                      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
++++ snap/SNAPLib/SAM.cpp	2015-08-04 10:46:28.000000000 -0400
 @@ -1123,6 +1123,7 @@ SAMFormat::writeRead(
      Read * read,
      AlignmentResult result, 

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

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