Mark DePristo 2c38310868 Create LIBS using new AlignmentStateMachine infrastructure ... -- Optimizations to AlignmentStateMachine -- Properly count deletions. Added unit test for counting routines -- AlignmentStateMachine.java is no longer recursive -- Traversals now use new LIBS, not the old one		2013-01-11 15:17:17 -05:00
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java	Create LIBS using new AlignmentStateMachine infrastructure	2013-01-11 15:17:17 -05:00