TreeLikelihoodExt auto update
ShortReadLikelihood auto updating
Add/Fix swapInfo
Add several operators
 - single/mutli base swap
 - single/multi base swap with equal probability
 - Recombination
 - Section swap
Add HaplotypeLogger
Working copy
 - Add SwapBaseEmpiricalOperator
Coerable operator working
srpLikelihood handles multiple base swap - still slow
Remove old files
Remove LikelihoodCalculation.java and related class
- Remove 3 initial benchmark class, jar files
faster srp likelihood: only calculate delta changes between each operation
Fast way (5x+) to calculate likelihood for multiple swaps. Only implements in uniformOperators (others break at moment). Need to update others.
Potentially can be even faster
Build MainMCMCFull_130516.jar
Running on DSCR with 7 haplotypes
with full tree search
high(ish) weight on srp operators
fixed various bugs, optimize weights
-MainMCMCFull_130603.jar
fix unittest
merge
fix merging errors
fix unittest files