LICENSE

       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

            http://www.apache.org/licenses/LICENSE-2.0

       Unless required by applicable law or agreed to in writing, software distributed under the
       License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
       either express or implied.  See the License for the specific language governing
       permissions and limitations under the License.

NAME

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

SYNOPSIS

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

DESCRIPTION

       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.

   Methods
       $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.

       $pileup->is_head
       $pileup->is_tail
           These fields are defined in bam.h but their interpretation is obscure.

AUTHOR

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

SEE ALSO

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