SNAP pipeline fixes (in progress)

Adding release scripts.

Updating active region threshold.

Adding fast aligner.

Adding a few fixes for running on a cluster.

Put extra logging under debug flag

More debug cleanup

SNAP pipeline fixes

Change ADAM version
Merge pull request #93 from rnpandya/ravip-snap-streaming

SNAP streaming changes
Merge branch 'master' of https://github.com/bigdatagenomics/avocado

Conflicts:
	avocado-cli/src/main/scala/org/bdgenomics/avocado/cli/Avocado.scala
	pom.xml