We created two source files (datafile and pedfile) with a small pedigree.
Next, we performed the backward phase, where we eliminate the variables in the following order: pl_1, ml_1, pl_3, pl_4, ml_4, pl_5, ml_5, ps_3, ms_3, ps_5, ms_5. During the elimination process we calculated the combined functions and the arg_max for each of the variables. The expected results as we calculated can be seen in the excel file.
The haplotyping query results (the assignment and the probability) matched the results that we expected from our calculations.
Haplotyping query results with K=6.
Haplotyping query results with K=6, epsilon=10.