What libraries are there for handling logic on intervals? I really want all the set operations on the intervals at genome scale. Bonus points if it has some persistence mechanism and can track the ancestor of an operation (i.e. interval X is the result of the intersection of Y and Z).
I looked at bx python, but the documentation is not great.
I don't think the IRanges objects track their own derivation history.
you can save an IRanges object using... save() Thumbs up for the most advanced interval library at present.
Looks pretty good, but how does persistence work with the ranges, or do you need to manually convert each time?
@Casbon: +1 David. Not sure about the persistence mechanism.