Fix BCF output

The command `convert --gvcf2vcf` was not filling the REF allele when BCF was output
because VCF API was not used, the alleles were rewritten directly. That works for
VCF, but not BCF output.

Fixes #243, finally

Author: pd3

NEWS

@@ -12,6 +12,10 @@ Changes affecting specific commands:
     - New experimental plugin for scoring variants and assess site noisiness (allelic frequency profiles)
       from a large number of unaffected parental samples
 
+* bcftools convert
+
+    - The command `convert --gvcf2vcf` was not filling the REF allele when BCF was output (#243)
+
 * bcftools query
 
     - The functions used in -i/-e filtering expressions (such as SUM, MEDIAN, etc) can be

test/test.pl

@@ -1541,6 +1541,7 @@ sub test_vcf_convert_gvcf
     my ($opts,%args) = @_;
     bgzip_tabix_vcf($opts,$args{in});
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert --no-version $args{args} -f $$opts{path}/$args{fa} $$opts{tmp}/$args{in}.vcf.gz");
+    test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools convert --no-version $args{args} -f $$opts{path}/$args{fa} $$opts{tmp}/$args{in}.vcf.gz -Ou | $$opts{bin}/bcftools view --no-version");
     test_cmd($opts,%args,cmd=>"$$opts{bin}/bcftools view -Ob $$opts{tmp}/$args{in}.vcf.gz | $$opts{bin}/bcftools convert $args{args} -f $$opts{path}/$args{fa} | grep -v ^##bcftools");
 }
 sub test_vcf_convert_tsv2vcf

vcfconvert.c

@@ -1,6 +1,6 @@
 /*  vcfconvert.c -- convert between VCF/BCF and related formats.
 
-    Copyright (C) 2013-2023 Genome Research Ltd.
+    Copyright (C) 2013-2024 Genome Research Ltd.
 
     Author: Petr Danecek <[email protected]>
 
@@ -1583,6 +1583,7 @@ static void gvcf_to_vcf(args_t *args)
             char *ref = faidx_fetch_seq(args->ref, (char*)bcf_hdr_id2name(hdr,line->rid), line->pos, line->pos, &len);
             if ( !ref ) error("faidx_fetch_seq failed at %s:%"PRId64"\n", bcf_hdr_id2name(hdr,line->rid),(int64_t) line->pos+1);
             strncpy(line->d.allele[0],ref,len);
+            bcf_update_alleles(hdr,line,(const char**)line->d.allele,line->n_allele);
             if ( bcf_write(out_fh,hdr,line)!=0 ) error("[%s] Error: cannot write to %s\n", __func__,args->outfname);
             free(ref);
         }