Merge pull request #683 from opencb/TASK-5457

TASK-5457 Fix CellBase annotation queries for SV variants
opencb · Jan 24, 2024 · 8be81e7 · 8be81e7
2 parents 3e4d16b + 32a5ecf
commit 8be81e7
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/...src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java b/...src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
@@ -611,9 +611,9 @@ private List<VariantAnnotation> runAnnotationProcess(List<Variant> normalizedVar
                         }
                     }
                 } catch (Exception e) {
-                    e.printStackTrace();
+                    variantAnnotation.setDisplayConsequenceType(VariantAnnotationUtils.FUNCTION_UNCERTAIN_VARIANT);
+                    variantAnnotation.setConsequenceTypes(Collections.emptyList());
                     logger.error("Something wrong happened when calculation consequence type for variant " + variant, e);
-                    throw e;
                 }
             }