Adding third column to bam types and remove name guessing.
--WARNING BAD TEMPORARY FIX WILL BREAK
Changing defaults to match this particular set of exomes.
Refactoring all of the scala scripts to centralize everything related to the bamtypes file.
--Creating a shared BamTypes.scala
----moving reading and writing to the bamtypes file
----moving AnnotatedFile and Abrv file into BamTypes.scala
----renaming AnnotatedFile to AnnotatedBamFile and AbrvFile to NamedFile
Moving BamTypes code into a better location and adding it to the build script.
--We shouldn't have to add -S BamTypes.scala to runs now.
Working with bamtypes to bring things up to date and make things coherent.
Combining AbbreviateFile with BamType again because I couldn't get the build to work.
Changed diffResults.tsv to falseNegativeCounts.tsv
Fixing the way the tumor name is decoded from the false negative results files.
Fixed warning about non-unique bam names, its logic was backwards.
Renaming make_graphs.r to make_graphs.R
--this way I don't get make_graphs.r.Rout, i get make_graphs.Rout instead.
Fixing build file and a forward reference in GenerateBenchmark.scala
Fixing typecast exception caused by not adherring to the contract of FileExtension
Adding runStrelkaDebug.sh for running debuggable strelka runs
--it doesn't delete the strelka intermediate files afterwards
Added a --bamtypes parameter for GatherResults.scala.
Fixing a bug in GatherResults.scala
  The inputs to make_graphs were not annotated as inputs properly.
  This was causing Queue to be unable to correctly order the steps of GatherResults
Improving the error message when there is an error reading a vcftools diff file.
Making the tumor name in falseNegatives-indels.tsv match the name of the base tumor file without the fraction added.
--It was causing a frustrating error when running GatherResults.scala
Adding a rate calculation for false positives. It assumes it's an exon with 32 MB.
Adding a comment and minor formatting.
Revert "Adding a comment and minor formatting."

This reverts commit 2ae38f8c756a2ea069d17f00209ff77de184474e.
--There were other changes in this commit that broke things.