If you don't mind, I think I'll wait till after you're finished testing before merging.
Please keep me up to date, Michael On Fri, Aug 2, 2013 at 7:43 AM, Hector Corrada Bravo <hcorr...@gmail.com>wrote: > Thanks again Kasper, > All of these are now fixed: > * empty subject seqlevel, > * out-of-order seqinfo's, > * show,GIntervalTree-method > > Michael, please merge from > https://github.com/hcorrada/IRanges [version 1.19.20] > https://github.com/hcorrada/GenomicRanges [version 1.13.36] > > I'll test the SummarizedExperiment stuff later today. > > Cheers, > Hector > > > > On Thu, Aug 1, 2013 at 5:21 PM, Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > >> If you're fixing tonight here is a possible related. I get an error when >> I do the findOverlaps and I have two GRanges with the same seqlevels but in >> different order (so, I guess, technically not the same seqlevels). If this >> is not supported, I suggest an upfront check. >> >> gr1 = GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(1:2, width = >> 1)) >> gr2 = gr1 >> seqlevels(gr2, force = TRUE) = c("chr2", "chr1") >> findOverlaps(GIntervalTree(gr1), GIntervalTree(gr2)) >> >> I also got a seqfault on a similar example (but with real data). I am >> trying to see if I can make a small reproducible example (which is how I >> got here), hypothesizing that it has something to do with the seqinfo slot >> in the two GRanges. >> >> Kasper >> >> >> >> >> >> >> On Thu, Aug 1, 2013 at 4:48 PM, Hector Corrada Bravo >> <hcorr...@gmail.com>wrote: >> >>> Thanks. I'll fix tonight. >>> >>> >>> On Thu, Aug 1, 2013 at 4:28 PM, Kasper Daniel Hansen < >>> kasperdanielhan...@gmail.com> wrote: >>> >>>> Bug: >>>> >>>> > library(GenomicRanges) ## 1.13.35 >>>> >>>> > gr = GRanges(seqnames = c("chr1", "chr2"), ranges = IRanges(1:2, >>>> width = 1)) >>>> >>>> > gr.tree <- GIntervalTree(gr) >>>> >>>> >>>> > findOverlaps(gr.tree, gr.tree) >>>> >>>> >>>> Hits of length 2 >>>> >>>> >>>> queryLength: 2 >>>> >>>> >>>> subjectLength: 2 >>>> >>>> >>>> queryHits subjectHits >>>> >>>> >>>> <integer> <integer> >>>> >>>> >>>> 1 1 1 >>>> >>>> >>>> 2 2 2 >>>> >>>> >>>> !> findOverlaps(gr.tree, gr.tree[1]) >>>> >>>> >>>> >>>> >>>> >>>> *** caught segfault *** >>>> >>>> >>>> address (nil), cause 'memory not mapped' >>>> >>>> >>>> >>>> >>>> >>>> Traceback: >>>> >>>> >>>> 1: .Call(.NAME, ..., PACKAGE = PACKAGE) >>>> >>>> >>>> 2: .Call2(fun, object@ptr, ..., PACKAGE = "IRanges") >>>> >>>> >>>> 3: .IntervalForestCall(subject, fun, query, partitionIndices, >>>> elementLengths(partitioning), query_ord) >>>> >>>> 4: .local(query, subject, maxgap, minoverlap, type, select, ...) >>>> >>>> >>>> 5: findOverlaps(qlist, subject@ranges, maxgap = maxgap, minoverlap = >>>> minoverlap, type = type, select = "all") >>>> >>>> 6: findOverlaps(qlist, subject@ranges, maxgap = maxgap, minoverlap = >>>> minoverlap, type = type, select = "all") >>>> >>>> 7: .local(query, subject, maxgap, minoverlap, type, select, ...) >>>> >>>> >>>> 8: findOverlaps(gr.tree, gr.tree[1]) >>>> >>>> >>>> 9: findOverlaps(gr.tree, gr.tree[1]) >>>> >>>> >>>> >>>> >>>> >>>> Possible actions: >>>> >>>> >>>> 1: abort (with core dump, if enabled) >>>> >>>> >>>> 2: normal R exit >>>> >>>> >>>> 3: exit R without saving workspace >>>> >>>> >>>> 4: exit R saving workspace >>>> >>>> >>>> Selection: >>>> >>>> >>>> On Thu, Aug 1, 2013 at 3:45 PM, Kasper Daniel Hansen < >>>> kasperdanielhan...@gmail.com> wrote: >>>> >>>>> Ah! Super-nice! I'll test as well, when I have time. >>>>> >>>>> Kasper >>>>> >>>>> >>>>> On Thu, Aug 1, 2013 at 3:34 PM, Hector Corrada Bravo < >>>>> hcorr...@gmail.com> wrote: >>>>> >>>>>> This is not tested, but... >>>>>> >>>>>> GIntervalTree extends GenomicRanges so, in principle, can be used in >>>>>> the rowData slot of SummarizedExperiment. I tried to make GIntervalTree >>>>>> support as much of the GenomicRanges interface as I could so this may >>>>>> work >>>>>> already for overlap queries where the SummarizedExperiment object is the >>>>>> subject. I'll test this soon and let you know. >>>>>> >>>>>> >>>>>> On Thu, Aug 1, 2013 at 3:12 PM, Kasper Daniel Hansen < >>>>>> kasperdanielhan...@gmail.com> wrote: >>>>>> >>>>>>> Now that we have GIntervalTree, I am really interested in a >>>>>>> SummarizedExperiment that stores its index in a slot, so it can be >>>>>>> indexed >>>>>>> once. I am sure other people are greedily eyeing this as well. >>>>>>> Either >>>>>>> changing the class or extending it. >>>>>>> >>>>>>> Unfortunately, I will not have time to work on this for some weeks, >>>>>>> but I >>>>>>> wanted to put the idea out there. >>>>>>> >>>>>>> Best, >>>>>>> Kasper >>>>>>> >>>>>>> [[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
