Fix CRAM reference region transitions.

src/main/java/htsjdk/samtools/cram/build/CRAMReferenceRegion.java

@@ -113,9 +113,14 @@ 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 SAMSequenceRecord newSequenceRecord = sequenceDictionary.getSequence(referenceIndex);
+        if (newSequenceRecord == null) {
+            throw new IllegalArgumentException(
+                    String.format("Requested reference sequence index %d not found", referenceIndex));
+        }
         if ((referenceIndex != this.referenceIndex) ||
                 regionStart != 0 ||
-                (regionLength < referenceBases.length)) {
+                (regionLength != newSequenceRecord.getSequenceLength())) {
             setCurrentSequence(referenceIndex);
             referenceBases = referenceSource.getReferenceBases(sequenceRecord, true);
             if (referenceBases == null) {

src/test/java/htsjdk/samtools/cram/ref/CRAMReferenceRegionTest.java

@@ -3,6 +3,7 @@
 import htsjdk.HtsjdkTest;
 import htsjdk.samtools.SAMSequenceRecord;
 import htsjdk.samtools.cram.build.CRAMReferenceRegion;
+import htsjdk.samtools.cram.structure.AlignmentContext;
 import htsjdk.samtools.cram.structure.CRAMStructureTestHelper;
 import htsjdk.samtools.reference.InMemoryReferenceSequenceFile;
 import org.testng.Assert;
@@ -167,6 +168,39 @@ public void testGetReferenceBasesByRegionPositive(
         Assert.assertEquals(bases, Arrays.copyOfRange(fullContigBases, requestedOffset, requestedOffset + requestedLength));
     }
 
+    // simulate the state transitions that occur when writing a CRAM file
+    @Test
+    public void testSerialStateTransitions() {
+        // start with an entire reference sequence
+        final CRAMReferenceRegion cramReferenceRegion = getAlternatingReferenceRegion();
+        cramReferenceRegion.fetchReferenceBases(CRAMStructureTestHelper.REFERENCE_SEQUENCE_ZERO);
+        final long fullRegionFragmentLength = cramReferenceRegion.getRegionLength();
+        Assert.assertEquals(fullRegionFragmentLength, CRAMStructureTestHelper.REFERENCE_CONTIG_LENGTH);
+
+        // transition to a shorter reference fragment using fetchReferenceBasesByRegion, then back to the full region
+        final int SHORT_FRAGMENT_LENGTH = 5;
+        Assert.assertTrue(SHORT_FRAGMENT_LENGTH < fullRegionFragmentLength);
+        cramReferenceRegion.fetchReferenceBasesByRegion(CRAMStructureTestHelper.REFERENCE_SEQUENCE_ZERO, 0, SHORT_FRAGMENT_LENGTH);
+        Assert.assertEquals(cramReferenceRegion.getRegionLength(), SHORT_FRAGMENT_LENGTH);
+
+        // now transition back to the full sequence
+        cramReferenceRegion.fetchReferenceBases(CRAMStructureTestHelper.REFERENCE_SEQUENCE_ZERO);
+        Assert.assertEquals(cramReferenceRegion.getRegionLength(), fullRegionFragmentLength);
+
+        // transition to a shorter region fragment length using fetchReferenceBasesByRegion(AlignmentContext), then back to the full region
+        Assert.assertTrue(SHORT_FRAGMENT_LENGTH < fullRegionFragmentLength);
+        cramReferenceRegion.fetchReferenceBasesByRegion(
+                new AlignmentContext(
+                        new ReferenceContext(CRAMStructureTestHelper.REFERENCE_SEQUENCE_ZERO),
+                        1,
+                        SHORT_FRAGMENT_LENGTH));
+        Assert.assertEquals(cramReferenceRegion.getRegionLength(), SHORT_FRAGMENT_LENGTH);
+
+        // now transition back to the full sequence
+        cramReferenceRegion.fetchReferenceBases(CRAMStructureTestHelper.REFERENCE_SEQUENCE_ZERO);
+        Assert.assertEquals(cramReferenceRegion.getRegionLength(), fullRegionFragmentLength);
+    }
+
     @Test
     public void testGetReferenceBasesByRegionExceedsContigLength() {
         int regionStart = CRAMStructureTestHelper.REFERENCE_CONTIG_LENGTH / 2;