Bio::DB::Bam::Query -- Object representing the query portion of a BAM/SAM alignment
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
This is a simple Bio::SeqFeatureI object that represents the query part of a SAM alignment.
The name of the read.
The read name (same as seq_id in this case).
The read display_name (same as seq_id in this case).
The string "match".
The string "sam/bam".
The start of the match in read coordinates.
The end of the match in read coordinates;
The length of the read.
A Bio::PrimarySeq representing the read sequence in REFERENCE orientation.
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.
The DNA string in reference sequence orientation.
If the query was reversed to align it, -1. Otherwise +1.
Return a Bio::PrimarySeq object representing the requested subsequence on the read.
Lincoln Stein <email@example.com>. <firstname.lastname@example.org>
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.