#endif
bool abort, realign, trim, trimera, save;
- string fastafile, templatefile, outputDir, search, namefile;
+ string fastafile, templatefile, outputDir, search, namefile, blastlocation;
int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
float divR;
Chimera* chimera;