[Bioc-devel] RFC: IntervalTrees for GRanges objects

[Hector Corrada Bravo]

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