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

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

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