CLI & mappability filter for region join, custom exceptions

Fixes #420, #297 

Several changes: 
* adding a filter for 'mappability' to the ``partitionAndJoin`` method, fixing (I hope) Christos's problem
* creating a CLI tool for accessing/testing RegionJoin (and for re-creating the bug) 
* adding a custom exception, for throwing errors related to unmapped reads or records (see #420) 
* added a ``hasReferenceRegion`` to ``ReferenceMapping`` -- to explicitly check for whether a value _can_ be converted to a ReferenceRegion
Can you eliminate this dead code?