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
Updating generateIndelocatorPFResults.py with new file structure.
Improvements to generateIndelocatorFPResults.py
Adding generateStrelkaFPResults.py, a slight modification of the indelocator version.
Work on GatherResults
Dealing with a case where vcftools doesn't output any files because there is nothing to compare.
Adding printout to GatherResults.scala.
Fixing output format.
Adding tool name to output.
Added a "matched" field to show how many actual positives were recorded.