[BioC] "internal equal" overlap mode for GRangesList
Cook, Malcolm
MEC at stowers.org
Wed Oct 26 18:21:31 CEST 2011
Yes, hear, hear
I too have what is probably pretty inefficient code in this space.
My needs are similar, but perhaps not identical, in that I need
I think it comes down to my wanting a 'any' version in addition to a 'within'.
My current approach is similarly to filter the result of a findOverlaps(..., 'any') ensuring that the subject / query pairs are identical in the region of overlap (as computed using pintersect).
So, I'm happy to hear any progress in this area....
Cheers
~Malcolm
> -----Original Message-----
> From: bioconductor-bounces at r-project.org [mailto:bioconductor-
> bounces at r-project.org] On Behalf Of Michael Lawrence
> Sent: Wednesday, October 26, 2011 7:34 AM
> To: bioconductor at r-project.org
> Subject: [BioC] "internal equal" overlap mode for GRangesList
>
> Hi,
>
> I wonder if it's worth having some sort of "internal equal" overlap mode for
> two GRangesLists. This would check not for total equality between e.g. a set
> of spliced reads and an exonsBy() GRL but instead only check that the
> internal starts and ends are equal and that the query outer start and end
> fall inside the subject (indicating a compatible splicing pattern). I have
> some pretty inefficient code that filters a "within" overlap result to this,
> but it might be nice to have it inside the infrastructure.
>
> Thanks,
> Michael
>
> [[alternative HTML version deleted]]
>
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