There are some really cool things going on - better handling of control data, better compares, and even saturation analysis made it in. Overall, I'm really impressed with how well things are working on that front.
The one thing that I'm disappointed to have not been able to include was support for SAM/BAM files. No one is really pushing for it yet, here at the GSC, but it's only a matter of time. Unfortunately, the integration is not trivial, and I made the executive decision to work on other things first.
Still, I can't say I'm unhappy at all - there's room for a fresh publication, if we decide to go down that route. If not, I have at least 2 possible publications in the novel applications of the code for the biology. That can't be a bad thing.
Anyhow, I'm off to put a few final updates on the code before tagging the final 3.3.x release.