  
  	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 {
+@@ -90,4 +151,4 @@ 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

diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/AlignmentResult.h snap/SNAPLib/AlignmentResult.h
--- tmp/snap/SNAPLib/AlignmentResult.h	2016-01-18 14:51:10.000000000 -0500
+++ snap/SNAPLib/AlignmentResult.h	2016-08-22 21:20:15.000000000 -0400
@@ -46,6 +46,68 @@ inline const char *AlignmentResultToStri
     }
 }
 

+		secondBestScorePair = _secondBestScorePair;
+		probabilityOfAllCandidates = _probabilityOfAllCandidates;
+		probabilityOfBestCandidate = _probabilityOfBestCandidate;
+		popularSeedsSkipped = _popularSeedsSkipped;
+		popularSeedsSkippedPair = _popularSeedsSkippedPair;
+		minHits = _minHits;
