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

[Michael Lawrence]

If it's not documented, it should be, because Patrick did it on purpose
(the output from the IntervalTree code is not sorted). We could add an
argument to disable the sorting for when the extra speed is desired. But it
has proven useful.

On Thu, Jan 15, 2015 at 6:42 AM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:

> 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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> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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