fix for chrom alias defaults

igvteam · Sep 30, 2024 · c644d51 · c644d51
1 parent 5629b43
commit c644d51
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Showing 2 changed files with 13 additions and 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
@@ -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
@@ -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);
 
             //