Mutation model conditioned on specific ancestral sequence

[jeromekelleher]

For some applications it will be useful to condition on a specific ancestral sequence. This should basically be the same as the MatrixMutationModel, except it takes as first parameter the ancestral_sequence. This should be a string (or maybe a numpy array) of length equal to the sequence length of the tree sequence we call mutate on. It is an error to use this mutation model if discrete is False.

We can add an option to this model also to add in sites at which no mutations occur. Ideally, I guess, we should also add in the ancestral sequence itself like SLiM does, but we don't have support for this in tskit yet, so that can wait.

I'm putting the 1.1 milestone on this for now, as there's already too much lined up for 1.0, but I'm happy to bump it up if someone would like to work on it.

[jeromekelleher]

Related: #2012