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

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.

Martin

Thanks,
Michael

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