#endif
string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
float match, misMatch, gapOpen, gapExtend, threshold;
int processors, kmerSize;
vector<string> candidateFileNames;
#endif
string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
float match, misMatch, gapOpen, gapExtend, threshold;
int processors, kmerSize;
vector<string> candidateFileNames;