|
0
|
1 =head1 LICENSE
|
|
|
2
|
|
|
3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
|
|
|
4 Genome Research Limited. All rights reserved.
|
|
|
5
|
|
|
6 This software is distributed under a modified Apache license.
|
|
|
7 For license details, please see
|
|
|
8
|
|
|
9 http://www.ensembl.org/info/about/code_licence.html
|
|
|
10
|
|
|
11 =head1 CONTACT
|
|
|
12
|
|
|
13 Please email comments or questions to the public Ensembl
|
|
|
14 developers list at <dev@ensembl.org>.
|
|
|
15
|
|
|
16 Questions may also be sent to the Ensembl help desk at
|
|
|
17 <helpdesk@ensembl.org>.
|
|
|
18
|
|
|
19 =cut
|
|
|
20
|
|
|
21 package Bio::EnsEMBL::Variation::IntergenicVariationAllele;
|
|
|
22
|
|
|
23 use strict;
|
|
|
24 use warnings;
|
|
|
25
|
|
|
26 use Bio::EnsEMBL::Variation::Utils::Constants qw(%OVERLAP_CONSEQUENCES);
|
|
|
27
|
|
|
28 use base qw(Bio::EnsEMBL::Variation::VariationFeatureOverlapAllele);
|
|
|
29
|
|
|
30 sub new_fast {
|
|
|
31 my ($self, $hashref) = @_;
|
|
|
32
|
|
|
33 # swap an intergenic_variation argument for a variation_feature_overlap one
|
|
|
34
|
|
|
35 if ($hashref->{intergenic_variation}) {
|
|
|
36 $hashref->{variation_feature_overlap} = delete $hashref->{intergenic_variation};
|
|
|
37 }
|
|
|
38
|
|
|
39 # and call the superclass
|
|
|
40
|
|
|
41 return $self->SUPER::new_fast($hashref);
|
|
|
42 }
|
|
|
43
|
|
|
44 sub intergenic_variation {
|
|
|
45 my $self = shift;
|
|
|
46 return $self->variation_feature_overlap(@_);
|
|
|
47 }
|
|
|
48
|
|
|
49 sub get_all_OverlapConsequences {
|
|
|
50 return [ $OVERLAP_CONSEQUENCES{intergenic_variant} ];
|
|
|
51 }
|
|
|
52
|
|
|
53 1;
|
