added regularization by the minimal possible clonality (on number of cloens seen) to the diagonal of the n by n matrix. Also, added a way by which the n by n covariance diagonals can be directly specified by the user. also, backward compatibility is broken, as I renamed the variance codes yet again. Also added a new variacne code where I use theta + (t(X) %*% X - theta)^+ as the diagonals of the n by n.