 +												 0xffff,
 +												 probabilityOfAllCandidates,
 +												 probabilityOfBestCandidate,
++												 probabilityOfSecondBestCandidate,
 +												 popularSeedsSkipped,
 +												 0,
 +												 lookupsThisRun,

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

     //
     // 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
