Improve test coverage

sgkit-dev · Jul 16, 2024 · a8fd845 · a8fd845
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Showing 7 changed files with 19 additions and 9 deletions.
diff --git a/tests/data/vcf/local_alleles.vcf.gz b/tests/data/vcf/local_alleles.vcf.gz
diff --git a/tests/data/vcf/local_alleles.vcf.gz.csi b/tests/data/vcf/local_alleles.vcf.gz.csi
diff --git a/tests/data/vcf/triploid2.vcf.gz b/tests/data/vcf/triploid2.vcf.gz
diff --git a/tests/data/vcf/triploid2.vcf.gz.csi b/tests/data/vcf/triploid2.vcf.gz.csi
diff --git a/tests/data/vcf/triploid3.vcf.gz b/tests/data/vcf/triploid3.vcf.gz
diff --git a/tests/data/vcf/triploid3.vcf.gz.csi b/tests/data/vcf/triploid3.vcf.gz.csi
diff --git a/tests/test_vcf_examples.py b/tests/test_vcf_examples.py
@@ -452,6 +452,8 @@ def test_call_LAA(self, ds):
             [[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]],
         ]
         nt.assert_array_equal(ds.call_LAA.values, call_LAA)
 
@@ -493,29 +495,37 @@ def test_call_LPL(self, ds):
                 [30, 30, 30, -2, -2, -2, -2, -2, -2, -2],
                 [30, -1, 0, -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, -1, -2, -2, -2, -2, -2, -2, -2, -2],
+                [-1, -1, -2, -2, -2, -2, -2, -2, -2, -2],
+            ],
         ]
         nt.assert_array_equal(ds.call_LPL.values, call_LPL)
 
 
 class TestTriploidExample:
-    data_path = "tests/data/vcf/triploid.vcf.gz"
-
-    @pytest.fixture(scope="class")
-    def ds(self, tmp_path_factory):
+    @pytest.fixture(scope="class", params=["triploid", "triploid2", "triploid3"])
+    def ds(self, tmp_path_factory, request):
+        data_path = f"tests/data/vcf/{request.param}.vcf.gz"
         out = tmp_path_factory.mktemp("data") / "example.vcf.zarr"
-        vcf2zarr.convert([self.data_path], out, local_alleles=False)
+        vcf2zarr.convert([data_path], out, local_alleles=False)
         return sg.load_dataset(out)
 
-    def test_error_with_local_alleles(self, tmp_path_factory):
-        icf_path = tmp_path_factory.mktemp("data") / "triploid.icf"
+    @pytest.mark.parametrize("name", ["triploid", "triploid2", "triploid3"])
+    def test_error_with_local_alleles(self, tmp_path_factory, name):
+        data_path = f"tests/data/vcf/{name}.vcf.gz"
+        icf_path = tmp_path_factory.mktemp("data") / f"{name}.icf"
         with pytest.raises(ValueError, match=re.escape("Cannot handle ploidy = 3")):
             vcf2zarr.explode(
-                icf_path, [self.data_path], worker_processes=0, local_alleles=True
+                icf_path, [data_path], worker_processes=0, local_alleles=True
             )
 
     def test_ok_without_local_alleles(self, ds):
         nt.assert_array_equal(ds.call_genotype.values, [[[0, 0, 0]]])
-        nt.assert_array_equal(ds.call_PL.values, [[[0, 0, 0, 0]]])
 
 
 class Test1000G2020Example: