---
name: "Bio::DB::Bam::Pileup"
section: "3pm"
platform: "linux"
package: "libbio-samtools-perl"
version: "1.43-5+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/Bio::DB::Bam::Pileup"
---

# Bio::DB::Bam::Pileup(3pm)

## 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.