- bool abort, keepprimer;
- string fastafile, oligosfile, taxfile, groupfile, namefile, ecolifile, outputDir, nomatch;
- int start, end, pdiffs, processors, length;
+ bool abort, keepprimer, keepdots;
+ string fastafile, oligosfile, taxfile, groupfile, namefile, countfile, ecolifile, outputDir, nomatch;
+ int start, end, processors, length;