Variant Recoder - remove duplicated MANE transcripts #1018
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| @@ -374,6 +374,21 @@ SKIP: { | |||
| 'recode - output MANE Select and fields' | |||
| ); | |||
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| my $vr_mane_hgvs = Bio::EnsEMBL::VEP::VariantRecoder->new({%$cfg_hash, %$db_cfg, offline => 0, database => 1, species => 'homo_vepiens', mane_select => 1, fields => 'spdi'}); | |||
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The new test reports
'Use of uninitialized value in subtraction (-) at ensembl/modules/Bio/EnsEMBL/TranscriptMapper.pm line 384 and line 384. This is for $self->{'cdna_coding_start'}. Is this expected?
Also get warnings when run variant_recoder with "GABPA:p.Trp189Ter" before and after the PR change.
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About the first warning in TranscriptMapper.pm, I'm going to open a ticket to investigate further. We found issues with TranscriptMapper before it could be related. Second warning: I'll add the example to the same ticket.
| $mane_object{'hgvsc'} = $mane_hgvsc; | ||
| $mane_object{'hgvsp'} = $mane_hgvsp; | ||
| push @{$mane_by_allele{$key_allele}->{'mane_select'}}, \%mane_object; | ||
| my $key_hgvsg = $object->{'hgvsg'}; |
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The initial code had my $mane_hgvsg = $object->{'hgvsg'} || '-';
in my $key_hgvsg = $object->{'hgvsg'}; is $object->{'hgvsg'} || '-'; needed?
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$object->{'hgvsg'} is supposed to be always defined that is why I removed my $mane_hgvsg = $object->{'hgvsg'} || '-';
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merged into master and release/105 |
mane_select returns duplicated results. Example: LAMA3:c.4998+1439G>A