Removal of purely homozygous loci valid?

[OJWatson]

Perhaps we should not immediately remove loci with only homozygous calls in these lines?

	##remove sites and individuals with too much missing data
	simpleS = data[In_ind,]
	simpleS = simpleS[,In_site]
	
	##remove sites with P=0 or 1
	P=rep(NA, ncol(simpleS))
	for (j in (1:ncol(simpleS))){
		temp= simpleS[,j]
		P[j]= (sum(temp==1) + 0.5*sum(temp!=0 & temp!=1& temp!=-1))/sum(temp!=-1)
	}
	In = (P!=Inf & P!="NaN" & P!=0 & P!=1)
	simpleS2= simpleS[, In]
	
	select_pos =colnames(data)[In_site][In]
	select_ind = rownames(data)[In_ind]

Perhaps it might be better to throw a warning for the user to be aware they will be removed from following MCMC, or throw an error that then prompts users to specify an additional function argument in order to force their inclusion.