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)