adding a --bamtypes parameter to specify the bamtypes file
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