General fixes to the Experimental PairHMM and cleanup of the other algorithms for clarity
Bug fixes to the ExperimentalPairHMM

fixed first column of the match matrix was being wrongfully initialized with 1's
fixed indices for insertion and deletion (i and j) in updateCell
Implementation of the FourMatrices hmm

-- simple implementation not yet using 4 matrices, but created constant class for clarity
-- added to Evaluate for testing
Better implementation of the FourMatrices hmm

cleaned up the code to make it more readable