Would it be feasible/acceptable to give Hector permission to commit? Michael
On Wed, May 29, 2013 at 2:12 PM, Hector Corrada Bravo <hcorr...@gmail.com>wrote: > That's great! There's some cleaning up to do there how should we do this > post-merge? > > > On Wed, May 29, 2013 at 4:19 PM, Valerie Obenchain <voben...@fhcrc.org>wrote: > >> 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.mich...@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 < >> >> hcorr...@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 >> >>> >> >> >> >> >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioc-devel@r-project.org mailing list >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel >> > >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
