Fail with helpful error message if 'region_index' is missing

tests/test_stats.py

@@ -1,6 +1,9 @@
 import pathlib
 from io import StringIO
 
+import pytest
+from bio2zarr import vcf2zarr
+
 from vcztools.stats import nrecords, stats
 
 from .utils import vcz_path_cache
@@ -29,3 +32,13 @@ def test_stats():
 X	.	1
 """
     )
+
+
+def test_stats__no_index(tmp_path):
+    original = pathlib.Path("tests/data/vcf") / "sample.vcf.gz"
+    # don't use cache here since we wnat to make sure vcz is not indexed
+    vcz = tmp_path.joinpath("intermediate.vcz")
+    vcf2zarr.convert([original], vcz, worker_processes=0, local_alleles=False)
+
+    with pytest.raises(ValueError, match="Could not load 'region_index' variable."):
+        stats(vcz, StringIO())

vcztools/stats.py

@@ -15,6 +15,12 @@ def nrecords(vcz, output):
 def stats(vcz, output):
     root = zarr.open(vcz, mode="r")
 
+    if "region_index" not in root:
+        raise ValueError(
+            "Could not load 'region_index' variable. "
+            "Use 'vcztools index' to create an index."
+        )
+
     with open_file_like(output) as output:
         contigs = root["contig_id"][:].astype("U").tolist()
         if "contig_length" in root: