def __init__(self, tree_sequence):
self._tree_sequence = tree_sequence
self._ll_ld_calculator = _tskit.LdCalculator(
tree_sequence.get_ll_tree_sequence())
# To protect low-level C code, only one method may execute on the
# low-level objects at one time.
self._instance_lock = threading.Lock()
def test_get_r2_array(self):
ts = self.get_example_tree_sequence()
calc = _tskit.LdCalculator(ts)
self.assertRaises(TypeError, calc.get_r2_array)
self.assertRaises(TypeError, calc.get_r2_array, None)
# Doesn't support buffer protocol, so raises typeerror
self.assertRaises(TypeError, calc.get_r2_array, None, 0)
n = ts.get_num_sites()
self.assertGreater(n, 2)
with self.assertRaises(BufferError):
calc.get_r2_array(bytes(100), 0)
buff = bytearray(1024)
with self.assertRaises(ValueError):
calc.get_r2_array(buff, 0, max_distance=-1)
with self.assertRaises(ValueError):
calc.get_r2_array(buff, 0, direction=1000)
# TODO this API is poor, we should explicitly catch these negative
# size errors.
for bad_max_mutations in [-2, -3, -2**32]:
with self.assertRaises(BufferError):
calc.get_r2_array(buff, 0, max_mutations=bad_max_mutations)
for bad_start_pos in [-1, n, n + 1]:
with self.assertRaises(_tskit.LibraryError):
calc.get_r2_array(buff, bad_start_pos)
def __init__(self, tree_sequence):
self._tree_sequence = tree_sequence
self._ll_ld_calculator = _tskit.LdCalculator(
tree_sequence.get_ll_tree_sequence())
item_size = struct.calcsize('d')
self._buffer = bytearray(tree_sequence.get_num_mutations() * item_size)
# To protect low-level C code, only one method may execute on the
# low-level objects at one time.
self._instance_lock = threading.Lock()
def test_get_r2(self):
ts = self.get_example_tree_sequence()
calc = _tskit.LdCalculator(ts)
n = ts.get_num_sites()
for bad_id in [-1, n, n + 1]:
with self.assertRaises(_tskit.LibraryError):
calc.get_r2(0, bad_id)
with self.assertRaises(_tskit.LibraryError):
calc.get_r2(bad_id, 0)