bionic (3) Bio::DB::Bam::Pileup.3pm.gz

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.