CLI & mappability filter for region join, custom exceptions

Fixes #420, #27 

Several changes: 
(1) adding a filter for 'mappability' to the ``partitionAndJoin`` method, fixing (I hope) Christos's problem
(2) creating a CLI tool for accessing/testing RegionJoin (and for re-creating the bug) 
(3) adding a custom exception, for throwing errors related to unmapped reads or records (see #420) 
(4) added a ``hasReferenceRegion`` to ``ReferenceMapping`` -- to explicitly check for whether a value _can_ be converted to a ReferenceRegion