chapmanb/cloudbiolinux — comment on commit 77b8cc5bee00e8600b1f08a451789e4cdf9e934c
File:  line 0
By chapmanb:

Paul;
That is definitely worrying. If you can reproduce with a small example. could you send to the TopHat authors? This behavior might affect quite a few people and it would be great to get an upstream fix.