      GenomeLocation genomeLocation,
      Direction direction,
      bool secondaryAlignment,
-@@ -1249,7 +1250,36 @@ SAMFormat::writeRead(
+@@ -1249,7 +1250,37 @@ SAMFormat::writeRead(
              readGroupString = read->getReadGroup();
          }
      }

                     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
+++ snap/SNAPLib/BaseAligner.h	2015-08-05 11:12:27.000000000 -0400
@@ -136,6 +136,9 @@ private:
     _int64 nReadsIgnoredBecauseOfTooManyNs;

+			diffbuf[2] = '\0';
+		}
+		ztzSeparator = "\tZT:Z:";
+		snprintf(ztzbuf, 1024, "%u,%d,%s,%.8e,%d,%d,%lld,%d,%d",
+				 features.bestPossible,
+				 -features.bestScore,
+				 diffbuf,
+				 features.probabilityOfBestCandidate /
