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Fix hgvsg for insertion with ref allele - #1124

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Fix hgvsg for insertion with ref allele - #1124

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3230acf
Fix hgvsg for insertion
nakib103 Sep 26, 2024
e5165b7
Fix for reverse trim
nakib103 Sep 27, 2024
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11 changes: 6 additions & 5 deletions modules/Bio/EnsEMBL/Variation/VariationFeature.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -1929,7 +1929,7 @@ sub hgvs_genomic {
my @all_alleles = split(/\//,$tr_vf->allele_string());
my $ref_allele = shift @all_alleles; ## remove reference allele - not useful for HGVS
my $original_ref_allele = $ref_allele;
my $original_ref_start = $ref_start;
my ($original_ref_start, $original_ref_end) = ($ref_start, $ref_end);

my $is_multi_allelic = scalar @all_alleles > 1;
foreach my $original_allele ( @all_alleles ) {
Expand Down Expand Up @@ -1966,11 +1966,12 @@ sub hgvs_genomic {

if ($is_multi_allelic) {
# fix for multi-allelic variants
my $old_chr_start = $chr_start;
($ref_allele, $allele, $chr_start, $chr_end) = @{trim_sequences($original_ref_allele, $allele, $chr_start)};
my ($old_chr_start, $old_chr_end) = ($chr_start, $chr_end);
($ref_allele, $allele, $chr_start, $chr_end) = @{trim_sequences($original_ref_allele, $allele, $chr_start, $chr_end)};
$allele ||= '-';
$offset = $chr_start - $old_chr_start;
$ref_start = $original_ref_start + $offset;

$ref_start = $original_ref_start + ($chr_start - $old_chr_start);
$ref_end = $original_ref_end + ($chr_end - $old_chr_end);
$ref_allele ||= '-';
}
my $var_class = $self->var_allele_class($ref_allele . '/' . $allele);
Expand Down