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.

AUTHOR

Lincoln Stein <[email protected]>. <[email protected]>

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.