          bool hasMate = false, bool firstInPair = false, Read * mate = NULL, 
          AlignmentResult mateResult = NotFound, GenomeLocation mateLocation = 0, Direction mateDirection = FORWARD,
          bool alignedAsPair = false) const; 
+diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/SortedDataWriter.cpp snap/SNAPLib/SortedDataWriter.cpp
+--- tmp/snap/SNAPLib/SortedDataWriter.cpp	2016-01-18 14:51:10.000000000 -0500
++++ snap/SNAPLib/SortedDataWriter.cpp	2016-01-18 14:44:34.000000000 -0500
+@@ -335,7 +335,7 @@ SortedDataFilterSupplier::mergeSort()
+     }
+     for (SortBlockVector::iterator i = blocks.begin(); i != blocks.end(); i++) {
+         i->reader = readerSupplier->getDataReader(1, MAX_READ_LENGTH * 8, 0.0,
+-            min(1UL << 23, max(1UL << 17, bufferSpace / blocks.size()))); // 128kB to 8MB buffer space per block
++            min(1ULL << 23, max(1ULL << 17, bufferSpace / blocks.size()))); // 128kB to 8MB buffer space per block
+         i->reader->init(tempFileName);
+         i->reader->reinit(i->start, i->bytes);
+     }
+diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/directions.h snap/SNAPLib/directions.h
+--- tmp/snap/SNAPLib/directions.h	2016-01-18 14:51:10.000000000 -0500
++++ snap/SNAPLib/directions.h	2015-10-12 16:54:59.000000000 -0400
+@@ -33,4 +33,4 @@ const int RC = 1;
+ inline Direction OppositeDirection(Direction direction) {
+     _ASSERT(FORWARD == direction || RC == direction);
+     return 1-direction;
+-}
+\ No newline at end of file
++}

+	hitsPerLookup(0.0f),
+	hitsPerLookupPair(0.0f) { }
+	
+	void init(unsigned _bestScore,
+			  unsigned _secondBestScore,
+			  double _probabilityOfAllCandidates,
+			  double _probabilityOfBestCandidate,

 			result->direction[r] = singleResult.direction;
 			result->location[r] = singleResult.location;
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/CommandProcessor.cpp snap/SNAPLib/CommandProcessor.cpp
--- tmp/snap/SNAPLib/CommandProcessor.cpp	2016-01-18 14:55:36.000000000 -0500
+++ snap/SNAPLib/CommandProcessor.cpp	2015-08-04 10:54:20.000000000 -0400
@@ -162,7 +162,8 @@ void RunDaemonMode(int argc, const char 
 
