Add normalise test using icechunk

tests/test_normalise.py

@@ -13,7 +13,7 @@
     variant_alleles_are_equivalent,
 )
 
-from .utils import compare_vcf_and_vcz, convert_vcf_to_vcz
+from .utils import compare_vcf_and_vcz, convert_vcf_to_vcz, convert_vcf_to_vcz_icechunk
 
 
 # TODO: replace this with make_vcz in vcztools/bio2zarr
@@ -342,3 +342,26 @@ def test_normalise_and_append(tmp_path):
     compare_vcf_and_vcz(
         tmp_path, "view --no-version", "sample-part1.vcf.gz", "view --no-version", vcz0
     )
+
+
+def test_normalise_and_append_icechunk(tmp_path):
+    pytest.importorskip("icechunk")
+    from vczstore.icechunk_utils import icechunk_transaction
+
+    # note that vcz0 is in icechunk, but the others needn't be
+    vcz0 = convert_vcf_to_vcz_icechunk("sample-variants.vcf.gz", tmp_path, ploidy=2)
+    vcz1 = convert_vcf_to_vcz("sample-part1.vcf.gz", tmp_path)
+    vcz1_norm = zarr.storage.MemoryStore()
+
+    with icechunk_transaction(vcz0, "main", message="append") as store:
+        normalise(store, vcz1, vcz1_norm)
+        append(store, vcz1_norm)
+
+    # check equivalence with original VCF
+    compare_vcf_and_vcz(
+        tmp_path,
+        "view --no-version",
+        "sample-part1.vcf.gz",
+        "view --no-version --zarr-backend-storage icechunk",
+        vcz0,
+    )

tests/utils.py

@@ -289,10 +289,18 @@ def compare_vcf_and_vcz(tmp_path, vcf_args, vcf_file, vcz_args, vcz):
     assert_vcfs_close(bcftools_out_file, vcztools_out_file)
 
 
-def convert_vcf_to_vcz_icechunk(vcf_name, tmp_path):
+def convert_vcf_to_vcz_icechunk(
+    vcf_name, tmp_path, variants_chunk_size=None, samples_chunk_size=None, ploidy=None
+):
     from vczstore.icechunk_utils import copy_store_to_icechunk
 
-    vcz = convert_vcf_to_vcz(vcf_name, tmp_path)
+    vcz = convert_vcf_to_vcz(
+        vcf_name,
+        tmp_path,
+        variants_chunk_size=variants_chunk_size,
+        samples_chunk_size=samples_chunk_size,
+        ploidy=ploidy,
+    )
 
     ic_tmp_path = tmp_path / "icechunk"
     ic_tmp_path.mkdir()