Count reads from a BamFile
Given the tiling of the genome created when the
object was created (or replaced via
getKaryotype), count reads
overlapping the bins, in preparation for estimating the threshold for
This method counts reads contained within the bins that make up the genome tiling. Bins are overlapping (by default 1Kb bins at 512b intervals) so reads are counted once for each bin that wholly contains them.
GreyList object, with added counts.
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