Update NearestExonJB #771
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Update NearestExonJB #771
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olaaustine
reviewed
Feb 14, 2025
| @@ -63,6 +71,7 @@ my $char_sep = "|"; | |||
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| my %CONFIG = ( | |||
| max_range => 10000, | |||
| intronic => 0 | |||
| ); | |||
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Suggesting we change the get_header_info since we support intron_variants now
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| my @exons_tmp; | ||
| # Reverse strand we get the exons from the end of the list | ||
| if($tva->transcript->strand < 0) { |
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Suggesting that we just directly modify the $exons like this
if ($tva->transcript->strand < 0) {
@$exons = ($exons->[-$intron_number], $exons->[-($intron_number + 1)]);
}
else {
@$exons = ($exons->[$intron_number - 1], $exons->[$intron_number]);
}
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The plugin only returns overlaping exons.
This PR introduces a new option
--intronicto report the closest exons (upstream and downstream) for intronic variants.Related to request: Ensembl/ensembl-vep#1834