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varfish-org · Feb 19, 2025 · f72f7fc · f72f7fc
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commit f72f7fc
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Showing 4 changed files with 55 additions and 1 deletion.
diff --git a/backend/variants/query_presets.py b/backend/variants/query_presets.py
@@ -607,7 +607,7 @@ class _ImpactPresets:
             "structural_variant",
             "transcript_ablation",
             # new mehari effects
-            "convervative_inframe_insertion",
+            "conservative_inframe_insertion",
             "conservative_inframe_deletion",
             "splice_donor_5th_base_variant",
             "splice_donor_region_variant",

diff --git a/backend/variants/tests/test_models_presets.py b/backend/variants/tests/test_models_presets.py
@@ -180,6 +180,7 @@ def test_create_as_copy_of_factory_preset(self):
                 "stop_lost",
                 "structural_variant",
                 "transcript_ablation",
+                "transcript_amplification",
             ],
         }
         self.assertDictEqual(result, expected)

diff --git a/backend/variants/tests/test_queries.py b/backend/variants/tests/test_queries.py
@@ -1988,6 +1988,15 @@ def test_effects_include_missing_annotation(self):
                     "synonymous_variant",
                     "transcript_ablation",
                     "upstream_gene_variant",
+                    "coding_sequence_variant",
+                    "conservative_inframe_deletion",
+                    "conservative_inframe_insertion",
+                    "intron_variant",
+                    "splice_donor_5th_base_variant",
+                    "splice_donor_region_variant",
+                    "splice_polypyrimidine_tract_variant",
+                    "start_retained_variant",
+                    "transcript_amplification",
                 ],
             },
             4,

diff --git a/backend/variants/tests/test_query_presets.py b/backend/variants/tests/test_query_presets.py
@@ -1033,6 +1033,10 @@ def testToSettingsAny(self):
 
 
 class TestEnumImpact(TestCase):
+    def setUp(self):
+        super().setUp()
+        self.maxDiff = None
+
     def testValues(self):
         self.assertEqual(query_presets.Impact.NULL_VARIANT.value, "null_variant")
         self.assertEqual(query_presets.Impact.AA_CHANGE_SPLICING.value, "aa_change_splicing")
@@ -1066,6 +1070,7 @@ def testToSettingsNullVariant(self):
                     "stop_lost",
                     "structural_variant",
                     "transcript_ablation",
+                    "transcript_amplification",
                 ],
             },
         )
@@ -1103,6 +1108,12 @@ def testToSettingsAaChangeSplicing(self):
                     "stop_lost",
                     "structural_variant",
                     "transcript_ablation",
+                    "conservative_inframe_insertion",
+                    "conservative_inframe_deletion",
+                    "splice_donor_5th_base_variant",
+                    "splice_donor_region_variant",
+                    "splice_polypyrimidine_tract_variant",
+                    "transcript_amplification",
                 ],
             },
         )
@@ -1142,6 +1153,15 @@ def testToSettingsAllCodingDeepIntronic(self):
                     "structural_variant",
                     "synonymous_variant",
                     "transcript_ablation",
+                    "coding_sequence_variant",
+                    "conservative_inframe_insertion",
+                    "conservative_inframe_deletion",
+                    "intron_variant",
+                    "splice_donor_5th_base_variant",
+                    "splice_donor_region_variant",
+                    "splice_polypyrimidine_tract_variant",
+                    "start_retained_variant",
+                    "transcript_amplification",
                 ],
             },
         )
@@ -1190,6 +1210,15 @@ def testToSettingsWholeTranscript(self):
                     "synonymous_variant",
                     "transcript_ablation",
                     "upstream_gene_variant",
+                    "coding_sequence_variant",
+                    "conservative_inframe_insertion",
+                    "conservative_inframe_deletion",
+                    "intron_variant",
+                    "splice_donor_5th_base_variant",
+                    "splice_donor_region_variant",
+                    "splice_polypyrimidine_tract_variant",
+                    "start_retained_variant",
+                    "transcript_amplification",
                 ],
             },
         )
@@ -1239,6 +1268,15 @@ def testToSettingsAny(self):
                     "synonymous_variant",
                     "transcript_ablation",
                     "upstream_gene_variant",
+                    "coding_sequence_variant",
+                    "conservative_inframe_insertion",
+                    "conservative_inframe_deletion",
+                    "intron_variant",
+                    "splice_donor_5th_base_variant",
+                    "splice_donor_region_variant",
+                    "splice_polypyrimidine_tract_variant",
+                    "start_retained_variant",
+                    "transcript_amplification",
                 ],
             },
         )
@@ -1737,6 +1775,12 @@ def testToSettingsDefaults(self):
                     "stop_lost",
                     "structural_variant",
                     "transcript_ablation",
+                    "conservative_inframe_insertion",
+                    "conservative_inframe_deletion",
+                    "splice_donor_5th_base_variant",
+                    "splice_donor_region_variant",
+                    "splice_polypyrimidine_tract_variant",
+                    "transcript_amplification",
                 ],
                 "exac_enabled": True,
                 "exac_frequency": 0.002,