fix: ensure null calls don't hit _any_ wildcard rules

VERSION

@@ -1 +1 @@
-0.9.0
+0.9.1

piezo/grammar_GARC1.py

@@ -1027,13 +1027,14 @@ def process_snp_variants(
 
         # PRIORITY=8: any nonsynoymous mutation at this specific position in the CDS or
         #   PROM  (e.g. rpoB@S450? or rpoB@c-15?)
-        row = rules.loc[
-            rules_mutation_type_vector
-            & rules_position_vector
-            & (rules.MUTATION.str[-1] == "?")
-        ]
-        # nonsyn SNP at specified position in the CDS
-        row_prediction(row, predictions, 8, minor)
+        if mutation[-1] not in ["X", "x"]:
+            row = rules.loc[
+                rules_mutation_type_vector
+                & rules_position_vector
+                & (rules.MUTATION.str[-1] == "?")
+            ]
+            # nonsyn SNP at specified position in the CDS
+            row_prediction(row, predictions, 8, minor)
 
     # PRIORITY=9: an exact match
     row = rules.loc[(rules_mutation_type_vector) & (rules.MUTATION == mutation)]

tests/test-catalogue/NC_004148.2_TEST_v1.0_GARC1_RFUS-FRS.csv

@@ -40,3 +40,5 @@ NC_004148.2,TEST,v1.0,GARC1,RFUS,DRUG_A,M2@G74!&M2@G74X,U,{},"{""row"": 37}",{}
 NC_004148.2,TEST,v1.0,GARC1,RFUS,DRUG_A,M2@F75V:0.03,R,{},"{""row"": 38}",{}
 NC_004148.2,TEST,v1.0,GARC1,RFUS,DRUG_B,M2@G74!:0.04&M2@G74X:0.02,U,{},"{""row"": 39}",{}
 NC_004148.2,TEST,v1.0,GARC1,RFUS,DRUG_B,M3@*_ins,R,{},"{""row"": 40}",{}
+NC_004148.2,TEST,v1.0,GARC1,RFUS,DRUG_B,M3@S450?,R,{},"{""row"": 41}",{}
+NC_004148.2,TEST,v1.0,GARC1,RFUS,DRUG_B,M3@*?,U,{},"{""row"": 42}",{}

tests/test_catalogue.py

@@ -582,3 +582,7 @@ def test_misc():
 
     # Double checking that a minor allele doesn't hit a general rule anymore
     assert test_catalogue.predict("M2@37_del_c:0.2") == {"DRUG_A": "S", "DRUG_B": "S"}
+
+    # Checking that a null call can't hit a wildcard rule
+    # This catalogue has M3@S450?, this shouldn't hit that and so should get a default "S"
+    assert test_catalogue.predict("M3@S450X") == "S"