      unsigned scoreLimit = maxK + extraSearchDepth;
  
      //
-@@ -350,6 +352,7 @@ IntersectingPairedEndAligner::align(
+@@ -350,6 +353,11 @@ IntersectingPairedEndAligner::align(
                  } else {
                      offset = readLen[whichRead] - seedLen - nextSeedToTest;
                  }
-+				minHashTableHits[whichRead][dir] = min(minHashTableHits[whichRead][dir], nHits[dir]);
++				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 +759,7 @@ IntersectingPairedEndAligner::align(
+@@ -756,6 +764,7 @@ IntersectingPairedEndAligner::align(
                                      (*nSecondaryResults)++;
  
                                  }

             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:
     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];
     unsigned                                readWithMoreHits;
     unsigned                                readWithFewerHits;
 

+			diffbufPair[2] = '\0';
+		}
+		ztzSeparator = "\tZT:Z:";
+		snprintf(ztzbuf, 1024, "%d,%s,%s,%d,%d,%d,%lld,%lld,%d,%d,%d,%d",
+				 -features.bestScore,
+				 diffbuf,
+				 diffbufPair,
