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.
Outputting vcf file of all the spiked in variants from SomaticSpike.
Added vcf header initialization.
Changing parameters to match the new usage.
-- -V, the input vcf file is now required
-- -vout, the output vcf file is now required
-- --spiked_intervals_out is now optional
Edited GenerateBenchmark.scala to match the changes to SomaticSpike.
Fixing invalid vcf output from SomaticSpike
--Adding samples to vcfHeader output
--Moved vcf header initialization into its own method
Added a shebang with -e to runIndelocator.sh so that it fails fast.
Removed the long obsolete SimulationCommon.pl
Removing extractIndels.sh, it is is redundant with SelectVariants
Changing runIndelocator.sh so that all stages of filtering are output as vcf.
--Adding conversion to vcf to all stages of indelocator output.
--Added a copy step to runIndelocator that creates the final.indels.vcf that is expected.
Adding runStrelka.sh, a wrapper script for RunBenchmark.scala to invoke.
--this has a hardcoded Strelka libdir that needs to be wired on whatever system it runs on
Moving runIndelocator.sh and runStrelka.sh into tool-scripts directory.