focal (3) Bio::DB::HTS::Pileup.3pm.gz

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