Minor cleanup.
--removed unused bamMapFile field from GenerateBenchmark.scala
--renamed chr20.interval_list to benchmark.interval list and adjusted GenerateBenchmark
--removed unused prefix field from GenerateBenchmark.scala
Updated README with basic instructions.  Probably missed a few things.
Added a step to generate coverage information for all of the output bams.
--Exposed output files to the script method
--Run DepthOfCoverage on these output files.
Merge branch 'master' into Analysis