Commit 1efacb84 authored by Yannis Duffourd's avatar Yannis Duffourd

Adding new option to support full cs sequence writing

parent 42b3a014
......@@ -27,6 +27,7 @@ int main(int argc, char* argv[])
cerr << "Starting Main" << endl;
bool countStop = false;
bool fullCS = false;
int currentThread = 0;
int depthThreshold;
......@@ -56,7 +57,7 @@ int main(int argc, char* argv[])
("output,o", po::value<string>( &outputFile ), "output result file variants." )
("logFile,l", po::value<string>( &logFile ), "Log file output." )
("codon,c", po::value<string>( &codonResultFile ), "output result file variants." )
("consensus,C", po::value<string>( &csFile ), "Consensus sequence file (fasta)." )
("consensus,C", po::value<string>( &csFile ), "Consensus sequence file to be written(fasta)." )
("integrase,I", po::value<string>( &integraseFile ), "File annotation for integrase prot." )
("rt,R" , po::value<string>( &rtFile ) , "File annotation for retrotranscriptase prot." )
......@@ -69,6 +70,7 @@ int main(int argc, char* argv[])
("ratio,a" , po::value<double>( &ratioThreshold )->default_value(0.1) , "Minimum ratio of alt reads to consider a mutation. (optional)" )
("pvalue,p" , po::value<double>( &pvalueThreshold )->default_value(0.05) , "pvalue threshold from FET to consider a mutation. (optional)" )
("stop,s" , "Activate stop codon detction." )
("fullcs,f", "Write full genome consensus instead of gene by gene.")
("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.");
......@@ -180,7 +182,13 @@ int main(int argc, char* argv[])
countStop = true;
}
Vihgo * App = new Vihgo( bamFile , geneFile , rtFile , integraseFile , proteaseFile, referenceFile,outputFile, codonResultFile, csFile, inRunControlBam,depthThreshold, nbThread,loggingLevel, ratioThreshold ,pvalueThreshold, countStop );
if( vm.count( "fullcs") )
{
fullCS = true;
}
Vihgo * App = new Vihgo( bamFile , geneFile , rtFile , integraseFile , proteaseFile, referenceFile,outputFile, codonResultFile, csFile, inRunControlBam,depthThreshold, nbThread,loggingLevel, ratioThreshold ,pvalueThreshold, countStop, fullCS );
App->mainLoop();
......
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