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Bio::DB::Bam::Query(3)User Contributed Perl DocumentatioBio::DB::Bam::Query(3)

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.

perl v5.14.2			  2012-08-23		Bio::DB::Bam::Query(3)
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