implementation of reference, genes and annotations reading

cpp/Vihgo.h

@@ -9,16 +9,23 @@ class Vihgo
 {
 	public:
 		Vihgo();
-		Vihgo( 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);
 		int mainLoop();
 		int getGenome();
 		int getGenes();
+		int getAnnotation();
+		int readRunControl();
+
+		bool isAnnotationDefined();
+		std::vector<std::string> getAnnotationFiles();
+
+		private :
 
-	private :
 		std::string sampleName;
 		std::string inputBamFile;
 		std::string integraseFile;
 		std::string proteaseFile;
+		std::string retrotranscriptaseFile;
 		std::string referenceFile;
 		std::string outputFile;
 		std::string codonResultFile;
@@ -34,10 +41,13 @@ class Vihgo
 		double pvalueThreshold;
 
 		bool countStop;
+		bool annotationIsOk;
 
-		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< int , std::string>> referenceCodon;
+		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< int , std::string> > referenceCodon;
+		std::map<std::string, std::map< int , std::string> > protCodon;
+		std::map<std::string, std::map< std::string , std::string> > knownMutationTable;
 
 		// method
 		void displayGenome();

cpp/main.cpp

@@ -178,7 +178,7 @@ int main(int argc, char* argv[])
 	}
 
 
-	Vihgo * App = new Vihgo( bamFile , geneFile , integraseFile , proteaseFile, referenceFile,outputFile, codonResultFile, csFile, inRunControlBam,depthThreshold, nbThread,loggingLevel, ratioThreshold ,pvalueThreshold, countStop );
+	Vihgo * App = new Vihgo( bamFile , geneFile , rtFile , integraseFile , proteaseFile, referenceFile,outputFile, codonResultFile, csFile, inRunControlBam,depthThreshold, nbThread,loggingLevel, ratioThreshold ,pvalueThreshold, countStop );
   App->mainLoop();
 
 

cpp/utils.cpp

@@ -4,6 +4,7 @@
 #include <fstream>
 #include <sstream>
 #include <stdexcept>
+#include <cstring>
 #include <sys/time.h>
 #include <sys/types.h>
 
@@ -77,11 +78,46 @@ string char_to_string(char incoming)
 	return s;
 }
 
+vector<string> parseOnSep( string inc , string sep )
+{
+	vector<string> ret;
+	istringstream issInc (inc);
+	string mot;
+	while ( getline( issInc, mot, string_to_char( sep ) ) )
+	{
+		ret.push_back( mot );
+	}
+	return ret;
+
+}
+
 
+char string_to_char( string inc )
+{
+	char cstr[inc.size() + 1];
+	inc.copy(cstr, inc.size() + 1);
+	cstr[inc.size()] = '\0';
+	return *cstr;
+}
 
 
 
 
+string strip( string inc )
+{
+	cerr << "Passing into strip << " << inc ;
+	string::size_type pos = 0;
+	while ( ( pos = inc.find ("\n",pos) ) != string::npos )
+	{
+		cerr << " ; pos = " << pos ;
+		inc.erase ( pos, 2 );
+	}
+	cerr << " to " << inc << endl;
+	return inc;
+}
+
+
+