Provided by: libbio-db-hts-perl_3.01-3_amd64 bug


       Copyright [2015-2018] EMBL-European Bioinformatics Institute

       Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file
       except in compliance with the License.  You may obtain a copy of the License at


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       Rishi Nag <<gt>


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


       Given an alignment retrieved from a Bio::DB::HTS 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


       This is a simple Bio::SeqFeatureI object that represents the query part of a SAM

       $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::Perl, Bio::DB::HTS, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants