[Bioc-devel] IntervalTree and Genomic Ranges

[Valerie Obenchain]

Hi Hector, Michael,

This sounds great. Bringing these into svn is fine with us. Michael, do 
you want to merge these in?

Val

On 05/24/2013 07:30 AM, Hector Corrada Bravo wrote:
> Thanks Michael,
>
> It has made significant difference for our visualization project. I would
> like to merge this into svn asap. Can I get a ruling from the rest of the
> core group? Please let me know if/when/how to proceed.
>
> Cheers,
> Hector
>
>
> On Wed, May 22, 2013 at 1:00 PM, Michael Lawrence <lawrence.michael at gene.com
>> wrote:
>
>> *Added bioc-devel; hope you don't mind*
>>
>> Hector,
>>
>> This is great stuff. The overall design is on the right track. As you
>> said, there's a bit of cleaning to do, but I think we should merge this
>> into svn and work the rest out from there. This will really benefit
>> performance, especially for visualization. Of course, I can't speak for the
>> others.
>>
>> Michael
>>
>>
>>
>> On Tue, May 21, 2013 at 11:52 AM, Hector Corrada Bravo <
>> hcorrada at umiacs.umd.edu> wrote:
>>
>>> Since the semester is over I finally finished this...
>>>
>>> Recall that I wanted a persistent set of IntervalTrees for GRanges
>>> objects for repeated querying. (The application is this:
>>> http://epiviz.cbcb.umd.edu/help/?page_id=62 which I hope to get out
>>> soon). Folding this into IRanges and GenomicRanges would make our life
>>> easier come installation time.
>>>
>>> I've implemented class 'IntervalForest' within IRanges following
>>> Michael's suggestion of storing this as an array of rbTree on the C side.
>>> I've implemented findOverlaps that operates with this array in C. There is
>>> code duplication in IntervalTree.c that could be reduced but that's if this
>>> makes it into the package.
>>>
>>> I've also implemented a 'GIntervalTree' that uses 'IntervalForest'
>>> underneath. findOverlaps-GenomicRanges-GIntervalTree-method is implemented
>>> for this class. I didn't touch the existing
>>> findOverlaps-GenomicRanges-GenomicRanges-method.
>>>
>>> You can pull these here:
>>> http://github.com/hcorrada/IRanges
>>> http://github.com/hcorrada/GenomicRanges
>>>
>>> These track the devel branch of the two packages. Let me know the best
>>> way to propagate to svn if you guys want this. It needs documentation, but
>>> I'll add that once implementation is settled.
>>>
>>> Kasper, I'm not sure if this would help with the 'too many seqlevels'
>>> problem but I'd be curious to know if you try it.
>>>
>>> Cheers,
>>> Hector
>>>
>>
>>
>
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