 +struct TS_MapqEstimationFeatures {
 +	
 +	TS_MapqEstimationFeatures() :
++	bestPossible(0),
 +	bestScore(0),
 +	secondBestScore(0),
 +	probabilityOfAllCandidates(0.0),

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

 
 	InitializeSeedSequencers();
 
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/Error.h snap/SNAPLib/Error.h
--- tmp/snap/SNAPLib/Error.h	2016-01-18 14:51:10.000000000 -0500
+++ snap/SNAPLib/Error.h	2015-10-12 16:54:55.000000000 -0400
@@ -31,4 +31,4 @@ WriteErrorMessage(const char *message, .
 WriteStatusMessage(const char *message, ...);
 
     void
-WriteProgressCounter(const char *counterName, _int64 increment);
\ No newline at end of file
+WriteProgressCounter(const char *counterName, _int64 increment);
diff -rupN -x Xcode -x .git tmp/snap/SNAPLib/FileFormat.h snap/SNAPLib/FileFormat.h
--- tmp/snap/SNAPLib/FileFormat.h	2016-01-18 14:51:10.000000000 -0500
+++ snap/SNAPLib/FileFormat.h	2015-07-28 15:03:35.000000000 -0400
@@ -92,7 +92,9 @@ public:
     virtual bool writeRead(
