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 pfasta("ffastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  15         CommandParameter prfasta("rfastq", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(prfasta);
  16         CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
  17                 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
  18                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
  19         CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
  20                 CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
  21         CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
  22
  23         CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "",false,false); parameters.push_back(palign);
  24         CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles);
  25                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  26                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  27                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  28                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  29         CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "",false,false); parameters.push_back(pthreshold);
  30                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  31                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  32                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  33
  34                 vector<string> myArray;
  35                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  36                 return myArray;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "MakeContigsCommand", "setParameters");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string MakeContigsCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 helpString += "The make.contigs command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.\n";
  48         helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
  49                 helpString += "The make.contigs command parameters are ffastq, rfastq, oligos, tdiffs, bdiffs, ldiffs, sdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, allfiles and processors.\n";
  50                 helpString += "The ffastq and rfastq parameters are required.\n";
  51                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh and needleman. The default is needleman.\n";
  52         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";
  53                 helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
  54                 helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
  55         helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
  56                 helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
  57                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  58                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  59                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  60                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  61         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";
  62         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  63         helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
  64         helpString += "The make.contigs command should be in the following format: \n";
  65                 helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
  66                 helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
  67                 return helpString;
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "MakeContigsCommand", "getHelpString");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75 string MakeContigsCommand::getOutputFileNameTag(string type, string inputName=""){
  76         try {
  77         string outputFileName = "";
  78                 map<string, vector<string> >::iterator it;
  79
  80         //is this a type this command creates
  81         it = outputTypes.find(type);
  82         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  83         else {
  84             if (type == "fasta")             {   outputFileName =  "contigs.fasta";         }
  85             else if (type == "qfile")        {   outputFileName =  "contigs.qual";          }
  86             else if (type == "group")            {   outputFileName =  "groups";   }
  87             else if (type == "mismatch")     {   outputFileName =  "contigs.mismatch";      }
  88             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  89         }
  90         return outputFileName;
  91         }
  92         catch(exception& e) {
  93                 m->errorOut(e, "MakeContigsCommand", "getOutputFileNameTag");
  94                 exit(1);
  95         }
  96 }
  97 //**********************************************************************************************************************
  98 MakeContigsCommand::MakeContigsCommand(){
  99         try {
 100                 abort = true; calledHelp = true;
 101                 setParameters();
 102                 vector<string> tempOutNames;
 103                 outputTypes["fasta"] = tempOutNames;
 104                 outputTypes["qfile"] = tempOutNames;
 105         outputTypes["group"] = tempOutNames;
 106         outputTypes["mismatch"] = tempOutNames;
 107         }
 108         catch(exception& e) {
 109                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 110                 exit(1);
 111         }
 112 }
 113 //**********************************************************************************************************************
 114 MakeContigsCommand::MakeContigsCommand(string option)  {
 115         try {
 116                 abort = false; calledHelp = false;
 117
 118                 //allow user to run help
 119                 if(option == "help") { help(); abort = true; calledHelp = true; }
 120                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 121
 122                 else {
 123                         vector<string> myArray = setParameters();
 124
 125                         OptionParser parser(option);
 126                         map<string, string> parameters = parser.getParameters();
 127
 128                         ValidParameters validParameter("pairwise.seqs");
 129                         map<string, string>::iterator it;
 130
 131                         //check to make sure all parameters are valid for command
 132                         for (it = parameters.begin(); it != parameters.end(); it++) {
 133                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 134                         }
 135
 136                         //initialize outputTypes
 137                         vector<string> tempOutNames;
 138                         outputTypes["fasta"] = tempOutNames;
 139                         outputTypes["qfile"] = tempOutNames;
 140             outputTypes["mismatch"] = tempOutNames;
 141             outputTypes["group"] = tempOutNames;
 142
 143
 144                         //if the user changes the input directory command factory will send this info to us in the output parameter
 145                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 146                         if (inputDir == "not found"){   inputDir = "";          }
 147                         else {
 148                                 string path;
 149                 it = parameters.find("ffastq");
 150                                 //user has given a template file
 151                                 if(it != parameters.end()){
 152                                         path = m->hasPath(it->second);
 153                                         //if the user has not given a path then, add inputdir. else leave path alone.
 154                                         if (path == "") {       parameters["ffastq"] = inputDir + it->second;           }
 155                                 }
 156
 157                 it = parameters.find("rfastq");
 158                                 //user has given a template file
 159                                 if(it != parameters.end()){
 160                                         path = m->hasPath(it->second);
 161                                         //if the user has not given a path then, add inputdir. else leave path alone.
 162                                         if (path == "") {       parameters["rfastq"] = inputDir + it->second;           }
 163                                 }
 164
 165                 it = parameters.find("oligos");
 166                                 //user has given a template file
 167                                 if(it != parameters.end()){
 168                                         path = m->hasPath(it->second);
 169                                         //if the user has not given a path then, add inputdir. else leave path alone.
 170                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 171                                 }
 172             }
 173
 174             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
 175                         if (ffastqfile == "not open") { ffastqfile = ""; abort = true; }
 176                         else if (ffastqfile == "not found") { ffastqfile = ""; abort=true;  m->mothurOut("The ffastq parameter is required.\n"); }
 177
 178                         rfastqfile = validParameter.validFile(parameters, "rfastq", true);
 179                         if (rfastqfile == "not open") { rfastqfile = ""; abort = true; }
 180                         else if (rfastqfile == "not found") { rfastqfile = ""; abort=true;  m->mothurOut("The rfastq parameter is required.\n"); }
 181
 182             oligosfile = validParameter.validFile(parameters, "oligos", true);
 183                         if (oligosfile == "not found")      {   oligosfile = "";        }
 184                         else if(oligosfile == "not open")   {   abort = true;       }
 185                         else {   m->setOligosFile(oligosfile);          }
 186
 187             //if the user changes the output directory command factory will send this info to us in the output parameter
 188                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(ffastqfile);             }
 189
 190
 191                         //check for optional parameter and set defaults
 192                         // ...at some point should added some additional type checking...
 193                         string temp;
 194                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 195                         m->mothurConvert(temp, match);
 196
 197                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 198                         m->mothurConvert(temp, misMatch);
 199             if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 200
 201                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 202                         m->mothurConvert(temp, gapOpen);
 203             if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 204
 205                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 206                         m->mothurConvert(temp, gapExtend);
 207             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 208
 209             temp = validParameter.validFile(parameters, "threshold", false);    if (temp == "not found"){       temp = "40";                    }
 210                         m->mothurConvert(temp, threshold);
 211             if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
 212
 213                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 214                         m->setProcessors(temp);
 215                         m->mothurConvert(temp, processors);
 216
 217             temp = validParameter.validFile(parameters, "bdiffs", false);               if (temp == "not found") { temp = "0"; }
 218                         m->mothurConvert(temp, bdiffs);
 219
 220                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 221                         m->mothurConvert(temp, pdiffs);
 222
 223             temp = validParameter.validFile(parameters, "ldiffs", false);               if (temp == "not found") { temp = "0"; }
 224                         m->mothurConvert(temp, ldiffs);
 225
 226             temp = validParameter.validFile(parameters, "sdiffs", false);               if (temp == "not found") { temp = "0"; }
 227                         m->mothurConvert(temp, sdiffs);
 228
 229                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs;  temp = toString(tempTotal); }
 230                         m->mothurConvert(temp, tdiffs);
 231
 232                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs + ldiffs + sdiffs;     }
 233
 234             temp = validParameter.validFile(parameters, "allfiles", false);             if (temp == "not found") { temp = "F"; }
 235                         allFiles = m->isTrue(temp);
 236
 237                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 238                         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"; }
 239         }
 240
 241         }
 242         catch(exception& e) {
 243                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 244                 exit(1);
 245         }
 246 }
 247 //**********************************************************************************************************************
 248 int MakeContigsCommand::execute(){
 249         try {
 250                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 251
 252         //read ffastq and rfastq files creating fasta and qual files.
 253         //this function will create a forward and reverse, fasta and qual files for each processor.
 254         //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual
 255         int numReads = 0;
 256         int start = time(NULL);
 257         longestBase = 1000;
 258         m->mothurOut("Reading fastq data...\n");
 259         vector< vector<string> > files = readFastqFiles(numReads);
 260         m->mothurOut("Done.\n");
 261
 262         if (m->control_pressed) { return 0; }
 263
 264         string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("fasta");
 265         string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("qfile");
 266         string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("mismatch");
 267         outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 268         outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
 269         outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
 270
 271         m->mothurOut("Making contigs...\n");
 272         createProcesses(files, outFastaFile, outQualFile, outMisMatchFile);
 273         m->mothurOut("Done.\n");
 274
 275         //remove temp fasta and qual files
 276         for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }  }
 277
 278         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 279
 280         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 281
 282         string currentFasta = "";
 283                 itTypes = outputTypes.find("fasta");
 284                 if (itTypes != outputTypes.end()) {
 285                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 286                 }
 287
 288         string currentQual = "";
 289                 itTypes = outputTypes.find("qfile");
 290                 if (itTypes != outputTypes.end()) {
 291                         if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
 292                 }
 293
 294         string currentGroup = "";
 295                 itTypes = outputTypes.find("group");
 296                 if (itTypes != outputTypes.end()) {
 297                         if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); }
 298                 }
 299
 300         //output files created by command
 301                 m->mothurOutEndLine();
 302                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 303                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 304                 m->mothurOutEndLine();
 305
 306         return 0;
 307     }
 308         catch(exception& e) {
 309                 m->errorOut(e, "MakeContigsCommand", "execute");
 310                 exit(1);
 311         }
 312 }
 313 //**********************************************************************************************************************
 314 int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputMisMatches) {
 315         try {
 316                 int num = 0;
 317                 vector<int> processIDS;
 318 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 319                 int process = 0;
 320
 321                 //loop through and create all the processes you want
 322                 while (process != processors-1) {
 323                         int pid = fork();
 324
 325                         if (pid > 0) {
 326                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 327                                 process++;
 328                         }else if (pid == 0){
 329                                 num = driver(files[process], outputFasta + toString(getpid()) + ".temp", outputQual + toString(getpid()) + ".temp", outputMisMatches + toString(getpid()) + ".temp");
 330
 331                                 //pass numSeqs to parent
 332                                 ofstream out;
 333                                 string tempFile = outputFasta + toString(getpid()) + ".num.temp";
 334                                 m->openOutputFile(tempFile, out);
 335                                 out << num << endl;
 336                                 out.close();
 337
 338                                 exit(0);
 339                         }else {
 340                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 341                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 342                                 exit(0);
 343                         }
 344                 }
 345
 346                 //do my part
 347                 num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
 348
 349                 //force parent to wait until all the processes are done
 350                 for (int i=0;i<processIDS.size();i++) {
 351                         int temp = processIDS[i];
 352                         wait(&temp);
 353                 }
 354
 355                 for (int i = 0; i < processIDS.size(); i++) {
 356                         ifstream in;
 357                         string tempFile =  outputFasta + toString(processIDS[i]) + ".num.temp";
 358                         m->openInputFile(tempFile, in);
 359                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 360                         in.close(); m->mothurRemove(tempFile);
 361         }
 362     #else
 363
 364         //////////////////////////////////////////////////////////////////////////////////////////////////////
 365                 //Windows version shared memory, so be careful when passing variables through the contigsData struct.
 366                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 367                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 368
 369                 vector<contigsData*> pDataArray;
 370                 DWORD   dwThreadIdArray[processors-1];
 371                 HANDLE  hThreadArray[processors-1];
 372
 373                 //Create processor worker threads.
 374                 for( int i=0; i<processors-1; i++ ){
 375                         string extension = toString(i) + ".temp";
 376
 377                         contigsData* tempcontig = new contigsData(files[i], (outputFasta + extension), (outputQual + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, i);
 378                         pDataArray.push_back(tempcontig);
 379                         processIDS.push_back(i);
 380
 381                         hThreadArray[i] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 382                 }
 383
 384         num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
 385
 386                 //Wait until all threads have terminated.
 387                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 388
 389                 //Close all thread handles and free memory allocations.
 390                 for(int i=0; i < pDataArray.size(); i++){
 391                         num += pDataArray[i]->count;
 392             CloseHandle(hThreadArray[i]);
 393                         delete pDataArray[i];
 394         }
 395
 396     #endif
 397
 398         for (int i = 0; i < processIDS.size(); i++) {
 399                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 400                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 401
 402                         m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
 403                         m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
 404
 405             m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 406                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 407                 }
 408
 409                 return num;
 410         }
 411         catch(exception& e) {
 412                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 413                 exit(1);
 414         }
 415 }
 416 //**********************************************************************************************************************
 417 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputMisMatches){
 418     try {
 419
 420         Alignment* alignment;
 421         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 422                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 423
 424         int num = 0;
 425         string thisffastafile = files[0];
 426         string thisfqualfile = files[1];
 427         string thisrfastafile = files[2];
 428         string thisrqualfile = files[3];
 429
 430         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 431
 432         ifstream inFFasta, inRFasta, inFQual, inRQual;
 433         m->openInputFile(thisffastafile, inFFasta);
 434         m->openInputFile(thisfqualfile, inFQual);
 435         m->openInputFile(thisrfastafile, inRFasta);
 436         m->openInputFile(thisrqualfile, inRQual);
 437
 438         ofstream outFasta, outQual, outMisMatch;
 439         m->openOutputFile(outputFasta, outFasta);
 440         m->openOutputFile(outputQual, outQual);
 441         m->openOutputFile(outputMisMatches, outMisMatch);
 442         outMisMatch << "Name\tLength\tMisMatches\n";
 443
 444         while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
 445
 446             if (m->control_pressed) { break; }
 447
 448             //read seqs and quality info
 449             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 450             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 451             QualityScores fQual(inFQual); m->gobble(inFQual);
 452             QualityScores rQual(inRQual); m->gobble(inRQual);
 453
 454             //flip the reverse reads
 455             rSeq.reverseComplement();
 456             rQual.flipQScores();
 457
 458             //pairwise align
 459             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 460             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 461             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 462             fSeq.setAligned(alignment->getSeqAAln());
 463             rSeq.setAligned(alignment->getSeqBAln());
 464             int length = fSeq.getAligned().length();
 465
 466             //traverse alignments merging into one contiguous seq
 467             string contig = "";
 468             vector<int> contigScores;
 469             int numMismatches = 0;
 470             string seq1 = fSeq.getAligned();
 471             string seq2 = rSeq.getAligned();
 472             vector<int> scores1 = fQual.getQualityScores();
 473             vector<int> scores2 = rQual.getQualityScores();
 474
 475            // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
 476             int overlapStart = fSeq.getStartPos();
 477             int seq2Start = rSeq.getStartPos();
 478             //bigger of the 2 starting positions is the location of the overlapping start
 479             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 480                 overlapStart = seq2Start;
 481                 for (int i = 0; i < overlapStart; i++) {
 482                     contig += seq1[i];
 483                     contigScores.push_back(scores1[ABaseMap[i]]);
 484                 }
 485             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 486                 for (int i = 0; i < overlapStart; i++) {
 487                     contig += seq2[i];
 488                     contigScores.push_back(scores2[BBaseMap[i]]);
 489                 }
 490             }
 491
 492             int seq1End = fSeq.getEndPos();
 493             int seq2End = rSeq.getEndPos();
 494             int overlapEnd = seq1End;
 495             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 496
 497             for (int i = overlapStart; i < overlapEnd; i++) {
 498                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 499                     contig += seq1[i];
 500                     contigScores.push_back(scores1[ABaseMap[i]]);
 501                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
 502                 }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
 503                     if (scores2[BBaseMap[i]] < threshold) { } //
 504                     else {
 505                         contig += seq2[i];
 506                         contigScores.push_back(scores2[BBaseMap[i]]);
 507                     }
 508                 }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
 509                     if (scores1[ABaseMap[i]] < threshold) { } //
 510                     else {
 511                         contig += seq1[i];
 512                         contigScores.push_back(scores1[ABaseMap[i]]);
 513                     }
 514                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 515                     char c = seq1[i];
 516                     contigScores.push_back(scores1[ABaseMap[i]]);
 517                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
 518                     contig += c;
 519                     numMismatches++;
 520                 }else { //should never get here
 521                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
 522                 }
 523             }
 524
 525             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
 526                 for (int i = overlapEnd; i < length; i++) {
 527                     contig += seq2[i];
 528                     contigScores.push_back(scores2[BBaseMap[i]]);
 529                 }
 530             }else { //seq2 ends before seq1 so take from overlap to length from seq1
 531                 for (int i = overlapEnd; i < length; i++) {
 532                     contig += seq1[i];
 533                     contigScores.push_back(scores1[ABaseMap[i]]);
 534                 }
 535
 536             }
 537             //if (num < 5) { cout << overlapStart << '\t' << overlapEnd << endl << seq1 << endl << seq2 << endl<< contig << endl; }
 538             //output
 539             outFasta << ">" << fSeq.getName() << endl << contig << endl;
 540             outQual << ">" << fSeq.getName() << endl;
 541             for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
 542             outQual << endl;
 543             outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
 544
 545             num++;
 546
 547                         //report progress
 548                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 549                 }
 550
 551                 //report progress
 552                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 553
 554         inFFasta.close();
 555         inFQual.close();
 556         inRFasta.close();
 557         inRQual.close();
 558         outFasta.close();
 559         outQual.close();
 560         outMisMatch.close();
 561         delete alignment;
 562
 563         if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta);  m->mothurRemove(outputMisMatches);}
 564
 565         return num;
 566     }
 567         catch(exception& e) {
 568                 m->errorOut(e, "MakeContigsCommand", "driver");
 569                 exit(1);
 570         }
 571 }
 572 //**********************************************************************************************************************
 573 vector< vector<string> > MakeContigsCommand::readFastqFiles(int& count){
 574     try {
 575         vector< vector<string> > files;
 576
 577         //maps processors number to file pointer
 578         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
 579         map<int, vector<ofstream*> >::iterator it;
 580
 581         //create files to write to
 582         for (int i = 0; i < processors; i++) {
 583             vector<ofstream*> temp;
 584             ofstream* outFF = new ofstream;     temp.push_back(outFF);
 585             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
 586             ofstream* outRF = new ofstream;     temp.push_back(outRF);
 587             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
 588             tempfiles[i] = temp;
 589
 590             vector<string> names;
 591             string ffastafilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "ffasta.temp";
 592             string rfastafilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rfasta.temp";
 593             string fqualfilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "fqual.temp";
 594             string rqualfilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rqual.temp";
 595             names.push_back(ffastafilename); names.push_back(fqualfilename);
 596             names.push_back(rfastafilename); names.push_back(rqualfilename);
 597             files.push_back(names);
 598
 599             m->openOutputFile(ffastafilename, *outFF);
 600             m->openOutputFile(rfastafilename, *outRF);
 601             m->openOutputFile(fqualfilename, *outFQ);
 602             m->openOutputFile(rqualfilename, *outRQ);
 603         }
 604
 605         if (m->control_pressed) {
 606             //close files, delete ofstreams
 607             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]; } }
 608             //remove files
 609             for (int i = 0; i < files.size(); i++) {
 610                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
 611             }
 612         }
 613
 614         ifstream inForward;
 615         m->openInputFile(ffastqfile, inForward);
 616
 617         ifstream inReverse;
 618         m->openInputFile(rfastqfile, inReverse);
 619
 620         count = 0;
 621         while ((!inForward.eof()) && (!inReverse.eof())) {
 622
 623             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; }
 624
 625             //get a read from forward and reverse fastq files
 626             fastqRead fread = readFastq(inForward);
 627             fastqRead rread = readFastq(inReverse);
 628             checkReads(fread, rread);
 629
 630             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; }
 631
 632             //if the reads are okay write to output files
 633             int process = count % processors;
 634
 635             *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
 636             *(tempfiles[process][1]) << ">" << fread.name << endl;
 637             for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
 638             *(tempfiles[process][1]) << endl;
 639             *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
 640             *(tempfiles[process][3]) << ">" << rread.name << endl;
 641             for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
 642             *(tempfiles[process][3]) << endl;
 643
 644             count++;
 645
 646             //report progress
 647                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 648
 649                 }
 650                 //report progress
 651                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 652
 653
 654
 655         //close files, delete ofstreams
 656         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]; } }
 657         inForward.close();
 658         inReverse.close();
 659
 660         //adjust for really large processors or really small files
 661         if (count < processors) {
 662             for (int i = count; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 663             files.resize(count);
 664             processors = count;
 665         }
 666
 667         return files;
 668     }
 669     catch(exception& e) {
 670         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
 671         exit(1);
 672     }
 673 }
 674 //**********************************************************************************************************************
 675 fastqRead MakeContigsCommand::readFastq(ifstream& in){
 676     try {
 677         fastqRead read;
 678
 679         //read sequence name
 680         string name = m->getline(in); m->gobble(in);
 681         if (name == "") {  m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 682         else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 683         else { name = name.substr(1); }
 684
 685         //read sequence
 686         string sequence = m->getline(in); m->gobble(in);
 687         if (sequence == "") {  m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 688
 689         //read sequence name
 690         string name2 = m->getline(in); m->gobble(in);
 691         if (name2 == "") {  m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 692         else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 693         else { name2 = name2.substr(1);  }
 694
 695         //read quality scores
 696         string quality = m->getline(in); m->gobble(in);
 697         if (quality == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 698
 699         //sanity check sequence length and number of quality scores match
 700         if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; return read; } }
 701         if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 702
 703         vector<int> qualScores;
 704                 int controlChar = int('@');
 705                 for (int i = 0; i < quality.length(); i++) {
 706                         int temp = int(quality[i]);
 707                         temp -= controlChar;
 708
 709                         qualScores.push_back(temp);
 710                 }
 711
 712         read.name = name;
 713         read.sequence = sequence;
 714         read.scores = qualScores;
 715
 716         return read;
 717     }
 718     catch(exception& e) {
 719         m->errorOut(e, "MakeContigsCommand", "readFastq");
 720         exit(1);
 721     }
 722 }
 723 //**********************************************************************************************************************
 724 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){
 725     try {
 726         bool good = true;
 727
 728         //fix names
 729         if ((forward.name.length() > 2) && (reverse.name.length() > 2)) {
 730             forward.name = forward.name.substr(0, forward.name.length()-2);
 731             reverse.name = reverse.name.substr(0, reverse.name.length()-2);
 732         }else { good = false; m->control_pressed = true; }
 733
 734         //do names match
 735         if (forward.name != reverse.name) {
 736             m->mothurOut("[ERROR]: read " + forward.name + " from " + ffastqfile + ", but read " + reverse.name + " from " + rfastqfile + ".\n");
 737             good = false; m->control_pressed = true;
 738         }
 739
 740         //do sequence lengths match
 741         if (forward.sequence.length() != reverse.sequence.length()) {
 742             m->mothurOut("[ERROR]: 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 + ".\n");
 743             good = false; m->control_pressed = true;
 744         }
 745
 746         //do number of qual scores match
 747         if (forward.scores.size() != reverse.scores.size()) {
 748             m->mothurOut("[ERROR]: For sequence " + forward.name + " I read " + toString(forward.scores.size()) + " quality scores from " + ffastqfile + ", but read  " + toString(reverse.scores.size()) + " quality scores from " + rfastqfile + ".\n");
 749             good = false; m->control_pressed = true;
 750         }
 751
 752         return good;
 753     }
 754     catch(exception& e) {
 755         m->errorOut(e, "MakeContigsCommand", "readFastq");
 756         exit(1);
 757     }
 758 }
 759 //***************************************************************************************************************
 760 //illumina data requires paired forward and reverse data
 761 //BARCODE   atgcatgc   atgcatgc    groupName
 762 //PRIMER   atgcatgc   atgcatgc    groupName
 763 //PRIMER   atgcatgc   atgcatgc
 764 bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames){
 765         try {
 766                 ifstream in;
 767                 m->openInputFile(oligosfile, in);
 768
 769                 ofstream test;
 770
 771                 string type, foligo, roligo, group;
 772
 773                 int indexPrimer = 0;
 774                 int indexBarcode = 0;
 775         set<string> uniquePrimers;
 776         set<string> uniqueBarcodes;
 777
 778                 while(!in.eof()){
 779
 780                         in >> type;
 781
 782                         if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
 783
 784                         if(type[0] == '#'){
 785                                 while (!in.eof())       {       char c = in.get();  if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
 786                                 m->gobble(in);
 787                         }
 788                         else{
 789                                 m->gobble(in);
 790                                 //make type case insensitive
 791                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
 792
 793                                 in >> foligo;
 794
 795                 if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); }
 796
 797                                 for(int i=0;i<foligo.length();i++){
 798                                         foligo[i] = toupper(foligo[i]);
 799                                         if(foligo[i] == 'U')    {       foligo[i] = 'T';        }
 800                                 }
 801
 802                                 if(type == "PRIMER"){
 803                                         m->gobble(in);
 804
 805                     in >> roligo;
 806
 807                     for(int i=0;i<roligo.length();i++){
 808                         roligo[i] = toupper(roligo[i]);
 809                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
 810                     }
 811                     roligo = reverseOligo(roligo);
 812
 813                     group = "";
 814
 815                                         // get rest of line in case there is a primer name
 816                                         while (!in.eof())       {
 817                                                 char c = in.get();
 818                                                 if (c == 10 || c == 13){        break;  }
 819                                                 else if (c == 32 || c == 9){;} //space or tab
 820                                                 else {  group += c;  }
 821                                         }
 822
 823                     oligosPair newPrimer(foligo, roligo);
 824
 825                                         //check for repeat barcodes
 826                     string tempPair = foligo+roligo;
 827                     if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine();  }
 828                     else { uniquePrimers.insert(tempPair); }
 829
 830                     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"); }  }
 831
 832                                         primers[indexPrimer]=newPrimer; indexPrimer++;
 833                                         primerNameVector.push_back(group);
 834                                 }else if(type == "BARCODE"){
 835                                         m->gobble(in);
 836
 837                     in >> roligo;
 838
 839                     for(int i=0;i<roligo.length();i++){
 840                         roligo[i] = toupper(roligo[i]);
 841                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
 842                     }
 843                     roligo = reverseOligo(roligo);
 844
 845                     oligosPair newPair(foligo, roligo);
 846
 847                     group = "";
 848                     while (!in.eof())   {
 849                                                 char c = in.get();
 850                                                 if (c == 10 || c == 13){        break;  }
 851                                                 else if (c == 32 || c == 9){;} //space or tab
 852                                                 else {  group += c;  }
 853                                         }
 854
 855                     if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
 856
 857                     //check for repeat barcodes
 858                     string tempPair = foligo+roligo;
 859                     if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse +  " is in your oligos file already, disregarding."); m->mothurOutEndLine();  }
 860                     else { uniqueBarcodes.insert(tempPair); }
 861
 862                     barcodes[indexBarcode]=newPair; indexBarcode++;
 863                                         barcodeNameVector.push_back(group);
 864                                 }else if(type == "LINKER"){
 865                                         linker.push_back(foligo);
 866                                 }else if(type == "SPACER"){
 867                                         spacer.push_back(foligo);
 868                                 }
 869                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); }
 870                         }
 871                         m->gobble(in);
 872                 }
 873                 in.close();
 874
 875                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 876
 877                 //add in potential combos
 878                 if(barcodeNameVector.size() == 0){
 879             oligosPair temp("", "");
 880                         barcodes[0] = temp;
 881                         barcodeNameVector.push_back("");
 882                 }
 883
 884                 if(primerNameVector.size() == 0){
 885             oligosPair temp("", "");
 886                         primers[0] = temp;
 887                         primerNameVector.push_back("");
 888                 }
 889
 890                 fastaFileNames.resize(barcodeNameVector.size());
 891                 for(int i=0;i<fastaFileNames.size();i++){
 892                         fastaFileNames[i].assign(primerNameVector.size(), "");
 893                 }
 894                 qualFileNames = fastaFileNames;
 895
 896                 if(allFiles){
 897                         set<string> uniqueNames; //used to cleanup outputFileNames
 898                         for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 899                                 for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 900
 901                                         string primerName = primerNameVector[itPrimer->first];
 902                                         string barcodeName = barcodeNameVector[itBar->first];
 903
 904                                         string comboGroupName = "";
 905                                         string fastaFileName = "";
 906                                         string qualFileName = "";
 907                                         string nameFileName = "";
 908                     string countFileName = "";
 909
 910                                         if(primerName == ""){
 911                                                 comboGroupName = barcodeNameVector[itBar->first];
 912                                         }
 913                                         else{
 914                                                 if(barcodeName == ""){
 915                                                         comboGroupName = primerNameVector[itPrimer->first];
 916                                                 }
 917                                                 else{
 918                                                         comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
 919                                                 }
 920                                         }
 921
 922
 923                                         ofstream temp;
 924                                         fastaFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".fasta";
 925                                         if (uniqueNames.count(fastaFileName) == 0) {
 926                                                 outputNames.push_back(fastaFileName);
 927                                                 outputTypes["fasta"].push_back(fastaFileName);
 928                                                 uniqueNames.insert(fastaFileName);
 929                                         }
 930
 931                                         fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
 932                                         m->openOutputFile(fastaFileName, temp);         temp.close();
 933
 934
 935                     qualFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".qual";
 936                     if (uniqueNames.count(qualFileName) == 0) {
 937                         outputNames.push_back(qualFileName);
 938                         outputTypes["qfile"].push_back(qualFileName);
 939                     }
 940
 941                     qualFileNames[itBar->first][itPrimer->first] = qualFileName;
 942                     m->openOutputFile(qualFileName, temp);              temp.close();
 943                                 }
 944                         }
 945                 }
 946
 947                 bool allBlank = true;
 948                 for (int i = 0; i < barcodeNameVector.size(); i++) {
 949                         if (barcodeNameVector[i] != "") {
 950                                 allBlank = false;
 951                                 break;
 952                         }
 953                 }
 954                 for (int i = 0; i < primerNameVector.size(); i++) {
 955                         if (primerNameVector[i] != "") {
 956                                 allBlank = false;
 957                                 break;
 958                         }
 959                 }
 960
 961                 if (allBlank) {
 962                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
 963                         allFiles = false;
 964                         return false;
 965                 }
 966
 967                 return true;
 968
 969         }
 970         catch(exception& e) {
 971                 m->errorOut(e, "MakeContigsCommand", "getOligos");
 972                 exit(1);
 973         }
 974 }
 975 //********************************************************************/
 976 string MakeContigsCommand::reverseOligo(string oligo){
 977         try {
 978         string reverse = "";
 979
 980         for(int i=oligo.length()-1;i>=0;i--){
 981
 982             if(oligo[i] == 'A')         {       reverse += 'T'; }
 983             else if(oligo[i] == 'T'){   reverse += 'A'; }
 984             else if(oligo[i] == 'U'){   reverse += 'A'; }
 985
 986             else if(oligo[i] == 'G'){   reverse += 'C'; }
 987             else if(oligo[i] == 'C'){   reverse += 'G'; }
 988
 989             else if(oligo[i] == 'R'){   reverse += 'Y'; }
 990             else if(oligo[i] == 'Y'){   reverse += 'R'; }
 991
 992             else if(oligo[i] == 'M'){   reverse += 'K'; }
 993             else if(oligo[i] == 'K'){   reverse += 'M'; }
 994
 995             else if(oligo[i] == 'W'){   reverse += 'W'; }
 996             else if(oligo[i] == 'S'){   reverse += 'S'; }
 997
 998             else if(oligo[i] == 'B'){   reverse += 'V'; }
 999             else if(oligo[i] == 'V'){   reverse += 'B'; }
1000
1001             else if(oligo[i] == 'D'){   reverse += 'H'; }
1002             else if(oligo[i] == 'H'){   reverse += 'D'; }
1003
1004             else                                                {       reverse += 'N'; }
1005         }
1006
1007
1008         return reverse;
1009     }
1010         catch(exception& e) {
1011                 m->errorOut(e, "MakeContigsCommand", "reverseOligo");
1012                 exit(1);
1013         }
1014 }
1015 //**********************************************************************************************************************
1016
1017
1018
1019