[Bioc-devel] Memory use and coverage from BamFile
mtmorgan at fhcrc.org
Wed Feb 12 15:15:34 CET 2014
On 02/12/2014 05:04 AM, Sean Davis wrote:
> On Wed, Feb 12, 2014 at 7:59 AM, Michael Lawrence <lawrence.michael at gene.com
>> 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).
>> On Wed, Feb 12, 2014 at 1:53 AM, Sean Davis <sdavis2 at 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
>>> 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.
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