-- These are like read filters but can be applied either on input, on output, of handled by the walker
-- Previous example of BAQ now uses the general framework
-- Resulted in massive conceptual cleanup of SAMDataSource and ReadProperties! Yeah!
-- BQSR now uses this framework. We can now do BQSR on input, on output, or within a walker
-- PrintReads now handles all read transformers in the walker in map, enabling us to parallelize PrintReads with BAQ and BQSR
-- Currently BQSR is excepting in parallel, which subsequent commit with fix
-- Removed global variable setting in GenomeAnalysisEngine for BAQ, as command line parameters are cleanly handled by ReadTransformer infrastructure
-- In principle ReadFilters are just a special kind of ReadTransformer, but this refactoring is larger than I can do. It's a JIRA entry
-- Many files touched simply due to the refactoring and renaming of classes
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