Fixes following https://github.com/pystatgen/sgkit/issues/81

Author: tomwhite

sgkit/io/vcfzarr_reader.py

@@ -75,7 +75,7 @@ def max_str_len(arr: ArrayLike) -> Any:
     )
 
     # Add a mask for variant ID
-    ds["variant/id_mask"] = (
+    ds["variant_id_mask"] = (
         [DIM_VARIANT],
         variants_id == ".",
     )

sgkit/tests/test_vcfzarr_reader.py

@@ -16,13 +16,13 @@ def test_read_vcfzarr(shared_datadir):
     ds = read_vcfzarr(path)
 
     assert ds.attrs["contigs"] == ["19", "20", "X"]
-    assert_array_equal(ds["variant/contig"], [0, 0, 1, 1, 1, 1, 1, 1, 2])
+    assert_array_equal(ds["variant_contig"], [0, 0, 1, 1, 1, 1, 1, 1, 2])
     assert_array_equal(
-        ds["variant/position"],
+        ds["variant_position"],
         [111, 112, 14370, 17330, 1110696, 1230237, 1234567, 1235237, 10],
     )
     assert_array_equal(
-        ds["variant/alleles"],
+        ds["variant_allele"],
         [
             [b"A", b"C", b"", b""],
             [b"A", b"G", b"", b""],
@@ -36,15 +36,15 @@ def test_read_vcfzarr(shared_datadir):
         ],
     )
     assert_array_equal(
-        ds["variant/id"],
+        ds["variant_id"],
         [".", ".", "rs6054257", ".", "rs6040355", ".", "microsat1", ".", "rsTest"],
     )
     assert_array_equal(
-        ds["variant/id_mask"],
+        ds["variant_id_mask"],
         [True, True, False, True, False, True, False, True, False],
     )
 
-    assert_array_equal(ds["sample/id"], ["NA00001", "NA00002", "NA00003"])
+    assert_array_equal(ds["sample_id"], ["NA00001", "NA00002", "NA00003"])
 
     call_genotype = np.array(
         [
@@ -60,9 +60,9 @@ def test_read_vcfzarr(shared_datadir):
         ],
         dtype="i1",
     )
-    assert_array_equal(ds["call/genotype"], call_genotype)
-    assert_array_equal(ds["call/genotype_mask"], call_genotype < 0)
-    assert "call/genotype_phased" not in ds
+    assert_array_equal(ds["call_genotype"], call_genotype)
+    assert_array_equal(ds["call_genotype_mask"], call_genotype < 0)
+    assert "call_genotype_phased" not in ds
 
 
 def test_ensure_2d():