From 24f3f3217018cfd70ea330b06cb419db8425bfc8 Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Thu, 8 May 2025 17:41:03 +0200
Subject: [PATCH] Use the highest VCF version when merging headers

Requires the htslib update https://github.com/samtools/htslib/pull/1912
Resolves #2395
---
 test/merge.symbolic.1.1.out | 2 +-
 test/merge.symbolic.1.b.vcf | 2 +-
 vcfmerge.c                  | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/test/merge.symbolic.1.1.out b/test/merge.symbolic.1.1.out
index 853bca50..b059b2b7 100644
--- 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
index afcfbf4f..9a189a7c 100644
--- 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
index cb75e7ba..6eef5127 100644
--- 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 )
     {