Fixup

Author: jeromekelleher

bio2zarr/vcf2zarr/vcz.py

@@ -848,17 +848,10 @@ def encode_local_alleles_partition(self, partition_index):
             store=self.wip_partition_array_path(partition_index, "call_genotype"),
             mode="r",
         )
-        alleles_array = zarr.open_array(
-            store=self.wip_partition_array_path(partition_index, "variant_allele"),
-            mode="r",
-        )
         for chunk_index in range(gt_array.cdata_shape[0]):
-            A = alleles_array.blocks[chunk_index]
-            G = gt_array.blocks[chunk_index]
-            for alleles, var in zip(A, G):
+            for genotypes in gt_array.blocks[chunk_index]:
                 j = call_LAA.next_buffer_row()
-                # TODO we should probably compute LAAs by chunk for efficiency
-                call_LAA.buff[j] = compute_laa_field(var, alleles)
+                call_LAA.buff[j] = compute_laa_field(genotypes)
 
         call_LAA.flush()
         self.finalise_partition_array(partition_index, "call_LAA")