fixed bug with trim.seqs allfiles=t

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 5deeff755de28c54b6f06ed2caa84482788c7d1a..d4cb57a3158a85008d30d9c875e331f5be5801e9 100644 (file)
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -715,7 +715,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
                        in >> chimeraFlag >> name;
                        
                        //fix name if needed
-                       if (templatefile != "self") { 
+                       if (templatefile == "self") { 
                                name = name.substr(0, name.length()-1); //rip off last /
                                name = name.substr(0, name.find_last_of('/'));
                        }

diff --git a/mothurout.cpp b/mothurout.cpp
index 3205ae794165a5b8c045c473403d8a66b1b54f90..5a0ea1281b3644e1c0b42035054f9f7f2e0cf0f6 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1229,6 +1229,33 @@ float MothurOut::ceilDist(float dist, int precision){
                exit(1);
        }
 }
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap) { 
+       try {
+               
+               //open input file
+               ifstream in;
+               openInputFile(namefile, in);
+               
+               while (!in.eof()) {
+                       if (control_pressed) { break; }
+                       
+                       string firstCol, secondCol;
+                       in >> firstCol >> secondCol; gobble(in);
+                       
+                       nameMap[firstCol] = secondCol;
+               }
+               in.close();
+               
+               return 0;
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "readNames");
+               exit(1);
+       }
+}
+
 /**********************************************************************************************************************/
 map<string, int> MothurOut::readNames(string namefile) { 
        try {

diff --git a/mothurout.h b/mothurout.h
index 8ac84007de59225ccffb9642a4d0dd023818e40a..7b71fcfbd48c823db529f0bc8d1a54f78422543d 100644 (file)
--- a/mothurout.h
+++ b/mothurout.h
@@ -66,6 +66,7 @@ class MothurOut {
                void gobble(istream&);
                void gobble(istringstream&);
                map<string, int> readNames(string);
+               int readNames(string, map<string, string>&);
                int readNames(string, vector<seqPriorityNode>&, map<string, string>&);
                
                //searchs and checks

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 61a58a4aaeddcdbde6a0b9bdd6f57c56c4079fe9..dad8b98b64f99026388b32c7d47e60dab33e1fba 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -16,6 +16,7 @@ vector<string> TrimSeqsCommand::setParameters(){
                CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
                CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
                CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
+               CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
                CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
                CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
                CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxhomop);
@@ -53,10 +54,11 @@ string TrimSeqsCommand::getHelpString(){
                string helpString = "";
                helpString += "The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n";
                helpString += "The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n";
-               helpString += "The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n";
+               helpString += "The trim.seqs command parameters are fasta, name, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n";
                helpString += "The fasta parameter is required.\n";
                helpString += "The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n";
                helpString += "The oligos parameter allows you to provide an oligos file.\n";
+               helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
                helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
                helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
                helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
@@ -100,6 +102,7 @@ TrimSeqsCommand::TrimSeqsCommand(){
                outputTypes["fasta"] = tempOutNames;
                outputTypes["qfile"] = tempOutNames;
                outputTypes["group"] = tempOutNames;
+               outputTypes["name"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
@@ -137,6 +140,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        outputTypes["fasta"] = tempOutNames;
                        outputTypes["qfile"] = tempOutNames;
                        outputTypes["group"] = tempOutNames;
+                       outputTypes["name"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -167,6 +171,14 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                                        if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
                                }
                                
+                               it = parameters.find("name");
+                               //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["name"] = inputDir + it->second;             }
+                               }
+                               
                        }
 
                        
@@ -226,6 +238,11 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        else if(temp == "not open")     {       abort = true;           }
                        else                                            {       qFileName = temp;       }
                        
+                       temp = validParameter.validFile(parameters, "name", true);      
+                       if (temp == "not found")        {       nameFile = "";          }
+                       else if(temp == "not open")     {       abort = true;           }
+                       else                                            {       nameFile = temp;        }
+                       
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
                        convert(temp, qThreshold);
                        
@@ -292,6 +309,7 @@ int TrimSeqsCommand::execute(){
                numRPrimers = 0;
                vector<vector<string> > fastaFileNames;
                vector<vector<string> > qualFileNames;
+               vector<vector<string> > nameFileNames;
                
                string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
                outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
@@ -301,6 +319,7 @@ int TrimSeqsCommand::execute(){
                
                string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
                string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
+               
                if (qFileName != "") {
                        outputNames.push_back(trimQualFile);
                        outputNames.push_back(scrapQualFile);
@@ -308,11 +327,24 @@ int TrimSeqsCommand::execute(){
                        outputTypes["qfile"].push_back(scrapQualFile); 
                }
                
+               string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim.names";
+               string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap.names";
+               
+               if (nameFile != "") {
+                       m->readNames(nameFile, nameMap);
+                       outputNames.push_back(trimNameFile);
+                       outputNames.push_back(scrapNameFile);
+                       outputTypes["name"].push_back(trimNameFile);
+                       outputTypes["name"].push_back(scrapNameFile); 
+               }
+               
+               if (m->control_pressed) { return 0; }
+               
                string outputGroupFileName;
                if(oligoFile != ""){
                        outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
                        outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
-                       getOligos(fastaFileNames, qualFileNames);
+                       getOligos(fastaFileNames, qualFileNames, nameFileNames);
                }
                
                vector<unsigned long int> fastaFilePos;
@@ -328,12 +360,12 @@ int TrimSeqsCommand::execute(){
                
                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                                if(processors == 1){
-                                       driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+                                       driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
                                }else{
-                                       createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames); 
+                                       createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames); 
                                }       
                #else
-                               driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, outputGroupFileName, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+                               driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
                #endif
                
                if (m->control_pressed) {  return 0; }                  
@@ -354,6 +386,11 @@ int TrimSeqsCommand::execute(){
                                                                        remove(qualFileNames[i][j].c_str());
                                                                        namesToRemove.insert(qualFileNames[i][j]);
                                                                }
+                                                               
+                                                               if(nameFile != ""){
+                                                                       remove(nameFileNames[i][j].c_str());
+                                                                       namesToRemove.insert(nameFileNames[i][j]);
+                                                               }
                                                        }else{  
                                                                it = uniqueFastaNames.find(fastaFileNames[i][j]);
                                                                if (it == uniqueFastaNames.end()) {     
@@ -409,6 +446,11 @@ int TrimSeqsCommand::execute(){
                        if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
                }
                
+               itTypes = outputTypes.find("name");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
+               }
+               
                itTypes = outputTypes.find("qfile");
                if (itTypes != outputTypes.end()) {
                        if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
@@ -435,7 +477,7 @@ int TrimSeqsCommand::execute(){
                
 /**************************************************************************************/
 
-int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, linePair* line, linePair* qline) {       
+int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair* line, linePair* qline) {   
                
        try {
                
@@ -452,6 +494,14 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        m->openOutputFile(scrapQFileName, scrapQualFile);
                }
                
+               ofstream trimNameFile;
+               ofstream scrapNameFile;
+               if(nameFile != ""){
+                       m->openOutputFile(trimNFileName, trimNameFile);
+                       m->openOutputFile(scrapNFileName, scrapNameFile);
+               }
+               
+               
                ofstream outGroupsFile;
                if (oligoFile != ""){   m->openOutputFile(groupFileName, outGroupsFile);   }
                if(allFiles){
@@ -463,6 +513,10 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                if(qFileName != ""){
                                                        m->openOutputFile(qualFileNames[i][j], temp);                   temp.close();
                                                }
+                                               
+                                               if(nameFile != ""){
+                                                       m->openOutputFile(nameFileNames[i][j], temp);                   temp.close();
+                                               }
                                        }
                                }
                        }
@@ -584,6 +638,12 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                currQual.printQScores(trimQualFile);
                                        }
                                        
+                                       if(nameFile != ""){
+                                               map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                                               if (itName != nameMap.end()) {  trimNameFile << itName->first << '\t' << itName->second << endl; }
+                                               else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+                                       }
+                                       
                                        if(barcodes.size() != 0){
                                                string thisGroup = barcodeNameVector[barcodeIndex];
                                                if (primers.size() != 0) { if (primerNameVector[primerIndex] != "") { thisGroup += "." + primerNameVector[primerIndex]; } }
@@ -608,6 +668,15 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                        currQual.printQScores(output);
                                                        output.close();                                                 
                                                }
+                                               
+                                               if(nameFile != ""){
+                                                       map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                                                       if (itName != nameMap.end()) { 
+                                                               m->openOutputFileAppend(nameFileNames[barcodeIndex][primerIndex], output);
+                                                               output << itName->first << '\t' << itName->second << endl; 
+                                                               output.close();
+                                                       }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+                                               }
                                        }
                                }
                                else{
@@ -618,6 +687,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                        if(qFileName != ""){
                                                currQual.printQScores(scrapQualFile);
                                        }
+                                       if(nameFile != ""){
+                                               map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                                               if (itName != nameMap.end()) {  scrapNameFile << itName->first << '\t' << itName->second << endl; }
+                                                       else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
+                                       }
                                }
                                count++;
                        }
@@ -642,6 +716,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                scrapFASTAFile.close();
                if (oligoFile != "") {   outGroupsFile.close();   }
                if(qFileName != "")     {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
+               if(nameFile != "")      {       scrapNameFile.close(); trimNameFile.close();    }
                
                return count;
        }
@@ -653,7 +728,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
 /**************************************************************************************************/
 
-int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames) {
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                int process = 1;
@@ -671,6 +746,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                
                                vector<vector<string> > tempFASTAFileNames = fastaFileNames;
                                vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
+                               vector<vector<string> > tempNameFileNames = nameFileNames;
 
                                if(allFiles){
                                        ofstream temp;
@@ -685,6 +761,10 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                                                        tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
                                                                        m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
                                                                }
+                                                               if(nameFile != ""){
+                                                                       tempNameFileNames[i][j] += toString(getpid()) + ".temp";
+                                                                       m->openOutputFile(tempNameFileNames[i][j], temp);               temp.close();
+                                                               }
                                                        }
                                                }
                                        }
@@ -696,9 +776,12 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                                                 (scrapFASTAFileName + toString(getpid()) + ".temp"),
                                                                 (trimQualFileName + toString(getpid()) + ".temp"),
                                                                 (scrapQualFileName + toString(getpid()) + ".temp"),
+                                                                (trimNameFileName + toString(getpid()) + ".temp"),
+                                                                (scrapNameFileName + toString(getpid()) + ".temp"),
                                                                 (groupFile + toString(getpid()) + ".temp"),
                                                                 tempFASTAFileNames,
                                                                 tempPrimerQualFileNames,
+                                                                tempNameFileNames,
                                                                 lines[process],
                                                                 qLines[process]);
                                
@@ -725,8 +808,10 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                m->openOutputFile(scrapFASTAFileName, temp);    temp.close();
                m->openOutputFile(trimQualFileName, temp);              temp.close();
                m->openOutputFile(scrapQualFileName, temp);             temp.close();
+               m->openOutputFile(trimNameFileName, temp);              temp.close();
+               m->openOutputFile(scrapNameFileName, temp);             temp.close();
 
-               driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
+               driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
                
                //force parent to wait until all the processes are done
                for (int i=0;i<processIDS.size();i++) { 
@@ -751,6 +836,13 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                remove((scrapQualFileName + toString(processIDS[i]) + ".temp").c_str());
                        }
                        
+                       if(nameFile != ""){
+                               m->appendFiles((trimNameFileName + toString(processIDS[i]) + ".temp"), trimNameFileName);
+                               remove((trimNameFileName + toString(processIDS[i]) + ".temp").c_str());
+                               m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
+                               remove((scrapNameFileName + toString(processIDS[i]) + ".temp").c_str());
+                       }
+                       
                        m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
                        remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
                        
@@ -766,6 +858,11 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                                                m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
                                                                remove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
                                                        }
+                                                       
+                                                       if(nameFile != ""){
+                                                               m->appendFiles((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"), nameFileNames[j][k]);
+                                                               remove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp").c_str());
+                                                       }
                                                }
                                        }
                                }
@@ -916,7 +1013,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned
 
 //***************************************************************************************************************
 
-void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames){
+void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
        try {
                ifstream inOligos;
                m->openInputFile(oligoFile, inOligos);
@@ -1004,7 +1101,8 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                for(int i=0;i<fastaFileNames.size();i++){
                        fastaFileNames[i].assign(primerNameVector.size(), "");
                }
-               if(qFileName != ""){    qualFileNames = fastaFileNames; }
+               if(qFileName != "")     {       qualFileNames = fastaFileNames; }
+               if(nameFile != "")      {       nameFileNames = fastaFileNames; }
                
                if(allFiles){
                        set<string> uniqueNames; //used to cleanup outputFileNames
@@ -1017,6 +1115,7 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        string comboGroupName = "";
                                        string fastaFileName = "";
                                        string qualFileName = "";
+                                       string nameFileName = "";
                                        
                                        if(primerName == ""){
                                                comboGroupName = barcodeNameVector[itBar->second];
@@ -1030,30 +1129,40 @@ void TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                                }
                                        }
                                        
-                                       if ((comboGroupName == "") || (comboGroupName == ".")) {}
-                                       else {
-                                               ofstream temp;
-                                               fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
+                                       
+                                       ofstream temp;
+                                       fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
+                                       if (uniqueNames.count(fastaFileName) == 0) {
+                                               outputNames.push_back(fastaFileName);
+                                               outputTypes["fasta"].push_back(fastaFileName);
+                                               uniqueNames.insert(fastaFileName);
+                                       }
+                                       
+                                       fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
+                                       m->openOutputFile(fastaFileName, temp);         temp.close();
+                                       
+                                       if(qFileName != ""){
+                                               qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
                                                if (uniqueNames.count(fastaFileName) == 0) {
-                                                       outputNames.push_back(fastaFileName);
-                                                       outputTypes["fasta"].push_back(fastaFileName);
-                                                       uniqueNames.insert(fastaFileName);
+                                                       outputNames.push_back(qualFileName);
+                                                       outputTypes["qfile"].push_back(qualFileName);
                                                }
                                                
-                                               fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
-                                               m->openOutputFile(fastaFileName, temp);         temp.close();
-                                               
-                                               if(qFileName != ""){
-                                                       qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
-                                                       if (uniqueNames.count(fastaFileName) == 0) {
-                                                               outputNames.push_back(qualFileName);
-                                                               outputTypes["qfile"].push_back(qualFileName);
-                                                       }
-                                                       
-                                                       qualFileNames[itBar->second][itPrimer->second] = qualFileName;
-                                                       m->openOutputFile(qualFileName, temp);          temp.close();
+                                               qualFileNames[itBar->second][itPrimer->second] = qualFileName;
+                                               m->openOutputFile(qualFileName, temp);          temp.close();
+                                       }
+                                       
+                                       if(nameFile != ""){
+                                               nameFileName = outputDir + m->getRootName(m->getSimpleName(nameFile)) + comboGroupName + ".names";
+                                               if (uniqueNames.count(fastaFileName) == 0) {
+                                                       outputNames.push_back(nameFileName);
+                                                       outputTypes["name"].push_back(nameFileName);
                                                }
+                                               
+                                               nameFileNames[itBar->second][itPrimer->second] = nameFileName;
+                                               m->openOutputFile(nameFileName, temp);          temp.close();
                                        }
+                                       
                                }
                        }
                }

diff --git a/trimseqscommand.h b/trimseqscommand.h
index c5a94839cd82427c193e3e78a71c8e8434636653..40c221a0ec61c051099d081f15dd87bea135a163 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -41,7 +41,7 @@ private:
                linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
        };
        
-       void getOligos(vector<vector<string> >&, vector<vector<string> >&);
+       void getOligos(vector<vector<string> >&, vector<vector<string> >&, vector<vector<string> >&);
        int stripBarcode(Sequence&, QualityScores&, int&);
        int stripForward(Sequence&, QualityScores&, int&);
        bool stripReverse(Sequence&, QualityScores&);
@@ -56,7 +56,7 @@ private:
        int countDiffs(string, string);
 
        bool abort;
-       string fastaFile, oligoFile, qFileName, groupfile, outputDir;
+       string fastaFile, oligoFile, qFileName, groupfile, nameFile, outputDir;
        
        bool flip, allFiles, qtrim;
        int numFPrimers, numRPrimers, maxAmbig, maxHomoP, minLength, maxLength, processors, tdiffs, bdiffs, pdiffs, comboStarts;
@@ -72,13 +72,14 @@ private:
        vector<string> primerNameVector;        //needed here?
        vector<string> barcodeNameVector;       //needed here?
        map<string, int> groupCounts;  
+       map<string, string> nameMap;
 
        vector<int> processIDS;   //processid
        vector<linePair*> lines;
        vector<linePair*> qLines;
        
-       int driverCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);   
-       int createProcessesCreateTrim(string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >);
+       int driverCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >, linePair*, linePair*);  
+       int createProcessesCreateTrim(string, string, string, string, string, string, string, string, string, vector<vector<string> >, vector<vector<string> >, vector<vector<string> >);
        int setLines(string, string, vector<unsigned long int>&, vector<unsigned long int>&);
 };