if(line->start == 0){
flowFile >> numFlows; m->gobble(flowFile);
- scrapFlowFile << maxFlows << endl;
+ scrapFlowFile << numFlows << endl;
trimFlowFile << maxFlows << endl;
if(allFiles){
for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
else if(type == "REVERSE"){
string oligoRC = reverseOligo(oligo);
revPrimer.push_back(oligoRC);
+ if (m->debug) { m->mothurOut("[DEBUG]: reverse oligos = " + oligoRC + ".\n"); }
}
else if(type == "BARCODE"){
oligosFile >> group;
primers[""] = 0;
primerNameVector.push_back("");
}
-
-
+
outFlowFileNames.resize(barcodeNameVector.size());
for(int i=0;i<outFlowFileNames.size();i++){
outFlowFileNames[i].assign(primerNameVector.size(), "");
for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
if (tempBarcodePrimerComboFileNames[i][j] != "") {
- tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
+ tempBarcodePrimerComboFileNames[i][j] += m->mothurGetpid(process) + ".temp";
ofstream temp;
m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
temp.close();
}
}
driverCreateTrim(flowFileName,
- (trimFlowFileName + toString(getpid()) + ".temp"),
- (scrapFlowFileName + toString(getpid()) + ".temp"),
- (fastaFileName + toString(getpid()) + ".temp"),
+ (trimFlowFileName + m->mothurGetpid(process) + ".temp"),
+ (scrapFlowFileName + m->mothurGetpid(process) + ".temp"),
+ (fastaFileName + m->mothurGetpid(process) + ".temp"),
tempBarcodePrimerComboFileNames, lines[process]);
exit(0);