Oh my head

Okay this may be lunacy as I've been coding all day but I'm fairly sure it should fix everything that's wrong in the world or at least in the pipeline for the moment. Or I don't know. Oh it doesn't handle hiseq xten runs. I guess I'll do that tomorrow. But it handles the Charon updating issues and I think something else.
great!!!! in this way if all data is in Charon we will atomically handle reruns that have not been aligned