[BioC] transcriptLocs2refLocs Bug when strand is negative

[Cook, Malcolm]

Herve et al,

I believe that transcriptLocs2refLocs is implemented incorrectly for
negative strands.

The bug appears in the example of its use you provided in
https://stat.ethz.ch/pipermail/bioconductor/2011-March/038173.html

I think you will agree that the third result should be:
[[3]]
[1] 5899 6291

As a workaround, I have implemented a version in R using a new generic,
named `at`

https://gist.github.com/3560692


I would be happy to receive confirmation that this is a bug, and comments
from anyone on the approach to the workaround I have adopted, especially
as regards performance comparison with

Thanks,

Malcolm Cook
Stowers Institute for Medical Research