 +			  unsigned _popularSeedsSkippedPair,
 +			  _int64 _minHits,
 +			  _int64 _minHitsInDirection,
++			  int _misses,
++			  int _missesInDirection,
 +			  float _hitsPerLookup,
 +			  float _hitsPerLookupPair)
 +	{

 
 	bool fromAlignTogether;                     // Was this alignment created by aligning both reads together, rather than from some combination of single-end aligners?
 	bool alignedAsPair;                         // Were the reads aligned as a pair, or separately?
@@ -90,4 +151,4 @@ struct PairedAlignmentResult {
 
     static int compareByContigAndScore(const void *first, const void *second);      // qsort()-style compare routine
     static int compareByScore(const void *first, const void *second);               // qsort()-style compare routine

     GenomeLocation genomeLocation,
     Direction direction,
     bool secondaryAlignment,
@@ -1249,7 +1250,47 @@ SAMFormat::writeRead(
             readGroupString = read->getReadGroup();
         }
     }
