package PGF::Newbler::PairNewblerReads;

=head1 NAME

PGF::Newbler::PairNewblerReads - pair reads from Newbler assembly.

=head1 SYNOPSIS

  use PGF::Newbler::PairNewblerReads;

  my $objPairReads = PGF::Newbler::PairNewblerReads->new();
  $objPairReads->addread("FE898RP06GYE5O_right.pr148");
  $objPairReads->addread("FE898RP06GYE5O_left.pr148");
  $objPairReads->addread("FE898RP06GYE5O_left.pr150");

  my @readpairs = $obj->getReadPair("FE898RP06GYE5O_right.pr148");

  # @readpairs contain:
  # [0] = FE898RP06GYE5O_left.pr148
  # [1] = FE898RP06GYE5O_left.pr150

=head1 DESCRIPTION

This module allows you to pair up Newbler reads whereby the pairing
is based on _left or _right word in the read name. 

=head1 AUTHOR(s)

Stephan Trong

=head1 HISTORY

=over

=item *

Stephan Trong 10/13/2008 Creation

=back

=cut

#============================================================================#
use strict;
use Carp;
use Carp qw(cluck);

my $VERSION = 1.00;

sub new {

    my ($class) = @_;
    my $self={};
    bless $self, $class;
    return $self;

}

sub addRead {

    my $self = shift;
    my $readname = shift;
    
    if ( my $clonename = _getCloneName($readname) ) {
        push @{$self->{_clone}{$clonename}}, $readname;
    } else {
        $self->{_unpaired}{$readname} = 1;
    }
    
}

sub _getCloneName {

    my $readname = shift;
    my $clonename = '';
    
    if ( $readname =~ /^([^\_]+)\_[left|right]/ ) {
        $clonename = $1;
    }
    
    return $clonename;
    
}

sub getReadPair {

    my $self = shift;
    my $readname = shift;
    
    my $clonename = _getCloneName($readname);
    my @readpairs = ();
    
    if ( $clonename && $readname =~ /\_(left|right)/ ) {
        my $dir = $1 eq 'left' ? 'right':'left';
        @readpairs = grep /\_$dir/, @{$self->{_clone}{$clonename}};
    }
    
    if ( wantarray ) {
        return @readpairs;
    } elsif ( @readpairs ) {
        return $readpairs[0];
    } else {
        return '';
    }
    
}

#============================================================================#
1;