Update unit tests

sgkit-dev · Oct 25, 2024 · d52069b · d52069b
1 parent 65c6963
commit d52069b
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Showing 2 changed files with 21 additions and 115 deletions.
diff --git a/bio2zarr/vcf2zarr/icf.py b/bio2zarr/vcf2zarr/icf.py
@@ -598,6 +598,7 @@ def compute_lpl_field(variant, laa_val: np.ndarray) -> np.ndarray:
         pl_val = np.broadcast_to(pl_val, n.shape)
     row_index = np.arange(pl_val.shape[0]).reshape(-1, 1)
     lpl_val = pl_val[row_index, n]
+    lpl_val[b == constants.INT_FILL] = constants.INT_FILL
 
     return lpl_val
 

diff --git a/tests/test_vcf_examples.py b/tests/test_vcf_examples.py
@@ -446,41 +446,41 @@ def ds(self, tmp_path_factory):
 
     def test_call_LAA(self, ds):
         call_LAA = [
-            [[1, -2, -2], [1, -2, -2]],
-            [[1, -2, -2], [1, -2, -2]],
-            [[1, 2, -2], [1, 2, -2]],
+            [[1, -2, -2], [-2, -2, -2]],
+            [[-2, -2, -2], [1, -2, -2]],
+            [[1, -2, -2], [2, -2, -2]],
             [[1, 2, 3], [2, 3, -2]],
-            [[1, -2, -2], [1, -2, -2]],
-            [[2, -2, -2], [1, -2, -2]],
+            [[-2, -2, -2], [-2, -2, -2]],
+            [[-2, -2, -2], [1, -2, -2]],
             [[1, -2, -2], [-1, -2, -2]],
             [[2, -2, -2], [2, -2, -2]],
-            [[1, -2, -2], [-2, -2, -2]],
             [[-2, -2, -2], [-2, -2, -2]],
-            [[1, -2, -2], [1, -2, -2]],
+            [[-2, -2, -2], [-2, -2, -2]],
+            [[-2, -2, -2], [1, -2, -2]],
         ]
         nt.assert_array_equal(ds.call_LAA.values, call_LAA)
 
     def test_call_LPL(self, ds):
         call_LPL = [
             [
                 [100, 0, 105, -2, -2, -2, -2, -2, -2, -2],
-                [0, 100, 200, -2, -2, -2, -2, -2, -2, -2],
+                [0, -2, -2, -2, -2, -2, -2, -2, -2, -2],
             ],
             [
-                [0, 100, 200, -2, -2, -2, -2, -2, -2, -2],
+                [0, -2, -2, -2, -2, -2, -2, -2, -2, -2],
                 [154, 22, 0, -2, -2, -2, -2, -2, -2, -2],
             ],
             [
-                [1002, 55, 1002, 0, 55, 1002, -2, -2, -2, -2],
-                [154, 154, 0, 154, 102, 102, -2, -2, -2, -2],
+                [1002, 55, 1002, -2, -2, -2, -2, -2, -2, -2],
+                [154, 154, 102, -2, -2, -2, -2, -2, -2, -2],
             ],
             [
                 [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
                 [-1, -1, -1, -1, -1, -1, -1, -1, -1, -1],
             ],
             [
-                [30, 30, 30, -2, -2, -2, -2, -2, -2, -2],
-                [30, 60, 0, -2, -2, -2, -2, -2, -2, -2],
+                [30, -2, -2, -2, -2, -2, -2, -2, -2, -2],
+                [30, -2, -2, -2, -2, -2, -2, -2, -2, -2],
             ],
             [
                 [0, 30, -2, -2, -2, -2, -2, -2, -2, -2],
@@ -495,12 +495,12 @@ def test_call_LPL(self, ds):
                 [10, 40, 60, -2, -2, -2, -2, -2, -2, -2],
             ],
             [
-                [30, 30, 30, -2, -2, -2, -2, -2, -2, -2],
-                [30, -1, 0, -2, -2, -2, -2, -2, -2, -2],
+                [30, -2, -2, -2, -2, -2, -2, -2, -2, -2],
+                [30, -2, -2, -2, -2, -2, -2, -2, -2, -2],
             ],
             [
-                [-1, -1, -1, -2, -2, -2, -2, -2, -2, -2],
-                [-1, -1, -1, -2, -2, -2, -2, -2, -2, -2],
+                [-1, -2, -2, -2, -2, -2, -2, -2, -2, -2],
+                [-1, -2, -2, -2, -2, -2, -2, -2, -2, -2],
             ],
             [
                 [-1, -1, -2, -2, -2, -2, -2, -2, -2, -2],
@@ -637,107 +637,12 @@ def test_call_AD(self, ds):
         nt.assert_array_equal(ds.call_AD.values, call_AD)
 
     def test_call_LAA(self, ds):
-        call_LAA = [
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, 2, -2, -2], [1, 2, -2, -2], [1, 2, -2, -2]],
-            [[1, 2, 3, -2], [1, 2, 3, -2], [1, 2, 3, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]],
-            [[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]],
-            [[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]],
-            [[1, 2, 3, -2], [1, 2, 3, -2], [1, 2, 3, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, 2, -2, -2], [1, 2, -2, -2], [1, 2, -2, -2]],
-            [[1, -2, -2, -2], [1, -2, -2, -2], [1, -2, -2, -2]],
-            [[1, 2, -2, -2], [1, 2, -2, -2], [1, 2, -2, -2]],
-            [[1, 2, 3, -2], [1, 2, 3, -2], [1, 2, 3, -2]],
-            [[1, 2, 3, 4], [1, 2, 3, 4], [1, 2, 3, 4]],
-            [[1, 2, 3, -2], [1, 2, 3, -2], [1, 2, 3, -2]],
-        ]
+        # All the genotypes are 0/0
+        call_LAA = np.full((23, 3, 1), -2)
         nt.assert_array_equal(ds.call_LAA.values, call_LAA)
 
     def test_call_LPL(self, ds):
-        # fmt: off
-        call_LPL = [
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]],  # noqa: E501
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800],  # noqa: E501
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800],  # noqa: E501
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]],  # noqa: E501
-            [[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800],  # noqa: E501
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800],  # noqa: E501
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]],  # noqa: E501
-            [[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800],  # noqa: E501
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800],  # noqa: E501
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]],  # noqa: E501
-            [[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]],  # noqa: E501
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, -2, -2, -2, -2, -2, -2, -2, -2, -2]],
-            [[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]],  # noqa: E501
-            [[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800],  # noqa: E501
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800],  # noqa: E501
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, 120, 1800, 1800, 1800, 1800]],  # noqa: E501
-            [[0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2],
-             [0, 120, 1800, 120, 1800, 1800, 120, 1800, 1800, 1800, -2, -2, -2, -2, -2]]
-        ]
-        # fmt: on
+        call_LPL = np.tile([0, -2, -2], (23, 3, 1))
         nt.assert_array_equal(ds.call_LPL.values, call_LPL)
 
     def test_call_PID(self, ds):