Bio::DB::Bam::Query

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.

AUTHOR

Lincoln Stein <[email protected]>. <[email protected]>

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.

2022-10-19

perl v5.36.0