[avocado-116] Remove need for spark configuration file.
[avocado-117] Add basic configuration file.
Merge pull request #118 from fnothaft/spark-1.1

Clarify configuration settings and provide basic configuration
[avocado-124] Fixing build issue due to upstream change to ADAM save command.
Merge pull request #124 from fnothaft/fix-build-110714

[avocado-124] Fixing build issue due to upstream change to ADAM save command
Making some filter().size() calls into .count()'s
[avocado-114] Mutect implementation.

Initial commit contains the implementations of read pre-processing and
filters for tumor and normal sample reads.
Adding the Mutect probabilistic models.