[qob] Fix IBD and enable tests

hail/python/hail/methods/relatedness/identity_by_descent.py

@@ -147,7 +147,7 @@ def identity_by_descent(dataset, maf=None, bounded=True, min=None, max=None) ->
         _e00=(2 * (p**2) * (q**2) * ((X - 1) / X) * ((Y - 1) / Y) * (T / (T - 1)) * (T / (T - 2)) * (T / (T - 3))),
         _e10=(
             4 * (p**3) * q * ((X - 1) / X) * ((X - 2) / X) * (T / (T - 1)) * (T / (T - 2)) * (T / (T - 3))
-            + 4 * p * (q**3) * ((Y - 1) / X) * ((Y - 2) / X) * (T / (T - 1)) * (T / (T - 2)) * (T / (T - 3))
+            + 4 * p * (q**3) * ((Y - 1) / Y) * ((Y - 2) / Y) * (T / (T - 1)) * (T / (T - 2)) * (T / (T - 3))
         ),
         _e20=(
             (p**4) * ((X - 1) / X) * ((X - 2) / X) * ((X - 3) / X) * (T / (T - 1)) * (T / (T - 2)) * (T / (T - 3))
@@ -164,7 +164,7 @@ def identity_by_descent(dataset, maf=None, bounded=True, min=None, max=None) ->
             + (p**2) * q * ((X - 1) / X) * (T / (T - 1)) * (T / (T - 2))
             + p * (q**2) * ((Y - 1) / Y) * (T / (T - 1)) * (T / (T - 2))
         ),
-        _e22=(T / 2),
+        _e22=1,
     )
 
     dataset = dataset.checkpoint(hl.utils.new_temp_file())

hail/python/test/hail/methods/relatedness/test_identity_by_descent.py

@@ -5,12 +5,19 @@
 
 import hail as hl
 import hail.utils as utils
-from ...helpers import get_dataset, test_timeout, qobtest
+from ...helpers import test_timeout, qobtest
 
 
-def plinkify(ds, min=None, max=None):
+@pytest.fixture(scope='module')
+def ds():
+    dataset = hl.balding_nichols_model(1, 100, 100)
+    dataset = dataset.key_cols_by(s=hl.str(dataset.sample_idx + 1))
+    return dataset
+
+
+def plinkify(dataset, min=None, max=None):
     vcf = utils.new_temp_file(prefix="plink", extension="vcf")
-    hl.export_vcf(ds, vcf)
+    hl.export_vcf(dataset, vcf)
 
     local_tmpdir = utils.new_local_temp_dir()
     plinkpath = f'{local_tmpdir}/plink-ibd'
@@ -45,9 +52,7 @@ def plinkify(ds, min=None, max=None):
 @qobtest
 @unittest.skipIf('HAIL_TEST_SKIP_PLINK' in os.environ, 'Skipping tests requiring plink')
 @test_timeout(local=10 * 60, batch=10 * 60)
-def test_ibd_default_arguments():
-    ds = get_dataset()
-
+def test_ibd_default_arguments(ds):
     plink_results = plinkify(ds)
     hail_results = hl.identity_by_descent(ds).collect()
 
@@ -62,11 +67,10 @@ def test_ibd_default_arguments():
         assert plink_results[key][1][2] == row.ibs2
 
 
+@qobtest
 @unittest.skipIf('HAIL_TEST_SKIP_PLINK' in os.environ, 'Skipping tests requiring plink')
 @test_timeout(local=10 * 60, batch=10 * 60)
-def test_ibd_0_and_1():
-    ds = get_dataset()
-
+def test_ibd_0_and_1(ds):
     plink_results = plinkify(ds, min=0.0, max=1.0)
     hail_results = hl.identity_by_descent(ds).collect()
 
@@ -81,15 +85,15 @@ def test_ibd_0_and_1():
         assert plink_results[key][1][2] == row.ibs2
 
 
+@qobtest
 @test_timeout(local=10 * 60, batch=10 * 60)
-def test_ibd_does_not_error_with_dummy_maf_float64():
-    dataset = get_dataset()
-    dataset = dataset.annotate_rows(dummy_maf=0.01)
-    hl.identity_by_descent(dataset, dataset['dummy_maf'], min=0.0, max=1.0)
+def test_ibd_does_not_error_with_dummy_maf_float64(ds):
+    ds = ds.annotate_rows(dummy_maf=0.01)
+    hl.identity_by_descent(ds, ds['dummy_maf'], min=0.0, max=1.0)
 
 
+@qobtest
 @test_timeout(local=10 * 60, batch=10 * 60)
-def test_ibd_does_not_error_with_dummy_maf_float32():
-    dataset = get_dataset()
-    dataset = dataset.annotate_rows(dummy_maf=0.01)
-    hl.identity_by_descent(dataset, hl.float32(dataset['dummy_maf']), min=0.0, max=1.0)
+def test_ibd_does_not_error_with_dummy_maf_float32(ds):
+    ds = ds.annotate_rows(dummy_maf=0.01)
+    hl.identity_by_descent(ds, hl.float32(ds['dummy_maf']), min=0.0, max=1.0)