Thanks for the answer!
Just wanted to make sure that I don't miss a relevant feature….

Best,
Stefanie

Am 17.10.2013 um 22:07 schrieb Hervé Pagès <hpages@fhcrc.org>:

> Hi Stephanie,
> 
> On 10/17/2013 07:37 AM, Stefanie Tauber wrote:
>> What is the best way to compute the coverage on a ReadGAlignments object
>> when I have many, many (about 50 000) seqlevels?
>> 
>> Just computing coverage(object) is terribly slow due to the huge amount of seqlevels.
>> 
>> At the moment, I am subsetting the ReadGAlignments object for each seqlevel,
>>  I omit the redundant seqlevels and calculate the coverage.
>> This is fast if you do it for a few seqlevels.
>> But if one really would like to compute the coverage for each seqlevel individually,
>> this really takes a long time..
> 
> Yes this is a known weakness in the current implementation of
> coverage(). It loops over the seqlevels and this loop is currently
> performed in R, which is slow. Unfortunately this is not the first
> time someone complains about this.
> 
> Time for us to bite the bullet I guess. I've just started to work
> on moving the loop to the C-level. That should speed up things
> significantly. I'll let you know when this is ready.
> 
> Thanks for the feedback.
> H.
> 
>> 
>> 
>> I would appreciate any comments!
>> 
>> Best,
>> Stefanie
>> 
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> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
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> 
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