ofstream outSfftxt, outFasta, outQual, outFlow;
string outFastaFileName, outQualFileName;
+ string rootName = outputDir + m->getRootName(m->getSimpleName(input));
+ if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
+
string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
if (trim) {