Fix CRAM reference region updating.

samtools · Apr 9, 2024 · d769bce · d769bce
1 parent 222d10b
commit d769bce
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java b/src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java
@@ -113,9 +113,10 @@ public void fetchReferenceBases(final int referenceIndex) {
 
         // Re-resolve the reference bases if we don't have a current region or if the region we have
         // doesn't span the *entire* contig requested.
+        final int newSequenceLength = sequenceDictionary.getSequence(referenceIndex).getSequenceLength();
         if ((referenceIndex != this.referenceIndex) ||
                 regionStart != 0 ||
-                (regionLength < referenceBases.length)) {
+                (regionLength != newSequenceLength)) {
             setCurrentSequence(referenceIndex);
             referenceBases = referenceSource.getReferenceBases(sequenceRecord, true);
             if (referenceBases == null) {