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.
- $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.
Lincoln Stein <firstname.lastname@example.org>. <email@example.com>
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.