[Bioc-devel] IRanges findOverlaps Result Different for Recent Update

[Michael Lawrence]

I bet there is a lot of code that depends on having the hits (conveniently)
ordered by query,subject index, so we should try to restore the previous
behavior.

On Wed, Jan 14, 2015 at 8:00 PM, Dario Strbenac <dstr7320 at uni.sydney.edu.au>
wrote:

> Hello,
>
> For an identical query, the matrix results are in a different order.
> Consider the subject hits of the last two rows :
>
> > mapping        # R Under development (unstable) (2015-01-13 r67453) and
> IRanges 2.1.35
>      queryHits subjectHits
> [1,]         1           1
> [2,]         1           4
> [3,]         2           2
> [4,]         4           1
> [5,]         4           4
> [6,]         6           7
> [7,]         6           6
>
> > mapping        # R Under development (unstable) (2015-01-13 r67453) and
> IRanges 2.0.1
>      queryHits subjectHits
> [1,]         1           1
> [2,]         1           4
> [3,]         2           2
> [4,]         4           1
> [5,]         4           4
> [6,]         6           6
> [7,]         6           7
>
> This causes some values to be extracted in a different order by our
> annotationLookup function, and causes an error for the development version
> of Repitools on a test case which uses all.equal to compare a list to a
> correct list, but not for the release version which uses the release
> version of IRanges. Should I update the test case to have a new expected
> result, or is this new characteristic of findOverlaps likely to revert to
> the previous output soon ?
>
> The two sets of intervals to produce this result are anno and probesGR,
> defined in the tests.R file in the Repitools package.
>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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