first implementation

main.cpp

+// C++ std libs
+#include <iostream>
+#include <vector>
+#include <map>
+#include <string>
+#include <fstream>
+#include <sstream>
+#include <stdexcept>
+#include <sys/time.h>
+#include <sys/types.h>
+
+// C++ Boost
+#include <boost/program_options.hpp>
+
+// utils
+#include "utils.h"
+
+// Classes
+#include "Galacs.h"
+
+
+using namespace std;
+namespace po = boost::program_options;
+
+int main(int argc, char* argv[])
+{
+    cerr << "Starting Main" << endl;
+
+	int currentThread = 0;
+	int nbThread = 1;
+	int loggingLevel;
+    int window; 
+    int step; 
+
+	double ratioThreshold;
+	double pvalueThreshold;
+    double zscore;
+	
+	string bamFile;
+	string outputFile;
+    string outputFilePairs;
+    string outputFileSplits;
+	string logFile;
+    string referenceFile;
+
+
+	po::options_description desc("Allowed options");
+	desc.add_options()
+	("help,h", "produce help message")
+	("input,i",  po::value<string>(&bamFile), "Input BAM file containing aligned read from sample.")
+	("output,o",  po::value<string>(&outputFile), "output result file variants.")
+    ("outputPairs,p",  po::value<string>(&outputFilePairs), "output result file containing discordant pairs.")
+    ("outputSplits,S",  po::value<string>(&outputFileSplits), "output result file containing split read.")
+	("logFile,l",  po::value<string>(&logFile), "Log file output.")
+	("reference,r" ,  po::value<string>(&referenceFile) , "Reference Fasta file." )
+	("window,w", po::value<int>(&window)->default_value(50), "Depth treshold to call a variant. (optional)")
+	("step,s" , po::value<int>(&step)->default_value(0.1) , "Minimum ratio of alt reads to consider a mutation. (optional)" )
+	("zscore,z" , po::value<double>(&zscore)->default_value(0.05) , "pvalue threshold from FET to consider a mutation. (optional)" )
+	("thread,t", po::value<int>(&nbThread)->default_value(50), "Number of thread to use. (NYI)")
+	("loglevel,L", po::value<int>(&loggingLevel)->default_value(1), "Logging level.");
+
+
+	po::variables_map vm;
+	po::store(po::parse_command_line(argc, argv, desc), vm);
+	po::notify(vm);
+
+	// Verif que le nb de thread n'est pas négatif ...
+	if( nbThread < 1 )
+	{
+		nbThread = 1;
+		cerr << "You entered a null or negative value for thread number, positionning it to 1. " << endl;
+	}
+
+
+	if( argc <= 1 )
+	{
+		cerr << "Error while checking program arguments" << endl;
+		cerr << desc << "\n";
+		return 1;
+	}
+
+
+	// check provided files
+	if( bamFile.length( ) > 0 )
+	{
+		if( !IsFileReadable( bamFile ) )
+		{
+			cerr << "File provided as input BAM : " << bamFile << " is not accessible : stopping" << endl;
+			return -1;
+		}
+	}
+	else
+	{
+		cerr << "No file provided as input BAM file : stopping" << endl;
+		return -1;
+	}
+
+
+	if( referenceFile.length( ) > 0 )
+	{
+		if( !IsFileReadable( referenceFile ) )
+		{
+			cerr << "File provided as reference : " << referenceFile << " is not accessible : stopping" << endl;
+			return -1;
+		}
+	}
+	else
+	{
+		cerr << "No file provided as reference file : stopping" << endl;
+		return -1;
+	}
+
+
+	Galacs * App = new Galacs(bamFile, referenceFile, outputFile, outputFilePairs, outputFileSplits, window, step, zscore, nbThread, loggingLevel);
+  App->mainLoop();
+
+
+	delete App;
+	cerr << "end of main" << endl;
+  return 0;
+}