              result->score[whichRead] = bestResultScore[whichRead];
 diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/IntersectingPairedEndAligner.h snap/SNAPLib/IntersectingPairedEndAligner.h
 --- tmp/snap/SNAPLib/IntersectingPairedEndAligner.h	2016-01-18 14:51:10.000000000 -0500
-+++ snap/SNAPLib/IntersectingPairedEndAligner.h	2016-08-22 21:02:56.000000000 -0400
-@@ -268,6 +268,7 @@ private:
++++ snap/SNAPLib/IntersectingPairedEndAligner.h	2016-08-23 10:50:16.000000000 -0400
+@@ -268,6 +268,8 @@ private:
      int                                     countOfHashTableLookups[NUM_READS_PER_PAIR];
      _int64                                  totalHashTableHits[NUM_READS_PER_PAIR][NUM_DIRECTIONS];
      _int64                                  largestHashTableHit[NUM_READS_PER_PAIR][NUM_DIRECTIONS];
 +    _int64                                  minHashTableHits[NUM_READS_PER_PAIR][NUM_DIRECTIONS];
++    int                                     misses[NUM_READS_PER_PAIR][NUM_DIRECTIONS];
      unsigned                                readWithMoreHits;
      unsigned                                readWithFewerHits;
  

                                 bestPairScore = pairScore;
                                 probabilityOfBestPair = pairProbability;
                                 bestResultGenomeLocation[readWithFewerHits] = candidate->readWithFewerHitsGenomeLocation + fewerEndGenomeLocationOffset;
@@ -771,6 +775,9 @@ IntersectingPairedEndAligner::align(
 
                                 isBestHit = true;
                             } else {

     unsigned scoreLimit = maxK + extraSearchDepth;
 
     //
@@ -350,6 +353,11 @@ IntersectingPairedEndAligner::align(
                 } else {
                     offset = readLen[whichRead] - seedLen - nextSeedToTest;
                 }
+				if(nHits[dir] > 0) {
+					minHashTableHits[whichRead][dir] = min(minHashTableHits[whichRead][dir], nHits[dir]);
+				} else {
+					misses[whichRead][dir]++;
+				}
                 if (nHits[dir] < maxBigHits) {
                     totalHashTableHits[whichRead][dir] += nHits[dir];
                     if (doesGenomeIndexHave64BitLocations) {
@@ -756,6 +764,7 @@ IntersectingPairedEndAligner::align(
                                     (*nSecondaryResults)++;
 
                                 }
