convert: fix logic bug in gvcf2vcf

Fixes samtools#641
ssimwa · Jul 8, 2017 · 9a1f6b2 · 9a1f6b2
1 parent f0ec4a3
commit 9a1f6b2
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/test/convert.gvcf.out b/test/convert.gvcf.out
@@ -112,7 +112,7 @@
 22	83	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
 22	84	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
 22	85	.	G	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-22	86	.	G	C	23	LowGQX	SNVSB=0;SNVHPOL=2	GT:GQ:GQX:DP:DPF:AD	0/1:56:23:22:0:16,6
+22	86	.	G	C	23	PASS	SNVSB=0;SNVHPOL=2	GT:GQ:GQX:DP:DPF:AD	0/1:56:23:22:0:16,6
 22	87	.	T	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
 22	88	.	C	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
 22	89	.	A	.	0	PASS	BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0

diff --git a/test/convert.gvcf.vcf b/test/convert.gvcf.vcf
@@ -80,7 +80,7 @@
 22	51	.	C	.	0	PASS	END=55;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:30:11:0
 22	56	.	G	.	0	PASS	END=72;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:42:15:0
 22	73	.	T	.	0	PASS	END=85;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:54:19:0
-22	86	.	G	C	23	LowGQX	SNVSB=0;SNVHPOL=2	GT:GQ:GQX:DP:DPF:AD	0/1:56:23:22:0:16,6
+22	86	.	G	C	23	PASS	SNVSB=0;SNVHPOL=2	GT:GQ:GQX:DP:DPF:AD	0/1:56:23:22:0:16,6
 22	87	.	T	.	0	PASS	END=101;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:69:24:0
 22	102	.	A	.	0	PASS	END=140;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:84:29:0
 22	141	.	G	.	0	PASS	END=185;BLOCKAVG_min30p3a	GT:GQX:DP:DPF	0/0:90:31:0

diff --git a/vcfconvert.c b/vcfconvert.c
@@ -1316,12 +1316,13 @@ static void gvcf_to_vcf(args_t *args)
         }
 
         // check if alleles compatible with being a gVCF record
+        // ALT must be one of ., <*>, <X>, <NON_REF>
+        // check for INFO/END is below
         int i, gallele = -1;
         if (line->n_allele==1)
             gallele = 0; // illumina/bcftools-call gvcf (if INFO/END present)
-        else
+        else if ( line->d.allele[1][0]=='<' )
         {
-            if ( line->d.allele[1][0]!='<' ) continue;
             for (i=1; i<line->n_allele; i++)
             {
                 if ( line->d.allele[i][1]=='*' && line->d.allele[i][2]=='>' && line->d.allele[i][3]=='\0' ) { gallele = i; break; } // mpileup/spec compliant gVCF