          qnameLen, read->getId(),
          flags,
          contigName,
-@@ -1263,7 +1295,10 @@ SAMFormat::writeRead(
+@@ -1263,7 +1300,10 @@ SAMFormat::writeRead(
          fullLength, quality,
          aux != NULL ? "\t" : "", auxLen, aux != NULL ? aux : "",
          readGroupSeparator, readGroupString,

 
     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 +111,8 @@ 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).

                     if (0 == addFrontClipping) {
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/SAM.cpp snap/SNAPLib/SAM.cpp
--- tmp/snap/SNAPLib/SAM.cpp	2015-07-28 15:15:02.000000000 -0400
+++ snap/SNAPLib/SAM.cpp	2015-08-05 11:25:54.000000000 -0400
@@ -1123,6 +1123,7 @@ SAMFormat::writeRead(
     Read * read,
     AlignmentResult result, 
