libbio-samtools-perl 1.43-1+b2 / usr / lib / x86_64-linux-gnu / perl5 / 5.24 / Bio / DB / Bam / Query.pm

package Bio::DB::Bam::Query;

# $Id$

=head1 NAME

Bio::DB::Bam::Query -- Object representing the query portion of a BAM/SAM alignment

=head1 SYNOPSIS

Given an alignment retrieved from a Bio::DB::Sam database,

 my $query = $alignment->query;

 my $name   = $query->display_name;
 my $start  = $query->start;
 my $end    = $query->end;
 my $dna    = $query->dna;    # dna string
 my $seq    = $query->seq;    # Bio::PrimarySeq object
 my @scores = $query->qscore; # quality score

=head1 DESCRIPTION

This is a simple Bio::SeqFeatureI object that represents the query
part of a SAM alignment.

=head2 Methods

=over 4

=cut

use strict;
use Bio::DB::Sam;
use Bio::DB::Sam::Constants qw(CIGAR_SYMBOLS BAM_CREF_SKIP BAM_CSOFT_CLIP BAM_CHARD_CLIP);

use constant CIGAR_SKIP      => {CIGAR_SYMBOLS->[BAM_CREF_SKIP]  => 1,
 				 CIGAR_SYMBOLS->[BAM_CSOFT_CLIP] => 1,
 				 CIGAR_SYMBOLS->[BAM_CHARD_CLIP] => 1};


sub new {
    my $self      = shift;
    my $alignment = shift;
    bless \$alignment,ref $self || $self;
}

=item $seqid = $query->seq_id

The name of the read.

=cut

sub seq_id {
    my $self = shift;
    $$self->qname;
}

=item $name = $query->name

The read name (same as seq_id in this case).

=cut

sub name {
    my $self = shift;
    $$self->qname;
}

=item $name = $query->display_name

The read display_name (same as seq_id in this case).

=cut

sub display_name {shift->name}

=item $tag = $query->primary_tag

The string "match".

=cut

sub primary_tag { ${shift()}->primary_tag }


=item $tag = $query->source_tag

The string "sam/bam".

=cut

sub source_tag  { ${shift()}->source_tag  }

=item $start = $query->start

The start of the match in read coordinates.

=cut

sub start {
    my $self = shift;
    return $self->low;
}

=item $end = $query->end

The end of the match in read coordinates;

=cut

sub end {
    my $self = shift;
    return $self->high;
}

sub low {
    my $self       = shift;
    my $cigar_arry = $$self->cigar_array;
    my $start      = 1;
    for my $c (@$cigar_arry) {
      next if CIGAR_SYMBOLS->[BAM_CHARD_CLIP] eq $c->[0];
      last unless CIGAR_SKIP->{$c->[0]};
      $start += $c->[1];
    }
    $start;
}

sub high {
    my $self      = shift;
    my $len       = $$self->cigar2qlen;
    my $cigar_arry = $$self->cigar_array;

    # alignment stops at first non-clip CIGAR position
    my $i = $len - 1;
    for my $c (reverse @$cigar_arry) {
      next if CIGAR_SYMBOLS->[BAM_CHARD_CLIP] eq $c->[0];
      last unless CIGAR_SKIP->{$c->[0]};
      $len -= $c->[1];
    }
    return $len;
}

=item $len = $query->length

The length of the read.

=cut

sub length {
    my $self = shift;
    $self->high-$self->low+1;
#    $$self->cigar2qlen;
}

=item $seq = $query->seq

A Bio::PrimarySeq representing the read sequence in REFERENCE
orientation.

=cut

sub seq {
    my $self = shift;
    my $dna  = $self->dna;
    return Bio::PrimarySeq->new(-seq => $dna,
				-id  => $$self->qname);
}

=item $scores = $query->qscore

The read quality scores. In a list context, a list of integers equal
in length to the read sequence length. In a scalar context, an array
ref. The qscores are in REFERENCE sequence orientation.

=cut

sub qscore {
    my $self = shift;
    my @qscore = $$self->qscore;
    return wantarray ? @qscore : \@qscore;
}

=item $dna = $query->dna

The DNA string in reference sequence orientation.

=cut

sub dna {
    my $self = shift;
    return $$self->qseq || ('N' x $self->length);
}

=item $strand = $query->strand

If the query was reversed to align it, -1. Otherwise +1.

=cut

sub strand {
    my $self = shift;
    return $$self->reversed ? -1 : 1;
}

=item $seq = $query->subseq($start,$end)

Return a Bio::PrimarySeq object representing the requested subsequence
on the read.

=cut

sub subseq {
    my $self = shift;
    my ($start,$end) = @_;
    $start = 1 if $start < 1;
    $end   = $self->high if $end > $self->high;
    ($end,$start) = ($start,$end) if $start > $end;
    return Bio::PrimarySeq->new(-seq=>substr($self->dna,
					     $start-1,
					     $end-$start+1)
				);
}


1;

=back

=head1 SEE ALSO

L<Bio::Perl>, L<Bio::DB::Sam>, L<Bio::DB::Bam::Alignment>, L<Bio::DB::Bam::Constants>

=head1 AUTHOR

Lincoln Stein E<lt>lincoln.stein@oicr.on.caE<gt>.
E<lt>lincoln.stein@bmail.comE<gt>

Copyright (c) 2009-2015 Ontario Institute for Cancer Research.

This package and its accompanying libraries are free software; you can
redistribute it and/or modify it under the terms of the Artistic
License 2.0, the Apache 2.0 License, or the GNU General Public License
(version 1 or higher).  Refer to LICENSE for the full license text.

=cut