Small changes trying to get a good test setup. Some parts working some not.
Working - I think - version of syntenic_paralogs() that goes through all candidate pairs in order and requires that a candidate pair be better than all alternative sister regions as well as exceeding null hypothesis (from randomizations).
Bunch of minor changes.
Implemented synteny only based short cut (if candidate completes "three in a row" then just accept) and cleaned up screen output.
Fixed minor - but significant - bug in shortcut.
More bug squashing. Shortcut seems to be working.