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]]
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