makecontigscommand.cpp

   1 //
   2 //  makecontigscommand.cpp
   3 //  Mothur
   4 //
   5 //  Created by Sarah Westcott on 5/15/12.
   6 //  Copyright (c) 2012 Schloss Lab. All rights reserved.
   7 //
   8
   9 #include "makecontigscommand.h"
  10
  11 //**********************************************************************************************************************
  12 vector<string> MakeContigsCommand::setParameters(){
  13         try {
  14                 CommandParameter pfastq("ffastq", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "fastqGroup","fasta-qfile",false,false,true); parameters.push_back(pfastq);
  15         CommandParameter prfastq("rfastq", "InputTypes", "", "", "none", "none", "fastqGroup","fasta-qfile",false,false,true); parameters.push_back(prfastq);
  16         CommandParameter pfasta("ffasta", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "fastaGroup","fasta",false,false,true); parameters.push_back(pfasta);
  17         CommandParameter prfasta("rfasta", "InputTypes", "", "", "none", "none", "none","fastaGroup",false,false,true); parameters.push_back(prfasta);
  18         CommandParameter pfqual("fqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(pfqual);
  19         CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(prqual);
  20         CommandParameter pfile("file", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "none","fasta-qfile",false,false,true); parameters.push_back(pfile);
  21         CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
  22                 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
  23                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
  24 //        CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
  25 //              CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
  26         CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
  27
  28         CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
  29         CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
  30                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
  31                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
  32                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
  33                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
  34         CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "","",false,false); parameters.push_back(pthreshold);
  35                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  36                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  37                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  38
  39                 vector<string> myArray;
  40                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "MakeContigsCommand", "setParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 string MakeContigsCommand::getHelpString(){
  50         try {
  51                 string helpString = "";
  52                 helpString += "The make.contigs command reads a file, forward fastq file and a reverse fastq file or forward fasta and reverse fasta files and outputs new fasta.  It will also provide new quality files if the fastq or file parameter is used.\n";
  53         helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
  54                 helpString += "The make.contigs command parameters are ffastq, rfastq, oligos, tdiffs, bdiffs, ldiffs, sdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, allfiles and processors.\n";
  55                 helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";
  56         helpString += "The file parameter is 2 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column.  Mothur will process each pair and create a combined fasta and qual file with all the sequences.\n";
  57         helpString += "The ffastq and rfastq parameters are used to provide a forward fastq and reverse fastq file to process.  If you provide one, you must provide the other.\n";
  58         helpString += "The ffasta and rfasta parameters are used to provide a forward fasta and reverse fasta file to process.  If you provide one, you must provide the other.\n";
  59         helpString += "The fqfile and rqfile parameters are used to provide a forward quality and reverse quality files to process with the ffasta and rfasta parameters.  If you provide one, you must provide the other.\n";
  60                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh and needleman. The default is needleman.\n";
  61         helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
  62                 helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
  63                 helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
  64         helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
  65                 helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
  66                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  67                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  68                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  69                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  70         helpString += "The threshold parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it. Default=40.\n";
  71         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  72         helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
  73         helpString += "The make.contigs command should be in the following format: \n";
  74                 helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
  75                 helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
  76                 return helpString;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "MakeContigsCommand", "getHelpString");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84 string MakeContigsCommand::getOutputPattern(string type) {
  85     try {
  86         string pattern = "";
  87
  88         if (type == "fasta") {  pattern = "[filename],[tag],contigs.fasta"; }
  89         else if (type == "qfile") {  pattern = "[filename],[tag],contigs.qual"; }
  90         else if (type == "group") {  pattern = "[filename],[tag],groups"; }
  91         else if (type == "mismatch") {  pattern = "[filename],[tag],contigs.mismatch"; }
  92         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  93
  94         return pattern;
  95     }
  96     catch(exception& e) {
  97         m->errorOut(e, "MakeContigsCommand", "getOutputPattern");
  98         exit(1);
  99     }
 100 }
 101 //**********************************************************************************************************************
 102 MakeContigsCommand::MakeContigsCommand(){
 103         try {
 104                 abort = true; calledHelp = true;
 105                 setParameters();
 106                 vector<string> tempOutNames;
 107                 outputTypes["fasta"] = tempOutNames;
 108                 outputTypes["qfile"] = tempOutNames;
 109         outputTypes["group"] = tempOutNames;
 110         outputTypes["mismatch"] = tempOutNames;
 111         }
 112         catch(exception& e) {
 113                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 114                 exit(1);
 115         }
 116 }
 117 //**********************************************************************************************************************
 118 MakeContigsCommand::MakeContigsCommand(string option)  {
 119         try {
 120                 abort = false; calledHelp = false;
 121
 122                 //allow user to run help
 123                 if(option == "help") { help(); abort = true; calledHelp = true; }
 124                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 125
 126                 else {
 127                         vector<string> myArray = setParameters();
 128
 129                         OptionParser parser(option);
 130                         map<string, string> parameters = parser.getParameters();
 131
 132                         ValidParameters validParameter("pairwise.seqs");
 133                         map<string, string>::iterator it;
 134
 135                         //check to make sure all parameters are valid for command
 136                         for (it = parameters.begin(); it != parameters.end(); it++) {
 137                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 138                         }
 139
 140                         //initialize outputTypes
 141                         vector<string> tempOutNames;
 142                         outputTypes["fasta"] = tempOutNames;
 143                         outputTypes["qfile"] = tempOutNames;
 144             outputTypes["mismatch"] = tempOutNames;
 145             outputTypes["group"] = tempOutNames;
 146
 147
 148                         //if the user changes the input directory command factory will send this info to us in the output parameter
 149                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 150                         if (inputDir == "not found"){   inputDir = "";          }
 151                         else {
 152                                 string path;
 153                 it = parameters.find("ffastq");
 154                                 //user has given a template file
 155                                 if(it != parameters.end()){
 156                                         path = m->hasPath(it->second);
 157                                         //if the user has not given a path then, add inputdir. else leave path alone.
 158                                         if (path == "") {       parameters["ffastq"] = inputDir + it->second;           }
 159                                 }
 160
 161                 it = parameters.find("rfastq");
 162                                 //user has given a template file
 163                                 if(it != parameters.end()){
 164                                         path = m->hasPath(it->second);
 165                                         //if the user has not given a path then, add inputdir. else leave path alone.
 166                                         if (path == "") {       parameters["rfastq"] = inputDir + it->second;           }
 167                                 }
 168
 169                 it = parameters.find("ffasta");
 170                                 //user has given a template file
 171                                 if(it != parameters.end()){
 172                                         path = m->hasPath(it->second);
 173                                         //if the user has not given a path then, add inputdir. else leave path alone.
 174                                         if (path == "") {       parameters["ffasta"] = inputDir + it->second;           }
 175                                 }
 176
 177                 it = parameters.find("rfasta");
 178                                 //user has given a template file
 179                                 if(it != parameters.end()){
 180                                         path = m->hasPath(it->second);
 181                                         //if the user has not given a path then, add inputdir. else leave path alone.
 182                                         if (path == "") {       parameters["rfasta"] = inputDir + it->second;           }
 183                                 }
 184
 185                 it = parameters.find("fqfile");
 186                                 //user has given a template file
 187                                 if(it != parameters.end()){
 188                                         path = m->hasPath(it->second);
 189                                         //if the user has not given a path then, add inputdir. else leave path alone.
 190                                         if (path == "") {       parameters["fqfile"] = inputDir + it->second;           }
 191                                 }
 192
 193                 it = parameters.find("rqfile");
 194                                 //user has given a template file
 195                                 if(it != parameters.end()){
 196                                         path = m->hasPath(it->second);
 197                                         //if the user has not given a path then, add inputdir. else leave path alone.
 198                                         if (path == "") {       parameters["rqfile"] = inputDir + it->second;           }
 199                                 }
 200
 201                 it = parameters.find("file");
 202                                 //user has given a template file
 203                                 if(it != parameters.end()){
 204                                         path = m->hasPath(it->second);
 205                                         //if the user has not given a path then, add inputdir. else leave path alone.
 206                                         if (path == "") {       parameters["file"] = inputDir + it->second;             }
 207                                 }
 208
 209                 it = parameters.find("oligos");
 210                                 //user has given a template file
 211                                 if(it != parameters.end()){
 212                                         path = m->hasPath(it->second);
 213                                         //if the user has not given a path then, add inputdir. else leave path alone.
 214                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 215                                 }
 216             }
 217
 218             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
 219                         if (ffastqfile == "not open") {  abort = true; }
 220                         else if (ffastqfile == "not found") { ffastqfile = ""; }
 221
 222                         rfastqfile = validParameter.validFile(parameters, "rfastq", true);
 223                         if (rfastqfile == "not open") {  abort = true; }
 224                         else if (rfastqfile == "not found") { rfastqfile = "";  }
 225
 226             ffastafile = validParameter.validFile(parameters, "ffasta", true);
 227                         if (ffastafile == "not open") {  abort = true; }
 228                         else if (ffastafile == "not found") { ffastafile = ""; }
 229
 230                         rfastafile = validParameter.validFile(parameters, "rfasta", true);
 231                         if (rfastafile == "not open") {  abort = true; }
 232                         else if (rfastafile == "not found") { rfastafile = "";  }
 233
 234             fqualfile = validParameter.validFile(parameters, "fqfile", true);
 235                         if (fqualfile == "not open") {  abort = true; }
 236                         else if (fqualfile == "not found") { fqualfile = ""; }
 237
 238                         rqualfile = validParameter.validFile(parameters, "rqfile", true);
 239                         if (rqualfile == "not open") {  abort = true; }
 240                         else if (rqualfile == "not found") { rqualfile = "";  }
 241
 242             file = validParameter.validFile(parameters, "file", true);
 243                         if (file == "not open") {  abort = true; }
 244                         else if (file == "not found") { file = "";  }
 245
 246             if ((file == "") && (ffastafile == "") && (ffastqfile == "")) { abort = true; m->mothurOut("[ERROR]: ffastq and rfastq parameters are required.\n"); }
 247             if ((ffastqfile != "") && (rfastqfile == "")) {  abort = true; }
 248             if ((ffastqfile == "") && (rfastqfile != "")) {  abort = true; }
 249
 250             oligosfile = validParameter.validFile(parameters, "oligos", true);
 251                         if (oligosfile == "not found")      {   oligosfile = "";        }
 252                         else if(oligosfile == "not open")   {   abort = true;       }
 253                         else {   m->setOligosFile(oligosfile);          }
 254
 255             //if the user changes the output directory command factory will send this info to us in the output parameter
 256                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(ffastqfile);             }
 257
 258
 259                         //check for optional parameter and set defaults
 260                         // ...at some point should added some additional type checking...
 261                         string temp;
 262                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 263                         m->mothurConvert(temp, match);
 264
 265                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 266                         m->mothurConvert(temp, misMatch);
 267             if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 268
 269                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 270                         m->mothurConvert(temp, gapOpen);
 271             if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 272
 273                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 274                         m->mothurConvert(temp, gapExtend);
 275             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 276
 277             temp = validParameter.validFile(parameters, "threshold", false);    if (temp == "not found"){       temp = "40";                    }
 278                         m->mothurConvert(temp, threshold);
 279             if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
 280
 281                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 282                         m->setProcessors(temp);
 283                         m->mothurConvert(temp, processors);
 284
 285             temp = validParameter.validFile(parameters, "bdiffs", false);               if (temp == "not found") { temp = "0"; }
 286                         m->mothurConvert(temp, bdiffs);
 287
 288                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 289                         m->mothurConvert(temp, pdiffs);
 290
 291   //          temp = validParameter.validFile(parameters, "ldiffs", false);             if (temp == "not found") { temp = "0"; }
 292 //                      m->mothurConvert(temp, ldiffs);
 293             ldiffs = 0;
 294
 295  //           temp = validParameter.validFile(parameters, "sdiffs", false);             if (temp == "not found") { temp = "0"; }
 296  //           m->mothurConvert(temp, sdiffs);
 297             sdiffs = 0;
 298
 299                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 300                         m->mothurConvert(temp, tdiffs);
 301
 302                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }  //+ ldiffs + sdiffs;
 303
 304             temp = validParameter.validFile(parameters, "allfiles", false);             if (temp == "not found") { temp = "F"; }
 305                         allFiles = m->isTrue(temp);
 306
 307                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 308                         if ((align != "needleman") && (align != "gotoh")) { m->mothurOut(align + " is not a valid alignment method. Options are needleman or gotoh. I will use needleman."); m->mothurOutEndLine(); align = "needleman"; }
 309         }
 310
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 314                 exit(1);
 315         }
 316 }
 317 //**********************************************************************************************************************
 318 int MakeContigsCommand::execute(){
 319         try {
 320                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 321
 322         //read ffastq and rfastq files creating fasta and qual files.
 323         //this function will create a forward and reverse, fasta and qual files for each processor.
 324         //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual
 325         unsigned long int numReads = 0;
 326         int start = time(NULL);
 327         longestBase = 1000;
 328         m->mothurOut("Reading fastq data...\n");
 329         vector< vector<string> > files = readFastqFiles(numReads);
 330         m->mothurOut("Done.\n");
 331
 332         if (m->control_pressed) { return 0; }
 333
 334         vector<vector<string> > fastaFileNames;
 335                 vector<vector<string> > qualFileNames;
 336         createGroup = false;
 337         string outputGroupFileName;
 338         map<string, string> variables;
 339         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(ffastqfile));
 340         variables["[tag]"] = "";
 341         if(oligosfile != ""){
 342                         createGroup = getOligos(fastaFileNames, qualFileNames);
 343             if (createGroup) {
 344                 outputGroupFileName = getOutputFileName("group",variables);
 345                 outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
 346             }
 347                 }
 348
 349         variables["[tag]"] = "trim";
 350         string outFastaFile = getOutputFileName("fasta",variables);
 351         string outQualFile = getOutputFileName("qfile",variables);
 352         variables["[tag]"] = "scrap";
 353         string outScrapFastaFile = getOutputFileName("fasta",variables);
 354         string outScrapQualFile = getOutputFileName("qfile",variables);
 355
 356         variables["[tag]"] = "";
 357         string outMisMatchFile = getOutputFileName("mismatch",variables);
 358         outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 359         outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
 360         outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
 361         outputNames.push_back(outScrapQualFile); outputTypes["qfile"].push_back(outScrapQualFile);
 362         outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
 363
 364         m->mothurOut("Making contigs...\n");
 365         createProcesses(files, outFastaFile, outQualFile, outScrapFastaFile, outScrapQualFile, outMisMatchFile, fastaFileNames, qualFileNames);
 366         m->mothurOut("Done.\n");
 367
 368         //remove temp fasta and qual files
 369         for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }  }
 370
 371         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 372
 373         if(allFiles){
 374                         map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
 375                         map<string, string>::iterator it;
 376                         set<string> namesToRemove;
 377                         for(int i=0;i<fastaFileNames.size();i++){
 378                                 for(int j=0;j<fastaFileNames[0].size();j++){
 379                                         if (fastaFileNames[i][j] != "") {
 380                                                 if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
 381                                                         if(m->isBlank(fastaFileNames[i][j])){
 382                                                                 m->mothurRemove(fastaFileNames[i][j]);
 383                                                                 namesToRemove.insert(fastaFileNames[i][j]);
 384
 385                                 m->mothurRemove(qualFileNames[i][j]);
 386                                 namesToRemove.insert(qualFileNames[i][j]);
 387                                                         }else{
 388                                                                 it = uniqueFastaNames.find(fastaFileNames[i][j]);
 389                                                                 if (it == uniqueFastaNames.end()) {
 390                                                                         uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
 391                                                                 }
 392                                                         }
 393                                                 }
 394                                         }
 395                                 }
 396                         }
 397
 398                         //remove names for outputFileNames, just cleans up the output
 399                         vector<string> outputNames2;
 400                         for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
 401                         outputNames = outputNames2;
 402
 403             for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
 404                 ifstream in;
 405                 m->openInputFile(it->first, in);
 406
 407                 ofstream out;
 408                 string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
 409                 thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
 410                 m->openOutputFile(thisGroupName, out);
 411
 412                 while (!in.eof()){
 413                     if (m->control_pressed) { break; }
 414
 415                     Sequence currSeq(in); m->gobble(in);
 416                     out << currSeq.getName() << '\t' << it->second << endl;
 417                 }
 418                 in.close();
 419                 out.close();
 420             }
 421         }
 422
 423         if (createGroup) {
 424             ofstream outGroup;
 425             m->openOutputFile(outputGroupFileName, outGroup);
 426             for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
 427                 outGroup << itGroup->first << '\t' << itGroup->second << endl;
 428             }
 429             outGroup.close();
 430         }
 431         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 432
 433         if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 434
 435                 //output group counts
 436                 m->mothurOutEndLine();
 437                 int total = 0;
 438                 if (groupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
 439                 for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 440             total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
 441                 }
 442                 if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
 443
 444                 if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 445
 446         string currentFasta = "";
 447                 itTypes = outputTypes.find("fasta");
 448                 if (itTypes != outputTypes.end()) {
 449                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 450                 }
 451
 452         string currentQual = "";
 453                 itTypes = outputTypes.find("qfile");
 454                 if (itTypes != outputTypes.end()) {
 455                         if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
 456                 }
 457
 458         string currentGroup = "";
 459                 itTypes = outputTypes.find("group");
 460                 if (itTypes != outputTypes.end()) {
 461                         if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); }
 462                 }
 463
 464         //output files created by command
 465                 m->mothurOutEndLine();
 466                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 467                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 468                 m->mothurOutEndLine();
 469
 470         return 0;
 471     }
 472         catch(exception& e) {
 473                 m->errorOut(e, "MakeContigsCommand", "execute");
 474                 exit(1);
 475         }
 476 }
 477 //**********************************************************************************************************************
 478 int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames) {
 479         try {
 480                 int num = 0;
 481                 vector<int> processIDS;
 482 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 483                 int process = 0;
 484
 485                 //loop through and create all the processes you want
 486                 while (process != processors-1) {
 487                         int pid = fork();
 488
 489                         if (pid > 0) {
 490                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 491                                 process++;
 492                         }else if (pid == 0){
 493                 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 494                                 vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 495
 496                                 if(allFiles){
 497                                         ofstream temp;
 498
 499                                         for(int i=0;i<tempFASTAFileNames.size();i++){
 500                                                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 501                                                         if (tempFASTAFileNames[i][j] != "") {
 502                                                                 tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
 503                                                                 m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 504
 505                                 tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
 506                                 m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
 507                                                         }
 508                                                 }
 509                                         }
 510                                 }
 511
 512                                 num = driver(files[process],
 513                              outputFasta + toString(getpid()) + ".temp",
 514                              outputQual + toString(getpid()) + ".temp",
 515                              outputScrapFasta + toString(getpid()) + ".temp",
 516                              outputScrapQual + toString(getpid()) + ".temp",
 517                              outputMisMatches + toString(getpid()) + ".temp",
 518                              tempFASTAFileNames,
 519                              tempPrimerQualFileNames);
 520
 521                                 //pass groupCounts to parent
 522                 ofstream out;
 523                 string tempFile = toString(getpid()) + ".num.temp";
 524                 m->openOutputFile(tempFile, out);
 525                 out << num << endl;
 526                                 if(createGroup){
 527                                         out << groupCounts.size() << endl;
 528
 529                                         for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 530                                                 out << it->first << '\t' << it->second << endl;
 531                                         }
 532
 533                     out << groupMap.size() << endl;
 534                     for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
 535                                                 out << it->first << '\t' << it->second << endl;
 536                                         }
 537                                 }
 538                 out.close();
 539
 540                                 exit(0);
 541                         }else {
 542                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 543                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 544                                 exit(0);
 545                         }
 546                 }
 547
 548         ofstream temp;
 549                 m->openOutputFile(outputFasta, temp);           temp.close();
 550                 m->openOutputFile(outputQual, temp);    temp.close();
 551         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 552         m->openOutputFile(outputScrapQual, temp);               temp.close();
 553
 554                 //do my part
 555                 num = driver(files[processors-1], outputFasta, outputQual, outputScrapFasta, outputScrapQual, outputMisMatches, fastaFileNames, qualFileNames);
 556
 557                 //force parent to wait until all the processes are done
 558                 for (int i=0;i<processIDS.size();i++) {
 559                         int temp = processIDS[i];
 560                         wait(&temp);
 561                 }
 562
 563                 for (int i = 0; i < processIDS.size(); i++) {
 564             ifstream in;
 565             string tempFile = toString(processIDS[i]) + ".num.temp";
 566             m->openInputFile(tempFile, in);
 567             int tempNum;
 568             in >> tempNum; num += tempNum; m->gobble(in);
 569
 570                         if(createGroup){
 571                                 string group;
 572                                 in >> tempNum; m->gobble(in);
 573
 574                                 if (tempNum != 0) {
 575                                         for (int j = 0; j < tempNum; j++) {
 576                         int groupNum;
 577                                                 in >> group >> groupNum; m->gobble(in);
 578
 579                                                 map<string, int>::iterator it = groupCounts.find(group);
 580                                                 if (it == groupCounts.end()) {  groupCounts[group] = groupNum; }
 581                                                 else { groupCounts[it->first] += groupNum; }
 582                                         }
 583                                 }
 584                 in >> tempNum; m->gobble(in);
 585                 if (tempNum != 0) {
 586                                         for (int j = 0; j < tempNum; j++) {
 587                         string group, seqName;
 588                                                 in >> seqName >> group; m->gobble(in);
 589
 590                                                 map<string, string>::iterator it = groupMap.find(seqName);
 591                                                 if (it == groupMap.end()) {     groupMap[seqName] = group; }
 592                                                 else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 593                                         }
 594                                 }
 595                         }
 596             in.close(); m->mothurRemove(tempFile);
 597         }
 598     #else
 599
 600         //////////////////////////////////////////////////////////////////////////////////////////////////////
 601                 //Windows version shared memory, so be careful when passing variables through the contigsData struct.
 602                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 603                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 604
 605                 vector<contigsData*> pDataArray;
 606                 DWORD   dwThreadIdArray[processors-1];
 607                 HANDLE  hThreadArray[processors-1];
 608
 609                 //Create processor worker threads.
 610                 for( int h=0; h<processors-1; h++ ){
 611                         string extension = "";
 612                         if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
 613             vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 614             vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 615
 616             if(allFiles){
 617                 ofstream temp;
 618
 619                 for(int i=0;i<tempFASTAFileNames.size();i++){
 620                     for(int j=0;j<tempFASTAFileNames[i].size();j++){
 621                         if (tempFASTAFileNames[i][j] != "") {
 622                             tempFASTAFileNames[i][j] += extension;
 623                             m->openOutputFile(tempFASTAFileNames[i][j], temp);                  temp.close();
 624
 625
 626                             tempPrimerQualFileNames[i][j] += extension;
 627                             m->openOutputFile(tempPrimerQualFileNames[i][j], temp);             temp.close();
 628                         }
 629                     }
 630                 }
 631             }
 632
 633
 634                         contigsData* tempcontig = new contigsData(files[h], (outputFasta + extension), (outputQual + extension), (outputScrapFasta + extension), (outputScrapQual + extension),(outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, barcodes, primers, tempFASTAFileNames, tempPrimerQualFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createGroup, allFiles, h);
 635                         pDataArray.push_back(tempcontig);
 636
 637                         hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
 638                 }
 639
 640         vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 641         vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 642
 643         if(allFiles){
 644             ofstream temp;
 645             string extension = toString(processors-1) + ".temp";
 646
 647             for(int i=0;i<tempFASTAFileNames.size();i++){
 648                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 649                     if (tempFASTAFileNames[i][j] != "") {
 650                         tempFASTAFileNames[i][j] += extension;
 651                         m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 652
 653
 654                         tempPrimerQualFileNames[i][j] += extension;
 655                         m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
 656                     }
 657                 }
 658             }
 659         }
 660
 661                 //parent do my part
 662                 ofstream temp;
 663                 m->openOutputFile(outputFasta, temp);           temp.close();
 664                 m->openOutputFile(outputQual, temp);    temp.close();
 665         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 666         m->openOutputFile(outputScrapQual, temp);               temp.close();
 667
 668
 669         //do my part
 670                 num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"), (outputQual+ toString(processors-1) + ".temp"), (outputScrapFasta+ toString(processors-1) + ".temp"), (outputScrapQual+ toString(processors-1) + ".temp"), (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames);
 671
 672                 //Wait until all threads have terminated.
 673                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 674
 675                 //Close all thread handles and free memory allocations.
 676                 for(int i=0; i < pDataArray.size(); i++){
 677                         num += pDataArray[i]->count;
 678             for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
 679                 map<string, int>::iterator it2 = groupCounts.find(it->first);
 680                 if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
 681                 else { groupCounts[it->first] += it->second; }
 682             }
 683             for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
 684                 map<string, string>::iterator it2 = groupMap.find(it->first);
 685                 if (it2 == groupMap.end()) {    groupMap[it->first] = it->second; }
 686                 else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 687             }
 688             CloseHandle(hThreadArray[i]);
 689                         delete pDataArray[i];
 690         }
 691
 692     #endif
 693
 694         for (int i = 0; i < processIDS.size(); i++) {
 695                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 696                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 697
 698                         m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
 699                         m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
 700
 701             m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
 702                         m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp"));
 703
 704                         m->appendFiles((outputScrapQual + toString(processIDS[i]) + ".temp"), outputScrapQual);
 705                         m->mothurRemove((outputScrapQual + toString(processIDS[i]) + ".temp"));
 706
 707             m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 708                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 709
 710             if(allFiles){
 711                                 for(int j=0;j<fastaFileNames.size();j++){
 712                                         for(int k=0;k<fastaFileNames[j].size();k++){
 713                                                 if (fastaFileNames[j][k] != "") {
 714                                                         m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
 715                                                         m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 716
 717                             m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
 718                             m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 719                                                 }
 720                                         }
 721                                 }
 722                         }
 723                 }
 724
 725                 return num;
 726         }
 727         catch(exception& e) {
 728                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 729                 exit(1);
 730         }
 731 }
 732 //**********************************************************************************************************************
 733 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames){
 734     try {
 735
 736         Alignment* alignment;
 737         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 738                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 739
 740         int num = 0;
 741         string thisffastafile = files[0];
 742         string thisfqualfile = files[1];
 743         string thisrfastafile = files[2];
 744         string thisrqualfile = files[3];
 745
 746         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 747
 748         ifstream inFFasta, inRFasta, inFQual, inRQual;
 749         m->openInputFile(thisffastafile, inFFasta);
 750         m->openInputFile(thisfqualfile, inFQual);
 751         m->openInputFile(thisrfastafile, inRFasta);
 752         m->openInputFile(thisrqualfile, inRQual);
 753
 754         ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
 755         m->openOutputFile(outputFasta, outFasta);
 756         m->openOutputFile(outputQual, outQual);
 757         m->openOutputFile(outputScrapFasta, outScrapFasta);
 758         m->openOutputFile(outputScrapQual, outScrapQual);
 759         m->openOutputFile(outputMisMatches, outMisMatch);
 760         outMisMatch << "Name\tLength\tMisMatches\n";
 761
 762         TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
 763
 764         while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
 765
 766             if (m->control_pressed) { break; }
 767
 768             int success = 1;
 769             string trashCode = "";
 770             int currentSeqsDiffs = 0;
 771
 772             //read seqs and quality info
 773             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 774             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 775             QualityScores fQual(inFQual); m->gobble(inFQual);
 776             QualityScores rQual(inRQual); m->gobble(inRQual);
 777
 778             int barcodeIndex = 0;
 779             int primerIndex = 0;
 780
 781             if(barcodes.size() != 0){
 782                 success = trimOligos.stripBarcode(fSeq, rSeq, fQual, rQual, barcodeIndex);
 783                 if(success > bdiffs)            {       trashCode += 'b';       }
 784                 else{ currentSeqsDiffs += success;  }
 785             }
 786
 787             if(primers.size() != 0){
 788                 success = trimOligos.stripForward(fSeq, rSeq, fQual, rQual, primerIndex);
 789                 if(success > pdiffs)            {       trashCode += 'f';       }
 790                 else{ currentSeqsDiffs += success;  }
 791             }
 792
 793             if (currentSeqsDiffs > tdiffs)      {       trashCode += 't';   }
 794
 795             //flip the reverse reads
 796             rSeq.reverseComplement();
 797             rQual.flipQScores();
 798
 799             //pairwise align
 800             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 801             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 802             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 803             fSeq.setAligned(alignment->getSeqAAln());
 804             rSeq.setAligned(alignment->getSeqBAln());
 805             int length = fSeq.getAligned().length();
 806
 807             //traverse alignments merging into one contiguous seq
 808             string contig = "";
 809             vector<int> contigScores;
 810             int numMismatches = 0;
 811             string seq1 = fSeq.getAligned();
 812             string seq2 = rSeq.getAligned();
 813             vector<int> scores1 = fQual.getQualityScores();
 814             vector<int> scores2 = rQual.getQualityScores();
 815
 816             // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
 817             int overlapStart = fSeq.getStartPos();
 818             int seq2Start = rSeq.getStartPos();
 819             //bigger of the 2 starting positions is the location of the overlapping start
 820             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 821                 overlapStart = seq2Start;
 822                 for (int i = 0; i < overlapStart; i++) {
 823                     contig += seq1[i];
 824                     contigScores.push_back(scores1[ABaseMap[i]]);
 825                 }
 826             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 827                 for (int i = 0; i < overlapStart; i++) {
 828                     contig += seq2[i];
 829                     contigScores.push_back(scores2[BBaseMap[i]]);
 830                 }
 831             }
 832
 833             int seq1End = fSeq.getEndPos();
 834             int seq2End = rSeq.getEndPos();
 835             int overlapEnd = seq1End;
 836             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 837
 838             for (int i = overlapStart; i < overlapEnd; i++) {
 839                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 840                     contig += seq1[i];
 841                     contigScores.push_back(scores1[ABaseMap[i]]);
 842                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
 843                 }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below threshold. In that case eliminate base
 844                     if (scores2[BBaseMap[i]] < threshold) { } //
 845                     else {
 846                         contig += seq2[i];
 847                         contigScores.push_back(scores2[BBaseMap[i]]);
 848                     }
 849                 }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below threshold. In that case eliminate base
 850                     if (scores1[ABaseMap[i]] < threshold) { } //
 851                     else {
 852                         contig += seq1[i];
 853                         contigScores.push_back(scores1[ABaseMap[i]]);
 854                     }
 855                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 856                     char c = seq1[i];
 857                     contigScores.push_back(scores1[ABaseMap[i]]);
 858                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
 859                     contig += c;
 860                     numMismatches++;
 861                 }else { //should never get here
 862                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
 863                 }
 864             }
 865
 866             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
 867                 for (int i = overlapEnd; i < length; i++) {
 868                     contig += seq2[i];
 869                     contigScores.push_back(scores2[BBaseMap[i]]);
 870                 }
 871             }else { //seq2 ends before seq1 so take from overlap to length from seq1
 872                 for (int i = overlapEnd; i < length; i++) {
 873                     contig += seq1[i];
 874                     contigScores.push_back(scores1[ABaseMap[i]]);
 875                 }
 876
 877             }
 878
 879             if(trashCode.length() == 0){
 880                 if (createGroup) {
 881                     if(barcodes.size() != 0){
 882                         string thisGroup = barcodeNameVector[barcodeIndex];
 883                         if (primers.size() != 0) {
 884                             if (primerNameVector[primerIndex] != "") {
 885                                 if(thisGroup != "") {
 886                                     thisGroup += "." + primerNameVector[primerIndex];
 887                                 }else {
 888                                     thisGroup = primerNameVector[primerIndex];
 889                                 }
 890                             }
 891                         }
 892
 893                         if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
 894
 895                         groupMap[fSeq.getName()] = thisGroup;
 896
 897                         map<string, int>::iterator it = groupCounts.find(thisGroup);
 898                         if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1; }
 899                         else { groupCounts[it->first] ++; }
 900
 901                     }
 902                 }
 903
 904                 if(allFiles){
 905                     ofstream output;
 906                     m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
 907                     output << ">" << fSeq.getName() << endl << contig << endl;
 908                     output.close();
 909
 910                     m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
 911                     output << ">" << fSeq.getName() << endl;
 912                     for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
 913                     output << endl;
 914                     output.close();
 915                 }
 916
 917                 //output
 918                 outFasta << ">" << fSeq.getName() << endl << contig << endl;
 919                 outQual << ">" << fSeq.getName() << endl;
 920                 for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
 921                 outQual << endl;
 922                 outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
 923             }else {
 924                 //output
 925                 outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
 926                 outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
 927                 for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
 928                 outScrapQual << endl;
 929             }
 930             num++;
 931
 932                         //report progress
 933                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 934                 }
 935
 936                 //report progress
 937                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 938
 939         inFFasta.close();
 940         inFQual.close();
 941         inRFasta.close();
 942         inRQual.close();
 943         outFasta.close();
 944         outQual.close();
 945         outScrapFasta.close();
 946         outScrapQual.close();
 947         outMisMatch.close();
 948         delete alignment;
 949
 950         if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta);   m->mothurRemove(outputScrapQual); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches);}
 951
 952         return num;
 953     }
 954         catch(exception& e) {
 955                 m->errorOut(e, "MakeContigsCommand", "driver");
 956                 exit(1);
 957         }
 958 }
 959 //**********************************************************************************************************************
 960 vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& count){
 961     try {
 962         vector< vector<string> > files;
 963
 964         //maps processors number to file pointer
 965         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
 966         map<int, vector<ofstream*> >::iterator it;
 967
 968         //create files to write to
 969         for (int i = 0; i < processors; i++) {
 970             vector<ofstream*> temp;
 971             ofstream* outFF = new ofstream;     temp.push_back(outFF);
 972             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
 973             ofstream* outRF = new ofstream;     temp.push_back(outRF);
 974             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
 975             tempfiles[i] = temp;
 976
 977             vector<string> names;
 978             string ffastafilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "ffasta.temp";
 979             string rfastafilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rfasta.temp";
 980             string fqualfilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "fqual.temp";
 981             string rqualfilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rqual.temp";
 982             names.push_back(ffastafilename); names.push_back(fqualfilename);
 983             names.push_back(rfastafilename); names.push_back(rqualfilename);
 984             files.push_back(names);
 985
 986             m->openOutputFile(ffastafilename, *outFF);
 987             m->openOutputFile(rfastafilename, *outRF);
 988             m->openOutputFile(fqualfilename, *outFQ);
 989             m->openOutputFile(rqualfilename, *outRQ);
 990         }
 991
 992         if (m->control_pressed) {
 993             //close files, delete ofstreams
 994             for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } }
 995             //remove files
 996             for (int i = 0; i < files.size(); i++) {
 997                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
 998             }
 999         }
1000
1001         ifstream inForward;
1002         m->openInputFile(ffastqfile, inForward);
1003
1004         ifstream inReverse;
1005         m->openInputFile(rfastqfile, inReverse);
1006
1007         count = 0;
1008         map<string, fastqRead> uniques;
1009         map<string, fastqRead>::iterator itUniques;
1010         while ((!inForward.eof()) || (!inReverse.eof())) {
1011
1012             if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) {  for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inForward.close(); inReverse.close(); return files; }
1013
1014             //get a read from forward and reverse fastq files
1015             bool ignoref, ignorer;
1016             fastqRead thisFread, thisRread;
1017             if (!inForward.eof()) {  thisFread = readFastq(inForward, ignoref); }
1018             else { ignoref = true; }
1019             if (!inReverse.eof()) { thisRread = readFastq(inReverse, ignorer);  }
1020             else { ignorer = true; }
1021
1022             vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
1023
1024             for (int i = 0; i < reads.size(); i++) {
1025                 fastqRead fread = reads[i].forward;
1026                 fastqRead rread = reads[i].reverse;
1027
1028                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
1029
1030                 if (checkReads(fread, rread)) {
1031                     if (m->control_pressed) { for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } } for (int i = 0; i < files.size(); i++) {  for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } } inForward.close(); inReverse.close(); return files; }
1032
1033                     //if the reads are okay write to output files
1034                     int process = count % processors;
1035
1036                     *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
1037                     *(tempfiles[process][1]) << ">" << fread.name << endl;
1038                     for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
1039                     *(tempfiles[process][1]) << endl;
1040                     *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
1041                     *(tempfiles[process][3]) << ">" << rread.name << endl;
1042                     for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
1043                     *(tempfiles[process][3]) << endl;
1044
1045                     count++;
1046
1047                     //report progress
1048                     if((count) % 10000 == 0){   m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1049                 }
1050             }
1051                 }
1052                 //report progress
1053                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1054
1055         if (uniques.size() != 0) {
1056             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
1057                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
1058             }
1059             m->mothurOutEndLine();
1060         }
1061
1062         //close files, delete ofstreams
1063         for (it = tempfiles.begin(); it!=tempfiles.end(); it++) { for (int i = 0; i < (it->second).size(); i++) { (*(it->second)[i]).close();  delete (it->second)[i]; } }
1064         inForward.close();
1065         inReverse.close();
1066
1067         //adjust for really large processors or really small files
1068         if (count == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
1069         if (count < processors) {
1070             for (int i = count; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
1071             files.resize(count);
1072             processors = count;
1073         }
1074
1075         return files;
1076     }
1077     catch(exception& e) {
1078         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1079         exit(1);
1080     }
1081 }
1082 //**********************************************************************************************************************
1083 vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques){
1084     try {
1085         vector<pairFastqRead> reads;
1086         map<string, fastqRead>::iterator itUniques;
1087
1088         if (!ignoref && !ignorer) {
1089             if (forward.name == reverse.name) {
1090                 pairFastqRead temp(forward, reverse);
1091                 reads.push_back(temp);
1092             }else {
1093                 bool match = false;
1094                 //if no match are the names only different by 1 and 2?
1095                 string tempFRead = forward.name.substr(0, forward.name.length()-1);
1096                 string tempRRead = reverse.name.substr(0, reverse.name.length()-1);
1097                 if (tempFRead == tempRRead) {
1098                     if ((forward.name[forward.name.length()-1] == '1') && (reverse.name[reverse.name.length()-1] == '2')) {
1099                         forward.name = tempFRead;
1100                         reverse.name = tempRRead;
1101                         pairFastqRead temp(forward, reverse);
1102                         reads.push_back(temp);
1103                         match = true;
1104                     }
1105                 }
1106
1107                 if (!match) {
1108                     //look for forward pair
1109                     itUniques = uniques.find(forward.name);
1110                     if (itUniques != uniques.end()) {  //we have the pair for this read
1111                         pairFastqRead temp(forward, itUniques->second);
1112                         reads.push_back(temp);
1113                         uniques.erase(itUniques);
1114                     }else { //save this read for later
1115                         uniques[forward.name] = forward;
1116                     }
1117
1118                     //look for reverse pair
1119                     itUniques = uniques.find(reverse.name);
1120                     if (itUniques != uniques.end()) {  //we have the pair for this read
1121                         pairFastqRead temp(itUniques->second, reverse);
1122                         reads.push_back(temp);
1123                         uniques.erase(itUniques);
1124                     }else { //save this read for later
1125                         uniques[reverse.name] = reverse;
1126                     }
1127                 }
1128
1129             }
1130         }else if (!ignoref && ignorer) { //ignore reverse keep forward
1131             //look for forward pair
1132             itUniques = uniques.find(forward.name);
1133             if (itUniques != uniques.end()) {  //we have the pair for this read
1134                 pairFastqRead temp(forward, itUniques->second);
1135                 reads.push_back(temp);
1136                 uniques.erase(itUniques);
1137             }else { //save this read for later
1138                 uniques[forward.name] = forward;
1139             }
1140
1141         }else if (ignoref && !ignorer) { //ignore forward keep reverse
1142             //look for reverse pair
1143             itUniques = uniques.find(reverse.name);
1144             if (itUniques != uniques.end()) {  //we have the pair for this read
1145                 pairFastqRead temp(itUniques->second, reverse);
1146                 reads.push_back(temp);
1147                 uniques.erase(itUniques);
1148             }else { //save this read for later
1149                 uniques[reverse.name] = reverse;
1150             }
1151         }//else ignore both and do nothing
1152
1153         return reads;
1154     }
1155     catch(exception& e) {
1156         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1157         exit(1);
1158     }
1159 }
1160 //**********************************************************************************************************************
1161 fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
1162     try {
1163         fastqRead read;
1164
1165         ignore = false;
1166
1167         //read sequence name
1168         string line = m->getline(in); m->gobble(in);
1169         vector<string> pieces = m->splitWhiteSpace(line);
1170         string name = "";  if (pieces.size() != 0) { name = pieces[0]; }
1171         if (name == "") {  m->mothurOut("[WARNING]: Blank fasta name, ignoring read."); m->mothurOutEndLine(); ignore=true;  }
1172         else if (name[0] != '@') { m->mothurOut("[WARNING]: reading " + name + " expected a name with @ as a leading character, ignoring read."); m->mothurOutEndLine(); ignore=true; }
1173         else { name = name.substr(1); }
1174
1175         //read sequence
1176         string sequence = m->getline(in); m->gobble(in);
1177         if (sequence == "") {  m->mothurOut("[WARNING]: missing sequence for " + name + ", ignoring."); ignore=true; }
1178
1179         //read sequence name
1180         line = m->getline(in); m->gobble(in);
1181         pieces = m->splitWhiteSpace(line);
1182         string name2 = "";  if (pieces.size() != 0) { name2 = pieces[0]; }
1183         if (name2 == "") {  m->mothurOut("[WARNING]: expected a name with + as a leading character, ignoring."); ignore=true; }
1184         else if (name2[0] != '+') { m->mothurOut("[WARNING]: reading " + name2 + " expected a name with + as a leading character, ignoring."); ignore=true; }
1185         else { name2 = name2.substr(1); if (name2 == "") { name2 = name; } }
1186
1187         //read quality scores
1188         string quality = m->getline(in); m->gobble(in);
1189         if (quality == "") {  m->mothurOut("[WARNING]: missing quality for " + name2 + ", ignoring."); ignore=true; }
1190
1191         //sanity check sequence length and number of quality scores match
1192         if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } }
1193         if (quality.length() != sequence.length()) { m->mothurOut("[WARNING]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores, ignoring read."); ignore=true; }
1194
1195         vector<int> qualScores;
1196                 int controlChar = int('!');
1197                 for (int i = 0; i < quality.length(); i++) {
1198                         int temp = int(quality[i]);
1199                         temp -= controlChar;
1200
1201                         qualScores.push_back(temp);
1202                 }
1203
1204         read.name = name;
1205         read.sequence = sequence;
1206         read.scores = qualScores;
1207
1208         return read;
1209     }
1210     catch(exception& e) {
1211         m->errorOut(e, "MakeContigsCommand", "readFastq");
1212         exit(1);
1213     }
1214 }
1215 //**********************************************************************************************************************
1216 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){
1217     try {
1218         bool good = true;
1219
1220         //do sequence lengths match
1221         if (forward.sequence.length() != reverse.sequence.length()) {
1222             m->mothurOut("[WARNING]: For sequence " + forward.name + " I read a sequence of length " + toString(forward.sequence.length()) + " from " + ffastqfile + ", but read a sequence of length " + toString(reverse.sequence.length()) + " from " + rfastqfile + ", ignoring.\n");
1223             good = false;
1224         }
1225
1226         //do number of qual scores match
1227         if (forward.scores.size() != reverse.scores.size()) {
1228             m->mothurOut("[WARNING]: For sequence " + forward.name + " I read " + toString(forward.scores.size()) + " quality scores from " + ffastqfile + ", but read  " + toString(reverse.scores.size()) + " quality scores from " + rfastqfile + ", ignoring.\n");
1229             good = false;
1230         }
1231
1232         return good;
1233     }
1234     catch(exception& e) {
1235         m->errorOut(e, "MakeContigsCommand", "checkReads");
1236         exit(1);
1237     }
1238 }
1239 //***************************************************************************************************************
1240 //illumina data requires paired forward and reverse data
1241 //BARCODE   atgcatgc   atgcatgc    groupName
1242 //PRIMER   atgcatgc   atgcatgc    groupName
1243 //PRIMER   atgcatgc   atgcatgc
1244 bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames){
1245         try {
1246                 ifstream in;
1247                 m->openInputFile(oligosfile, in);
1248
1249                 ofstream test;
1250
1251                 string type, foligo, roligo, group;
1252
1253                 int indexPrimer = 0;
1254                 int indexBarcode = 0;
1255         set<string> uniquePrimers;
1256         set<string> uniqueBarcodes;
1257
1258                 while(!in.eof()){
1259
1260                         in >> type;
1261
1262                         if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
1263
1264                         if(type[0] == '#'){
1265                                 while (!in.eof())       {       char c = in.get();  if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
1266                                 m->gobble(in);
1267                         }
1268                         else{
1269                                 m->gobble(in);
1270                                 //make type case insensitive
1271                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
1272
1273                                 in >> foligo;
1274
1275                 if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); }
1276
1277                                 for(int i=0;i<foligo.length();i++){
1278                                         foligo[i] = toupper(foligo[i]);
1279                                         if(foligo[i] == 'U')    {       foligo[i] = 'T';        }
1280                                 }
1281
1282                                 if(type == "FORWARD"){
1283                                         m->gobble(in);
1284
1285                     in >> roligo;
1286
1287                     for(int i=0;i<roligo.length();i++){
1288                         roligo[i] = toupper(roligo[i]);
1289                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1290                     }
1291                     //roligo = reverseOligo(roligo);
1292
1293                     group = "";
1294
1295                                         // get rest of line in case there is a primer name
1296                                         while (!in.eof())       {
1297                                                 char c = in.get();
1298                                                 if (c == 10 || c == 13){        break;  }
1299                                                 else if (c == 32 || c == 9){;} //space or tab
1300                                                 else {  group += c;  }
1301                                         }
1302
1303                     oligosPair newPrimer(foligo, roligo);
1304
1305                                         //check for repeat barcodes
1306                     string tempPair = foligo+roligo;
1307                     if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine();  }
1308                     else { uniquePrimers.insert(tempPair); }
1309
1310                     if (m->debug) {  if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); }  }
1311
1312                                         primers[indexPrimer]=newPrimer; indexPrimer++;
1313                                         primerNameVector.push_back(group);
1314                                 }else if(type == "BARCODE"){
1315                                         m->gobble(in);
1316
1317                     in >> roligo;
1318
1319                     for(int i=0;i<roligo.length();i++){
1320                         roligo[i] = toupper(roligo[i]);
1321                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1322                     }
1323                     //roligo = reverseOligo(roligo);
1324
1325                     oligosPair newPair(foligo, roligo);
1326
1327                     group = "";
1328                     while (!in.eof())   {
1329                                                 char c = in.get();
1330                                                 if (c == 10 || c == 13){        break;  }
1331                                                 else if (c == 32 || c == 9){;} //space or tab
1332                                                 else {  group += c;  }
1333                                         }
1334
1335                     if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
1336
1337                     //check for repeat barcodes
1338                     string tempPair = foligo+roligo;
1339                     if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse +  " is in your oligos file already, disregarding."); m->mothurOutEndLine();  }
1340                     else { uniqueBarcodes.insert(tempPair); }
1341
1342                     barcodes[indexBarcode]=newPair; indexBarcode++;
1343                                         barcodeNameVector.push_back(group);
1344                                 }else if(type == "LINKER"){
1345                                         linker.push_back(foligo);
1346                     m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");
1347                                 }else if(type == "SPACER"){
1348                                         spacer.push_back(foligo);
1349                     m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n");
1350                                 }
1351                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); }
1352                         }
1353                         m->gobble(in);
1354                 }
1355                 in.close();
1356
1357                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
1358
1359                 //add in potential combos
1360                 if(barcodeNameVector.size() == 0){
1361             oligosPair temp("", "");
1362                         barcodes[0] = temp;
1363                         barcodeNameVector.push_back("");
1364                 }
1365
1366                 if(primerNameVector.size() == 0){
1367             oligosPair temp("", "");
1368                         primers[0] = temp;
1369                         primerNameVector.push_back("");
1370                 }
1371
1372                 fastaFileNames.resize(barcodeNameVector.size());
1373                 for(int i=0;i<fastaFileNames.size();i++){
1374                         fastaFileNames[i].assign(primerNameVector.size(), "");
1375                 }
1376                 qualFileNames = fastaFileNames;
1377
1378                 if(allFiles){
1379                         set<string> uniqueNames; //used to cleanup outputFileNames
1380                         for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1381                                 for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1382
1383                                         string primerName = primerNameVector[itPrimer->first];
1384                                         string barcodeName = barcodeNameVector[itBar->first];
1385
1386                                         string comboGroupName = "";
1387                                         string fastaFileName = "";
1388                                         string qualFileName = "";
1389                                         string nameFileName = "";
1390                     string countFileName = "";
1391
1392                                         if(primerName == ""){
1393                                                 comboGroupName = barcodeNameVector[itBar->first];
1394                                         }
1395                                         else{
1396                                                 if(barcodeName == ""){
1397                                                         comboGroupName = primerNameVector[itPrimer->first];
1398                                                 }
1399                                                 else{
1400                                                         comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
1401                                                 }
1402                                         }
1403
1404
1405                                         ofstream temp;
1406                                         fastaFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".fasta";
1407                                         if (uniqueNames.count(fastaFileName) == 0) {
1408                                                 outputNames.push_back(fastaFileName);
1409                                                 outputTypes["fasta"].push_back(fastaFileName);
1410                                                 uniqueNames.insert(fastaFileName);
1411                                         }
1412
1413                                         fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
1414                                         m->openOutputFile(fastaFileName, temp);         temp.close();
1415
1416
1417                     qualFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".qual";
1418                     if (uniqueNames.count(qualFileName) == 0) {
1419                         outputNames.push_back(qualFileName);
1420                         outputTypes["qfile"].push_back(qualFileName);
1421                     }
1422
1423                     qualFileNames[itBar->first][itPrimer->first] = qualFileName;
1424                     m->openOutputFile(qualFileName, temp);              temp.close();
1425                                 }
1426                         }
1427                 }
1428
1429                 bool allBlank = true;
1430                 for (int i = 0; i < barcodeNameVector.size(); i++) {
1431                         if (barcodeNameVector[i] != "") {
1432                                 allBlank = false;
1433                                 break;
1434                         }
1435                 }
1436                 for (int i = 0; i < primerNameVector.size(); i++) {
1437                         if (primerNameVector[i] != "") {
1438                                 allBlank = false;
1439                                 break;
1440                         }
1441                 }
1442
1443                 if (allBlank) {
1444                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
1445                         allFiles = false;
1446                         return false;
1447                 }
1448
1449                 return true;
1450
1451         }
1452         catch(exception& e) {
1453                 m->errorOut(e, "MakeContigsCommand", "getOligos");
1454                 exit(1);
1455         }
1456 }
1457 //********************************************************************/
1458 string MakeContigsCommand::reverseOligo(string oligo){
1459         try {
1460         string reverse = "";
1461
1462         for(int i=oligo.length()-1;i>=0;i--){
1463
1464             if(oligo[i] == 'A')         {       reverse += 'T'; }
1465             else if(oligo[i] == 'T'){   reverse += 'A'; }
1466             else if(oligo[i] == 'U'){   reverse += 'A'; }
1467
1468             else if(oligo[i] == 'G'){   reverse += 'C'; }
1469             else if(oligo[i] == 'C'){   reverse += 'G'; }
1470
1471             else if(oligo[i] == 'R'){   reverse += 'Y'; }
1472             else if(oligo[i] == 'Y'){   reverse += 'R'; }
1473
1474             else if(oligo[i] == 'M'){   reverse += 'K'; }
1475             else if(oligo[i] == 'K'){   reverse += 'M'; }
1476
1477             else if(oligo[i] == 'W'){   reverse += 'W'; }
1478             else if(oligo[i] == 'S'){   reverse += 'S'; }
1479
1480             else if(oligo[i] == 'B'){   reverse += 'V'; }
1481             else if(oligo[i] == 'V'){   reverse += 'B'; }
1482
1483             else if(oligo[i] == 'D'){   reverse += 'H'; }
1484             else if(oligo[i] == 'H'){   reverse += 'D'; }
1485
1486             else                                                {       reverse += 'N'; }
1487         }
1488
1489
1490         return reverse;
1491     }
1492         catch(exception& e) {
1493                 m->errorOut(e, "MakeContigsCommand", "reverseOligo");
1494                 exit(1);
1495         }
1496 }
1497 //**********************************************************************************************************************
1498
1499
1500
1501