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.\" ========================================================================
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.IX Title "Bio::DB::HTS::Query 3pm"
.TH Bio::DB::HTS::Query 3pm "2020-11-09" "perl v5.32.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "LICENSE"
.IX Header "LICENSE"
Copyright [2015\-2018] EMBL-European Bioinformatics Institute
.PP
Licensed under the Apache License, Version 2.0 (the \*(L"License\*(R");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
.PP
.Vb 1
\&     http://www.apache.org/licenses/LICENSE\-2.0
.Ve
.PP
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an \*(L"\s-1AS IS\*(R" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,\s0 either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
.SH "AUTHOR"
.IX Header "AUTHOR"
Rishi Nag <rishi@ebi.ac.uk<gt>
.SH "NAME"
Bio::DB::HTS::Query \-\- Object representing the query portion of a BAM/SAM alignment
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Given an alignment retrieved from a Bio::DB::HTS 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::HTS, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants