Proposed changes to Python object hierarchy

The part that bothers me is needing to bind that intermediate to a separate name, because here we’ll need to use fields that aren’t in the namespace previous to calling filter_alleles.

Man, this is hard.

Agreed. Manipulating alelles is not all a natural operation. I don’t know who else is doing it better than us (can GATK filter alleles?) and I we’re clearly still not thinking about it correctly.