[Bioc-devel] RFC: IntervalTrees for GRanges objects

Hector Corrada Bravo hcorrada at gmail.com
Wed Apr 3 02:40:26 CEST 2013

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

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.


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