 +		popularSeedsSkippedPair = _popularSeedsSkippedPair;
 +		minHits = _minHits;
 +		minHitsInDirection = _minHitsInDirection;
++		misses = _misses;
++		missesInDirection = _missesInDirection;
 +		hitsPerLookup = _hitsPerLookup;
 +		hitsPerLookupPair = _hitsPerLookupPair;
 +	}

+												 0,
+												 minHits,
+												 minHitsInDirection,
+												 hitsPerLookup,
+												 0);
                     primaryResult->mapq = computeMAPQ(probabilityOfAllCandidates, probabilityOfBestCandidate, bestScore, popularSeedsSkipped);

         *spaceUsed = bamSize;
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/BaseAligner.cpp snap/SNAPLib/BaseAligner.cpp
--- tmp/snap/SNAPLib/BaseAligner.cpp	2016-01-18 14:51:10.000000000 -0500
+++ snap/SNAPLib/BaseAligner.cpp	2016-08-23 10:47:40.000000000 -0400
@@ -289,7 +289,7 @@ Return Value:
     primaryResult->score = UnusedScoreValue;
     primaryResult->status = NotFound;
