 +	secondBestScorePair(0),
 +	probabilityOfAllCandidates(0.0),
 +	probabilityOfBestCandidate(0.0),
-+	probabilityOfSecondBestCandidate(0.0),
 +	popularSeedsSkipped(0),
 +	popularSeedsSkippedPair(0),
 +	minHits(0),

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

 
     static int compareByContigAndScore(const void *first, const void *second);      // qsort()-style compare routine
     static int compareByScore(const void *first, const void *second);               // qsort()-style compare routine
@@ -81,6 +140,8 @@ struct PairedAlignmentResult {
 	int score[NUM_READS_PER_PAIR];              // score of each end if matched
 
 	int mapq[NUM_READS_PER_PAIR];               // mapping quality of each end, encoded like a Phred score (but as an integer, not ASCII Phred + 33).
