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
Merge branch 'master' into exome

Conflicts:
	GenerateBenchmark.scala