In function returnPunnetValues if the value of the cell is 0,
add .00001 so as to avoid log(0) computations from being attempted
later on by pgmsnp. I know this is not perfect, but its best hack
I could come up with.

Added function generateAllReferenceGenotypesAssignment:
return the genotype assignment of all samples being homoz_ref
Altered the following:
Call ExpFactorNormalize for the GLFactor
When calling ComputeExactMarginalsBP will also return the joint distribution factor

Computes the QUAL value from the joint distirbution by figuring out what the
homozygous genotype is and computing what assignment this corresponds to in the
joint distrbution factor's value array. The error prob. in this case is
eveyrone being homoz ref, and we phred scale this probablity.