[Bioc-devel] Memory use and coverage from BamFile

[Martin Morgan]

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
>> 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 <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
>> 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
>>>
>>>          [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>          [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793