Mark DePristo 2039ce6102 Default values now displayed in arguments ... DiffEngine fixed so that newInstance() would work. Pretty quickly encountered a situation where newInstance() failed. Debug output now written when this occurs in the log. Logger now used instead of standard out, with INFO the default level.		2011-07-24 22:56:55 -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	Default values now displayed in arguments	2011-07-24 22:56:55 -04:00
test	Merge branch 'master' into NoDistributedGATK	2011-07-23 20:04:50 -04:00