fixed edge case for M2 palindrome transformer (#5080)

src/main/java/org/broadinstitute/hellbender/transformers/PalindromeArtifactClipReadTransformer.java

@@ -64,7 +64,7 @@ public PalindromeArtifactClipReadTransformer(final ReferenceDataSource reference
     @Override
     public GATKRead apply(final GATKRead read) {
         final int adaptorBoundary = read.getAdaptorBoundary();
-        if (adaptorBoundary == ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY) {
+        if (!read.isProperlyPaired() || adaptorBoundary == ReadUtils.CANNOT_COMPUTE_ADAPTOR_BOUNDARY) {
             return read;
         }