Initial implementation, some existing plugins may need to be updated.

Experimental.
A bolus of changes to allow for naive overlaps.

Also includes fixes to tests to allow them to run faster and a number of off-by-one error checks.
Remove repeats
Only suppress overlaps with yourself, not with SNV at the same position.
wrong ID
Include the inverse for more interest
fix typo
Reactivate broken tests
Merge pull request #8 from SeqWare/feature/naive_overlaps

Feature/naive overlaps