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.mich...@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 < > dstr7...@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
