Hi Hector,

That's interesting, thanks for passing this along. I'm still wishing that
somehow GRanges itself could abstract the way it stores ranges. I know that
Herve/Patrick had some reasons for depending specifically on GRanges. One
reason was probably convenience at the C level, but it wouldn't be hard to
create a Ranges abstraction at the C level, as well.

Michael



On Tue, Apr 2, 2013 at 5:40 PM, Hector Corrada Bravo <hcorrada@gmail.com>wrote:

> Hello bioc-develers,
>
> I'm writing an application where lots findOverlap calls are made on
> static GRanges objects. For IRanges we can create persistent
> IntervalTree objects that would serve the multiple overlap query
> use-case. There is no equivalent for GenomicRanges objects, so I'm
> proposing an implementation for this.
>
> Please check
> http://github.com/hcorrada/GenomicIntervalTree
>
> There's a first cut implementation there you can test by installing
> this skeleton package. E.g,
>
> > library(devtools)
> > install_github("GenomicIntervalTree", username="hcorrada", subdir="pkg")
> > library(GenomicIntervalTree)
>
> Let me know what you think.
>
> Cheers,
> Hector
>
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