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Fix SVTYPE when using IUPAC nucleotide codes #1636

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merged 4 commits into from
Apr 8, 2024
Merged

Fix SVTYPE when using IUPAC nucleotide codes #1636

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3eda626
Fix SVTYPE when using IUPAC nucleotide codes
nuno-agostinho Mar 14, 2024
0b706f2
Improve warning message for unsupported SV types
nuno-agostinho Mar 14, 2024
486f60e
Fix unit tests
nuno-agostinho Mar 15, 2024
1ec63c4
Merge remote-tracking branch 'upstream/postreleasefix/112' into fix/s…
nuno-agostinho Apr 8, 2024
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Parser.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -723,7 +723,7 @@ sub get_SO_term {
my $res = $terms{$abbrev};
## unsupported SV types
if ($self->isa('Bio::EnsEMBL::VEP::Parser')) {
$self->skipped_variant_msg("$abbrev type is not supported") unless $res;
$self->skipped_variant_msg("$abbrev is not a supported structural variant type") unless $res;
}
return $res;
}
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10 changes: 8 additions & 2 deletions modules/Bio/EnsEMBL/VEP/Parser/VCF.pm
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Expand Up @@ -460,9 +460,15 @@ sub create_StructuralVariationFeatures {
$parser->get_IDs,
);

## get structural variant type from SVTYPE tag (deprecated in VCF 4.4) or ALT
## get structural variant type from ALT or (deprecated) SVTYPE tag
my $alt = join("/", @$alts);
my $type = $alt ne '.' ? $alt : $info->{SVTYPE};
my $type = $alt;

# replace with SVTYPE tag if ALT does not follow VCF 4.4 specs
if ($info->{SVTYPE} && $alt !~ /^<?(DEL|INS|DUP|INV|CNV|CN=?[0-9]+)/) {
$type = $info->{SVTYPE};
}

my $so_term = $self->get_SO_term($type);
unless ($so_term) {
$skip_line = 1;
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4 changes: 2 additions & 2 deletions t/Parser_VCF.t
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Expand Up @@ -621,14 +621,14 @@ is_deeply($cvf, bless( {
'inner_start' => '774570',
'strand' => 1,
'seq_region_end' => 828435,
'class_SO_term' => '<CPX>',
'class_SO_term' => 'CPX',
'variation_name' => 'gnomAD_v2_CPX_1_1',
'start' => 774570
},
'Bio::EnsEMBL::Variation::StructuralVariationFeature' ) , 'StructuralVariationFeature - CPX skipped');


like($tmp, qr/CPX type is not supported/, 'StructuralVariationFeature - skip CPX warning');
like($tmp, qr/CPX is not a supported structural variant type/, 'StructuralVariationFeature - skip CPX warning');

open(STDERR, ">&SAVE") or die "Can't restore STDERR\n";

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