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norm: left-align <DUP> with INFO/END but no INFO/SVLEN #2602

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Merged
pd3 merged 1 commit into from
Oct 16, 2026
+20 −4
Merged

norm: left-align <DUP> with INFO/END but no INFO/SVLEN #2602

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10 changes: 10 additions & 0 deletions test/norm.symbolic.4.1.out
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##contig=<ID=1>
#CHROM POS ID REF ALT QUAL FILTER INFO
1 11 . G GGATTACA . PASS SVTYPE=DUP
1 11 . G <DUP> . PASS SVTYPE=DUP;END=18
1 11 . G <DUP> . PASS SVTYPE=DUP;SVLEN=7;END=18
8 changes: 8 additions & 0 deletions test/norm.symbolic.4.vcf
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@@ -0,0 +1,8 @@
##fileformat=VCFv4.2
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
#CHROM POS ID REF ALT QUAL FILTER INFO
1 26 . G GATTACAG . PASS SVTYPE=DUP
1 26 . G <DUP> . PASS SVTYPE=DUP;END=33
1 26 . G <DUP> . PASS SVTYPE=DUP;SVLEN=7;END=33
1 change: 1 addition & 0 deletions test/test.pl
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Expand Up @@ -312,6 +312,7 @@
run_test(\&test_vcf_norm,$opts,in=>'norm.join-missing-ploidy',out=>'norm.join-missing-ploidy.1.out',args=>'-m +both');
run_test(\&test_vcf_norm,$opts,in=>'norm.split.5',out=>'norm.split.5.1.out',args=>'-m - --multi-overlaps .');
run_test(\&test_vcf_norm,$opts,in=>'norm.symbolic.3',out=>'norm.symbolic.3.1.out',fai=>'norm.symbolic.3',args=>'');
run_test(\&test_vcf_norm,$opts,in=>'norm.symbolic.4',out=>'norm.symbolic.4.1.out',fai=>'norm.symbolic.3',args=>'');
run_test(\&test_vcf_norm,$opts,in=>'norm',out=>'norm.out',fai=>'norm',args=>'-cx');
run_test(\&test_vcf_norm,$opts,in=>'norm.split',out=>'norm.split.out',args=>'-m-');
run_test(\&test_vcf_norm,$opts,in=>'norm.split',out=>'norm.split.1.out',args=>'-m- -a');
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5 changes: 1 addition & 4 deletions vcfnorm.c
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Expand Up @@ -697,10 +697,7 @@ static int realign(args_t *args, bcf1_t *line)
// TODO: there should be check for symbolic allele length. If too big, perhaps should not attempt realignment
int32_t sv_len = 0;
if ( !strncmp("<DEL",line->d.allele[i],4) ) sv_len = -line->rlen;
else if ( !strncmp("<DUP",line->d.allele[i],4) )
{
if ( bcf_get_info_int32(args->hdr,line,"SVLEN",&args->int32_arr,&args->nint32_arr)==1 ) sv_len = args->int32_arr[0];
}
else if ( !strncmp("<DUP",line->d.allele[i],4) ) sv_len = line->rlen - 1; // like <DEL>, htslib sets rlen from INFO/END or INFO/SVLEN
if ( !sv_len ) return ERR_SYMBOLIC;

als[i].l = 0;
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