Add a simple script to be used by Jenkins for testing
Add new pileup and genotype formats for variant calling
Upgrade to Parquet 1.2.4 and fixup jenkins test script
Add all Spark context parameters to commandline
Updated the AdamCommand trait to make non-commandline use easier

This commit separate the commandline processing concerns from the
AdamCommands. This allows command to be used more easily as
part of a library or for testing.
Quick fix to the mpileup command
Add a simple utility class for creation schema projections
Cleanup imports
Created benchmark to test the cost of reading varying amounts of fields from ADAMRecord using projection.
Added GetReadLengthAndQuality benchmark. Having trouble with reads returning all nulls.