[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.)
Merge pull request #482 from tdanford/coverage-regions

[ADAM-462] Coverage region calculation
[ADAM-442] Adds .2bit file reader

Fixes #442
[ADAM-518] Move distribution stage into a profile.