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
..
net/sf	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00
org/broadinstitute	Complete rewrite of low-level machinery of LIBS, not hooked up	2013-01-11 15:17:16 -05:00