Fixing trivial warnings in Intellij.

Minor refactoring for clarity
-FractureBams became a object instead of a class
-Cleaned up unecessary parentheses

Specified exception type as Throwable.

Removed unecessary _ in RunBenchmark.scala
Added isIntermediate = true to the filter stage of makeSingleFractureJob.
-This should cause the intermediate bams to be deleted when no longer necessary.