def test_ssl2ihh_a():
# 2 haplotypes, 1 pair
ssl = np.array([3], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = (4 * (1 + 1) / 2) + (2 * (1 + 1) / 2) + (1 * (1 + 0) / 2)
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
eq(expect, actual)
def test_ssl2ihh_h():
# 3 haplotypes, 3 pairs
ssl = np.array([0, 1, 3], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0.5
expect = 4 * (2 / 3 + 1 / 3) / 2
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
eq(expect, actual)
def test_ssl2ihh_f():
# 2 haplotypes, 1 pair
# never falls to min_ehh
ssl = np.array([4], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
assert np.isnan(actual), actual
def test_ssl2ihh_h():
# 3 haplotypes, 3 pairs
ssl = np.array([0, 1, 3], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0.5
expect = 4 * (2/3 + 1/3) / 2
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
eq(expect, actual)
def test_ssl2ihh_f():
# 2 haplotypes, 1 pair
# never falls to min_ehh
ssl = np.array([4], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
assert np.isnan(actual), actual
def test_ssl2ihh_a():
# 2 haplotypes, 1 pair
ssl = np.array([3], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = (4 * (1 + 1) / 2) + (2 * (1 + 1) / 2) + (1 * (1 + 0) / 2)
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
eq(expect, actual)
def test_ssl2ihh_g():
# 2 haplotypes, 1 pair
# never falls to min_ehh, but include_edges
ssl = np.array([4], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = (4 + 2 + 1)
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh, include_edges=True)
eq(expect, actual)
def test_ssl2ihh_e():
# 2 haplotypes, 1 pair
# no matches beyond current variant
ssl = np.array([1], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = 4 * (1 + 0) / 2
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
eq(expect, actual)
def test_ssl2ihh_d():
# 3 haplotypes, 3 pairs
ssl = np.array([0, 1, 3], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = (4 * (2/3 + 1/3) / 2) + (2 * (1/3 + 1/3) / 2) + \
(1 * (1/3 + 0) / 2)
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
eq(expect, actual)
def test_ssl2ihh_c():
# 3 haplotypes, 3 pairs
ssl = np.array([3, 2, 1], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = (4 * (1 + 2/3) / 2) + (2 * (2/3 + 1/3) / 2) + \
(1 * (1/3 + 0) / 2)
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
assert expect == actual
def test_ssl2ihh_g():
# 2 haplotypes, 1 pair
# never falls to min_ehh, but include_edges
ssl = np.array([4], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = (4 + 2 + 1)
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh, include_edges=True)
eq(expect, actual)
def test_ssl2ihh_e():
# 2 haplotypes, 1 pair
# no matches beyond current variant
ssl = np.array([1], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = 4 * (1 + 0) / 2
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
eq(expect, actual)
def test_ssl2ihh_d():
# 3 haplotypes, 3 pairs
ssl = np.array([0, 1, 3], dtype='i4')
gaps = np.array([1, 2, 4], dtype='f8')
vidx = 3
min_ehh = 0
expect = (4 * (2/3 + 1/3) / 2) + (2 * (1/3 + 1/3) / 2) + \
(1 * (1/3 + 0) / 2)
actual = ssl2ihh(ssl, max(ssl), vidx, gaps, min_ehh)
eq(expect, actual)