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

[Dario Strbenac]

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