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vihgo
Commit 42b3a014 authored by Yannis Duffourd's avatar Yannis Duffourd
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adding new method to write the full consensus sequence

parent 525abefc
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Showing with 3 additions and 1 deletion
cpp/Vihgo.h
View file @ 42b3a014
...@@ -9,7 +9,7 @@ class Vihgo ...@@ -9,7 +9,7 @@ class Vihgo
{ {
public: public:
Vihgo(); 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 mainLoop();
int getGenome(); int getGenome();
int getGenes(); int getGenes();
...@@ -49,6 +49,7 @@ class Vihgo ...@@ -49,6 +49,7 @@ class Vihgo
bool countStop; bool countStop;
bool annotationIsOk; bool annotationIsOk;
bool fullCS;
std::map<std::string, std::map<int, char> > referenceSequence; std::map<std::string, std::map<int, char> > referenceSequence;
std::map<std::string, std::map< std::string , std::string> > genes; std::map<std::string, std::map< std::string , std::string> > genes;
...@@ -67,6 +68,7 @@ class Vihgo ...@@ -67,6 +68,7 @@ class Vihgo
std::string isInGene( std::string , int ); std::string isInGene( std::string , int );
bool detectStopInRead( bam1_t * , int32_t , std::string ); bool detectStopInRead( bam1_t * , int32_t , std::string );
void writeConsensus(); void writeConsensus();
void writeFullConsensus();
std::string getChrFromProt( std::string ); std::string getChrFromProt( std::string );
bool isThereAControl(); bool isThereAControl();
std::string getAAfromCodon( std::string ); std::string getAAfromCodon( std::string );
......
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