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 Ontario Institute for Cancer Research.

       This package and its accompanying libraries is free software; you can redistribute it
       and/or modify it under the terms of the GPL (either version 1, or at your option, any
       later version) or the Artistic License 2.0.  Refer to LICENSE for the full license text.
       In addition, please see DISCLAIMER.txt for disclaimers of warranty.