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 v5.18.1                                       2013-10-20                           Bio::DB::Bam::Query(3pm)