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.IX Title "Bio::DB::Bam::Query 3pm"
.TH Bio::DB::Bam::Query 3pm "2012-01-29" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::DB::Bam::Query \-\- Object representing the query portion of a BAM/SAM alignment
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Given an alignment retrieved from a Bio::DB::Sam database,
.PP
.Vb 1
\& 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 = $query\->qscore; # quality score
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a simple Bio::SeqFeatureI object that represents the query
part of a \s-1SAM\s0 alignment.
.SS "Methods"
.IX Subsection "Methods"
.ie n .IP "$seqid = $query\->seq_id" 4
.el .IP "\f(CW$seqid\fR = \f(CW$query\fR\->seq_id" 4
.IX Item "$seqid = $query->seq_id"
The name of the read.
.ie n .IP "$name = $query\->name" 4
.el .IP "\f(CW$name\fR = \f(CW$query\fR\->name" 4
.IX Item "$name = $query->name"
The read name (same as seq_id in this case).
.ie n .IP "$name = $query\->display_name" 4
.el .IP "\f(CW$name\fR = \f(CW$query\fR\->display_name" 4
.IX Item "$name = $query->display_name"
The read display_name (same as seq_id in this case).
.ie n .IP "$tag = $query\->primary_tag" 4
.el .IP "\f(CW$tag\fR = \f(CW$query\fR\->primary_tag" 4
.IX Item "$tag = $query->primary_tag"
The string \*(L"match\*(R".
.ie n .IP "$tag = $query\->source_tag" 4
.el .IP "\f(CW$tag\fR = \f(CW$query\fR\->source_tag" 4
.IX Item "$tag = $query->source_tag"
The string \*(L"sam/bam\*(R".
.ie n .IP "$start = $query\->start" 4
.el .IP "\f(CW$start\fR = \f(CW$query\fR\->start" 4
.IX Item "$start = $query->start"
The start of the match in read coordinates.
.ie n .IP "$end = $query\->end" 4
.el .IP "\f(CW$end\fR = \f(CW$query\fR\->end" 4
.IX Item "$end = $query->end"
The end of the match in read coordinates;
.ie n .IP "$len = $query\->length" 4
.el .IP "\f(CW$len\fR = \f(CW$query\fR\->length" 4
.IX Item "$len = $query->length"
The length of the read.
.ie n .IP "$seq = $query\->seq" 4
.el .IP "\f(CW$seq\fR = \f(CW$query\fR\->seq" 4
.IX Item "$seq = $query->seq"
A Bio::PrimarySeq representing the read sequence in \s-1REFERENCE\s0
orientation.
.ie n .IP "$scores = $query\->qscore" 4
.el .IP "\f(CW$scores\fR = \f(CW$query\fR\->qscore" 4
.IX Item "$scores = $query->qscore"
The read quality scores. In a list context, a list of integers equal
in length to the read sequence length. In a scalar context, an array
ref. The qscores are in \s-1REFERENCE\s0 sequence orientation.
.ie n .IP "$dna = $query\->dna" 4
.el .IP "\f(CW$dna\fR = \f(CW$query\fR\->dna" 4
.IX Item "$dna = $query->dna"
The \s-1DNA\s0 string in reference sequence orientation.
.ie n .IP "$strand = $query\->strand" 4
.el .IP "\f(CW$strand\fR = \f(CW$query\fR\->strand" 4
.IX Item "$strand = $query->strand"
If the query was reversed to align it, \-1. Otherwise +1.
.ie n .IP "$seq = $query\->subseq($start,$end)" 4
.el .IP "\f(CW$seq\fR = \f(CW$query\fR\->subseq($start,$end)" 4
.IX Item "$seq = $query->subseq($start,$end)"
Return a Bio::PrimarySeq object representing the requested subsequence
on the read.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Perl, Bio::DB::Sam, Bio::DB::Bam::Alignment, Bio::DB::Bam::Constants
.SH "AUTHOR"
.IX Header "AUTHOR"
Lincoln Stein <lincoln.stein@oicr.on.ca>.
<lincoln.stein@bmail.com>
.PP
Copyright (c) 2009 Ontario Institute for Cancer Research.
.PP
This package and its accompanying libraries is free software; you can
redistribute it and/or modify it under the terms of the \s-1GPL\s0 (either
version 1, or at your option, any later version) or the Artistic
License 2.0.  Refer to \s-1LICENSE\s0 for the full license text. In addition,
please see \s-1DISCLAIMER\s0.txt for disclaimers of warranty.