package Bio::DB::Bam::Pileup;
# $Id$
# documentation only
1;
=head1 NAME
Bio::DB::Bam::Pileup -- Object passed to pileup() callback
=head1 SYNOPSIS
See L<Bio::DB::Sam/The generic fetch() and pileup() methods> for how
this object is passed to pileup callbacks.
=head1 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.
=head2 Methods
=over 4
=item $alignment = $pileup->alignment
Return the Bio::DB::Bam::Alignment or Bio::DB::Bam::AlignWrapper
object representing the aligned read.
=item $alignment = $pileup->b
This method is an alias for alignment(). It is available for
compatibility with the C API.
=item $qpos = $pileup->qpos
Return the position of this aligned column in read coordinates, using
zero-based coordinates.
=item $pos = $pileup->pos
Return the position of this aligned column in read coordinates, using
1-based coordinates.
=item $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.
=item $is_del = $pileup->is_del
True if the base on the padded read is a deletion.
=item $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.
=item $pileup->is_head
=item $pileup->is_tail
These fields are defined in bam.h but their interpretation is obscure.
=back
=head1 SEE ALSO
L<Bio::Perl>, L<Bio::DB::Sam>, L<Bio::DB::Bam::Alignment>, L<Bio::DB::Bam::Constants>
=head1 AUTHOR
Lincoln Stein E<lt>lincoln.stein@oicr.on.caE<gt>.
E<lt>lincoln.stein@bmail.comE<gt>
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.
=cut