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

in run control is now an option

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