NAME¶
Bio::DB::Bam::Pileup -- Object passed to pileup() callback
SYNOPSIS¶
See "The generic
fetch() and
pileup() methods" in
Bio::DB::Sam for how this object is passed to pileup callbacks.
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->
pileup() 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
alignment() method, at the cost of some
performance loss.
Methods¶
- $alignment = $pileup->alignment
- Return the Bio::DB::Bam::Alignment or Bio::DB::Bam::AlignWrapper object
representing the aligned read.
- $alignment = $pileup->b
- This method is an alias for alignment(). It is available for
compatibility with the C API.
- $qpos = $pileup->qpos
- Return the position of this aligned column in read coordinates, using
zero-based coordinates.
- $pos = $pileup->pos
- Return the position of this aligned column in read coordinates, using
1-based coordinates.
- $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.
- $is_del = $pileup->is_del
- True if the base on the padded read is a deletion.
- $level = $pileup->level
- If pileup() or fast_pileup() 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.
- $pileup->is_head
- $pileup->is_tail
- These fields are defined in bam.h but their interpretation is
obscure.
SEE ALSO¶
Bio::Perl, Bio::DB::Sam, Bio::DB::Bam::Alignment, Bio::DB::Bam::Constants
AUTHOR¶
Lincoln Stein <lincoln.stein@oicr.on.ca>. <lincoln.stein@bmail.com>
Copyright (c) 2009 Ontario Institute for Cancer Research.
This package and its accompanying libraries is free software; you can
redistribute it and/or modify it under the terms of the GPL (either version 1,
or at your option, any later version) or the Artistic License 2.0. Refer to
LICENSE for the full license text. In addition, please see DISCLAIMER.txt for
disclaimers of warranty.