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.IX Title "Bio::DB::Bam::Pileup 3pm"
.TH Bio::DB::Bam::Pileup 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
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.SH NAME
Bio::DB::Bam::Pileup \-\- Object passed to pileup() callback
.SH SYNOPSIS
.IX Header "SYNOPSIS"
See "The generic \fBfetch()\fR and \fBpileup()\fR methods" in Bio::DB::Sam for how
this object is passed to pileup callbacks.
.SH DESCRIPTION
.IX Header "DESCRIPTION"
A Bio::DB::Bam::Pileup object (or a Bio::DB::Bam::PileupWrapper
object) is passed to the callback passed to the Bio::DB::Sam\->\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::Bam::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 = $pileup->alignment"
Return the Bio::DB::Bam::Alignment or Bio::DB::Bam::AlignWrapper
object representing the aligned read.
.ie n .IP "$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 "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\-2015 Ontario Institute for Cancer Research.
.PP
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.