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 pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
- CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
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);
if (path == "") { parameters["oligos"] = inputDir + it->second; }
}
-
-// it = parameters.find("group");
-// //user has given a template file
-// if(it != parameters.end()){
-// path = m->hasPath(it->second);
-// //if the user has not given a path then, add inputdir. else leave path alone.
-// if (path == "") { parameters["group"] = inputDir + it->second; }
-// }
}
// ...at some point should added some additional type checking...
string temp;
- temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "360"; }
+ temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
convert(temp, minFlows);
- temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "720"; }
+ temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
convert(temp, maxFlows);
temp = validParameter.validFile(parameters, "oligos", true);
if (temp == "not found") { oligoFileName = ""; }
else if(temp == "not open") { abort = true; }
- else { oligoFileName = temp; }
+ else { oligoFileName = temp; m->setOligosFile(oligoFileName); }
temp = validParameter.validFile(parameters, "fasta", false); if (temp == "not found"){ fasta = 0; }
else if(m->isTrue(temp)) { fasta = 1; }
temp = validParameter.validFile(parameters, "noise", false); if (temp == "not found"){ temp = "0.70"; }
convert(temp, noise);
-
- temp = validParameter.validFile(parameters, "minlength", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, minLength);
-
- temp = validParameter.validFile(parameters, "maxlength", false); if (temp == "not found"){ temp = "0"; }
- convert(temp, maxLength);
-
+
temp = validParameter.validFile(parameters, "bdiffs", false); if (temp == "not found"){ temp = "0"; }
convert(temp, bdiffs);
convert(temp, tdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs; }
- temp = validParameter.validFile(parameters, "allfiles", false); if (temp == "not found"){ temp = "T"; }
- allFiles = m->isTrue(temp);
-
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
convert(temp, processors);
m->mothurOut("The value of the order option must be four bases long\n");
}
- if(oligoFileName == ""){ allFiles = 0; }
+ if(oligoFileName == "") { allFiles = 0; }
+ else { allFiles = 1; }
numFPrimers = 0;
numRPrimers = 0;
if (pFile==NULL) perror ("Error opening file");
else{
fseek (pFile, 0, SEEK_END);
- size=ftell (pFile);
+ size=ftell(pFile);
fclose (pFile);
}
if(size < 10){
- remove(barcodePrimerComboFileNames[i][j].c_str());
+ m->mothurRemove(barcodePrimerComboFileNames[i][j]);
}
else{
output << barcodePrimerComboFileNames[i][j] << endl;
+ outputNames.push_back(barcodePrimerComboFileNames[i][j]);
+ outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
}
}
}
output.close();
}
outputTypes["flow.files"].push_back(flowFilesFileName);
- outputNames.push_back(flowFileName);
+ outputNames.push_back(flowFilesFileName);
- //set fasta file as new current fastafile
- string current = "";
- itTypes = outputTypes.find("fasta");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
- }
+// set fasta file as new current fastafile
+// string current = "";
+// itTypes = outputTypes.find("fasta");
+// if (itTypes != outputTypes.end()) {
+// if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
+// }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
trashCode += 'l';
}
- if(minLength > 0 || maxLength > 0){ //screen to see if sequence is above and below a specific number of bases
- int seqLength = currSeq.getNumBases();
- if(seqLength < minLength || seqLength > maxLength){
- success = 0;
- trashCode += 'l';
- }
- }
-
int primerIndex = 0;
int barcodeIndex = 0;
fileName = outputDir + m->getRootName(m->getSimpleName(flowFileName)) + comboGroupName + ".flow";
}
- outputNames.push_back(fileName);
- outputTypes["flow"].push_back(fileName);
outFlowFileNames[itBar->second][itPrimer->second] = fileName;
ofstream temp;
if (barcodes.size() > 0) {
map<string,int>::iterator it=barcodes.begin();
- for(it;it!=barcodes.end();it++){
+ for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
if(it->first.length() > maxLength){
maxLength = it->first.length();
}
m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
- remove((trimFlowFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((trimFlowFileName + toString(processIDS[i]) + ".temp"));
// m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
- remove((scrapFlowFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((scrapFlowFileName + toString(processIDS[i]) + ".temp"));
// m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
if(fasta){
m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
- remove((fastaFileName + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((fastaFileName + toString(processIDS[i]) + ".temp"));
// m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
}
if(allFiles){
for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
- remove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
}
}
}