Testing/Less Cooked

Adding tests and not sorting every attribute as only INFO fields were sensitive
to header ordering.

Author: ACEnglish

bio2zarr/vcf2zarr/icf.py

@@ -116,24 +116,24 @@ class VcfPartition:
 )
 
 
-@dataclasses.dataclass(order=True)
+@dataclasses.dataclass
 class Contig:
     id: str
     length: int = None
 
 
-@dataclasses.dataclass(order=True)
+@dataclasses.dataclass
 class Sample:
     id: str
 
 
-@dataclasses.dataclass(order=True)
+@dataclasses.dataclass
 class Filter:
     id: str
     description: str = ""
 
 
-@dataclasses.dataclass(order=True)
+@dataclasses.dataclass
 class IcfMetadata(core.JsonDataclass):
     samples: list
     contigs: list
@@ -195,10 +195,12 @@ def fromdict(d):
     def __eq__(self, other):
         if not isinstance(other, IcfMetadata):
             return NotImplemented
-        return (sorted(self.samples) == sorted(other.samples) and
-                sorted(self.contigs) == sorted(other.contigs) and
-                sorted(self.filters) == sorted(other.filters) and
-                sorted(self.fields) == sorted(other.fields))
+        return (
+                self.samples == other.samples and 
+                self.contigs == other.contigs and
+                self.filters == other.filters and
+                sorted(self.fields) == sorted(other.fields)
+               )
 
 
 def fixed_vcf_field_definitions():

tests/data/vcf/out_of_order_fields/input1.bcf

@@ -1100,3 +1100,61 @@ def test_missing_filter(tmp_path):
     zarr_path = tmp_path / "zarr"
     with pytest.raises(ValueError, match="Filter 'q10' was not defined in the header"):
         vcf2zarr.convert([path], zarr_path)
+
+class TestOutOfOrderFields:
+    data_paths = ["tests/data/vcf/out_of_order_fields/input1.bcf",
+                  "tests/data/vcf/out_of_order_fields/input2.bcf"]
+
+    @pytest.fixture(scope="class")
+    def ds(self, tmp_path_factory):
+        out = tmp_path_factory.mktemp("data") / "ooo_example.vcf.zarr"
+        vcf2zarr.convert(self.data_paths, out)
+        return sg.load_dataset(out)
+
+    def test_filters(self, ds):
+        nt.assert_array_equal(ds["filter_id"], ["PASS", "FAIL"])
+        nt.assert_array_equal(
+            ds["variant_filter"],
+            [
+                [True, False],
+                [False, True],
+                [True, False],
+            ],
+        )
+
+    def test_source(self, ds):
+        assert ds.attrs["source"] == f"bio2zarr-{provenance.__version__}"
+
+    def test_contigs(self, ds):
+        nt.assert_array_equal(ds["contig_id"], ["chr20", "chr21"])
+        nt.assert_array_equal(ds['contig_length'], [64444167., 46709983.])
+        nt.assert_array_equal(ds["variant_contig"], [0, 1, 1])
+
+    def test_position(self, ds):
+        nt.assert_array_equal(ds["variant_position"], [63971, 64506, 64507])
+
+    def test_length(self, ds):
+        nt.assert_array_equal(ds["variant_length"], [11, 1, 1])
+
+    def test_info_fields(self, ds):
+        nt.assert_array_equal(
+            ds["variant_QNAME"],
+            ['cluster19_000000F', '.', 'cluster19_000000F'],
+        )
+        nt.assert_array_equal(ds["variant_QSTART"], [25698928, 25698928, -1])
+
+    def test_allele(self, ds):
+        fill = constants.STR_FILL
+        nt.assert_array_equal(
+            ds["variant_allele"].values.tolist(),
+            [
+                ['TTCCATTCCAC', 'T'],
+                ['C', 'CTCCAT'],
+                ['G', 'A']
+            ]
+        )
+        assert ds["variant_allele"].dtype == "O"
+
+    def test_call_DPs(self, ds):
+        nt.assert_array_equal(ds["call_DP"], [[5], [-1], [5]])
+        nt.assert_array_equal(ds["call_DP2"], [[1], [1], [-1]])