Note that rtracklayer has a function called FileForFormat that given a path
will return a high-level file object, from either rtracklayer or Rsamtools,
or anything that uses the naming convention [Format]File. rtracklayer could
have coverage methods for the non-SAM/BAM files.
On Wed, Feb 12, 2014
On 02/12/2014 05:04 AM, Sean Davis wrote:
On Wed, Feb 12, 2014 at 7:59 AM, Michael Lawrence
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 m
On Wed, Feb 12, 2014 at 7:59 AM, Michael Lawrence 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.
This is a nice suggestion. What about integration with BiocParallel?
Michael
On Wed, Feb 12, 2014 at 1:53 AM, Sean Davis 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 doe
