On Tue, Apr 13, 2010 at 2:38 AM, Robert Castelo <robert.castelo@upf.edu>wrote:

> dear list and, particularly, IRanges developers,
>
> i've noticed a change shown below in the functionality of the
> findOverlap function from the IRanges package from the current BioC
> release version 2.10 to the current BioC devel (about to become release)
> version 2.11 (i've checked-out the latest IRanges version at the svn
> repository).
>
> this change seems to alter the way in which findOverlaps() return the
> hits. in the current release findOverlaps() was returning the index of
> the hits with respect to the entire RangedData object while in the
> current devel version it does it with respect to the corresponding
> space. is this an intended change or is it a bug? (i was happier with
> the behavior of the release..)
>
>
It's a bug. Dimensions got switched around in RangesMatching, which confused
RangesMatchingList. It's been broken since 2/26/10, in case anyone wants to
re-run their scripts.

Thanks a lot for catching this,

Michael


> thanks!
> robert.
>
> =========================current release 2.10==================
> suppressPackageStartupMessages(library(IRanges))
>
> x <- RangedData(IRanges(start=c(1,6), end=c(5,10)),
>                        space=c("chr1","chr2"))
> x
> RangedData with 2 rows and 0 value columns across 2 spaces
>        space    ranges |
>  <character> <IRanges> |
> 1        chr1   [1,  5] |
> 2        chr2   [6, 10] |
>
> y <- RangedData(IRanges(start=8, end=10),
>                        space="chr2")
> y
> RangedData with 1 row and 0 value columns across 1 space
>        space    ranges |
>  <character> <IRanges> |
> 1        chr2   [8, 10] |
>
> as.matrix(findOverlaps(x, y))
>     query subject
> [1,]     2       1
> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] IRanges_1.4.14
> ===============================================================
>
> ========================current devel 2.11=====================
> suppressPackageStartupMessages(library(IRanges))
>
> x <- RangedData(IRanges(start=c(1,6), end=c(5,10)),
>                        space=c("chr1","chr2"))
> x
> RangedData with 2 rows and 0 value columns across 2 spaces
>        space    ranges |
>  <character> <IRanges> |
> 1        chr1   [1,  5] |
> 2        chr2   [6, 10] |
> y <- RangedData(IRanges(start=8, end=10),
>                        space="chr2")
> y
> RangedData with 1 row and 0 value columns across 1 space
>        space    ranges |
>  <character> <IRanges> |
> 1        chr2   [8, 10] |
> as.matrix(findOverlaps(x, y))
>     query subject
> [1,]     1       1
> R version 2.11.0 Under development (unstable) (2010-02-25 r51180)
> x86_64-unknown-linux-gnu
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods
> base
>
> other attached packages:
> [1] IRanges_1.5.76
>
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