Making the first input in spike_in_only mode the normal, the rest are tumors.
Changing from first bam being normal to last bam being normal.
Changing from using global tumor bams to determining them from the list of mergedBams
Removing localizing BamFileNameCalculator dependencies to the fracture and merge stage.
Added "getName" to fix output directory.
Working on refactoring GenerateBenchmark.scala
--moving file name determination code into 1 location
--removing global variables