def test_count_call_alleles__chunked():
rs = np.random.RandomState(0)
calls = rs.randint(0, 1, size=(50, 10, 2))
ds = get_dataset(calls)
ac1 = count_call_alleles(ds)
# Coerce from numpy to multiple chunks in all dimensions
ds["call_genotype"] = ds["call_genotype"].chunk(chunks=(5, 5, 1)) # type: ignore[arg-type]
ac2 = count_call_alleles(ds)
xr.testing.assert_equal(ac1, ac2) # type: ignore[no-untyped-call]
def test_count_call_alleles__chunked():
rs = np.random.RandomState(0)
calls = rs.randint(0, 1, size=(50, 10, 2))
ds = get_dataset(calls)
ac1 = count_call_alleles(ds)
# Coerce from numpy to multiple chunks in all dimensions
ds["call_genotype"] = ds["call_genotype"].chunk(chunks=(5, 5, 1))
ac2 = count_call_alleles(ds)
assert isinstance(ac2["call_allele_count"].data, da.Array)
xr.testing.assert_equal(ac1, ac2)
def test_count_call_alleles__higher_ploidy():
ds = count_call_alleles(
get_dataset(
[
[[-1, -1, 0], [-1, -1, 1], [-1, -1, 2]],
[[0, 1, 2], [1, 2, 3], [-1, -1, -1]],
],
n_allele=4,
n_ploidy=3,
))
ac = ds["call_allele_count"]
np.testing.assert_equal(
ac,
np.array([
[[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0]],
[[1, 1, 1, 0], [0, 1, 1, 1], [0, 0, 0, 0]],
]),
)
def test_count_call_alleles__missing_data():
ds = count_call_alleles(
get_dataset([
[[-1, -1], [-1, -1], [-1, -1]],
[[-1, -1], [0, 0], [-1, 1]],
[[1, 1], [-1, -1], [-1, 0]],
[[1, 1], [1, 1], [1, 1]],
]))
ac = ds["call_allele_count"]
np.testing.assert_equal(
ac,
np.array([
[[0, 0], [0, 0], [0, 0]],
[[0, 0], [2, 0], [0, 1]],
[[0, 2], [0, 0], [1, 0]],
[[0, 2], [0, 2], [0, 2]],
]),
)
def test_count_call_alleles__multi_variant_multi_sample():
ds = count_call_alleles(
get_dataset([
[[0, 0], [0, 0], [0, 0]],
[[0, 0], [0, 0], [0, 1]],
[[1, 1], [0, 1], [1, 0]],
[[1, 1], [1, 1], [1, 1]],
]))
ac = ds["call_allele_count"]
np.testing.assert_equal(
ac,
np.array([
[[2, 0], [2, 0], [2, 0]],
[[2, 0], [2, 0], [1, 1]],
[[0, 2], [1, 1], [1, 1]],
[[0, 2], [0, 2], [0, 2]],
]),
)
def test_count_call_alleles__single_variant_single_sample():
ds = count_call_alleles(get_dataset([[[1, 0]]]))
ac = ds["call_allele_count"]
np.testing.assert_equal(ac, np.array([[[1, 1]]]))
