Mark DePristo 80d9b7011c Complete rewrite of low-level machinery of LIBS, not hooked up ... -- AlignmentStateMachine does what SAMRecordAlignmentState should really do. It's correct in that it's more accurate than the LIB_position tests themselves. This is a non-broken, correct implementation. Needs cleanup, contracts, etc. -- This version is like 6x slower than the original implementation (according to the google caliper benchmark here). Obvious optimizations for future commit		2013-01-11 15:17:16 -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	Complete rewrite of low-level machinery of LIBS, not hooked up	2013-01-11 15:17:16 -05:00
test	Complete rewrite of low-level machinery of LIBS, not hooked up	2013-01-11 15:17:16 -05:00