Commit 552afefb authored by Yannis Duffourd's avatar Yannis Duffourd

in run control is now an option

parent 4ca3fb2b
......@@ -18,6 +18,7 @@
// Classes
#include "Vihgo.h"
using namespace std;
namespace po = boost::program_options;
......@@ -157,11 +158,7 @@ int main(int argc, char* argv[])
return -1;
}
}
else
{
cerr << "No file provided as control sample BAM file : stopping" << endl;
return -1;
}
if( geneFile.length( ) > 0 )
{
......@@ -178,6 +175,11 @@ int main(int argc, char* argv[])
}
if( vm.count( "stop") )
{
countStop = true;
}
Vihgo * App = new Vihgo( bamFile , geneFile , rtFile , integraseFile , proteaseFile, referenceFile,outputFile, codonResultFile, csFile, inRunControlBam,depthThreshold, nbThread,loggingLevel, ratioThreshold ,pvalueThreshold, countStop );
App->mainLoop();
......
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