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.