string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
- convert(temp, ksize);
+ m->mothurConvert(temp, ksize);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "50"; }
- convert(temp, window);
+ m->mothurConvert(temp, window);
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; }
- convert(temp, match);
+ m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; }
- convert(temp, mismatch);
+ m->mothurConvert(temp, mismatch);
temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; }
- convert(temp, divR);
+ m->mothurConvert(temp, divR);
temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; }
- convert(temp, minSimilarity);
+ m->mothurConvert(temp, minSimilarity);
temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; }
- convert(temp, minCoverage);
+ m->mothurConvert(temp, minCoverage);
temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
- convert(temp, minBS);
+ m->mothurConvert(temp, minBS);
temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
- convert(temp, minSNP);
+ m->mothurConvert(temp, minSNP);
temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
- convert(temp, parents);
+ m->mothurConvert(temp, parents);
temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; }
realign = m->isTrue(temp);
search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "blast"; }
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; }
- convert(temp, increment);
+ m->mothurConvert(temp, increment);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; }
- convert(temp, numwanted);
+ m->mothurConvert(temp, numwanted);
blastlocation = validParameter.validFile(parameters, "blastlocation", false);
if (blastlocation == "not found") { blastlocation = ""; }