On Fri, Aug 2, 2013 at 10:53 AM, Martin Morgan wrote:
> On 08/02/2013 07:33 AM, Michael Lawrence wrote:
>
>> This has come up several times I think, and I'm totally naive, but what
>> about
>> making R smart enough to do that itself? One nice thing about the
>> vectorization
>> is that R knows ho
The code that's there now is already unit tested and should be merged.
The test I mentioned was a small check that the following works (this is
what started this thread):
> m <- matrix(1, 5, 3, dimnames=list(NULL, NULL))
> gr <- GRanges("chr1", IRanges(1:5, 10))
> colData <- DataFrame(x=letters[1:
On 08/02/2013 07:33 AM, Michael Lawrence wrote:
This has come up several times I think, and I'm totally naive, but what about
making R smart enough to do that itself? One nice thing about the vectorization
is that R knows how many CHARSXPs it needs to allocate up-front, or at least an
upper-bound
If you don't mind, I think I'll wait till after you're finished testing
before merging.
Please keep me up to date,
Michael
On Fri, Aug 2, 2013 at 7:43 AM, Hector Corrada Bravo wrote:
> Thanks again Kasper,
> All of these are now fixed:
> * empty subject seqlevel,
> * out-of-order seqinfo's,
> *
Thanks again Kasper,
All of these are now fixed:
* empty subject seqlevel,
* out-of-order seqinfo's,
* show,GIntervalTree-method
Michael, please merge from
https://github.com/hcorrada/IRanges [version 1.19.20]
https://github.com/hcorrada/GenomicRanges [version 1.13.36]
I'll test the SummarizedExp
This has come up several times I think, and I'm totally naive, but what
about making R smart enough to do that itself? One nice thing about the
vectorization is that R knows how many CHARSXPs it needs to allocate
up-front, or at least an upper-bound when they're all unique. Is the issue
that the R
On 07/31/2013 04:05 PM, Hervé Pagès wrote:
Hi Dario,
Thanks for providing the file.
The file has 55780092 records in it and yes it only contains primary
alignments so this is the best situation for the pairing algorithm.
Here are the timings I get for the readBamGappedAlignmentPairs()
function
Thanks Val!
I've been playing some more with that function and I was wondering if it would
make sense to introduce an arguments to filter out synthetic exons if they are
smaller than a given size. I.e. In my data I often get 1bp exons, which are
obviously of no interest in the downstream analys
