 +	unsigned secondBestScorePair;
 +	double probabilityOfAllCandidates;
 +	double probabilityOfBestCandidate;
++	double probabilityOfSecondBestCandidate;
 +	unsigned popularSeedsSkipped;
 +	unsigned popularSeedsSkippedPair;
 +	_int64 countOfHashTableLookups;

 
     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 +136,8 @@ 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).

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 16:50:23.000000000 -0400
@@ -46,6 +46,64 @@ inline const char *AlignmentResultToStri
     }
 }
 
