Commit 42b3a014 authored by Yannis Duffourd's avatar Yannis Duffourd

adding new method to write the full consensus sequence

parent 525abefc
......@@ -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 );
......
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