broadgsa/gatk-protected — pull request #9 by mlinderm (2014-08-18 23:13:02+00:00)
Title: Update extension generator to recognize RodBindingCollection as 'taggable'

The Queue wrapper for CombineVariants and other walkers that use RodBindingCollection do not pass TaggedFiles through. The issue is that RodBindingCollection is not recognized as something that could be 'tag gable'. I changed the extension generator to recognize that type and to not create Tribble index dependencies when fed a ".list" file. That latter check is unfortunately hard-coded, but so so is ".list" in the RodBindingCollection parser.