 +		
 +		// ZT:Z
 +		ztzSeparator = "\tZT:Z:";
-+		snprintf(ztzbuf, 1024, "%0.8f,%0.8f,%d", features.probabilityOfAllCandidates, features.probabilityOfBestCandidate, features.popularSeedsSkipped);
++		snprintf(ztzbuf, 1024, "%0.8f,%0.8f,%d",
++				 features.probabilityOfBestCandidate,
++				 features.probabilityOfAllCandidates - features.probabilityOfBestCandidate,
++				 features.popularSeedsSkipped);
 +		ztzString = ztzbuf;
 +	}
 +	

                     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();
         }
     }
