Bio::DB::HTS::Query(3pm)

LICENSE
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

     http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

AUTHOR
Rishi Nag <rishi@ebi.ac.uk<gt>

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

SYNOPSIS
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

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::HTS, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants