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Downstream changes for get_end fix in VCF parser #1773

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Downstream changes for get_end fix in VCF parser #1773

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0a09aef
SV del can have start = end
nakib103 Oct 20, 2024
53a7ae8
Fix unit test cases
nakib103 Oct 20, 2024
c8b0095
Skip SV deletions if SVLEN/END missing
nakib103 Oct 20, 2024
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2 changes: 1 addition & 1 deletion modules/Bio/EnsEMBL/VEP/Parser/VCF.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -551,7 +551,7 @@ sub create_StructuralVariationFeatures {
$parser->get_outer_end,
);

if($start >= $end && $so_term =~ /del/i) {
if(($start > $end || (!defined $info->{SVLEN} && !defined $info->{END})) && $so_term =~ /del/i) {
$self->skipped_variant_msg("deletion looks incomplete");
$skip_line = 1;
}
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2 changes: 1 addition & 1 deletion t/AnnotationSource_File_VCF.t
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Expand Up @@ -431,7 +431,7 @@ SKIP: {
config => $cfg,
parser => Bio::EnsEMBL::VEP::Parser::VCF->new({
config => $cfg,
file => $test_cfg->create_input_file([qw(21 25585735 . G . . . SVTYPE=DEL;SVLEN=2)]),
file => $test_cfg->create_input_file([qw(21 25585735 . T . . . SVTYPE=DEL;SVLEN=1)]),
valid_chromosomes => [21]
})
});
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18 changes: 9 additions & 9 deletions t/Parser_VCF.t
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Original file line number Diff line number Diff line change
Expand Up @@ -767,11 +767,11 @@ is_deeply($bnd_vf, bless( {
'start' => 68914093,
'inner_start' => 68914093,
'outer_start' => 68914093,
'end' => 68914095,
'inner_end' => 68914095,
'outer_end' => 68914095,
'end' => 68914093,
'inner_end' => 68914093,
'outer_end' => 68914093,
'seq_region_start' => 68914093,
'seq_region_end' => 68914095
'seq_region_end' => 68914093
},
'Bio::EnsEMBL::Variation::StructuralVariationFeature' ) ,
'StructuralVariationFeature - BND with unsupported INFO/END field');
Expand Down Expand Up @@ -869,14 +869,14 @@ is_deeply($bnd5_vf, bless( {
'start' => 68914093,
'inner_start' => 68914093,
'outer_start' => 68914093,
'end' => 68914095,
'inner_end' => 68914095,
'outer_end' => 68914095,
'end' => 68914094,
'inner_end' => 68914094,
'outer_end' => 68914094,
'seq_region_start' => 68914093,
'seq_region_end' => 68914095
'seq_region_end' => 68914094
},
'Bio::EnsEMBL::Variation::StructuralVariationFeature' ) ,
'StructuralVariationFeature - BND with unsupported INFO/END field');
'StructuralVariationFeature - BND with undefined INFO/END field');

## test tandem repeats

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