[Biojava-dev] b-tree of annotation

[Ryan Golhar]

nevermind.  I see FeatureList is able to sort Features.

On Fri, Sep 21, 2012 at 3:40 PM, Ryan Golhar <ngsbioinformatics at gmail.com>wrote:

> HI - I have a need to scan through a bunch of genomic locations I have.
>  For each location, I need to identify the overlapping gene/exon.  If there
> isn't one, I need to find the closest gene upstream or downstream.
>
> I thought BEDTools at first would do this, but I need some additional
> information from the annotation as well.  I thought maybe BioJava would
> have a class that I can read in a GFF file and quickly search it, sort of a
> b-tree implementation.  I think IGV does something like this.  Is anything
> like this available in Biojava?
>
>
>