Added ReferencePosition.UNMAPPED and handling in GRP.

Added a special "unmapped" value for the ReferencePosition class, and updated the GenomicRegionPartitioner to handle it as a special case by mapping it into a single partition separate from all the others.

Also added a few more comments.

Frank / Matt, if this looks alright to you, I'll rebase it down into a single commit and update it to be based on the latest master.