NAME

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

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

DESCRIPTION

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

Methods

$seqid = $query->seq_id

The name of the read.

$name = $query->name

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

$name = $query->display_name

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

$tag = $query->primary_tag

The string "match".

$tag = $query->source_tag

The string "sam/bam".

$start = $query->start

The start of the match in read coordinates.

$end = $query->end

The end of the match in read coordinates;

$len = $query->length

The length of the read.

$seq = $query->seq

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

$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.

$dna = $query->dna

The DNA string in reference sequence orientation.

$strand = $query->strand

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

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

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

SEE ALSO

Bio::Perl, Bio::DB::Sam, Bio::DB::Bam::Alignment, Bio::DB::Bam::Constants

AUTHOR

Lincoln Stein <lincoln.stein@oicr.on.ca>. <lincoln.stein@bmail.com>

Copyright (c) 2009 Ontario Institute for Cancer Research.

This package and its accompanying libraries is free software; you can redistribute it and/or modify it under the terms of the GPL (either version 1, or at your option, any later version) or the Artistic License 2.0. Refer to LICENSE for the full license text. In addition, please see DISCLAIMER.txt for disclaimers of warranty.