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Use the highest VCF version when merging headers #2404

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Merged
jkbonfield merged 1 commit into from
May 19, 2025
+3 −3
Merged

Use the highest VCF version when merging headers #2404

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2 changes: 1 addition & 1 deletion test/merge.symbolic.1.1.out
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Original file line number Diff line number Diff line change
@@ -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">
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2 changes: 1 addition & 1 deletion test/merge.symbolic.1.b.vcf
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Original file line number Diff line number Diff line change
@@ -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">
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2 changes: 1 addition & 1 deletion vcfmerge.c
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Expand Up @@ -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 )
{
Expand All @@ -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 )
{
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