From 32a5ecfb72b6df06f178a1d74074e6d4cccdf41c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Joaqu=C3=ADn=20T=C3=A1rraga=20Gim=C3=A9nez?=
 <joaquintarraga@gmail.com>
Date: Tue, 16 Jan 2024 08:53:55 +0100
Subject: [PATCH] lib: catch the exception, but do not propagate it; instead,
 continue processing the variant annotation, #TASK-5457

---
 .../lib/variant/annotation/VariantAnnotationCalculator.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
index a16239e87..db87a51de 100644
--- a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java
+++ b/cellbase-lib/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;
                 }
             }