Re: IRanges findOverlaps potential bug?

Thanks. Fixed in 1.99.25. We had never actually implemented select="last".


On Thu, Aug 28, 2014 at 1:09 PM, Arunkumar Srinivasan <[email protected]
> wrote:

> Hi BioC list,
>
> I just came across something I believe is an unexpected result (potential
> bug) in IRanges. I'm using the development version, but the same happens in
> stable version as well. My sincerest apologies if it's a misunderstanding
> on my part.
>
> In the example below, I'd expect the result for 'ans2' to be a vector of
> length 6, but with all values = 4L instead of 3L. By looking at
> `?findOverlaps`, it seems like `select` should work with all values of
> argument 'type'.
>
> ## code
> require(IRanges)
> ii = IRanges(start=3L, end=c(5L, 5L, 16L, 20L, 24L, 47L))
> # IRanges of length 6
> #     start end width
> # [1]     3   5     3
> # [2]     3   5     3
> # [3]     3  16    14
> # [4]     3  20    18
> # [5]     3  24    22
> # [6]     3  47    45
>
> xx = IRanges(start=c(1L,2L,3L,3L,6L), end=c(646L, 481L, 672L, 1037L, 153L))
> # IRanges of length 5
> #     start  end width
> # [1]     1  646   646
> # [2]     2  481   480
> # [3]     3  672   670
> # [4]     3 1037  1035
> # [5]     6  153   148
>
> ## works fine, as expected
> ans1 = as.data.frame(findOverlaps(ii, xx, type="start", select="all"))
> #    query subject
> # 1      1       3
> # 2      1       4
> # 3      2       3
> # 4      2       4
> # 5      3       3
> # 6      3       4
> # 7      4       3
> # 8      4       4
> # 9      5       3
> # 10     5       4
> # 11     6       3
> # 12     6       4
>
> ## potential bug?
> ans2 = findOverlaps(ii, xx, type="start", select="last")
> # [1] 3 3 3 3 3 3
>
> This seems like a bug to me. If not, could you please explain? Thank you.
>
> ---
>
> sessionInfo()
> # R version 3.1.1 (2014-07-10)
> # Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> # locale:
> # [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> # attached base packages:
> # [1] parallel  graphics  grDevices datasets  stats     utils     methods
>   base
>
> # other attached packages:
> # [1] IRanges_1.99.24     S4Vectors_0.1.2     BiocGenerics_0.11.4
> bit64_0.9-4
> # [5] bit_1.1-12
>
> # loaded via a namespace (and not attached):
> # [1] stats4_3.1.1 tools_3.1.1
>
> Arun
>
>
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>
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