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

 
 	bool fromAlignTogether;                     // Was this alignment created by aligning both reads together, rather than from some combination of single-end aligners?
 	bool alignedAsPair;                         // Were the reads aligned as a pair, or separately?
@@ -90,4 +155,4 @@ struct PairedAlignmentResult {
 
     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

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