Raw content of Bio::EnsEMBL::Variation::ReadCoverage
<![CDATA[# 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 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=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;
]]>