def test_pack_unpack_diploid(self):
"""Check that genotypes survive pack/unpack round trip."""
genotypes = np.array([[[0, 0], [0, 1]],
[[1, 1], [-1, -1]],
[[6, 6], [7, 7]],
[[10, 10], [14, 14]]], dtype='i1')
packed = pack_diploid(genotypes)
self.assertEqual(BHOM00, packed[0, 0])
self.assertEqual(BHET01, packed[0, 1])
self.assertEqual(BHOM11, packed[1, 0])
self.assertEqual(BMISSING, packed[1, 1])
actual = unpack_diploid(packed)
self.assertTrue(np.array_equal(genotypes, actual))
def test_pack_diploid_ref_zero(self):
"""Check that hom ref calls are encoded as 0 for sparse matrices."""
genotypes = np.array([[[0, 0]]], dtype='i1')
packed = pack_diploid(genotypes)
self.assertEqual(0, packed[0, 0])
