|Bio::DB::HTS::Pileup(3pm)||User Contributed Perl Documentation||Bio::DB::HTS::Pileup(3pm)|
Copyright [2015-2018] EMBL-European Bioinformatics Institute
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Bio::DB::HTS::Pileup -- Object passed to pileup() callback
See "The generic fetch() and pileup() methods" in Bio::DB::HTS for how this object is passed to pileup callbacks.
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.
- $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.
- These fields are defined in bam.h but their interpretation is obscure.
Rishi Nag <firstname.lastname@example.org<gt>
Bio::Perl, Bio::DB::HTS, Bio::DB::HTS::Alignment, Bio::DB::HTS::Constants