adding new method to write the full consensus sequence

cpp/Vihgo.h

@@ -9,7 +9,7 @@ class Vihgo
 {
 	public:
 		Vihgo();
-		Vihgo( std::string , std::string , std::string , std::string ,  std::string , std::string, std::string,std::string,std::string,std::string, int, int , int , double, double, bool);
+		Vihgo( std::string , std::string , std::string , std::string ,  std::string , std::string, std::string,std::string,std::string,std::string, int, int , int , double, double, bool, bool);
 		int mainLoop();
 		int getGenome();
 		int getGenes();
@@ -49,6 +49,7 @@ class Vihgo
 
 		bool countStop;
 		bool annotationIsOk;
+    bool fullCS;
 
 		std::map<std::string, std::map<int, char> > referenceSequence;
 		std::map<std::string, std::map< std::string , std::string> > genes;
@@ -67,6 +68,7 @@ class Vihgo
 		std::string isInGene( std::string , int );
 		bool detectStopInRead( bam1_t * , int32_t , std::string );
 		void writeConsensus();
+    void writeFullConsensus();
 		std::string getChrFromProt( std::string );
 		bool isThereAControl();
 		std::string getAAfromCodon( std::string );