[BioC] transcriptLocs2refLocs Bug when strand is negative

Cook, Malcolm MEC at stowers.org
Sat Sep 1 01:22:39 CEST 2012

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

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

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


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


Malcolm Cook
Stowers Institute for Medical Research

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