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Author image Lincoln D. Stein


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.


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


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