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.