 +	unsigned popularSeedsSkipped;
 +	unsigned popularSeedsSkippedPair;
 +	_int64 countOfHashTableLookups;
-+	_int64 countOfHashTableLookupsPair;
 +	float hitsPerLookup;
 +	float hitsPerLookupPair;
 +};

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

         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	2015-07-28 15:15:02.000000000 -0400
+++ snap/SNAPLib/IntersectingPairedEndAligner.cpp	2015-08-05 14:07:33.000000000 -0400
@@ -852,9 +852,22 @@ doneScoring:
 #endif  // DEBUG
         }
     } else {
