didnt use new allele for state

src/ga4gh/vrs/normalize.py

@@ -158,10 +158,9 @@ def _normalize_allele(input_allele, data_proxy):
             # a Location specified by the coordinates of the new ival, a length
             # specified by the length of the alternate allele, and a repeat subunit
             # length
-            allele.state = models.ReferenceLengthExpression(
+            new_allele.state = models.ReferenceLengthExpression(
                 length=len(new_alleles[1]),
-                sequence=models.SequenceString(new_ref_seq),
-                repeat_subunit_length=repeat_subunit_len
+                repeatSubunitLength=repeat_subunit_len
             )
     except ValueError:
         # Occurs for ref agree Alleles (when alt = ref)

tests/test_vrs_normalize.py

@@ -36,6 +36,22 @@
 }
 
 
+allele_dict2_normalized = {
+    "type": "Allele",
+    "location": {
+        "type": "SequenceLocation",
+        "sequence": "refseq:NC_000023.11",
+        "start": [None, 155980375],
+        "end": [155980377, None]
+    },
+    "state": {
+        "length": 0,
+        "repeatSubunitLength": 2,
+        "type": "ReferenceLengthExpression"
+    }
+}
+
+
 allele_dict3 = {
     "type": "Allele",
     "location": {
@@ -59,7 +75,8 @@ def test_normalize_allele(rest_dataproxy):
 
     allele1 = models.Allele(**allele_dict2)
     allele2 = normalize(allele1, rest_dataproxy)
-    assert allele1 == allele2
+    assert allele1 != allele2
+    assert allele2 == models.Allele(**allele_dict2_normalized)
 
     # Definite ranges are not normalized
     allele3 = models.Allele(**allele_dict3)