          qnameLen, read->getId(),
          flags,
          contigName,
-@@ -1263,7 +1292,10 @@ SAMFormat::writeRead(
+@@ -1263,7 +1295,10 @@ SAMFormat::writeRead(
          fullLength, quality,
          aux != NULL ? "\t" : "", auxLen, aux != NULL ? aux : "",
          readGroupSeparator, readGroupString,

                     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	2015-07-28 17:20:08.000000000 -0400
@@ -1123,6 +1123,7 @@ SAMFormat::writeRead(
     Read * read,
     AlignmentResult result, 

     GenomeLocation genomeLocation,
     Direction direction,
     bool secondaryAlignment,
@@ -1249,7 +1250,38 @@ SAMFormat::writeRead(
             readGroupString = read->getReadGroup();
         }
     }
