Bio::DB::Bam::Pileup3pm

Usage

See "The generic fetch() and pileup() methods" in Bio::DB::Sam for how this object is passed to pileup callbacks.

Overview

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.

Releases

8 releases since Debian 6.0 (Squeeze); the text changed 7 times.