On 02/12/2014 05:04 AM, Sean Davis wrote:
On Wed, Feb 12, 2014 at 7:59 AM, Michael Lawrence <lawrence.mich...@gene.com
wrote:
This is a nice suggestion. What about integration with BiocParallel?
Yep, makes good sense. Since there is IO involved, one needs to be a bit
careful about parallel ops, but I suspect that moderate parallel operation
would be useful.
I'd also suggest a method on character(), since a file (BAM or otherwise) seems
the most likely interpretation. Presumably this would chunk across a single file
and parallelize across multiple files, like summarizeOverlaps (which uses bplapply).
Martin
Michael
On Wed, Feb 12, 2014 at 1:53 AM, Sean Davis <sdav...@mail.nih.gov> wrote:
It seems that the coverage method for BamFile() reads the entire BAM file
into memory and then calls coverage. Is there a coverage method for
BamFiles that does not read the entire BAM file into memory first? If
not,
does it make sense to augment the BamFile coverage method to do so in
chunks? It is easy enough to write code to do so and there is even an
example in the GenomicRanges HowTos, but having the method handle the use
case would simplify matters just a bit.
Thanks,
Sean
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