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

[Kasper Daniel Hansen]

Has it ever been documented that the return object is sorted in a specific
way?  I just want to make sure we think about whether that is something we
want to enforce giving the possibility of using a different algorithm in
the future.

We could also address this by implementing (perhaps it already exists) a
sort() method for the return object.  That would still break existing code
though.

Best,
Kasper

On Wed, Jan 14, 2015 at 11:13 PM, Michael Lawrence <
lawrence.michael at gene.com> wrote:

> 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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