=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 METHODS
=cut
$Bio::EnsEMBL::Utils::VegaCuration::Gene::VERSION = '112.0_55'; # TRIAL
$Bio::EnsEMBL::Utils::VegaCuration::Gene::VERSION = '112.055';
use strict;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Utils::ConversionSupport);
=head2 find_gaps
Args : arrayref of B::E::Transcripts
Example : my $gaps = find_gaps($all_transcripts)
Description: identifies regions of a gene that are not covered by any transcript
Returntype : int
Exceptions : none
Caller : internal
=cut
sub find_gaps {
my $self = shift;
my ($all_transcripts) = @_;
my $gaps = 0;
my @sorted_transcripts = sort {$a->start <=> $b->start || $b->end <=> $a->end} @{$all_transcripts};
if ( my $first_transcript = shift @sorted_transcripts ) {
my $pos = $first_transcript->end;
foreach my $transcript (@sorted_transcripts) {
next if ($transcript->end < $pos );
if ($transcript->start < $pos && $transcript->end > $pos ) {
$pos = $transcript->end;
next;
}
elsif ($transcript->end > $pos) {
$gaps++;
$pos = $transcript->end;
}
}
}
return $gaps;
}