NonSynonymousFilter.pm

=head1 LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2017] 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

     http://www.apache.org/licenses/LICENSE-2.0

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.

=head1 CONTACT

 Graham Ritchie <grsr@ebi.ac.uk>
    
=cut

=head1 NAME

 NonSynonymousFilter

=head1 SYNOPSIS

 mv NonSynonymousFilter.pm ~/.vep/Plugins
 ./vep -i variations.vcf --plugin NonSynonymousFilter

=head1 DESCRIPTION

 A simple example VEP filter plugin that limits output to non-synonymous variants

=cut

package NonSynonymousFilter;

use strict;
use warnings;

use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepFilterPlugin);

sub feature_types {
    return ['Transcript'];
}

sub include_line {
    my ($self, $tva) = @_;

    # just check if there are alternative amino acids in the 
    # pep_allele_string, this means we'll catch stop gained
    # or lost as well

    if (my $pep_alleles = $tva->pep_allele_string) {
        return $pep_alleles =~ /\//;
    }

    return 0;
}

1;