Merge pull request #8558 from kalletlak/fix-8555

SV: Proper handle intragenic variant type
cBioPortal · Apr 29, 2021 · 1bf469a · 1bf469a
2 parents 89bc588 + b7a95f4
commit 1bf469a
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/service/src/main/java/org/cbioportal/service/util/MutationMapperUtils.java b/service/src/main/java/org/cbioportal/service/util/MutationMapperUtils.java
@@ -90,6 +90,11 @@ public List<StructuralVariant> mapFusionsToStructuralVariants(List<Mutation> fus
                             // this is in format of <gene>-<variant-type>. ex: TUFT1-intragenic
                             site1GeneSymbol = matcher.group(1);
                             variantType = EnumUtils.getEnum(VariantType.class, matcher.group(2).toUpperCase());
+                            if(variantType != null && variantType.equals(VariantType.INTRAGENIC)) {
+                                //convert it to oncokb deletion type
+                                variantType = VariantType.DELETION;
+                                site2GeneSymbol = site1GeneSymbol;
+                            }
                         } else {
                             // this is in format of <gene1>-<gene2>-<optional variant-type>. ex.
                             // ZSWIM4-SLC1A6 or ZNF595-TERT fusion