Bio::DB::Bam::Query -- Object representing the query portion of a BAM/SAM alignment

       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.

perl v5.40.0                                       2024-10-20                           Bio::DB::Bam::Query(3pm)

       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.

       Bio::DB::Bam::Query -- Object representing the query portion of a BAM/SAM alignment

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

       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