Mask VCF missing rather than fill values

Closes sgkit-dev#1196

sgkit/io/vcf/vcf_writer_utils.py

@@ -494,16 +494,16 @@ def vcf_genotypes_to_byte_buf_size(call_genotype):
 
 
 def create_mask(arr):
-    """Return a mask array of shape ``arr.shape[0]` for masking out fill values."""
+    """Return a mask array of shape ``arr.shape[0]` for masking out missing values."""
     axis = tuple(range(1, len(arr.shape)))
     if arr.dtype == bool:
         return ~arr
     elif arr.dtype in (np.int8, np.int16, np.int32):
-        return np.all(arr == INT_FILL, axis=axis)
+        return np.all(arr == INT_MISSING, axis=axis)
     elif arr.dtype == np.float32:
-        return np.all(arr.view("i4") == FLOAT32_FILL_AS_INT32, axis=axis)
+        return np.all(arr.view("i4") == FLOAT32_MISSING_AS_INT32, axis=axis)
     elif arr.dtype.kind == "S":
-        return np.all(arr == STR_FILL_BYTE, axis=axis)
+        return np.all(arr == STR_MISSING_BYTE, axis=axis)
     else:
         raise ValueError(f"Unsupported dtype: {arr.dtype}")
 

sgkit/tests/io/vcf/test_vcf_writer.py

@@ -73,7 +73,6 @@ def test_zarr_to_vcf(shared_datadir, tmp_path, output_is_path):
     )
 
 
-@pytest.mark.skip("Temporarily disabling pending bugfix; #1196")
 @pytest.mark.parametrize("in_memory_ds", [True, False])
 @pytest.mark.filterwarnings(
     "ignore::sgkit.io.vcfzarr_reader.DimensionNameForFixedFormatFieldWarning",