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
>>>>
>>>>
>>>
>>
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