 +											 secondBestPairScore,
 +											 probabilityOfAllPairs,
 +											 probabilityOfBestPair,
++											 probabilityOfSecondBestPair,
 +											 popularSeedsSkipped[whichRead],
 +											 popularSeedsSkipped[0] + popularSeedsSkipped[1],
 +											 countOfHashTableLookups[whichRead],

         bool alignedAsPair = false) const = 0; 
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/IntersectingPairedEndAligner.cpp snap/SNAPLib/IntersectingPairedEndAligner.cpp
--- tmp/snap/SNAPLib/IntersectingPairedEndAligner.cpp	2016-01-18 14:55:36.000000000 -0500
+++ snap/SNAPLib/IntersectingPairedEndAligner.cpp	2016-08-22 13:48:33.000000000 -0400
@@ -277,6 +277,7 @@ IntersectingPairedEndAligner::align(
     localBestPairProbability[1] = 0;
     double probabilityOfAllPairs = 0;
     unsigned bestPairScore = 65536;

     //
     // A bitvector indexed by offset in the read indicating whether this seed is used.
     // This is here to avoid doing a memory allocation in the aligner.
@@ -257,6 +260,7 @@ private:
     unsigned lvScoresAfterBestFound;
     double probabilityOfAllCandidates;
     double probabilityOfBestCandidate;
+    double probabilityOfSecondBestCandidate;
     int firstPassSeedsNotSkipped[NUM_DIRECTIONS];
     _int64 smallestSkippedSeed[NUM_DIRECTIONS];
     unsigned highestWeightListChecked;
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/ChimericPairedEndAligner.cpp snap/SNAPLib/ChimericPairedEndAligner.cpp
--- tmp/snap/SNAPLib/ChimericPairedEndAligner.cpp	2016-01-18 14:51:10.000000000 -0500
+++ snap/SNAPLib/ChimericPairedEndAligner.cpp	2015-08-05 09:03:57.000000000 -0400
