Remove references to issue #180

Author: tomwhite

tests/test_bcftools_validation.py

@@ -50,8 +50,6 @@ def run_vcztools(args: str, expect_error=False) -> tuple[str, str]:
         # https://github.com/sgkit-dev/vcztools/issues/189
         # ("view --no-version -i 'ID == \"rs6054257\"'", "sample.vcf.gz"),
         ("view --no-version -i 'INFO/DP > 10'", "sample.vcf.gz"),
-        # Filters based on FMT values are currently disabled.
-        # https://github.com/sgkit-dev/vcztools/issues/180
         ("view --no-version -i 'FMT/DP >= 5'", "sample.vcf.gz"),
         ("view --no-version -i 'FMT/DP >= 5 && FMT/GQ > 10'", "sample.vcf.gz"),
         ("view --no-version -i 'FMT/DP >= 5 & FMT/GQ>10'", "sample.vcf.gz"),

tests/test_filter.py

@@ -70,7 +70,6 @@ class TestFilterExpressionSample:
         [
             ("POS < 1000", [1, 1, 0, 0, 0, 0, 0, 0, 1]),
             ("INFO/DP > 10", [0, 0, 1, 1, 0, 1, 0, 0, 0]),
-            # Not supporting format fields for now: #180
             (
                 "FMT/GQ > 20",
                 [
@@ -85,14 +84,76 @@ class TestFilterExpressionSample:
                     [0, 0, 0],
                 ],
             ),
-            # ("FMT/DP >= 5 && FMT/GQ > 10", [0, 0, 1, 1, 1, 0, 0, 0, 0]),
-            # ("GT > 0", [1, 1, 1, 1, 1, 0, 1, 0, 1]),
-            # ("GT > 0 & FMT/HQ >= 10", [0, 0, 1, 1, 1, 0, 0, 0, 0]),
-            # ("FMT/DP >= 5 & FMT/GQ>10", [0, 0, 1, 0, 1, 0, 0, 0, 0]),
-            # ("QUAL > 10 || FMT/GQ>10", [0, 0, 1, 1, 1, 1, 1, 0, 0]),
-            # ("(QUAL > 10 || FMT/GQ>10) && POS > 100000", [0, 0, 0, 0, 1, 1, 1, 0, 0]),
-            # ("(FMT/DP >= 8 | FMT/GQ>40) && POS > 100000",
-            #     [0, 0, 0, 0, 0, 1, 0, 0, 0]),
+            (
+                "FMT/DP >= 5 && FMT/GQ > 10",
+                [
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [1, 1, 1],
+                    [1, 1, 1],
+                    [1, 0, 1],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                ],
+            ),
+            (
+                "FMT/DP >= 5 & FMT/GQ > 10",
+                [
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 1, 1],
+                    [0, 0, 0],
+                    [1, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                ],
+            ),
+            (
+                "QUAL > 10 || FMT/GQ > 10",
+                [
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [1, 1, 1],
+                    [1, 1, 1],
+                    [1, 1, 1],
+                    [1, 1, 1],
+                    [1, 1, 1],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                ],
+            ),
+            (
+                "(QUAL > 10 || FMT/GQ > 10) && POS > 100000",
+                [
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [1, 1, 1],
+                    [1, 1, 1],
+                    [1, 1, 1],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                ],
+            ),
+            (
+                "(FMT/DP >= 8 | FMT/GQ > 40) && POS > 100000",
+                [
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [1, 1, 1],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                    [0, 0, 0],
+                ],
+            ),
         ],
     )
     def test(self, expression, expected_result):

tests/test_vcf_writer.py

@@ -222,13 +222,11 @@ def test_write_vcf__no_samples(tmp_path):
     assert v.samples == []
 
 
-# @pytest.mark.skip("Sample filtering not implemented: #180")
 @pytest.mark.parametrize(
     ("regions", "targets", "samples", "include", "expected_chrom_pos"),
     [
         # Test that sample filtering takes place after include filtering.
-        # Not supporting format fields in filtering for now: #180
-        # ("20", None, "NA00001", "FMT/GQ > 60", [("20", 1230237)]),
+        ("20", None, "NA00001", "FMT/GQ > 60", [("20", 1230237)]),
         # Test that region filtering and include expression are combined.
         ("19", None, "NA00001", "POS > 200", []),
         # Test that target filtering and include expression are combined.