Fix an NPE in CRAMRecordReadFeatures.restoreReadBases (#1655)

* Fix an NPE in CRAMRecordReadFeatures.restoreReadBases() when reading crams with embedded references.
* Fix for igvteam/igv#1286

src/main/java/htsjdk/samtools/cram/structure/CRAMRecordReadFeatures.java

@@ -495,6 +495,9 @@ public static byte[] restoreReadBases(
     }
 
     private static byte getByteOrDefault(final byte[] array, final int pos, final byte outOfBoundsValue) {
+        if (array == null) {
+            return outOfBoundsValue;
+        }
         return pos >= array.length ?
                 outOfBoundsValue :
                 array[pos];

src/test/java/htsjdk/samtools/CRAMReferencelessTest.java

@@ -14,7 +14,7 @@ public class CRAMReferencelessTest extends HtsjdkTest {
     private static final File TEST_DATA_DIR = new File("src/test/resources/htsjdk/samtools/cram");
 
     @Test
-    private void testReadCRAMWithEmbeddedReference() throws IOException {
+    public void testReadCRAMWithEmbeddedReference() throws IOException {
         try (final SamReader cramReader = SamReaderFactory.makeDefault()
                 .validationStringency(ValidationStringency.LENIENT)
                 .referenceSource(new ReferenceSource(new File(TEST_DATA_DIR, "human_g1k_v37.20.21.1-100.fasta")))
@@ -24,16 +24,44 @@ private void testReadCRAMWithEmbeddedReference() throws IOException {
                      .open(new File(TEST_DATA_DIR, "referenceEmbedded.NA12878.20.21.1-100.100-SeqsPerSlice.500-unMapped.cram"))) {
             final Iterator<SAMRecord> cramIterator = cramReader.iterator();
             final Iterator<SAMRecord> cramEmbeddedIterator = cramReaderEmbedded.iterator();
+            int count = 0;
             while (cramIterator.hasNext() && cramEmbeddedIterator.hasNext()) {
+                count++;
                 final SAMRecord cramRecord = cramIterator.next();
                 final SAMRecord cramRecordEmbedded = cramEmbeddedIterator.next();
                 Assert.assertEquals(cramRecordEmbedded, cramRecord);
             }
+            Assert.assertTrue( count >0, "Expected reads but there were none.");
         }
     }
 
+    // test for https://github.com/igvteam/igv/issues/1286
+    // cram was generated subset from an example cram using samtools and -O no_ref
     @Test
-    private void testReadCRAMNoReferenceRequired() throws IOException {
+    public void testForNPE() throws IOException {
+        try (final SamReader cramReader = SamReaderFactory.makeDefault()
+                .validationStringency(ValidationStringency.LENIENT)
+                .open(new File(TEST_DATA_DIR, "testIGV1286.sam"));
+             final SamReader cramReaderEmbedded = SamReaderFactory.makeDefault()
+                     .validationStringency(ValidationStringency.LENIENT)
+                     .open(new File(TEST_DATA_DIR, "testIGV1286.cram"))) {
+            final Iterator<SAMRecord> cramIterator = cramReader.iterator();
+            final Iterator<SAMRecord> cramEmbeddedIterator = cramReaderEmbedded.iterator();
+            int count = 0;
+            while (cramIterator.hasNext() && cramEmbeddedIterator.hasNext()) {
+                count++;
+                final SAMRecord cramRecord = cramIterator.next();
+                final SAMRecord cramRecordEmbedded = cramEmbeddedIterator.next();
+                Assert.assertEquals(cramRecordEmbedded, cramRecord);
+            }
+            Assert.assertEquals(count, 2);
+            Assert.assertFalse(cramIterator.hasNext());
+            Assert.assertFalse(cramEmbeddedIterator.hasNext());
+        }
+    }
+
+    @Test
+    public void testReadCRAMNoReferenceRequired() throws IOException {
         // test reading a cram with no reference compression (RR=false in compression header)
         try (final SamReader samReader = SamReaderFactory.makeDefault()
                              .validationStringency(ValidationStringency.LENIENT)