+    if (args->non_normalize_alleles != 1) normalize_alleles(ma->out_als, ma->nout_als);
     bcf_update_alleles(out_hdr, out, (const char**) ma->out_als, ma->nout_als);
     free(al_idxs);
     for (i=0; i<ma->nout_als; i++) free(ma->out_als[i]);
@@ -2799,7 +2799,7 @@ int can_merge(args_t *args)
                     // All alleles of the tested record must be present in the
                     // selected maux record plus variant types must be the same
                     if ( (maux->var_types & line_type) != line_type ) continue;
-                    if ( vcmp_set_ref(args->vcmp,maux->als[0],line->d.allele[0]) < 0 ) continue;   // refs not compatible
+                    if ( vcmp_set_ref(args->vcmp,maux->als[0],line->d.allele[0]) <= 0 ) continue;   // refs not perfect match
                     for (k=1; k<line->n_allele; k++)
                     {
                         if ( vcmp_find_allele(args->vcmp,maux->als+1,maux->nals-1,line->d.allele[k])>=0 ) break;
@@ -3134,6 +3134,7 @@ static void usage(void)
     fprintf(stderr, "    -R, --regions-file FILE           Restrict to regions listed in a file\n");
     fprintf(stderr, "        --regions-overlap 0|1|2       Include if POS in the region (0), record overlaps (1), variant overlaps (2) [1]\n");
     fprintf(stderr, "        --threads INT                 Use multithreading with <int> worker threads [0]\n");
+    fprintf(stderr, "    -N, --non_normalize_alleles       Do not normalize_alleles\n");
     fprintf(stderr, "\n");
     exit(1);
 }
@@ -3150,6 +3151,7 @@ int main_vcfmerge(int argc, char *argv[])
     args->record_cmd_line = 1;
     args->collapse = COLLAPSE_BOTH;
     args->clevel = -1;
+    args->non_normalize_alleles = 0;
     int regions_is_file = 0;
     int regions_overlap = 1;
 
@@ -3175,11 +3177,13 @@ int main_vcfmerge(int argc, char *argv[])
         {"no-version",no_argument,NULL,8},
         {"no-index",no_argument,NULL,10},
         {"filter-logic",required_argument,NULL,'F'},
+        {"non_normalize_alleles",no_argument,NULL,'N'},
         {NULL,0,NULL,0}
     };
     char *tmp;
-    while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:l:g:F:0L:",loptions,NULL)) >= 0) {
+    while ((c = getopt_long(argc, argv, "hm:f:r:R:o:O:i:l:g:F:0L:N",loptions,NULL)) >= 0) {
         switch (c) {
+            case 'N': args->non_normalize_alleles = 1; break;
             case 'L':
                 args->local_alleles = strtol(optarg,&tmp,10);
                 if ( *tmp ) error("Could not parse argument: --local-alleles %s\n", optarg);

vcmp.c

@@ -58,7 +58,7 @@ int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2)
 
     char *a = ref1, *b = ref2;
     while ( *a && *b && toupper(*a)==toupper(*b) ) { a++; b++; }
-    if ( !*a && !*b ) return 0;
+    if ( !*a && !*b ) return 1; // perfect match
     if ( *a && *b ) return -1;  // refs not compatible
 
     int i;
@@ -70,18 +70,19 @@ int vcmp_set_ref(vcmp_t *vcmp, char *ref1, char *ref2)
         hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
         for (i=0; i<vcmp->ndref; i++) vcmp->dref[i] = toupper(ref1[vcmp->nmatch+i]);
         vcmp->dref[vcmp->ndref] = 0;
-        return 0;
+        return 0; // compatible
+    } else if ( *b ) { // ref2 is longer
+        vcmp->nmatch = a-ref1;
+        while ( *b ) b++;
+        vcmp->ndref = (b-ref2) - vcmp->nmatch;
+        hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
+        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; // compatible
+    } else {
+        return -1; // should not happen
     }
-
-    // ref2 is longer
-    vcmp->nmatch = a-ref1;
-    while ( *b ) b++;
-    vcmp->ndref = (b-ref2) - vcmp->nmatch;
-    hts_expand(char,vcmp->ndref+1,vcmp->mdref,vcmp->dref);
-    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;
 }
 
 int vcmp_find_allele(vcmp_t *vcmp, char **als1, int nals1, char *al2)