[ADAM-462] Coverage region calculation

This commit includes an new class, Coverage, which contains methods for
calculating coverage RDDs from RDDs of Region values.

Also included is a helper class, the PairingRDD class, which calculates
simple 'sliding' and 'pair' methods on sorted RDDs using the
"zipWithIndex trick."

(Joint work with Carl Yeksigian, and fixes #462) 
I got tired of writing out ReferenceRegion the whole time.

Also, it used to be a type parameter.