def test_tree_sequence_simulated_mutations(self):
ts = msprime.simulate(20, mutation_rate=10, recombination_rate=10)
self.assertGreater(ts.get_num_trees(), 10)
ts = tsutil.subsample_sites(ts, self.num_test_sites)
self.verify_matrix(ts)
self.verify_max_distance(ts)
self.verify_max_mutations(ts)
def test_deprecated_aliases(self):
ts = msprime.simulate(20, mutation_rate=10, random_seed=15)
ts = tsutil.subsample_sites(ts, self.num_test_sites)
ldc = msprime.LdCalculator(ts)
A = ldc.get_r2_matrix()
B = ldc.r2_matrix()
self.assertTrue(np.array_equal(A, B))
a = ldc.get_r2_array(0)
b = ldc.r2_array(0)
self.assertTrue(np.array_equal(a, b))
self.assertEqual(ldc.get_r2(0, 1), ldc.r2(0, 1))
def get_tree_sequence(self):
ts = msprime.simulate(20,
mutation_rate=10,
recombination_rate=10,
random_seed=8)
return tsutil.subsample_sites(ts, self.num_test_sites)
def test_single_tree_simulated_mutations(self):
ts = msprime.simulate(20, mutation_rate=10, random_seed=15)
ts = tsutil.subsample_sites(ts, self.num_test_sites)
self.verify_matrix(ts)
self.verify_max_distance(ts)
