Eric Banks 4bb7a99f08 Given that all classes implementing output stubs already have getters for the underlying OutputStream and File, it makes sense to unify that functionality into the Stub interface. Now it is possible to have an Engine utility method that iterates over all registered stubs to find the one representing a given OutputStream and return the File associated with it.		2012-09-12 11:51:44 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Given that all classes implementing output stubs already have getters for the underlying OutputStream and File, it makes sense to unify that functionality into the Stub interface. Now it is possible to have an Engine utility method that iterates over all registered stubs to find the one representing a given OutputStream and return the File associated with it.	2012-09-12 11:51:44 -04:00
test	VCF/BCF writers once again automatically write out no-call genotypes for samples in the VCFHeader but not in the VC itself	2012-09-12 06:46:26 -04:00