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.