def ls_viterbi_tree(h, alleles, ts, rho, mu, precision=30, use_lib=True):
"""
Viterbi path computation based on a tree sequence.
"""
if use_lib:
acgt_alleles = tuple(alleles) == tskit.ALLELES_ACGT
ls_hmm = _tskit.LsHmm(
ts.ll_tree_sequence, recombination_rate=rho, mutation_rate=mu,
precision=precision, acgt_alleles=acgt_alleles)
vm = _tskit.ViterbiMatrix(ts.ll_tree_sequence)
ls_hmm.viterbi_matrix(h, vm)
return vm
else:
va = ViterbiAlgorithm(ts, rho, mu, alleles, precision=precision)
return va.run(h)
def ls_forward_tree(h, alleles, ts, rho, mu, precision=30, use_lib=True):
"""
Forward matrix computation based on a tree sequence.
"""
if use_lib:
acgt_alleles = tuple(alleles) == tskit.ALLELES_ACGT
ls_hmm = _tskit.LsHmm(
ts.ll_tree_sequence, recombination_rate=rho, mutation_rate=mu,
precision=precision, acgt_alleles=acgt_alleles)
cm = _tskit.CompressedMatrix(ts.ll_tree_sequence)
ls_hmm.forward_matrix(h, cm)
return cm
else:
fa = ForwardAlgorithm(ts, rho, mu, alleles, precision=precision)
return fa.run(h)