Adding generateIndelocatorFPResults.py.
-a tool for scanning the pure false positive directories and reporting how many false positives indelocator found.
-outputs a column for each stage of filtering
-functionality should be moved into RunBenchmark.scala
Split getCommands into getFalsePositiveCommands and getSpikedCommands.
Modified both to return a output directories as well as their commands.
Removing python and perl scripts that are no longer needed.
-make_fn_sim_datasets.pl has had its functionality moved into GenerateBenchmark.scala
-runAllCombinations.py has been replaced by RunBenchmark.scala
-setupbams.py was replaced by GenerateBenchmark.scala