merge_format_string: Enlarge array for BCF_VL_A/BCF_VL_R too

Fixes samtools#1353. Lengthen strings in merge.6.b.vcf to such an extent that merge_format_string() crashes on this test case without this fix.
ssimwa · Nov 30, 2020 · ff5dc52 · ff5dc52
1 parent 0987715
commit ff5dc52
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Showing 4 changed files with 6 additions and 5 deletions.
diff --git a/test/merge.6.a.vcf b/test/merge.6.a.vcf
@@ -5,5 +5,5 @@
 ##contig=<ID=1,length=248956422>
 ##reference=file:///home/dnanexus/genome.fa
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	t1
-1	11080563	.	A	C	.	.	.	GT:RFS:AFS	0/1:a,c:c
-1	11080564	.	A	C	.	.	.	GT:RFS:AFS	0/1:a,c:c
+1	11080563	.	A	C	.	.	.	GT:RFS:AFS	0/1:aa,c:c
+1	11080564	.	A	C	.	.	.	GT:RFS:AFS	0/1:a,cc:c
diff --git a/test/merge.6.b.vcf b/test/merge.6.b.vcf
@@ -7,4 +7,4 @@
 ##reference=file:///home/dnanexus/genome.fa
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	t2
 1	11080563	.	A	C	.	.	.	GT:FFS:AFS:RFS	0/1:xx,yy:C:A,C
-1	11080564	.	A	T	.	.	.	GT:FFS:AFS:RFS	0/1:xx,yy:T:A,T
+1	11080564	.	A	T	.	.	.	GT:FFS:AFS:RFS	0/1:xx,yy:TTTTATGCATGCATGCTTTTTTTTATGCATGCATGCTTTT:A,T
diff --git a/test/merge.6.out b/test/merge.6.out
@@ -7,5 +7,5 @@
 ##reference=file:///home/dnanexus/genome.fa
 ##FORMAT=<ID=FFS,Number=2,Type=String,Description="Some string">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	t1	t2
-1	11080563	.	A	C	.	.	.	GT:RFS:AFS:FFS	0/1:a,c:c:.	0/1:A,C:C:xx,yy
-1	11080564	.	A	C,T	.	.	.	GT:RFS:AFS:FFS	0/1:a,c,.:c,.:.	0/2:A,.,T:.,T:xx,yy
+1	11080563	.	A	C	.	.	.	GT:RFS:AFS:FFS	0/1:aa,c:c:.	0/1:A,C:C:xx,yy
+1	11080564	.	A	C,T	.	.	.	GT:RFS:AFS:FFS	0/1:a,cc,.:c,.:.	0/2:A,.,T:.,TTTTATGCATGCATGCTTTTTTTTATGCATGCATGCTTTT:xx,yy
diff --git a/vcfmerge.c b/vcfmerge.c
@@ -1726,6 +1726,7 @@ void merge_format_string(args_t *args, const char *key, bcf_fmt_t **fmt_map, bcf
                     int ret = copy_string_field(src, iori - ifrom, fmt_ori->size, str, inew);
                     if ( ret<-1 ) error("[E::%s] fixme: internal error at %s:%"PRId64" .. %d\n",__func__,bcf_seqname(hdr,line),(int64_t) line->pos+1,ret);
                 }
+                if ( nmax < str->l ) nmax = str->l;
                 src += fmt_ori->size;
             }
             continue;