Support multiple alleles

[jeromekelleher]

In the simplest case, the reference panel can contain values > 1. Initial version can assume that mutation rates among the k existing alleles are equal. We should keep the possibility open of providing arbitrary transition matrix between states.

May be as easy to do in the first pass as a kxk uniform transition matrix that we create, and then worry about making a parameter later.

[astheeggeggs]

we currently consider the simplest case, whereby multiple alleles are allowed at a given site but where mutation probabilities to each are equal.

[szhan]

It should be now easy to switch the emission probability matrix to support multiple alleles.