Thanks a lot, Martin! Will work on fixing things on my end. b
On Feb 12, 2014 12:49 PM, "Martin Morgan" wrote:
> On 02/11/2014 05:03 PM, Benilton Carvalho wrote:
>
>> Hi,
>>
>> I'm trying to understand why FeatureSet objects behave slightly different
>> than eSet objects.
>>
>
> There's a combina
On 02/11/2014 05:03 PM, Benilton Carvalho wrote:
Hi,
I'm trying to understand why FeatureSet objects behave slightly different
than eSet objects.
There's a combination of things going on, some of which are unfortunate /
unintended.
The basic problem is that, with regard to row names, subset
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
On Tue, Feb 11, 2014 at 6:58 PM, Hervé Pagès wrote:
> Hi,
>
> Why not. But I don't expect a significant speed up. Here is why:
>
> There are actually 2 algos implemented by coverage(): one called "sort"
> that computes the coverage directly into "Rle space", and one called
> "hash" that computes
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? I
