added zap method to classify.seqs and changed bayesian method name to wang.

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 6f5bb979a4d45b9fc3d8201848aa9f6b2d2dddb7..bbb0b367a59de85b94e6dd9e561b697d37832b00 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -11,13 +11,15 @@
 #include "needlemanoverlap.hpp"
 #include "trimoligos.h"
 
 #include "needlemanoverlap.hpp"
 #include "trimoligos.h"
 

+

 //**********************************************************************************************************************
 vector<string> TrimSeqsCommand::setParameters(){       
        try {
                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);
 //**********************************************************************************************************************
 vector<string> TrimSeqsCommand::setParameters(){       
        try {
                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 pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);

                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);
                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);


@@ -58,11 +60,12 @@ 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";
                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, name, 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, count, 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 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 count parameter allows you to provide a count 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";
                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";


@@ -97,6 +100,30 @@ string TrimSeqsCommand::getHelpString(){
                exit(1);
        }
 }
                exit(1);
        }
 }

+//**********************************************************************************************************************
+string TrimSeqsCommand::getOutputFileNameTag(string type, string inputName=""){        
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "qfile")            {   outputFileName =  "qual";   }
+            else if (type == "fasta")            {   outputFileName =  "fasta";   }
+            else if (type == "group")            {   outputFileName =  "groups";   }
+            else if (type == "name")            {   outputFileName =  "names";   }
+            else if (type == "count")            {   outputFileName =  "count_table";   }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "TrimSeqsCommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}

 
 
 //**********************************************************************************************************************
 
 
 //**********************************************************************************************************************


@@ -110,6 +137,7 @@ TrimSeqsCommand::TrimSeqsCommand(){
                outputTypes["qfile"] = tempOutNames;
                outputTypes["group"] = tempOutNames;
                outputTypes["name"] = tempOutNames;
                outputTypes["qfile"] = tempOutNames;
                outputTypes["group"] = tempOutNames;
                outputTypes["name"] = tempOutNames;

+        outputTypes["count"] = tempOutNames;

        }
        catch(exception& e) {
                m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
        }
        catch(exception& e) {
                m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");


@@ -148,6 +176,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        outputTypes["qfile"] = tempOutNames;
                        outputTypes["group"] = tempOutNames;
                        outputTypes["name"] = tempOutNames;
                        outputTypes["qfile"] = tempOutNames;
                        outputTypes["group"] = tempOutNames;
                        outputTypes["name"] = tempOutNames;

+            outputTypes["count"] = 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);              
                        
                        //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);              


@@ -185,6 +214,14 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["name"] = inputDir + it->second;             }
                                }

+                
+                it = parameters.find("count");
+                               //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["count"] = inputDir + it->second;            }
+                               }

                                
                        }
 
                                
                        }
 


@@ -256,6 +293,13 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                        if (temp == "not found")        {       nameFile = "";          }
                        else if(temp == "not open")     {       nameFile = "";  abort = true;           }
                        else                                            {       nameFile = temp;        m->setNameFile(nameFile); }
                        if (temp == "not found")        {       nameFile = "";          }
                        else if(temp == "not open")     {       nameFile = "";  abort = true;           }
                        else                                            {       nameFile = temp;        m->setNameFile(nameFile); }

+            
+            countfile = validParameter.validFile(parameters, "count", true);
+                       if (countfile == "not open") { abort = true; countfile = ""; }  
+                       else if (countfile == "not found") { countfile = ""; }
+                       else { m->setCountTableFile(countfile); }
+                       
+            if ((countfile != "") && (nameFile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }

                        
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
                        m->mothurConvert(temp, qThreshold);
                        
                        temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
                        m->mothurConvert(temp, qThreshold);


@@ -308,10 +352,12 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                                abort = true;
                        }
                        
                                abort = true;
                        }
                        

-                       if (nameFile == "") {
-                               vector<string> files; files.push_back(fastaFile);
-                               parser.getNameFile(files);
-                       }
+            if (countfile == "") {
+                if (nameFile == "") {
+                    vector<string> files; files.push_back(fastaFile);
+                    parser.getNameFile(files);
+                }
+            }

                }
 
        }
                }
 
        }


@@ -336,14 +382,14 @@ int TrimSeqsCommand::execute(){
                vector<vector<string> > qualFileNames;
                vector<vector<string> > nameFileNames;
                
                vector<vector<string> > qualFileNames;
                vector<vector<string> > nameFileNames;
                

-               string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
+               string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("fasta");

                outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
                
                outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
                

-               string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
+               string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("fasta");

                outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
                
                outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
                

-               string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
-               string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
+               string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("qfile");
+               string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("qfile");

                
                if (qFileName != "") {
                        outputNames.push_back(trimQualFile);
                
                if (qFileName != "") {
                        outputNames.push_back(trimQualFile);


@@ -352,8 +398,8 @@ int TrimSeqsCommand::execute(){
                        outputTypes["qfile"].push_back(scrapQualFile); 
                }
                
                        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";
+               string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim." + getOutputFileNameTag("name");
+               string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap." + getOutputFileNameTag("name");

                
                if (nameFile != "") {
                        m->readNames(nameFile, nameMap);
                
                if (nameFile != "") {
                        m->readNames(nameFile, nameMap);


@@ -362,14 +408,28 @@ int TrimSeqsCommand::execute(){
                        outputTypes["name"].push_back(trimNameFile);
                        outputTypes["name"].push_back(scrapNameFile); 
                }
                        outputTypes["name"].push_back(trimNameFile);
                        outputTypes["name"].push_back(scrapNameFile); 
                }

+        
+        string trimCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "trim." + getOutputFileNameTag("count");
+               string scrapCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "scrap." + getOutputFileNameTag("count");
+               
+               if (countfile != "") {
+            CountTable ct;
+            ct.readTable(countfile);
+            nameCount = ct.getNameMap();
+                       outputNames.push_back(trimCountFile);
+                       outputNames.push_back(scrapCountFile);
+                       outputTypes["count"].push_back(trimCountFile);
+                       outputTypes["count"].push_back(scrapCountFile); 
+               }
+

                
                if (m->control_pressed) { return 0; }
                
                string outputGroupFileName;
                if(oligoFile != ""){
                        createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
                
                if (m->control_pressed) { return 0; }
                
                string outputGroupFileName;
                if(oligoFile != ""){
                        createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);

-                       if (createGroup) {
-                               outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
+                       if ((createGroup) && (countfile == "")){
+                               outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("group");

                                outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
                        }
                }
                                outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
                        }
                }


@@ -378,9 +438,9 @@ int TrimSeqsCommand::execute(){
                setLines(fastaFile, qFileName);
                
         if(processors == 1){
                setLines(fastaFile, qFileName);
                
         if(processors == 1){

-            driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
+            driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, trimCountFile, scrapCountFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);

         }else{
         }else{

-            createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames); 
+            createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, trimCountFile, scrapCountFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames); 

         }      
                
                
         }      
                
                


@@ -423,35 +483,62 @@ int TrimSeqsCommand::execute(){
                        for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
                        outputNames = outputNames2;
                        
                        for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
                        outputNames = outputNames2;
                        

-                       for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
-                               ifstream in;
-                               m->openInputFile(it->first, in);
-                               
-                               ofstream out;
-                               string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first)) + "groups";
-                               outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
-                               m->openOutputFile(thisGroupName, out);
-                               
-                               while (!in.eof()){
-                                       if (m->control_pressed) { break; }
-                                       
-                                       Sequence currSeq(in); m->gobble(in);
-                                       out << currSeq.getName() << '\t' << it->second << endl;
+            for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
+                ifstream in;
+                m->openInputFile(it->first, in);
+                
+                ofstream out;
+                string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
+                if (countfile == "") { thisGroupName += getOutputFileNameTag("group"); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
+                else {  thisGroupName += getOutputFileNameTag("count"); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName);  }
+                m->openOutputFile(thisGroupName, out);
+                
+                if (countfile != "") {  out << "Representative_Sequence\ttotal\t" << it->second << endl;  }
+                
+                while (!in.eof()){
+                    if (m->control_pressed) { break; }

                     
                     

-                    if (nameFile != "") {
-                        map<string, string>::iterator itName = nameMap.find(currSeq.getName());
-                        if (itName != nameMap.end()) { 
-                            vector<string> thisSeqsNames; 
-                            m->splitAtChar(itName->second, thisSeqsNames, ',');
-                            for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
-                                out << thisSeqsNames[k] << '\t' << it->second << endl;
-                            }
-                        }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }                                                  
+                    Sequence currSeq(in); m->gobble(in);
+                    if (countfile == "") {  
+                        out << currSeq.getName() << '\t' << it->second << endl;  
+                        
+                        if (nameFile != "") {
+                            map<string, string>::iterator itName = nameMap.find(currSeq.getName());
+                            if (itName != nameMap.end()) { 
+                                vector<string> thisSeqsNames; 
+                                m->splitAtChar(itName->second, thisSeqsNames, ',');
+                                for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
+                                    out << thisSeqsNames[k] << '\t' << it->second << endl;
+                                }
+                            }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }                                                      
+                        }
+                    }else { 
+                        map<string, int>::iterator itTotalReps = nameCount.find(currSeq.getName());
+                        if (itTotalReps != nameCount.end()) { out << currSeq.getName() << '\t' << itTotalReps->second << '\t' << itTotalReps->second << endl; }
+                        else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }

                     }
                     }

-                               }
-                               in.close();
-                               out.close();
-                       }
+                }
+                in.close();
+                out.close();
+            }
+            
+            if (countfile != "") { //create countfile with group info included
+                CountTable* ct = new CountTable();
+                ct->readTable(trimCountFile);
+                map<string, int> justTrimmedNames = ct->getNameMap();
+                delete ct;
+                
+                CountTable newCt;
+                for (map<string, int>::iterator itCount = groupCounts.begin(); itCount != groupCounts.end(); itCount++) { newCt.addGroup(itCount->first); }
+                vector<int> tempCounts; tempCounts.resize(groupCounts.size(), 0);
+                for (map<string, int>::iterator itNames = justTrimmedNames.begin(); itNames != justTrimmedNames.end(); itNames++) {
+                    newCt.push_back(itNames->first, tempCounts); //add it to the table with no abundance so we can set the groups abundance
+                    map<string, string>::iterator it2 = groupMap.find(itNames->first);
+                    if (it2 != groupMap.end()) { newCt.setAbund(itNames->first, it2->second, itNames->second); }
+                    else { m->mothurOut("[ERROR]: missing group info for " + itNames->first + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+                }
+                newCt.printTable(trimCountFile);
+            }

                }
                
                if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
                }
                
                if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }


@@ -488,6 +575,11 @@ int TrimSeqsCommand::execute(){
                if (itTypes != outputTypes.end()) {
                        if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
                }
                if (itTypes != outputTypes.end()) {
                        if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
                }

+        
+        itTypes = outputTypes.find("count");
+               if (itTypes != outputTypes.end()) {
+                       if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+               }

 
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 
                m->mothurOutEndLine();
                m->mothurOut("Output File Names: "); m->mothurOutEndLine();


@@ -504,8 +596,7 @@ int TrimSeqsCommand::execute(){
 }
                
 /**************************************************************************************/
 }
                
 /**************************************************************************************/

-
-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) {     
+int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string trimCFileName, string scrapCFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair line, linePair qline) {        

                
        try {
                
                
        try {
                


@@ -529,9 +620,16 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                        m->openOutputFile(scrapNFileName, scrapNameFile);
                }
                
                        m->openOutputFile(scrapNFileName, scrapNameFile);
                }
                

+        ofstream trimCountFile;
+               ofstream scrapCountFile;
+               if(countfile != ""){
+                       m->openOutputFile(trimCFileName, trimCountFile);
+                       m->openOutputFile(scrapCFileName, scrapCountFile);
+            if (line.start == 0) { trimCountFile << "Representative_Sequence\ttotal" << endl; scrapCountFile << "Representative_Sequence\ttotal" << endl; }
+               }

                
                ofstream outGroupsFile;
                
                ofstream outGroupsFile;

-               if (createGroup){       m->openOutputFile(groupFileName, outGroupsFile);   }
+               if ((createGroup) && (countfile == "")){        m->openOutputFile(groupFileName, outGroupsFile);   }

                if(allFiles){
                        for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
                                for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
                if(allFiles){
                        for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
                                for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file


@@ -568,14 +666,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                
                        if (m->control_pressed) { 
                                inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
                                
                        if (m->control_pressed) { 
                                inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();

-                               if (createGroup) {       outGroupsFile.close();   }
-
-                               if(qFileName != ""){
-                                       qFile.close();
-                               }
-                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); }
-
-                               return 0;
+                               if ((createGroup) && (countfile == "")) {        outGroupsFile.close();   }
+                if(qFileName != "")    {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
+                if(nameFile != "")     {       scrapNameFile.close(); trimNameFile.close();    }
+                if(countfile != "")    {       scrapCountFile.close(); trimCountFile.close();  }
+                               for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;

                        }
                        
                        int success = 1;
                        }
                        
                        int success = 1;


@@ -584,9 +679,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
                        Sequence currSeq(inFASTA); m->gobble(inFASTA);
                        //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
 
                        Sequence currSeq(inFASTA); m->gobble(inFASTA);
                        //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;

+            

                        QualityScores currQual;
                        if(qFileName != ""){
                                currQual = QualityScores(qFile);  m->gobble(qFile);
                        QualityScores currQual;
                        if(qFileName != ""){
                                currQual = QualityScores(qFile);  m->gobble(qFile);

+                //cout << currQual.getName() << endl;

                        }
                        
                        string origSeq = currSeq.getUnaligned();
                        }
                        
                        string origSeq = currSeq.getUnaligned();


@@ -679,6 +776,8 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                        }
                                }
                                
                                        }
                                }
                                

+                if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + ", trashcode= " + trashCode); if (trashCode.length() != 0) { m->mothurOutEndLine(); } }
+                

                                if(trashCode.length() == 0){
                                        currSeq.setAligned(currSeq.getUnaligned());
                                        currSeq.printSequence(trimFASTAFile);
                                if(trashCode.length() == 0){
                                        currSeq.setAligned(currSeq.getUnaligned());
                                        currSeq.printSequence(trimFASTAFile);


@@ -693,6 +792,15 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                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 (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(); }
                                        }

+                    
+                    int numRedundants = 0;
+                    if (countfile != "") {
+                        map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
+                        if (itCount != nameCount.end()) { 
+                            trimCountFile << itCount->first << '\t' << itCount->second << endl;
+                            numRedundants = itCount->second-1;
+                        }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
+                    }

                                        
                                        if (createGroup) {
                                                if(barcodes.size() != 0){
                                        
                                        if (createGroup) {
                                                if(barcodes.size() != 0){


@@ -707,9 +815,11 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                                } 
                                                        }
                                                        
                                                                } 
                                                        }
                                                        

-                                                       outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl;
+                            if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
+                            
+                                                       if (countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
+                            else {   groupMap[currSeq.getName()] = thisGroup; }

                                                        
                                                        

-                            int numRedundants = 0;

                                                        if (nameFile != "") {
                                                                map<string, string>::iterator itName = nameMap.find(currSeq.getName());
                                                                if (itName != nameMap.end()) { 
                                                        if (nameFile != "") {
                                                                map<string, string>::iterator itName = nameMap.find(currSeq.getName());
                                                                if (itName != nameMap.end()) { 


@@ -757,6 +867,13 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                                                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(); }
                                        }
                                                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(); }
                                        }

+                    if (countfile != "") {
+                        map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
+                        if (itCount != nameCount.end()) { 
+                            trimCountFile << itCount->first << '\t' << itCount->second << endl;
+                        }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
+                    }
+                    

                                        currSeq.setName(currSeq.getName() + '|' + trashCode);
                                        currSeq.setUnaligned(origSeq);
                                        currSeq.setAligned(origSeq);
                                        currSeq.setName(currSeq.getName() + '|' + trashCode);
                                        currSeq.setUnaligned(origSeq);
                                        currSeq.setAligned(origSeq);


@@ -790,6 +907,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
                if (createGroup) {       outGroupsFile.close();   }
                if(qFileName != "")     {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
                if(nameFile != "")      {       scrapNameFile.close(); trimNameFile.close();    }
                if (createGroup) {       outGroupsFile.close();   }
                if(qFileName != "")     {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
                if(nameFile != "")      {       scrapNameFile.close(); trimNameFile.close();    }

+        if(countfile != "")    {       scrapCountFile.close(); trimCountFile.close();  }

                
                return count;
        }
                
                return count;
        }


@@ -801,7 +919,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 
 /**************************************************************************************************/
 
 
 /**************************************************************************************************/
 

-int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
+int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string trimCountFileName, string scrapCountFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {

        try {
         
         int process = 1;
        try {
         
         int process = 1;


@@ -852,12 +970,16 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                                                 (scrapQualFileName + toString(getpid()) + ".temp"),
                                                                 (trimNameFileName + toString(getpid()) + ".temp"),
                                                                 (scrapNameFileName + toString(getpid()) + ".temp"),
                                                                 (scrapQualFileName + toString(getpid()) + ".temp"),
                                                                 (trimNameFileName + toString(getpid()) + ".temp"),
                                                                 (scrapNameFileName + toString(getpid()) + ".temp"),

+                                 (trimCountFileName + toString(getpid()) + ".temp"),
+                                                                (scrapCountFileName + toString(getpid()) + ".temp"),

                                                                 (groupFile + toString(getpid()) + ".temp"),
                                                                 tempFASTAFileNames,
                                                                 tempPrimerQualFileNames,
                                                                 tempNameFileNames,
                                                                 lines[process],
                                                                 qLines[process]);
                                                                 (groupFile + toString(getpid()) + ".temp"),
                                                                 tempFASTAFileNames,
                                                                 tempPrimerQualFileNames,
                                                                 tempNameFileNames,
                                                                 lines[process],
                                                                 qLines[process]);

+                
+                if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }

                                
                                //pass groupCounts to parent
                                if(createGroup){
                                
                                //pass groupCounts to parent
                                if(createGroup){


@@ -870,6 +992,11 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                        for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
                                                out << it->first << '\t' << it->second << endl;
                                        }
                                        for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
                                                out << it->first << '\t' << it->second << endl;
                                        }

+                    
+                    out << groupMap.size() << endl;
+                    for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
+                                               out << it->first << '\t' << it->second << endl;
+                                       }

                                        out.close();
                                }
                                exit(0);
                                        out.close();
                                }
                                exit(0);


@@ -892,8 +1019,12 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                        m->openOutputFile(trimNameFileName, temp);              temp.close();
                        m->openOutputFile(scrapNameFileName, temp);             temp.close();
                }
                        m->openOutputFile(trimNameFileName, temp);              temp.close();
                        m->openOutputFile(scrapNameFileName, temp);             temp.close();
                }

+        if (countfile != "") {
+                       m->openOutputFile(trimCountFileName, temp);             temp.close();
+                       m->openOutputFile(scrapCountFileName, temp);            temp.close();
+               }

 
 

-               driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
+               driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, trimCountFileName, scrapCountFileName, 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++) { 
                
                //force parent to wait until all the processes are done
                for (int i=0;i<processIDS.size();i++) { 


@@ -943,13 +1074,15 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
 
             
                        trimData* tempTrim = new trimData(filename,
 
             
                        trimData* tempTrim = new trimData(filename,

-                                              qFileName, nameFile,
+                                              qFileName, nameFile, countfile,

                                               (trimFASTAFileName+extension),
                                               (scrapFASTAFileName+extension),
                                               (trimQualFileName+extension),
                                               (scrapQualFileName+extension),
                                               (trimNameFileName+extension),
                                               (scrapNameFileName+extension),
                                               (trimFASTAFileName+extension),
                                               (scrapFASTAFileName+extension),
                                               (trimQualFileName+extension),
                                               (scrapQualFileName+extension),
                                               (trimNameFileName+extension),
                                               (scrapNameFileName+extension),

+                                              (trimCountFileName+extension),
+                                              (scrapCountFileName+extension),

                                               (groupFile+extension),
                                               tempFASTAFileNames,
                                               tempPrimerQualFileNames,
                                               (groupFile+extension),
                                               tempFASTAFileNames,
                                               tempPrimerQualFileNames,


@@ -958,7 +1091,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                               pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer, 
                                              primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
                                               qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
                                               pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, rbarcodes, revPrimer, linker, spacer, 
                                              primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
                                               qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,

-                                             minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap);
+                                             minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap, nameCount);

                        pDataArray.push_back(tempTrim);
             
                        hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   
                        pDataArray.push_back(tempTrim);
             
                        hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);   


@@ -977,7 +1110,7 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                        m->openOutputFile(scrapNameFileName, temp);             temp.close();
                }
         
                        m->openOutputFile(scrapNameFileName, temp);             temp.close();
                }
         

-               driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);
+               driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);

         processIDS.push_back(processors-1);
 
         
         processIDS.push_back(processors-1);
 
         


@@ -991,6 +1124,11 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                 if (it2 == groupCounts.end()) {        groupCounts[it->first] = it->second; }
                 else { groupCounts[it->first] += it->second; }
             }
                 if (it2 == groupCounts.end()) {        groupCounts[it->first] = it->second; }
                 else { groupCounts[it->first] += it->second; }
             }

+            for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
+                map<string, string>::iterator it2 = groupMap.find(it->first);
+                if (it2 == groupMap.end()) {   groupMap[it->first] = it->second; }
+                else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
+            }

             CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }
             CloseHandle(hThreadArray[i]);
                        delete pDataArray[i];
                }


@@ -1021,8 +1159,15 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
                                m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
                        }
                                m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
                                m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
                        }

+            
+            if(countfile != ""){
+                               m->appendFiles((trimCountFileName + toString(processIDS[i]) + ".temp"), trimCountFileName);
+                               m->mothurRemove((trimCountFileName + toString(processIDS[i]) + ".temp"));
+                               m->appendFiles((scrapCountFileName + toString(processIDS[i]) + ".temp"), scrapCountFileName);
+                               m->mothurRemove((scrapCountFileName + toString(processIDS[i]) + ".temp"));
+                       }

                        
                        

-                       if(createGroup){
+                       if((createGroup)&&(countfile == "")){

                                m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
                                m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
                        }
                                m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
                                m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
                        }


@@ -1060,14 +1205,27 @@ int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName
                                in >> tempNum; m->gobble(in);
                                
                                if (tempNum != 0) {
                                in >> tempNum; m->gobble(in);
                                
                                if (tempNum != 0) {

-                                       while (!in.eof()) { 
-                                               in >> group >> tempNum; m->gobble(in);
+                                       for (int i = 0; i < tempNum; i++) { 
+                        int groupNum;
+                                               in >> group >> groupNum; m->gobble(in);

                         
                                                map<string, int>::iterator it = groupCounts.find(group);
                         
                                                map<string, int>::iterator it = groupCounts.find(group);

-                                               if (it == groupCounts.end()) {  groupCounts[group] = tempNum; }
-                                               else { groupCounts[it->first] += tempNum; }
+                                               if (it == groupCounts.end()) {  groupCounts[group] = groupNum; }
+                                               else { groupCounts[it->first] += groupNum; }
+                                       }
+                               }
+                in >> tempNum; m->gobble(in);
+                if (tempNum != 0) {
+                                       for (int i = 0; i < tempNum; i++) { 
+                        string group, seqName;
+                                               in >> seqName >> group; m->gobble(in);
+                        
+                                               map<string, string>::iterator it = groupMap.find(seqName);
+                                               if (it == groupMap.end()) {     groupMap[seqName] = group; }
+                                               else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }

                                        }
                                }
                                        }
                                }

+                

                                in.close(); m->mothurRemove(tempFile);
                        }
             #endif
                                in.close(); m->mothurRemove(tempFile);
                        }
             #endif


@@ -1162,6 +1320,7 @@ int TrimSeqsCommand::setLines(string filename, string qfilename) {
         }
         
         for (int i = 0; i < (fastaFilePos.size()-1); i++) {
         }
         
         for (int i = 0; i < (fastaFilePos.size()-1); i++) {

+            if (m->debug) { m->mothurOut("[DEBUG]: " + toString(i) +'\t' + toString(fastaFilePos[i]) + '\t' + toString(fastaFilePos[i+1]) + '\n'); }

                        lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
                        if (qfilename != "") {  qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)]));  }
                }       
                        lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
                        if (qfilename != "") {  qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)]));  }
                }       


@@ -1227,7 +1386,9 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                while(!inOligos.eof()){
 
                        inOligos >> type; 
                while(!inOligos.eof()){
 
                        inOligos >> type; 

-                                       
+            
+                       if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }      
+            

                        if(type[0] == '#'){
                                while (!inOligos.eof()) {       char c = inOligos.get();  if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
                                m->gobble(inOligos);
                        if(type[0] == '#'){
                                while (!inOligos.eof()) {       char c = inOligos.get();  if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
                                m->gobble(inOligos);


@@ -1238,6 +1399,8 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
                                
                                inOligos >> oligo;
                                for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
                                
                                inOligos >> oligo;

+                
+                if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }

                                
                                for(int i=0;i<oligo.length();i++){
                                        oligo[i] = toupper(oligo[i]);
                                
                                for(int i=0;i<oligo.length();i++){
                                        oligo[i] = toupper(oligo[i]);


@@ -1259,6 +1422,8 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        map<string, int>::iterator itPrime = primers.find(oligo);
                                        if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        
                                        map<string, int>::iterator itPrime = primers.find(oligo);
                                        if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
                                        

+                    if (m->debug) {  if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); }  }
+                    

                                        primers[oligo]=indexPrimer; indexPrimer++;              
                                        primerNameVector.push_back(group);
                                }
                                        primers[oligo]=indexPrimer; indexPrimer++;              
                                        primerNameVector.push_back(group);
                                }


@@ -1283,15 +1448,22 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        
                     //then this is illumina data with 4 columns
                     if (temp != "") {  
                                        
                     //then this is illumina data with 4 columns
                     if (temp != "") {  

-                        string reverseBarcode = reverseOligo(group); //reverse barcode
-                        group = temp;

                         
                         

+                        for(int i=0;i<group.length();i++){
+                            group[i] = toupper(group[i]);
+                            if(group[i] == 'U')        {       group[i] = 'T'; }
+                        }
+                        
+                        if (m->debug) { m->mothurOut("[DEBUG]: reading reverse " + group + ", and group = " + temp + ".\n"); }
+                        
+                        string reverseBarcode = reverseOligo(group); //reverse barcode

                         //check for repeat barcodes
                         map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);
                         //check for repeat barcodes
                         map<string, int>::iterator itBar = rbarcodes.find(reverseBarcode);

-                        if (itBar != rbarcodes.end()) { m->mothurOut("barcode " + reverseBarcode + " is in your oligos file already."); m->mothurOutEndLine();  }
-                                               
+                        if (itBar != rbarcodes.end()) { m->mothurOut("reverse barcode " + group + " is in your oligos file already."); m->mothurOutEndLine();  }
+                        
+                        group = temp;

                         rbarcodes[reverseBarcode]=indexBarcode; 
                         rbarcodes[reverseBarcode]=indexBarcode; 

-                    }
+                    }else { if (m->debug) { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); } }

                         
                                        //check for repeat barcodes
                                        map<string, int>::iterator itBar = barcodes.find(oligo);
                         
                                        //check for repeat barcodes
                                        map<string, int>::iterator itBar = barcodes.find(oligo);


@@ -1304,7 +1476,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                }else if(type == "SPACER"){
                                        spacer.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();  }
+                               else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }

                        }
                        m->gobble(inOligos);
                }       
                        }
                        m->gobble(inOligos);
                }       


@@ -1342,6 +1514,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                        string fastaFileName = "";
                                        string qualFileName = "";
                                        string nameFileName = "";
                                        string fastaFileName = "";
                                        string qualFileName = "";
                                        string nameFileName = "";

+                    string countFileName = "";

                                        
                                        if(primerName == ""){
                                                comboGroupName = barcodeNameVector[itBar->second];
                                        
                                        if(primerName == ""){
                                                comboGroupName = barcodeNameVector[itBar->second];


@@ -1388,7 +1561,6 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                                nameFileNames[itBar->second][itPrimer->second] = nameFileName;
                                                m->openOutputFile(nameFileName, temp);          temp.close();
                                        }
                                                nameFileNames[itBar->second][itPrimer->second] = nameFileName;
                                                m->openOutputFile(nameFileName, temp);          temp.close();
                                        }

-                                       

                                }
                        }
                }
                                }
                        }
                }


@@ -1410,7 +1582,7 @@ bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<
                                break;
                        }
                }
                                break;
                        }
                }

-               
+

                if (allBlank) {
                        m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
                        allFiles = false;
                if (allBlank) {
                        m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
                        allFiles = false;