Creating EvaluateCallSet.scala
    A QScript to run the single call set evaluation and produce plots.
Moving EvaluateCallSet and adding some initial functionality.
Adding an R script to draw graphs directly from the mutsig maf.
Improvements to the graphs of extract.R
Changing cosmic/dbsnp plot to have percentages as well as absolute counts.
Updates to extract.R
Fixup
Add minimum graph height
More graph updates.
Making the script friendlier.
--Added usage information
--Added very basic checks for invalid inputs
Switching argument order so that it is <input.maf> <outputdir>
Renamed extract.R to graphs_from_maf.R
Changed usage text to match new name.
Pulling in changes Mara made to get it to run on firehose.
Adding lego plot script and modifying wrapper to invoke it.
Updated the allele fraction vs tumor depth charts.
    printing them with and without density lines
    log scaling the x-axis
    shrinking the points and making them semi-transparent
Coloring Allele Fraction vs Tumor Depth plots by dbsnp/cosmic membership
In progress updates to graphs_from_maf.R
Added indel graphs
Removing useless box plots.