More slight changes
--Changed logging level of input files from INFO to DEBUG
--Added method stubs for analysis
Changed expected output file from sample.final.indel.vcf to final.indel.vcf.
Updating old false positives counting script to work with new file names.
Adding a false negative summary generator.  INCOMPLETE
Added a step to generate coverage information for all of the output bams.
--Exposed output files to the script method
--Run DepthOfCoverage on these output files.
Merge branch 'master' into Analysis
Fixed bug in runBenchmark that was causing certain combinations to be skipped.
Updating generateIndelocatorPFResults.py to work with the current expected directory structure.

--misc other minor improvements to generateIndelocatorFPResults.py
Adding generateStrelkaFPResults.py, a slight modification of the indelocator version.
Work on GatherResults

--Adding exception handling for the case where vcftools doesn't output any files because there is nothing to compare.

--Adding printout to GatherResults.scala.
Merge branch 'Analysis' because it is now stable enough to produce some of the results and not blow up.