- bool abort, trim;
- int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers;
- int numFlows, numFPrimers, numRPrimers, processors;
- float signal, noise;
+ bool abort, trim, large, flip, allFiles, keepforward, append, makeGroup;
+ int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs;
+ int processors, maxIters, largeSize;
+ float signal, noise, cutoff, sigma;
+ int keepFirst, removeLast, maxAmbig;