                      if (primaryResult->mapq >= MAPQ_LIMIT_FOR_SINGLE_HIT) {
                          primaryResult->status = SingleHit;
 diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/BaseAligner.h snap/SNAPLib/BaseAligner.h
---- tmp/snap/SNAPLib/BaseAligner.h	2015-07-28 15:15:02.000000000 -0400
+--- tmp/snap/SNAPLib/BaseAligner.h	2016-01-18 14:51:10.000000000 -0500
 +++ snap/SNAPLib/BaseAligner.h	2015-08-05 11:12:27.000000000 -0400
 @@ -136,6 +136,9 @@ private:
      _int64 nReadsIgnoredBecauseOfTooManyNs;

 struct SingleAlignmentResult {
 	AlignmentResult status;
 
@@ -54,6 +100,7 @@ struct SingleAlignmentResult {
     int             score;		// score of each end if matched
 
     int             mapq;		// mapping quality, encoded like a Phred score (but as an integer, not ASCII Phred + 33).

 
 	bool fromAlignTogether;                     // Was this alignment created by aligning both reads together, rather than from some combination of single-end aligners?
 	bool alignedAsPair;                         // Were the reads aligned as a pair, or separately?
@@ -90,4 +143,4 @@ struct PairedAlignmentResult {
 
     static int compareByContigAndScore(const void *first, const void *second);      // qsort()-style compare routine
     static int compareByScore(const void *first, const void *second);               // qsort()-style compare routine
-};
\ No newline at end of file
+};
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/Bam.cpp snap/SNAPLib/Bam.cpp
--- tmp/snap/SNAPLib/Bam.cpp	2016-01-18 14:51:10.000000000 -0500
+++ snap/SNAPLib/Bam.cpp	2015-07-28 15:04:32.000000000 -0400
@@ -682,7 +682,9 @@ public:
     virtual bool writeRead(
