+
+ temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
+ m->mothurConvert(temp, minFlows);
+
+ temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
+ m->mothurConvert(temp, maxFlows);
+
+ temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found"){ temp = "9"; }
+ m->mothurConvert(temp, maxHomoP);
+
+ temp = validParameter.validFile(parameters, "signal", false); if (temp == "not found"){ temp = "0.50"; }
+ m->mothurConvert(temp, signal);
+
+ temp = validParameter.validFile(parameters, "noise", false); if (temp == "not found"){ temp = "0.70"; }
+ m->mothurConvert(temp, noise);
+
+ temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, bdiffs);
+
+ temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, pdiffs);
+
+ temp = validParameter.validFile(parameters, "ldiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, ldiffs);
+
+ temp = validParameter.validFile(parameters, "sdiffs", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, sdiffs);
+
+ temp = validParameter.validFile(parameters, "tdiffs", false); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
+ m->mothurConvert(temp, tdiffs);
+
+ if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
+
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ flowOrder = validParameter.validFile(parameters, "order", false);
+ if (flowOrder == "not found"){ flowOrder = "TACG"; }
+ else if(flowOrder.length() != 4){
+ m->mothurOut("The value of the order option must be four bases long\n");
+ }
+
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found"){ temp = "0.01"; }
+ m->mothurConvert(temp, cutoff);
+
+ temp = validParameter.validFile(parameters, "mindelta", false); if (temp == "not found"){ temp = "0.000001"; }
+ m->mothurConvert(temp, minDelta);
+
+ temp = validParameter.validFile(parameters, "maxiter", false); if (temp == "not found"){ temp = "1000"; }
+ m->mothurConvert(temp, maxIters);
+
+ temp = validParameter.validFile(parameters, "large", false); if (temp == "not found"){ temp = "0"; }
+ m->mothurConvert(temp, largeSize);
+ if (largeSize != 0) { large = true; }
+ else { large = false; }
+ if (largeSize < 0) { m->mothurOut("The value of the large cannot be negative.\n"); }
+
+ temp = validParameter.validFile(parameters, "sigma", false);if (temp == "not found") { temp = "60"; }
+ m->mothurConvert(temp, sigma);
+
+ temp = validParameter.validFile(parameters, "flip", false);
+ if (temp == "not found") { flip = 0; }
+ else { flip = m->isTrue(temp); }
+
+ temp = validParameter.validFile(parameters, "maxambig", false); if (temp == "not found") { temp = "-1"; }
+ m->mothurConvert(temp, maxAmbig);
+
+ temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, minLength);
+
+ temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, maxLength);
+
+ temp = validParameter.validFile(parameters, "qthreshold", false); if (temp == "not found") { temp = "0"; }
+ m->mothurConvert(temp, qThreshold);
+
+ temp = validParameter.validFile(parameters, "qtrim", false); if (temp == "not found") { temp = "t"; }
+ qtrim = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "rollaverage", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, qRollAverage);
+
+ temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
+ convert(temp, qWindowAverage);
+
+ temp = validParameter.validFile(parameters, "qwindowsize", false); if (temp == "not found") { temp = "50"; }
+ convert(temp, qWindowSize);
+
+ temp = validParameter.validFile(parameters, "qstepsize", false); if (temp == "not found") { temp = "1"; }
+ convert(temp, qWindowStep);
+
+ temp = validParameter.validFile(parameters, "qaverage", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, qAverage);
+
+ temp = validParameter.validFile(parameters, "keepfirst", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, keepFirst);
+
+ temp = validParameter.validFile(parameters, "removelast", false); if (temp == "not found") { temp = "0"; }
+ convert(temp, removeLast);
+
+ temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found") { temp = "F"; }
+ allFiles = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "keepforward", false); if (temp == "not found") { temp = "F"; }
+ keepforward = m->isTrue(temp);
+
+ numFPrimers = 0;
+ numRPrimers = 0;
+ numLinkers = 0;
+ numSpacers = 0;