Remove deprecated variables in ShortReadsSpectrumLikelihood.java
Refactoring shortReadLikelihood, creating abstractShortReadSpectrumLikelihood
fix import bugs
adding abstractShortReadSpectrumLikelihood and categoriesSpectrumLikelihood
renaming package, moved from haplotype/spectrum.likelihood to likelihood.spectrum/halpotype
Refactoring, going to create the new Haplotype/HaplotypeModel data structure
OldHayplotyp MCMC can run again, might break a few things
A lot of refactoring, shoulde be multiple commit
Attempt to use spectrum code for haplotype calculation
Factor out abstract alignmentModel
minor bug fix
Refactoring data structure
JUnit for Haplotype
Refactor old haplotype operator to operator.haplotype.old package
Implemented single operator
Implemented multi operator
fix bugs created from operator.haplotype.old
fix bugs created from operator.haplotype.old
Make ShortReadLikelihood @Depracated.
Implemented baseSingleOperator and unittest
Modified main() to run HaplotypeModel
Change ArrayList<Haplotype> to Haplotype[]
Update HaplotypeModel to new data structure
Implementing shortReadLikelihood