Mark DePristo b3ecfbfce8 Refactor LIBS into component parts, expand unit tests, some code cleanup ... -- Split out all of the inner classes of LIBS into separate independent classes -- Split / add unit tests for many of these components. -- Radically expand unit tests for SAMRecordAlignmentState (the lowest level piece of code) making sure at least some of it works -- No need to change unit tests or integration tests. No change in functionality. -- Added (currently disabled) code to track all submitted reads to LIBS, but this isn't accessible or tested		2013-01-11 15:17:16 -05:00
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net/sf	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
org/broadinstitute	Refactor LIBS into component parts, expand unit tests, some code cleanup	2013-01-11 15:17:16 -05:00