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);
+ CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
+ CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
+ CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
CommandParameter psignal("signal", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(psignal);
CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "",false,false); parameters.push_back(pnoise);
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);
- if(tdiffs == 0){ tdiffs = bdiffs + 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);
- 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();
}
TrimOligos trimOligos(pdiffs, bdiffs, primers, barcodes, revPrimer);
while(moreSeqs) {
- //cout << "driver " << count << endl;
-
-
+
if (m->control_pressed) { break; }
int success = 1;
int primerIndex = 0;
int barcodeIndex = 0;
+ if(numLinkers != 0){
+ success = trimOligos.stripLinker(currSeq);
+ if(success > ldiffs) { trashCode += 'k'; }
+ else{ currentSeqDiffs += success; }
+
+ }
+
if(barcodes.size() != 0){
success = trimOligos.stripBarcode(currSeq, barcodeIndex);
if(success > bdiffs) { trashCode += 'b'; }
else{ currentSeqDiffs += success; }
}
+ if(numSpacers != 0){
+ success = trimOligos.stripSpacer(currSeq);
+ if(success > sdiffs) { trashCode += 's'; }
+ else{ currentSeqDiffs += success; }
+
+ }
+
if(numFPrimers != 0){
success = trimOligos.stripForward(currSeq, primerIndex);
if(success > pdiffs) { trashCode += 'f'; }
barcodes[oligo]=indexBarcode; indexBarcode++;
barcodeNameVector.push_back(group);
+ }else if(type == "LINKER"){
+ linker.push_back(oligo);
+ }else if(type == "SPACER"){
+ spacer.push_back(oligo);
}
else{
m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
numFPrimers = primers.size();
numRPrimers = revPrimer.size();
+ numLinkers = linker.size();
+ numSpacers = spacer.size();
}
catch(exception& e) {