#3481 updated codeQL version to v2 and #3482 Fix user searches for va…

…riants where the N is accidentally ommitted from NM_

genes/hgvs/hgvs_matcher.py

@@ -516,7 +516,8 @@ def clean_hgvs(self, hgvs_string) -> Tuple[str, List[str]]:
         cleaned_hgvs = clean_string(hgvs_string)  # remove non-printable characters
         cleaned_hgvs = cleaned_hgvs.replace(" ", "")  # No whitespace in HGVS
         cleaned_hgvs = cleaned_hgvs.replace("::", ":")  # Fix double colon
-        cleaned_hgvs = "N" + cleaned_hgvs if cleaned_hgvs.startswith("M_") else cleaned_hgvs  # Fix M_ prefix
+        if cleaned_hgvs.startswith("M_") or cleaned_hgvs.startswith("m_"):
+            cleaned_hgvs = "NM_" + cleaned_hgvs[2:]
         # Lowercase mutation types, e.g. NM_032638:c.1126_1133DUP - won't matter if also changes gene name as that's
         # case-insensitive
         MUTATION_TYPES = ["ins", "del", "dup", "inv"]  # Will also handle delins and del...ins

genes/tests/test_clean_hgvs.py

@@ -12,7 +12,11 @@ def test_clean_hgvs(self):
         test_cases = [
             ("M_206933.3(USH2A):c.4298G>A", "NM_206933.3(USH2A):c.4298G>A"),
             ("NM_206933.3(USH2A)::c.4298G>A", "NM_206933.3(USH2A):c.4298G>A"),
-            ("M_206933.3USH2A):c.4298G>A", "NM_206933.3USH2A:c.4298G>A")
+            ("M_206933.3USH2A):c.4298G>A", "NM_206933.3USH2A:c.4298G>A"),
+            ("m_206933.3USH2A):c.4298G>A", "NM_206933.3USH2A:c.4298G>A"),
+            ("nm_206933.3(USH2A):c.4298G>A", "NM_206933.3(USH2A):c.4298G>A"),
+            ("m_206933.3(USH2A)::c.4298G>A", "NM_206933.3(USH2A):c.4298G>A"),
+            ("m_206933.3(USH2A):c.4298G>A", "NM_206933.3(USH2A):c.4298G>A"),
         ]
 
         for input_hgvs, expected_result in test_cases: