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
