Extended DirectoryMetaData to work on false positive directories.
Merging generateIndelocatorFPResults with generateStrelkaFPResults.
--renamed to generateFPResults.py
Trivial refactorings.
Fixed problems with new generateFPResults.py

--Making generateFPResults print Normal and Tumor columns instead of directory

--Changed output file name of generateFPResults

--Autoformatted generateFPResults so intellij would stop complaining.
Removed generateIndelocatorFPResults and generateStrelkaFPResults.
Adding false postive counting to gather results.
Misc refactorings to GatherResults.scala
Fixing frequency output which was Some(#) rather than just \#
Added a collection step to gather all the depth information into 1 R friendly file.
Merge branch 'FPEval'
Merging in the new false positive evaluation tool in GatherResults.scala
Adding a script make_graphs.r to automatically make the false positives graphs.
Added false negative graph (not perfect yet)
Updating gitignore to include various images, datafiles, and the droppings of R and the OSX Finder.
Changes to output files.
--renamed falsePositiveCounts to falsePositiveCounts.tsv
--moved graphs into a graphs folder
Update .gitignore
Merge branch 'master' into ConvertMakeVcfsToScala
Updating ConvertMakeVcfsToScala to current version
Conflicts:
	GenerateBenchmark.scala