Bio::DB::Bam::Pileup -- Object passed to pileup() callback
See "The generic
fetch() and
pileup() methods" in
Bio::DB::Sam for how this object is passed to pileup callbacks.
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.
- $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.
Bio::Perl, Bio::DB::Sam, Bio::DB::Bam::Alignment, Bio::DB::Bam::Constants
Lincoln Stein <
[email protected]>. <
[email protected]>
Copyright (c) 2009-2015 Ontario Institute for Cancer Research.
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.