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Copyright [2015-2018] EMBL-European Bioinformatics Institute

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


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


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


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.


$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.


These fields are defined in bam.h but their interpretation is obscure.


Rishi Nag <rishi@ebi.ac.uk<gt>


Bio::Perl, Bio::DB::HTS, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants