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1 =head1 LICENSE
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2 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
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3 Copyright [2016-2018] EMBL-European Bioinformatics Institute
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4 Licensed under the Apache License, Version 2.0 (the "License");
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5 you may not use this file except in compliance with the License.
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6 You may obtain a copy of the License at
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7 http://www.apache.org/licenses/LICENSE-2.0
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8 Unless required by applicable law or agreed to in writing, software
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9 distributed under the License is distributed on an "AS IS" BASIS,
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10 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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11 See the License for the specific language governing permissions and
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12 limitations under the License.
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13
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14 =head1 CONTACT
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15
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16 Ensembl <http://www.ensembl.org/info/about/contact/index.html>
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17
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18 =cut
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19
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20 =head1 NAME
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21
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22 HGVSReferenceBase
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23
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24 =head1 SYNOPSIS
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25
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26 mv HGVSReferenceBase.pm ~/.vep/Plugins
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27 ./vep -i variations.vcf --cache --hgvs --plugin HGVSReferenceBase
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28
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29 =head1 DESCRIPTION
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30
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31 This is a plugin for the Ensembl Variant Effect Predictor (VEP) that
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32 reports the reference base for the variant, as used in the longer form.
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33 of HGVS. To be used with --hgvs option.
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34
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35 =cut
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36
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37
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38 package HGVSReferenceBase;
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39
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40 use strict;
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41 use warnings;
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42
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43 use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
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44 use Bio::EnsEMBL::Variation::DBSQL::TranscriptVariationAdaptor;
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45 use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;
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46 use Bio::EnsEMBL::Variation::TranscriptVariationAllele;
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47
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48 use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
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49
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50
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51 sub feature_types {
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52 return ['Transcript'];
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53 }
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54
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55 sub variant_feature_types {
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56 return ['VariationFeature'];
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57 }
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58
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59 sub get_header_info {
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60 my $self = shift;
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61
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62 return {
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63 'HGVS_ref' => 'Reference base as may be reported in HGVS transcript level notation',
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64 };
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65 }
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66
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67 sub run {
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68 my ($self, $tva) = @_;
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69
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70 # check var class, this is only useful for deletions
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71 # or duplications - a subset of insertions
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72 return {} unless $tva->variation_feature->var_class() =~ /del|ins/;
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73
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74 return $tva->hgvs_transcript_reference() ? {'HGVS_ref' => $tva->hgvs_transcript_reference()} : {};
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75
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76 }
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77
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78 1;
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