[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.)
Removed isAdjacent from Coverage

Also, updated the implementation of ReferenceRegion.isAdjacent.
And removed the ordering implementation for ReferenceRegion in Coverage.
Fixing comment editing.
Reworked sliding to use a flatMap/groupBy impl.

Frank had suggested moving from a sequence-of-joins to a
flatMap/groupBy-based implementation -- this commit makes that change,
and includes an extra test of the sliding method.
Creating RegionRDDFunctions

helper functions for RDD[ReferenceRegion] and RDD[(ReferenceRegion, T)]
Finished basic implementations of joinByOverlap and filterWithinRange
Revising the list of methods

Adding the join/filter/group methods for each of Overlap/WithinRange
wip added windowCounts method.
Formatting.