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
Merge branch 'master' into Analysis
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.