[BioC] "internal equal" overlap mode for GRangesList

[Cook, Malcolm]

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
> 
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