Bio::DB::Bam::Pileup -- Object passed to pileup() callback
See "The generic fetch() and pileup() methods" in Bio::DB::Sam for how this object is passed to pileup callbacks.
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.
Return the Bio::DB::Bam::Alignment or Bio::DB::Bam::AlignWrapper object representing the aligned read.
This method is an alias for alignment(). It is available for compatibility with the C API.
Return the position of this aligned column in read coordinates, using zero-based coordinates.
Return the position of this aligned column in read coordinates, using 1-based coordinates.
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.
True if the base on the padded read is a deletion.
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.
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Copyright (c) 2009-2015 Ontario Institute for Cancer Research.
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