From 8ac1649d3d965155cc2978fb9e5955883632ed26 Mon Sep 17 00:00:00 2001
From: korikuzma <korikuzma@gmail.com>
Date: Thu, 24 Aug 2023 00:35:37 -0400
Subject: [PATCH] didnt use new allele for state

---
 src/ga4gh/vrs/normalize.py  |  5 ++---
 tests/test_vrs_normalize.py | 19 ++++++++++++++++++-
 2 files changed, 20 insertions(+), 4 deletions(-)

diff --git a/src/ga4gh/vrs/normalize.py b/src/ga4gh/vrs/normalize.py
index c4f98ce2..819fa677 100644
--- a/src/ga4gh/vrs/normalize.py
+++ b/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)
diff --git a/tests/test_vrs_normalize.py b/tests/test_vrs_normalize.py
index 908080bb..7bdcaa73 100644
--- a/tests/test_vrs_normalize.py
+++ b/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)