fix: effects all does not catch empty annotations (#1578)

varfish-org · Apr 22, 2024 · 32f0267 · 32f0267
1 parent eca30d3
commit 32f0267
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diff --git a/variants/queries.py b/variants/queries.py
@@ -49,6 +49,7 @@
     SmallVariantSummary,
 )
 from variants.plugins import PLUGIN_TYPE_EXTEND_QUERY_INFO, get_active_plugins
+from variants.query_presets import IMPACT_PRESETS
 from variants.utils import class_from_string
 
 
@@ -1007,6 +1008,8 @@ def extend_conditions(self, _query_parts):
 
 class ExtendQueryPartsEffectsFilter(ExtendQueryPartsBase):
     def extend_conditions(self, _query_parts):
+        if set(self.kwargs["effects"]) == set(IMPACT_PRESETS.any["effects"]):
+            return []
         return [
             OVERLAP(
                 getattr(SmallVariant.sa, "%s_effect" % self.transcript_db),

diff --git a/variants/tests/test_queries.py b/variants/tests/test_queries.py
@@ -1902,6 +1902,11 @@ def setUp(self):
             refseq_effect=["missense_variant", "frameshift_variant"],
             variant_set=variant_set,
         )
+        SmallVariantFactory(
+            release=self.case.release,
+            refseq_effect=[],
+            variant_set=variant_set,
+        )
         SmallVariantFactory(
             release=self.case.release, refseq_effect=["frameshift_variant"], variant_set=variant_set
         )
@@ -1954,6 +1959,50 @@ def test_effects_all_vcf(self):
             3,
         )
 
+    def test_effects_include_missing_annotation(self):
+        self.run_query(
+            CasePrefetchQuery,
+            {
+                "effects": [
+                    "3_prime_UTR_exon_variant",
+                    "3_prime_UTR_intron_variant",
+                    "5_prime_UTR_exon_variant",
+                    "5_prime_UTR_intron_variant",
+                    "coding_transcript_intron_variant",
+                    "complex_substitution",
+                    "direct_tandem_duplication",
+                    "disruptive_inframe_deletion",
+                    "disruptive_inframe_insertion",
+                    "downstream_gene_variant",
+                    "exon_loss_variant",
+                    "feature_truncation",
+                    "frameshift_elongation",
+                    "frameshift_truncation",
+                    "frameshift_variant",
+                    "inframe_deletion",
+                    "inframe_insertion",
+                    "intergenic_variant",
+                    "internal_feature_elongation",
+                    "missense_variant",
+                    "mnv",
+                    "non_coding_transcript_exon_variant",
+                    "non_coding_transcript_intron_variant",
+                    "splice_acceptor_variant",
+                    "splice_donor_variant",
+                    "splice_region_variant",
+                    "start_lost",
+                    "stop_gained",
+                    "stop_lost",
+                    "stop_retained_variant",
+                    "structural_variant",
+                    "synonymous_variant",
+                    "transcript_ablation",
+                    "upstream_gene_variant",
+                ],
+            },
+            4,
+        )
+
 
 class TestCaseOneQueryExonDistance(SupportQueryTestBase):
     """Test exon distance settings"""