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])