From 72891b07be8f18429040762786e709ba9aff3178 Mon Sep 17 00:00:00 2001
From: Calvin Lu <59149377+calvinlu3@users.noreply.github.com>
Date: Fri, 6 Sep 2024 16:53:53 -0400
Subject: [PATCH] Update

---
 .../org/mskcc/oncokb/curation/util/AlterationUtils.java   | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/main/java/org/mskcc/oncokb/curation/util/AlterationUtils.java b/src/main/java/org/mskcc/oncokb/curation/util/AlterationUtils.java
index 4c9a67c9..edbe6c30 100644
--- a/src/main/java/org/mskcc/oncokb/curation/util/AlterationUtils.java
+++ b/src/main/java/org/mskcc/oncokb/curation/util/AlterationUtils.java
@@ -100,7 +100,7 @@ private Alteration parseExonAlteration(String alteration) {
         alt.setType(AlterationType.STRUCTURAL_VARIANT);
         alt.setConsequence(consequence);
 
-        Pattern pattern = Pattern.compile(EXON_ALT_REGEX);
+        Pattern pattern = Pattern.compile(EXON_ALT_REGEX, Pattern.CASE_INSENSITIVE);
         Matcher matcher = pattern.matcher(alteration);
         List<String> splitResults = new ArrayList<>();
         Set<String> consequenceTermSet = new HashSet<>();
@@ -112,13 +112,17 @@ private Alteration parseExonAlteration(String alteration) {
 
             switch (consequenceTerm.toLowerCase()) {
                 case "insertion":
+                    consequenceTerm = "Insertion";
                     consequence.setTerm(SVConsequence.SV_INSERTION.name());
                     break;
                 case "duplication":
+                    consequenceTerm = "Duplication";
                     consequence.setTerm(SVConsequence.SV_DUPLICATION.name());
                     break;
                 case "deletion":
+                    consequenceTerm = "Deletion";
                     consequence.setTerm(SVConsequence.SV_DELETION.name());
+                    break;
                 default:
                     break;
             }
@@ -535,7 +539,7 @@ public static Boolean isGenomicChange(String alteration) {
     }
 
     public static Boolean isExon(String alteration) {
-        Pattern p = Pattern.compile(EXON_ALTS_REGEX);
+        Pattern p = Pattern.compile(EXON_ALTS_REGEX, Pattern.CASE_INSENSITIVE);
         Matcher m = p.matcher(alteration);
         return m.matches();
     }