Moving more of the various CommandLineFunctions over to using the predefined ones.

-Changed from my custom SomaticSpike wrapper to the autogenerated one.
-Changed from a custom picard SortSam to using the already existing one.
Removed sortSamPath
Changed MergeBams to use the Picard MergeSamFiles wrapper.
WARNING:  I changed the behavior of merge bams, it no longer copies the output .bai file as a bam.bai file.  I think these must have been produced for strelka or some other downstream caller, but I'm not sure what exactly.
-deleted my MergeBams class
-removed mergeBamsPath and PICARD_PATH fields because they were no longer necessary
-removed several unused fields
-fixed two typos
Minor refactor.  Moved command argument to the top of GenerateBenchmark.
Replaced several of my own CommandLineFunctions with pre-made gatk ones.
Merge branch 'ReplacingCommandLineFuncs'

Conflicts:
	GenerateBenchmark.scala