From f554a11eec4b9debb9701966f635dcf2453ed49a Mon Sep 17 00:00:00 2001
From: Julie Sullivan <julie.sullivan@gmail.com>
Date: Mon, 21 Nov 2022 11:06:54 +0000
Subject: [PATCH] fix consequence types for CNVs with 2 copies

---
 .../lib/variant/annotation/VariantAnnotationCalculator.java     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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 fdbd0fd35b..051cc047ba 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
@@ -1279,7 +1279,7 @@ private ConsequenceTypeCalculator getConsequenceTypeCalculator(Variant variant)
             case CNV:
             case COPY_NUMBER_GAIN:
             case COPY_NUMBER:
-                if (variant.getSv().getCopyNumber() == null) {
+                if (variant.getSv().getCopyNumber() == null || variant.getSv().getCopyNumber() == 2) {
                     return new ConsequenceTypeGenericRegionCalculator();
                 } else if (variant.getSv().getCopyNumber() > 2) {
                     return new ConsequenceTypeCNVGainCalculator();