Replaced loadBamMap.
-It now calculates the mapping rather than loading it from a file.
-It is extremely brittle to changes in parameters.
Eliminated field bamDigitToName map.
-renamed loadBamMap to generateBamMap
-eliminated parameters
-replaced fields only usage with a call to generateBamMap
Removed duplication of a formatting string and moved it into getSplitFileName.
Removed bamMap file because it is no longer needed.
Automatic code formatting.
Commented getBams.
Added --is_test flag to GenerateBenchmark.
-currently it only reduces the number of merge jobs

Fixed the ordering of the libraries and added a comment about the importance of the ordering.
Changed the hardcoded indel source file to the new recommended gsa gold standard variants.
It is aligned to b37_decoy.
WARNING:  This file also contains snps, so analysis steps will have to do some filtering.
Merge branch 'RemoveBamMap'
Removing the need for the bam map file as well as adding a slightly faster test mode.