Bio::DB::HTS::Query

LICENSE

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 <[email protected]<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.