From c644d51a0393962d519f8f4b7b439614afe3d94b Mon Sep 17 00:00:00 2001
From: jrobinso <933148+jrobinso@users.noreply.github.com>
Date: Mon, 30 Sep 2024 12:06:33 -0700
Subject: [PATCH] fix for chrom alias defaults

---
 .../broad/igv/feature/genome/ChromAlias.java  | 20 +++++++++++--------
 .../feature/genome/ChromAliasDefaults.java    |  1 +
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAlias.java b/src/main/java/org/broad/igv/feature/genome/ChromAlias.java
index 2dac9e06d..dc1de69ab 100644
--- a/src/main/java/org/broad/igv/feature/genome/ChromAlias.java
+++ b/src/main/java/org/broad/igv/feature/genome/ChromAlias.java
@@ -5,34 +5,38 @@
 import java.util.Map;
 
 public class ChromAlias {
-    
+
     private String chr;
+
+    /**
+     * Map of name set -> alias
+     */
     private Map<String, String> aliases;
 
     public ChromAlias(String chr) {
         this.chr = chr;
         this.aliases = new HashMap<>();
     }
-    
+
     public String getChr() {
         return chr;
     }
-    
+
     public void put(String nameSet, String alias) {
         aliases.put(nameSet, alias);
     }
+
     public String get(String nameSet) {
         return aliases.get(nameSet);
     }
-    
+
     public boolean containsKey(String nameSet) {
         return aliases.containsKey(nameSet);
     }
-    
+
     public Collection<String> values() {
         return aliases.values();
     }
-    
-    
-    
+
+
 }
diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java b/src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java
index 964967508..f930e4353 100644
--- a/src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java
+++ b/src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java
@@ -23,6 +23,7 @@ private void init(String id, List<String> chromosomeNames) {
 
             boolean skipRest = false;
             ChromAlias record = new ChromAlias(name);
+            record.put("__CANONICAL__", name);
             aliasRecords.add(record);
 
             //