Fix LTF8 9-byte write bug: wrong bit shift (>> 28 instead of >> 24)

src/main/java/htsjdk/samtools/cram/io/LTF8.java

@@ -195,7 +195,7 @@ public static int writeUnsignedLTF8(final long value, final OutputStream outputS
             outputStream.write((int) ((value >> 48) & 0xFF));
             outputStream.write((int) ((value >> 40) & 0xFF));
             outputStream.write((int) ((value >> 32) & 0xFF));
-            outputStream.write((int) ((value >> 28) & 0xFF));
+            outputStream.write((int) ((value >> 24) & 0xFF));
             outputStream.write((int) ((value >> 16) & 0xFF));
             outputStream.write((int) ((value >> 8) & 0xFF));
             outputStream.write((int) (value & 0xFF));

src/test/java/htsjdk/samtools/cram/io/LTF8Test.java

@@ -71,6 +71,47 @@ public void testPredefined (long value, byte[] ltf8) throws IOException {
         }
     }
 
+    /**
+     * Tests the 9-byte (full 64-bit) LTF8 encoding with a value where bits [35:32] differ from
+     * bits [27:24], which exposes the >> 28 vs >> 24 bug in writeUnsignedLTF8.
+     *
+     * For 0x0123456789ABCDEFL:
+     *   (value >> 28) & 0xFF == 0x78  (wrong, old behavior)
+     *   (value >> 24) & 0xFF == 0x89  (correct)
+     *
+     * The 9-byte encoding writes a 0xFF prefix followed by bytes at shifts 56,48,40,32,24,16,8,0.
+     */
+    @Test
+    public void testNineByteEncodingWithDistinctBitsAt24And28() throws IOException {
+        final long value = 0x0123456789ABCDEFL;
+
+        // Expected encoding: 0xFF prefix + 8 bytes at shifts 56,48,40,32,24,16,8,0
+        final byte[] expectedBytes = {
+            (byte) 0xFF,
+            (byte) 0x01, // >> 56
+            (byte) 0x23, // >> 48
+            (byte) 0x45, // >> 40
+            (byte) 0x67, // >> 32
+            (byte) 0x89, // >> 24  (would be 0x78 with the >> 28 bug)
+            (byte) 0xAB, // >> 16
+            (byte) 0xCD, // >> 8
+            (byte) 0xEF, // >> 0
+        };
+
+        try (ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
+            final int bitsWritten = LTF8.writeUnsignedLTF8(value, baos);
+            Assert.assertEquals(bitsWritten, 72);
+
+            final byte[] actualBytes = baos.toByteArray();
+            Assert.assertEquals(actualBytes, expectedBytes, "9-byte LTF8 encoded bytes do not match expected");
+
+            try (ByteArrayInputStream bais = new ByteArrayInputStream(actualBytes)) {
+                final long decoded = LTF8.readUnsignedLTF8(bais);
+                Assert.assertEquals(decoded, value, "Round-trip encode/decode mismatch for 9-byte LTF8 value");
+            }
+        }
+    }
+
     @Test(expectedExceptions = RuntimeEOFException.class)
     public void emptyStreamTest() throws IOException {
         try (InputStream emptyStream = new ByteArrayInputStream(new byte[0])) {