[Bioc-devel] coverage method on BamFile would be nice

Martin Morgan mtmorgan at fhcrc.org
Wed May 11 20:01:28 CEST 2011

On 05/10/2011 01:46 PM, Michael Lawrence wrote:
> Hi,
> It would be great if BamFile could have more methods like applyPileups but
> with the block handler implemented in C instead of R. One obvious one would
> be coverage. The idea here is that people on laptops will not be able to
> read in large portions of BAM files, and aggregating the results could be
> slow.

Yes this is something I'll do. But for what it's worth something like

param <- PileupParam(which=GRanges("chr1", IRanges(1, width=247249719)),
              what="seq", yieldBy="position", yieldSize=4000000)

does 4 million C-level non-zero pileups before coming back to R for 
processing; there are R overheads that I'll work on, but this is 
relatively memory and speed efficient.


> Thanks,
> Michael
> 	[[alternative HTML version deleted]]
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