-- Previously these core progress metering functions were all in TraversalEngine, and available to subclasses like TraverseLoci via inheritance. The problem here is that the upcoming data threads x cpu threads parallelism requires one master copy of the progress metering shared among all traversals, but multiple instantiations of traverse engines themselves.
-- Because the progress metering code has horrible anyway, I've refactored and vastly cleaned up and simplified all of these capabilities into TraversalProgressMeter class. I've simplified down the classes it uses to work (STILL SOME TODOs in there) so that it doesn't reach into the core GATK engine all the time. It should be possible to write some nice tests for it now. By making it its own class, it can protect itself from multi-threaded access with a single synchronized printProgress function instead of carrying around multiple lock objects as before
-- Cleaned up the start up of the progress meter. It's now handled when the meter is created, so each micro scheduler doesn't have to deal with proper initialization timing any longer
-- Simplified and made clear the interface for shutting down the traversal engines. There's no a shutdown method in TraversalEngine that's called once by the MicroScheduler when the entire traversing in over. Nano traversals now properly shut down (was subtle bug I undercovered here). The printing of on traversal done metering is now handled by MicroScheduler
-- The MicroScheduler holds the single master copy of the progress meter, and doles it out to the TraversalEngines (currently 1 but in future commit there will be N).
-- Added a nice function to GenomeAnalysisEngine that returns the regions we will be processing, either the intervals requested or the whole genome. Useful for progress meter but also probably for other infrastructure as well
-- Remove a lot of the sh*ting Bean interface getting and setting in MicroScheduler that's no longer useful. The generic bean is just a shell interface with nothing in it.
-- By removing a lot of these bean accessors and setters many things are now final that used to be dynamic.
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