-- Verified now to be correct at runtime
-- UnitTest covers this
-- createTypeDefault now takes a Type, not a Class, so that parameterized classes can have their parameter fetched in the defaults.
-- CombineVariants now uses the new RodBinding syntax, -V / --variants. Passed all integration tests on first run
-- Exposed gapping bug in the List<RodBinding<T>> system now fixed. ParserEngine now has a addRodBinding() that is called by RodBindingArgumentTypeDescriptor when it encounters each RodBinding. This allows the system to work with collection types that are recursively parsed by the system.
Initial version of RodBinding class.
Flow from walker Rodbinding @Arguments -> RMDTriplet (old system) -> GATK engine (standard). Will need refactoring.
Mark DePristo
Matt Hanna
David Roazen