Skeleton outline of MakeVcfs.  Does not compile.
Fleshing out MakeVcfs.  Currently in an incomplete state.
More work in progress.
--Removing sample names from hardcoded file names and replacing them with variables.
Finished initial pass at moving make_vcfs.pl in GenerateBenchmark.scala
Fixing UnifiedGenotyper creation, which was causing a compilation error.
Changed a hardcoded filename to one constructed from the sample names.
Making changes to the WriteIntervals CommandLineFunction.
--probably still isn't right, I am confused about what it's supposed to looks like.
Merge branch 'master' into ConvertMakeVcfsToScala
Updating ConvertMakeVcfsToScala to current version
Conflicts:
	GenerateBenchmark.scala
Merge branch 'master' into ConvertMakeVcfsToScala
Fixing command line parameters.
Made intervals part of GeneraterArguments because I kept forgetting it.
--had to override it in SomaticSpike call

Added indels and snps boolean parameters to enable/disable inclusion into the spike files
--currently only indels works
--modfied call to UnifiedGenotyper to set the genotyping model based on which spike ins are designated.