- if (outputDir == "") { outputDir += hasPath(candidateFileNames[s]); }
- string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
- string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
- string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
+ if (outputDir == "") { outputDir += m->hasPath(candidateFileNames[s]); }
+ string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align";
+ string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "align.report";
+ string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + "flip.accnos";