removed unused code from GatherResults added RCommandLineFunction
GatherResult now invokes make_graphs.r
Fixing a bug which was causing somatic spike to be passed the incorrect interval list.
Added a comment to SomaticSpike
Added a skeleton tool script called runExampleScript.
--to add a new tool copy this and fill in your details
Removing irrelevant text from runExampleScript.
Added a brief README to the tool-script directory explaining how to add a new wrapper script.
Modifying runExampleScript.sh so that it includes creating the output directory.
Added dbSnp file to GenerateBenchmark for use in snp calling.
Adding flags to run only FP or only FN analysis in RunBenchmark
Adding runMutect.sh a wrapper to run MuTect

--linked to the benchmark.interval_list to lower mutect runtime
Merge branch 'master' into exome
--bringing exome branch up to date

Conflicts:
	RunBenchmark.scala