LICENSE

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::DB::HTS::Pileup -- Object passed to pileup() callback

SYNOPSIS

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

DESCRIPTION

A Bio::DB::HTS::Pileup object (or a Bio::DB::HTS::PileupWrapper object) is passed to the callback passed to the Bio::DB::HTS->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::HTS::AlignWrapper objects in response to the alignment() method, at the cost of some performance loss.

Methods

$alignment = $pileup->alignment: Return the Bio::DB::HTS::Alignment or Bio::DB::HTS::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.

AUTHOR