- string method, fastafile, templatefile, consfile;
- bool filter, correction;
- int processors, midpoint, averageLeft, averageRight, window, iters, increment;
+ string method, fastafile, templatefile, consfile, quanfile, maskfile, namefile;
+ bool filter, correction, svg;
+ int processors, midpoint, averageLeft, averageRight, window, iters, increment, numwanted, ksize;