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.IX Title "Bio::DB::HTS::Pileup 3pm"
.TH Bio::DB::HTS::Pileup 3pm 2024-01-10 "perl v5.38.2" "User Contributed Perl Documentation"
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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 "License");
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 "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.
.SH NAME
Bio::DB::HTS::Pileup \-\- Object passed to pileup() callback
.SH SYNOPSIS
.IX Header "SYNOPSIS"
See "The generic \fBfetch()\fR and \fBpileup()\fR methods" in Bio::DB::HTS for how
this object is passed to pileup callbacks.
.SH DESCRIPTION
.IX Header "DESCRIPTION"
A Bio::DB::HTS::Pileup object (or a Bio::DB::HTS::PileupWrapper
object) is passed to the callback passed to the Bio::DB::HTS\->\fBpileup()\fR
method for each column in a sequence alignment. The only difference
between the two is that the latter returns the more convenient
Bio::DB::HTS::AlignWrapper objects in response to the \fBalignment()\fR
method, at the cost of some performance loss.
.SS Methods
.IX Subsection "Methods"
.ie n .IP "$alignment = $pileup\->alignment" 4
.el .IP "\f(CW$alignment\fR = \f(CW$pileup\fR\->alignment" 4
.IX Item "$alignment = $pileup->alignment"
Return the Bio::DB::HTS::Alignment or Bio::DB::HTS::AlignWrapper
object representing the aligned read.
.ie n .IP "$alignment = $pileup\->b" 4
.el .IP "\f(CW$alignment\fR = \f(CW$pileup\fR\->b" 4
.IX Item "$alignment = $pileup->b"
This method is an alias for \fBalignment()\fR. It is available for
compatibility with the C API.
.ie n .IP "$qpos = $pileup\->qpos" 4
.el .IP "\f(CW$qpos\fR = \f(CW$pileup\fR\->qpos" 4
.IX Item "$qpos = $pileup->qpos"
Return the position of this aligned column in read coordinates, using
zero-based coordinates.
.ie n .IP "$pos  = $pileup\->pos" 4
.el .IP "\f(CW$pos\fR  = \f(CW$pileup\fR\->pos" 4
.IX Item "$pos = $pileup->pos"
Return the position of this aligned column in read coordinates, using
1\-based coordinates.
.ie n .IP "$indel = $pileup\->indel" 4
.el .IP "\f(CW$indel\fR = \f(CW$pileup\fR\->indel" 4
.IX Item "$indel = $pileup->indel"
If this column is an indel, return a positive integer for an insertion
relative to the reference, a negative integer for a deletion relative
to the reference, or 0 for no indel at this column.
.ie n .IP "$is_del = $pileup\->is_del" 4
.el .IP "\f(CW$is_del\fR = \f(CW$pileup\fR\->is_del" 4
.IX Item "$is_del = $pileup->is_del"
True if the base on the padded read is a deletion.
.ie n .IP "$level  = $pileup\->level" 4
.el .IP "\f(CW$level\fR  = \f(CW$pileup\fR\->level" 4
.IX Item "$level = $pileup->level"
If \fBpileup()\fR or \fBfast_pileup()\fR was invoked with the "keep_level" flag,
then this method will return a positive integer indicating the level
of the read in a printed multiple alignment.
.ie n .IP $pileup\->is_head 4
.el .IP \f(CW$pileup\fR\->is_head 4
.IX Item "$pileup->is_head"
.PD 0
.ie n .IP $pileup\->is_tail 4
.el .IP \f(CW$pileup\fR\->is_tail 4
.IX Item "$pileup->is_tail"
.PD
These fields are defined in bam.h but their interpretation is obscure.
.SH AUTHOR
.IX Header "AUTHOR"
Rishi Nag <rishi@ebi.ac.uk<gt>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::Perl, Bio::DB::HTS, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants