David Roazen 932cd3ada7 Fix 3rd-party library dependency issues in the HC/PairHMM tests ... In general, test classes cannot use 3rd-party libraries that are not also dependencies of the GATK proper without causing problems when, at release time, we test that the GATK jar has been packaged correctly with all required dependencies. If a test class needs to use a 3rd-party library that is not a GATK dependency, write wrapper methods in the GATK utils/* classes, and invoke those wrapper methods from the test class.		2013-12-06 13:16:55 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Fix 3rd-party library dependency issues in the HC/PairHMM tests	2013-12-06 13:16:55 -05:00
test	Throw a GVCFIndexException when the user doesn't specify the optimal indexing strategy	2013-12-03 23:12:14 -05:00