CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pflow);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "",false,false); parameters.push_back(pmaxhomop);
- CommandParameter pmaxflows("maxflows", "Number", "", "720", "", "", "",false,false); parameters.push_back(pmaxflows);
- CommandParameter pminflows("minflows", "Number", "", "360", "", "", "",false,false); parameters.push_back(pminflows);
+ CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pmaxflows);
+ CommandParameter pminflows("minflows", "Number", "", "450", "", "", "",false,false); parameters.push_back(pminflows);
CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
string temp;
temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
- convert(temp, minFlows);
+ m->mothurConvert(temp, minFlows);
temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
- convert(temp, maxFlows);
+ m->mothurConvert(temp, maxFlows);
temp = validParameter.validFile(parameters, "oligos", true);
else if(m->isTrue(temp)) { fasta = 1; }
temp = validParameter.validFile(parameters, "maxhomop", false); if (temp == "not found"){ temp = "9"; }
- convert(temp, maxHomoP);
+ m->mothurConvert(temp, maxHomoP);
temp = validParameter.validFile(parameters, "signal", false); if (temp == "not found"){ temp = "0.50"; }
- convert(temp, signal);
+ m->mothurConvert(temp, signal);
temp = validParameter.validFile(parameters, "noise", false); if (temp == "not found"){ temp = "0.70"; }
- convert(temp, noise);
+ m->mothurConvert(temp, noise);
temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, bdiffs);
+ m->mothurConvert(temp, bdiffs);
temp = validParameter.validFile(parameters, "pdiffs", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, pdiffs);
+ m->mothurConvert(temp, pdiffs);
temp = validParameter.validFile(parameters, "tdiffs", false);
if (temp == "not found"){ int tempTotal = pdiffs + bdiffs; temp = toString(tempTotal); }
- convert(temp, tdiffs);
+ m->mothurConvert(temp, tdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs; }
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
flowOrder = validParameter.validFile(parameters, "order", false);
if (flowOrder == "not found"){ flowOrder = "TACG"; }
}
catch(exception& e) {
- m->errorOut(e, "TrimFlowsCommand", "TrimSeqsCommand");
+ m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
exit(1);
}
}
m->mothurRemove(barcodePrimerComboFileNames[i][j]);
}
else{
- output << barcodePrimerComboFileNames[i][j] << endl;
+ output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
outputNames.push_back(barcodePrimerComboFileNames[i][j]);
outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
}
flowFilesFileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + "flow.files";
m->openOutputFile(flowFilesFileName, output);
- output << trimFlowFileName << endl;
+ output << m->getFullPathName(trimFlowFileName) << endl;
output.close();
}