release v0.3 : Adding features : read in run control optionnaly, cs generation,…

cpp/Vihgo.h

@@ -3,7 +3,7 @@
 
 #include <vector>
 #include <map>
-
+#include <htslib/sam.h>
 
 class Vihgo
 {
@@ -15,6 +15,13 @@ class Vihgo
 		int getGenes();
 		int getAnnotation();
 		int readRunControl();
+		int readSample();
+		int variantCalling();
+		std::string getControlBamFile();
+		std::string getBamFile();
+		bool isInGeneList( std::string );
+		bool getCountStop();
+		std::string getConsensusFile();
 
 		bool isAnnotationDefined();
 		std::vector<std::string> getAnnotationFiles();
@@ -47,11 +54,31 @@ class Vihgo
 		std::map<std::string, std::map< std::string , std::string> > genes;
 		std::map<std::string, std::map< int , std::string> > referenceCodon;
 		std::map<std::string, std::map< int , std::string> > protCodon;
+		std::map<std::string, std::map<int , int> > refProtCorresp;
 		std::map<std::string, std::map< std::string , std::string> > knownMutationTable;
 
 		// method
 		void displayGenome();
 		void displayGenes();
+		void displayCodons();
+		void displayData( std::string );
+		void displayReferenceCodons();
+		void writeCodonFile( std::string );
+		std::string isInGene( std::string , int );
+		bool detectStopInRead( bam1_t * , int32_t , std::string );
+		void writeConsensus();
+		std::string getChrFromProt( std::string );
+		bool isThereAControl();
+		std::string getAAfromCodon( std::string );
+
+		// map of codon
+		std::map<std::string , std::string > codonTable;
+
+		// control data
+		std::map<std::string , std::map<int , std::map< std::string , int> > >  controlData;
+		// sample data
+		std::map<std::string , std::map<int , std::map< std::string , int> > >  sampleData;
+
 
 };
 #endif