Mercurial > repos > mahtabm > ensembl
view variant_effect_predictor/Bio/EnsEMBL/Variation/ReadCoverage.pm @ 3:d30fa12e4cc5 default tip
Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.
author | devteam <devteam@galaxyproject.org> |
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date | Mon, 13 Jan 2014 10:38:30 -0500 |
parents | 1f6dce3d34e0 |
children |
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=head1 LICENSE Copyright (c) 1999-2012 The European Bioinformatics Institute and Genome Research Limited. All rights reserved. This software is distributed under a modified Apache license. For license details, please see http://www.ensembl.org/info/about/code_licence.html =head1 CONTACT Please email comments or questions to the public Ensembl developers list at <dev@ensembl.org>. Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>. =cut # Ensembl module for Bio::EnsEMBL::Variation::ReadCoverage # # Copyright (c) 2005 Ensembl # =head1 NAME Bio::EnsEMBL::Variation::ReadCoverage - A coverage reagion for a read. =head1 SYNOPSIS # Read coverage feature representing a genomic region covered by 1 read $rc = Bio::EnsEMBL::Variation::ReadCoverage->new (-start => 100, -end => 200, -slice => $slice, -level => 1. -sample => $individual); $rc = $rc->transform('supercontig'); print $rc->start(), "-", $rc->end(), "\n"; =head1 DESCRIPTION This is a class representing the read coverage information from the ensembl-variation database. A ReadCoverage behaves as any other Ensembl feature. See B<Bio::EnsEMBL::Feature>. =head1 METHODS =cut use strict; use warnings; package Bio::EnsEMBL::Variation::ReadCoverage; use Bio::EnsEMBL::Feature; use Bio::EnsEMBL::Utils::Exception qw(throw warning); use Bio::EnsEMBL::Utils::Argument qw(rearrange); our @ISA = ('Bio::EnsEMBL::Feature'); =head2 new Arg [-ADAPTOR] : see superclass constructor Arg [-START] : see superclass constructor Arg [-END] : see superclass constructor Arg [-SLICE] : see superclass constructor Arg [-LEVEL] : int - the number of times the region represented by start and end has been seen Arg [-SAMPLE] : Bio::EnsEMBL::Variation::Individual - the individual in which the allele was recorded Example : $rc = Bio::EnsEMBL::Variation::ReadCoverage->new (-start => 100, -end => 100, -slice => $slice, -level => 1, -sample => $individual); Description: Constructor. Instantiates a new ReadCoverage object. Returntype : Bio::EnsEMBL::Variation::ReadCoverage Exceptions : none Caller : general Status : At Risk =cut sub new { my $caller = shift; my $class = ref($caller) || $caller; my $self = $class->SUPER::new(@_); my ($level, $individual) = rearrange([qw(LEVEL SAMPLE)], @_); $self->{'level'} = $level; $self->{'sample'} = $individual; return $self; } =head2 level Arg[1] : int $newval (optional) The new value to set the level attribute to Example : $depth = $obj->level(); Description : Getter/Setter for the level attribute. The level is the number of times this feature has been seen in the genome ReturnType : int Exceptions : none Caller : general Status : At Risk =cut sub level{ my $self = shift; return $self->{'level'} = shift if (@_); return $self->{'level'}; } =head2 sample Arg [1] : Bio::EnsEMBL::Variation::Individual $newval (optional) The new value to set the sample attribute to Example : $individual = $rc->sample(); Description: Getter/Setter for the individual attribute Returntype : Bio::EnsEMBL::Variation::Individual Exceptions : throw on incorrect argument Caller : general Status : At Risk =cut sub sample{ my $self = shift; if(@_) { if(!ref($_[0]) || !$_[0]->isa('Bio::EnsEMBL::Variation::Individual')) { throw('Bio::EnsEMBL::Variation::Individual argument expected.'); } $self->{'sample'} = shift; } return $self->{'sample'}; } 1;