Use the highest VCF version when merging headers

pd3 · pd3 · commit 3f620f603942 · 2025-05-08T17:41:03.000+02:00
Requires the htslib update samtools/htslib#1912 Resolves #2395
diff --git a/test/merge.symbolic.1.1.out b/test/merge.symbolic.1.1.out
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.4
 ##FILTER=<ID=PASS,Description="All filters passed">
 ##contig=<ID=chr1,length=248956422>
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
diff --git a/test/merge.symbolic.1.b.vcf b/test/merge.symbolic.1.b.vcf
@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.4
 ##contig=<ID=chr1,length=248956422>
 ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
diff --git a/vcfmerge.c b/vcfmerge.c
@@ -3424,6 +3424,7 @@ void merge_vcf(args_t *args)
     if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));
     if ( args->n_threads ) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p); //hts_set_threads(args->out_fh, args->n_threads);
     args->out_hdr = bcf_hdr_init("w");
+    bcf_hdr_set_version(args->out_hdr, bcf_hdr_get_version(args->files->readers[0].header));
 
     if ( args->header_fname )
     {
@@ -3445,7 +3446,6 @@ void merge_vcf(args_t *args)
     info_rules_init(args);
     missing_rules_init(args);
 
-    bcf_hdr_set_version(args->out_hdr, bcf_hdr_get_version(args->files->readers[0].header));
     if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);
     if ( args->header_only )
     {

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-##fileformat=VCFv4.1`
	`1`	`+##fileformat=VCFv4.4`
`2`	`2`	`##FILTER=<ID=PASS,Description="All filters passed">`
`3`	`3`	`##contig=<ID=chr1,length=248956422>`
`4`	`4`	`##INFO=<ID=END,Number=1,Type=Integer,Description="End position of structural variation">`
Original file line number	Diff line number	Diff line change
`@@ -3424,6 +3424,7 @@ void merge_vcf(args_t *args)`
`3424`	`3424`	`if ( args->out_fh == NULL ) error("Can't write to \"%s\": %s\n", args->output_fname, strerror(errno));`
`3425`	`3425`	`if ( args->n_threads ) hts_set_opt(args->out_fh, HTS_OPT_THREAD_POOL, args->files->p); //hts_set_threads(args->out_fh, args->n_threads);`
`3426`	`3426`	`args->out_hdr = bcf_hdr_init("w");`
	`3427`	`+ bcf_hdr_set_version(args->out_hdr, bcf_hdr_get_version(args->files->readers[0].header));`
`3427`	`3428`
`3428`	`3429`	`if ( args->header_fname )`
`3429`	`3430`	`{`
`@@ -3445,7 +3446,6 @@ void merge_vcf(args_t *args)`
`3445`	`3446`	`info_rules_init(args);`
`3446`	`3447`	`missing_rules_init(args);`
`3447`	`3448`
`3448`		`- bcf_hdr_set_version(args->out_hdr, bcf_hdr_get_version(args->files->readers[0].header));`
`3449`	`3449`	`if ( bcf_hdr_write(args->out_fh, args->out_hdr)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->output_fname);`
`3450`	`3450`	`if ( args->header_only )`
`3451`	`3451`	`{`