Add iter_id

Author: benjeffery

bio2zarr/vcf2zarr/icf.py

@@ -920,6 +920,13 @@ def iter_alleles(self, start, stop, num_alleles):
             alleles[1 : 1 + len(alt)] = alt
             yield alleles
 
+    def iter_id(self, start, stop):
+        for value in self.fields["ID"].iter_values(start, stop):
+            if value is not None:
+                yield value[0]
+            else:
+                yield None
+
     def iter_field(self, field_name, shape, start, stop):
         source_field = self.fields[field_name]
         sanitiser = source_field.sanitiser_factory(shape)

bio2zarr/writer.py

@@ -531,14 +531,13 @@ def encode_id_partition(self, partition_index):
         vid = self.init_partition_array(partition_index, "variant_id")
         vid_mask = self.init_partition_array(partition_index, "variant_id_mask")
         partition = self.metadata.partitions[partition_index]
-        field = self.source.fields["ID"]
 
-        for value in field.iter_values(partition.start, partition.stop):
+        for value in self.source.iter_id(partition.start, partition.stop):
             j = vid.next_buffer_row()
             k = vid_mask.next_buffer_row()
             assert j == k
             if value is not None:
-                vid.buff[j] = value[0]
+                vid.buff[j] = value
                 vid_mask.buff[j] = False
             else:
                 vid.buff[j] = constants.STR_MISSING