Commit 46a446ac authored by Arek Icrapzych's avatar Arek Icrapzych
Browse files

fixed 'disappearing exon' bug

parent 93b7ddf0
......@@ -866,9 +866,11 @@ sub get_MarkerFeatures {
sub get_all_Genes {
my ($self, $supporting) = @_;
my (%gene,%trans,%exon,%exonconverted);
foreach my $contig ($self->_vmap->get_all_RawContigs) {
foreach my $gene ( $contig->get_all_Genes($supporting) ) {
foreach my $gene ( $contig->get_all_Genes($supporting) ) {
$gene{$gene->id()} = $gene;
}
}
......@@ -989,16 +991,15 @@ sub _gene_query{
$internalExon = 1;
$exonconverted{$exon->id} = 1;
} else {$internalExon=0;}
}
}
}
unless ($internalExon) {
delete $gene{$gene->id};
}
}
# get out unique set of translation objects
foreach my $gene ( values %gene ) {
foreach my $transcript ( $gene->each_Transcript ) {
......@@ -1055,6 +1056,9 @@ sub _gene_query{
delete $gene{$trans_gene{$t->id}};
}
}
return values %gene;
}
......
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