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

                     primaryResult->mapq = computeMAPQ(probabilityOfAllCandidates, probabilityOfBestCandidate, bestScore, popularSeedsSkipped);
                     if (primaryResult->mapq >= MAPQ_LIMIT_FOR_SINGLE_HIT) {
                         primaryResult->status = SingleHit;
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/BaseAligner.h snap/SNAPLib/BaseAligner.h
--- tmp/snap/SNAPLib/BaseAligner.h	2016-01-18 14:51:10.000000000 -0500
+++ snap/SNAPLib/BaseAligner.h	2015-08-05 11:12:27.000000000 -0400
@@ -136,6 +136,9 @@ private:
     _int64 nReadsIgnoredBecauseOfTooManyNs;
     _int64 nIndelsMerged;

     GenomeLocation genomeLocation,
     Direction direction,
     bool secondaryAlignment,
@@ -1249,7 +1250,46 @@ SAMFormat::writeRead(
             readGroupString = read->getReadGroup();
         }
     }
