Modifying gather results to run for snps and indels.
Adding cmdline parameter to make_graphs.r to specify output directory.
Adding nofp and nofn arguments to GatherResults.
--Warning they are not wired up yet.
Glueing bits together
--Changed RCommandLineFunction to RscriptCommandLineFunction
----moved from using R CMD BATCH to Rscript
----removed extraneous parameters and added a args list parameter

--Activated nofp and norp flags
--Changed runAnalysis to pass an output directory name to make_graphs.R
Passing variantType through the analysis functions
--prevent the output files from overwriting each other by creating unique names
Adding commandline parameters to make_graphs to pass in the tsv files
--WARNING: Not wired yet.
Passing file names as parameters to make_graphs.r
--WARNING: Ugly, refactor.
Refactoring make_graphs.r
Minor refactor of GatherResults.scala
Adding check for non-existant counts files.
Merge branch 'gatherSnps' into expandedBamtypes
--Merging in updated graph code.
Conflicts:
	GatherResults.scala