  
  
  #ifdef  _DEBUG
-@@ -764,6 +765,18 @@ Return Value:
+@@ -764,6 +766,19 @@ Return Value:
                  primaryResult->score = bestScore;
                  if (bestScore <= maxK) {
                      primaryResult->location = bestScoreGenomeLocation;

     unsigned scoreLimit = maxK + extraSearchDepth;
 
     //
@@ -756,6 +757,7 @@ IntersectingPairedEndAligner::align(
                                     (*nSecondaryResults)++;
 
                                 }
+								secondBestPairScore = bestPairScore;
                                 bestPairScore = pairScore;
                                 probabilityOfBestPair = pairProbability;
                                 bestResultGenomeLocation[readWithFewerHits] = candidate->readWithFewerHitsGenomeLocation + fewerEndGenomeLocationOffset;
@@ -852,9 +854,24 @@ doneScoring:
 #endif  // DEBUG
         }
     } else {

+			  unsigned _secondBestScorePair,
+			  double _probabilityOfAllCandidates,
+			  double _probabilityOfBestCandidate,
+			  double _probabilityOfSecondBestCandidate,
+			  unsigned _popularSeedsSkipped,
+			  unsigned _popularSeedsSkippedPair,
+			  _int64 _countOfHashTableLookups,
