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.
Update .gitignore
Merge branch 'master' into ConvertMakeVcfsToScala
Updating ConvertMakeVcfsToScala to current version
Conflicts:
	GenerateBenchmark.scala
Fixing broken path to panel of normals.
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.
Removed LibraryReadFilter, it is now available as part of the base gatk.
--removed filters folder from inclusion in the build since it was now empty
Modifying runStrelka script to delete the large strelka chromosomes after running.
Made is_test set the allele-fraction in GenerateBenchmark like it should always have.
Updating runIndelocator to use filter criteria from Production Pairs instead of production algorithms