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igvteam · Oct 4, 2023 · 5bc968b · 5bc968b
1 parent 63b2ea7
commit 5bc968b
Showing 1 changed file with 10 additions and 3 deletions.
diff --git a/src/main/java/org/broad/igv/bbfile/BBDataSource.java b/src/main/java/org/broad/igv/bbfile/BBDataSource.java
@@ -258,7 +258,7 @@ protected synchronized DataTile getRawData(String chr, int start, int end) {
         IntArrayList endsList = new IntArrayList(100000);
         FloatArrayList valuesList = new FloatArrayList(100000);
 
-        String chrAlias = chrNameMap.containsKey(chr) ? chrNameMap.get(chr) : chr;
+        final String chrAlias = getChrAlias(chr);
         //Iterator<WigItem> iter = reader.getBigWigIterator(chrAlias, start, chrAlias, end, false);
         int chromId = reader.chromTree.nameToIdMap.get(chrAlias);
         try {
@@ -280,6 +280,10 @@ protected synchronized DataTile getRawData(String chr, int start, int end) {
 
     }
 
+    private String getChrAlias(String chr) {
+        return chrNameMap.containsKey(chr) ? chrNameMap.get(chr) : chr;
+    }
+
 
     private List<LocusScore> getWholeGenomeScores() {
 
@@ -301,9 +305,12 @@ private List<LocusScore> getWholeGenomeScores() {
                 BBZoomHeader lowestResHeader = this.getZoomLevelForScale(scale);
                 if (lowestResHeader == null) return null;
 
-                Set<String> wgChrNames = new HashSet<>(genome.getLongChromosomeNames());
+                Set<String> wgChrNames = new HashSet<>(genome.getLongChromosomeNames().stream().map(nm -> getChrAlias(nm)).toList());
 
-                List<Integer> chromIDs = new ArrayList<>(wgChrNames.stream().map(nm -> reader.chromTree.nameToIdMap.get(nm)).toList());
+                List<Integer> chromIDs = new ArrayList<>(
+                        wgChrNames.stream().map(nm -> reader.chromTree.nameToIdMap.get(nm))
+                                .filter(o -> o != null)
+                                .toList());
                 chromIDs.sort(Comparator.comparingInt(o -> o));
                 int firstChromId = chromIDs.get(0);
                 int lastChromId = chromIDs.get(chromIDs.size() - 1);