Provided by: libbio-samtools-perl_1.43-2_amd64
Bio::DB::Bam::Query -- Object representing the query portion of a BAM/SAM alignment
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
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::Perl, Bio::DB::Sam, Bio::DB::Bam::Alignment, Bio::DB::Bam::Constants
Lincoln Stein <firstname.lastname@example.org>. <email@example.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.