Minor refactorings.
-Changed outputDir to be named spikedOutputDir for clarity.
-Removed unused variable vcfOut.
Parameterized make_vcs.pl so that the vcf_data directory could be set programatically.
-renamed output argument of GenerateBenchmark to output_dir to remove confusion with local variables
-made spikedOutputDir and vcfDataDir lazily initialized so that they capture the runtime argument value
JobQueueArguments were redundant with already provided Queue argument --job_queue.
-removed hard coded queue = "week"
-renamed JobQueue arguments to base arguments.  They are currently empty.
--possibly will remove the trait completely later, but keeping for now in case I have use case in the near future.