Tested boolean operator precedence is correct

Author: jeromekelleher

tests/test_bcftools_validation.py

@@ -204,6 +204,32 @@ def test_query_arithmethic(tmp_path, expr):
     assert vcztools_output == "112\n"
 
 
+@pytest.mark.parametrize(
+    "expr",
+    [
+        # Check boolean logic evaluation. Will evaluate this with
+        # POS=112, so POS=112 is True and POS!=112 is False
+        "POS==112 || POS!=112",  # True
+        "POS==112 && POS!=112",  # True
+        "POS==112 || POS!=112 && POS!= 112",  # True
+        "(POS==112 || POS!=112) && POS!= 112",  # False
+    ],
+)
+def test_query_logic_precendence(tmp_path, expr):
+
+    args = r"query -f '%POS\n'" + f" -i 'POS=112 && ({expr})'"
+    vcf_name = "sample.vcf.gz"
+    vcf_path = pathlib.Path("tests/data/vcf") / vcf_name
+    vcz_path = vcz_path_cache(vcf_path)
+
+    bcftools_output, _ = run_bcftools(f"{args} {vcf_path}")
+    vcztools_output, _ = run_vcztools(f"{args} {vcz_path}")
+
+    assert vcztools_output == bcftools_output
+    num_lines = len(list(vcztools_output.splitlines()))
+    assert num_lines in [0, 1]
+
+
 @pytest.mark.parametrize(
     ("args", "vcf_name"),
     [

tests/test_filter.py

@@ -220,6 +220,9 @@ def test_boolean_operator_expressions(self, expr, expected):
             ("a | b", {"a": [0, 1], "b": [1, 1]}, [True, True]),
             ("a || b", {"a": [0, 1], "b": [1, 1]}, [True, True]),
             ("(a < 2) & (b > 1)", {"a": [0, 1], "b": [1, 2]}, [False, True]),
+            # AND has precedence over OR
+            ("t | f & f", {"t": [1], "f": [0]}, [True or False and False]),
+            ("(t | f) & f", {"t": [1], "f": [0]}, [(True or False) and False]),
         ],
     )
     def test_boolean_operator_expressions_data(self, expr, data, expected):

vcztools/retrieval.py

@@ -1,6 +1,9 @@
 import collections.abc
 
 
+# NOTE:  this class is just a skeleton for now. The idea is that this
+# will provide readahead, caching etc, and will be the central location
+# for fetching bulk Zarr data.
 class VariantChunkReader(collections.abc.Sequence):
     """
     Retrieve data from a Zarr store and return chunk-by-chunk in the