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) 2009-2015 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.