  
  	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 +155,4 @@ struct PairedAlignmentResult {
+@@ -90,4 +151,4 @@ 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

diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/AlignmentResult.h snap/SNAPLib/AlignmentResult.h
--- tmp/snap/SNAPLib/AlignmentResult.h	2016-01-18 14:51:10.000000000 -0500
+++ snap/SNAPLib/AlignmentResult.h	2016-08-22 21:20:15.000000000 -0400
@@ -46,6 +46,68 @@ inline const char *AlignmentResultToStri
     }
 }
 

 
     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
@@ -81,6 +140,8 @@ struct PairedAlignmentResult {
 	int score[NUM_READS_PER_PAIR];              // score of each end if matched
 
 	int mapq[NUM_READS_PER_PAIR];               // mapping quality of each end, encoded like a Phred score (but as an integer, not ASCII Phred + 33).
