Fine with me, as long as he is acquainted with the build/test before commit practices that we are supposed to follow. Breaking IRanges can have severe repercussions.
On Wed, May 29, 2013 at 6:36 PM, Michael Lawrence <lawrence.mich...@gene.com > wrote: > 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 > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
