def __init__(self, tree_sequence, breakpoints=None):
self._tree_sequence = tree_sequence
self._sites = []
# TODO this code here is expressed in terms of the low-level
# tree sequence for legacy reasons. It probably makes more sense
# to describe it in terms of the tables now if we want to have an
# independent implementation.
ll_ts = self._tree_sequence._ll_tree_sequence
def make_mutation(id_):
site, node, derived_state, parent, metadata = ll_ts.get_mutation(id_)
return tskit.Mutation(
id_=id_,
site=site,
node=node,
derived_state=derived_state,
parent=parent,
metadata=metadata,
)
for j in range(tree_sequence.num_sites):
pos, ancestral_state, ll_mutations, id_, metadata = ll_ts.get_site(j)
self._sites.append(
tskit.Site(
id_=id_,
position=pos,
ancestral_state=ancestral_state,
mutations=[make_mutation(ll_mut) for ll_mut in ll_mutations],
metadata=metadata,
)
)
def __init__(self, tree_sequence, breakpoints=None):
self._tree_sequence = tree_sequence
self._num_samples = tree_sequence.get_num_samples()
self._breakpoints = breakpoints
self._sites = []
def make_mutation(id_):
site, node, derived_state, parent, metadata = tree_sequence.get_mutation(
id_)
return tskit.Mutation(id_=id_,
site=site,
node=node,
derived_state=derived_state,
parent=parent,
metadata=metadata)
for j in range(tree_sequence.get_num_sites()):
pos, ancestral_state, ll_mutations, id_, metadata = tree_sequence.get_site(
j)
self._sites.append(
tskit.Site(id_=id_,
position=pos,
ancestral_state=ancestral_state,
mutations=[
make_mutation(ll_mut) for ll_mut in ll_mutations
],
metadata=metadata))