[ADAM-510] fix for bash syntax error; add ADDL_JARS check to adam-submit
Merge pull request #515 from heuermh/addl-jars

[ADAM-510] fix for bash syntax error; add ADDL_JARS check to adam-submit
[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.
quieting wget output
Merge pull request #521 from shaneknapp/cleaning_wget

quieting wget output
don't open non-.adam-extension files as ADAM files

  fixes #522
Merge pull request #523 from ryan-williams/adam-file

don't open non-.adam-extension files as ADAM files