modified:   gatk.qpp.scala
	    Changed comments and the order of optional @Inputs and @Arguments

modified:   gatk.qpp.sh
	    Added comments and cleaned up the script a bit
modified:   gatk.qpp.scala
	    Deleted definition of knownSites input file, and hard coded the file to the script

modified:   gatk.qpp.sh
	    Removed line with knownSites