Only add LAA if PL is present

Author: Will-Tyler

bio2zarr/vcf2zarr/icf.py

@@ -239,6 +239,7 @@ def scan_vcf(path, target_num_partitions, *, local_alleles):
         # Indicates whether vcf2zarr can introduce local alleles
         can_localize = False
         should_add_laa_field = True
+        has_PL = False
         fields = fixed_vcf_field_definitions()
         for h in vcf.header_iter():
             if h["HeaderType"] in ["INFO", "FORMAT"]:
@@ -247,12 +248,15 @@ def scan_vcf(path, target_num_partitions, *, local_alleles):
                     field.vcf_type = "Integer"
                     field.vcf_number = "."
                 fields.append(field)
-                if field.category == "FORMAT" and field.name in {"GT", "AD"}:
-                    can_localize = True
-                if (field.category, field.name) == ("FORMAT", "LAA"):
-                    should_add_laa_field = False
-
-        if local_alleles and can_localize and should_add_laa_field:
+                if field.category == "FORMAT":
+                    if field.name in {"GT", "AD", "PL"}:
+                        can_localize = True
+                    if field.name == "PL":
+                        has_PL = True
+                    if field.name == "LAA":
+                        should_add_laa_field = False
+
+        if local_alleles and can_localize and should_add_laa_field and has_PL:
             laa_field = VcfField(
                 category="FORMAT",
                 name="LAA",

tests/test_icf.py

@@ -27,11 +27,6 @@ def icf(self, tmp_path_factory):
         out = tmp_path_factory.mktemp("data") / "example.exploded"
         return vcf2zarr.explode(out, [self.data_path], local_alleles=False)
 
-    @pytest.fixture(scope="class")
-    def icf_local_alleles(self, tmp_path_factory):
-        out = tmp_path_factory.mktemp("data") / "example.exploded"
-        return vcf2zarr.explode(out, [self.data_path])
-
     def test_format_version(self, icf):
         assert icf.metadata.format_version == icf_mod.ICF_METADATA_FORMAT_VERSION
 
@@ -54,13 +49,6 @@ def test_summary_table(self, icf):
         fields = [d["name"] for d in data]
         assert tuple(sorted(fields)) == self.fields
 
-    def test_summary_table_local_allleles(self, icf_local_alleles):
-        data = icf_local_alleles.summary_table()
-        fields = [d["name"] for d in data]
-        fields.sort()
-        expected = tuple(sorted((*self.fields, "FORMAT/LAA")))
-        assert tuple(fields) == expected
-
     def test_inspect(self, icf):
         assert icf.summary_table() == vcf2zarr.inspect(icf.path)
 
@@ -103,6 +91,44 @@ def test_INFO_NS(self, icf):
         assert icf["INFO/NS"].values == [None, None, 3, 3, 2, 3, 3, None, None]
 
 
+class TestLocalAllelesExample:
+    data_path = "tests/data/vcf/local_alleles.vcf.gz"
+
+    fields = (
+        "ALT",
+        "CHROM",
+        "FILTERS",
+        "FORMAT/AD",
+        "FORMAT/DP",
+        "FORMAT/GQ",
+        "FORMAT/GT",
+        "FORMAT/LAA",
+        "FORMAT/PL",
+        "ID",
+        "INFO/AA",
+        "INFO/AC",
+        "INFO/AF",
+        "INFO/AN",
+        "INFO/DB",
+        "INFO/DP",
+        "INFO/H2",
+        "INFO/NS",
+        "POS",
+        "QUAL",
+        "REF",
+    )
+
+    @pytest.fixture(scope="class")
+    def icf(self, tmp_path_factory):
+        out = tmp_path_factory.mktemp("data") / "example.exploded"
+        return vcf2zarr.explode(out, [self.data_path])
+
+    def test_summary_table(self, icf):
+        data = icf.summary_table()
+        fields = [d["name"] for d in data]
+        assert tuple(sorted(fields)) == self.fields
+
+
 class TestIcfWriterExample:
     data_path = "tests/data/vcf/sample.vcf.gz"
 

tests/test_vcf_examples.py

@@ -233,18 +233,8 @@ def test_call_HQ(self, ds):
         nt.assert_array_equal(ds["call_HQ"], call_HQ)
 
     def test_call_LAA(self, ds):
-        call_LAA = [
-            [[-2, -2], [-2, -2], [1, -2]],
-            [[-2, -2], [-2, -2], [1, -2]],
-            [[-2, -2], [1, -2], [1, -2]],
-            [[-2, -2], [1, -2], [-2, -2]],
-            [[1, 2], [1, 2], [2, -2]],
-            [[-2, -2], [-2, -2], [-2, -2]],
-            [[1, -2], [2, -2], [-2, -2]],
-            [[-2, -2], [-2, -2], [-2, -2]],
-            [[-2, -2], [1, -2], [2, -2]],
-        ]
-        nt.assert_array_equal(ds["call_LAA"], call_LAA)
+        # The small example VCF does not have a PL field
+        assert "call_LA" not in ds
 
     def test_no_genotypes(self, ds, tmp_path):
         path = "tests/data/vcf/sample_no_genotypes.vcf.gz"