On Wed, Feb 12, 2014 at 7:59 AM, Michael Lawrence <lawrence.michael@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.


> Michael
>
>
> On Wed, Feb 12, 2014 at 1:53 AM, Sean Davis <sdavis2@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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> >
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