Fixup max_v_chunks

Author: jeromekelleher

bio2zarr/vcf.py

@@ -1670,7 +1670,7 @@ def init(
         root = zarr.group(store=store)
 
         for column in self.schema.columns.values():
-            self.init_array(root, column)
+            self.init_array(root, column, partitions[-1].stop_index)
 
         logger.info("Writing WIP metadata")
         with open(self.wip_path / "metadata.json", "w") as f:
@@ -1718,13 +1718,16 @@ def encode_filter_id(self, root):
         )
         array.attrs["_ARRAY_DIMENSIONS"] = ["filters"]
 
-    def init_array(self, root, variable):
+    def init_array(self, root, variable, variants_dim_size):
         object_codec = None
         if variable.dtype == "O":
             object_codec = numcodecs.VLenUTF8()
+        shape = list(variable.shape)
+        # Truncate the variants dimension is max_variant_chunks was specified
+        shape[0] = variants_dim_size
         a = root.empty(
             variable.name,
-            shape=variable.shape,
+            shape=shape,
             chunks=variable.chunks,
             dtype=variable.dtype,
             compressor=numcodecs.get_codec(variable.compressor),