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         vector<vector<string> > fastaFileNames;
 265                 vector<vector<string> > qualFileNames;
 266         createGroup = false;
 267         string outputGroupFileName;
 268         if(oligosfile != ""){
 269                         createGroup = getOligos(fastaFileNames, qualFileNames);
 270             if (createGroup) {
 271                 outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("group");
 272                 outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
 273             }
 274                 }
 275
 276         string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "trim." + getOutputFileNameTag("fasta");
 277         string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "trim." + getOutputFileNameTag("qfile");
 278         string outScrapFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "scrap." + getOutputFileNameTag("fasta");
 279         string outScrapQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "scrap." + getOutputFileNameTag("qfile");
 280
 281         string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("mismatch");
 282         outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 283         outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
 284         outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
 285         outputNames.push_back(outScrapQualFile); outputTypes["qfile"].push_back(outScrapQualFile);
 286         outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
 287
 288         m->mothurOut("Making contigs...\n");
 289         createProcesses(files, outFastaFile, outQualFile, outScrapFastaFile, outScrapQualFile, outMisMatchFile, fastaFileNames, qualFileNames);
 290         m->mothurOut("Done.\n");
 291
 292         //remove temp fasta and qual files
 293         for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }  }
 294
 295         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 296
 297         if(allFiles){
 298                         map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
 299                         map<string, string>::iterator it;
 300                         set<string> namesToRemove;
 301                         for(int i=0;i<fastaFileNames.size();i++){
 302                                 for(int j=0;j<fastaFileNames[0].size();j++){
 303                                         if (fastaFileNames[i][j] != "") {
 304                                                 if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
 305                                                         if(m->isBlank(fastaFileNames[i][j])){
 306                                                                 m->mothurRemove(fastaFileNames[i][j]);
 307                                                                 namesToRemove.insert(fastaFileNames[i][j]);
 308
 309                                 m->mothurRemove(qualFileNames[i][j]);
 310                                 namesToRemove.insert(qualFileNames[i][j]);
 311                                                         }else{
 312                                                                 it = uniqueFastaNames.find(fastaFileNames[i][j]);
 313                                                                 if (it == uniqueFastaNames.end()) {
 314                                                                         uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
 315                                                                 }
 316                                                         }
 317                                                 }
 318                                         }
 319                                 }
 320                         }
 321
 322                         //remove names for outputFileNames, just cleans up the output
 323                         vector<string> outputNames2;
 324                         for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
 325                         outputNames = outputNames2;
 326
 327             for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
 328                 ifstream in;
 329                 m->openInputFile(it->first, in);
 330
 331                 ofstream out;
 332                 string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
 333                 thisGroupName += getOutputFileNameTag("group"); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
 334                 m->openOutputFile(thisGroupName, out);
 335
 336                 while (!in.eof()){
 337                     if (m->control_pressed) { break; }
 338
 339                     Sequence currSeq(in); m->gobble(in);
 340                     out << currSeq.getName() << '\t' << it->second << endl;
 341                 }
 342                 in.close();
 343                 out.close();
 344             }
 345         }
 346
 347         if (createGroup) {
 348             ofstream outGroup;
 349             m->openOutputFile(outputGroupFileName, outGroup);
 350             for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
 351                 outGroup << itGroup->first << '\t' << itGroup->second << endl;
 352             }
 353             outGroup.close();
 354         }
 355         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 356
 357         if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 358
 359                 //output group counts
 360                 m->mothurOutEndLine();
 361                 int total = 0;
 362                 if (groupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
 363                 for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 364             total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
 365                 }
 366                 if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
 367
 368                 if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 369
 370         string currentFasta = "";
 371                 itTypes = outputTypes.find("fasta");
 372                 if (itTypes != outputTypes.end()) {
 373                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 374                 }
 375
 376         string currentQual = "";
 377                 itTypes = outputTypes.find("qfile");
 378                 if (itTypes != outputTypes.end()) {
 379                         if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
 380                 }
 381
 382         string currentGroup = "";
 383                 itTypes = outputTypes.find("group");
 384                 if (itTypes != outputTypes.end()) {
 385                         if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); }
 386                 }
 387
 388         //output files created by command
 389                 m->mothurOutEndLine();
 390                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 391                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 392                 m->mothurOutEndLine();
 393
 394         return 0;
 395     }
 396         catch(exception& e) {
 397                 m->errorOut(e, "MakeContigsCommand", "execute");
 398                 exit(1);
 399         }
 400 }
 401 //**********************************************************************************************************************
 402 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) {
 403         try {
 404                 int num = 0;
 405                 vector<int> processIDS;
 406 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 407                 int process = 0;
 408
 409                 //loop through and create all the processes you want
 410                 while (process != processors-1) {
 411                         int pid = fork();
 412
 413                         if (pid > 0) {
 414                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 415                                 process++;
 416                         }else if (pid == 0){
 417                 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 418                                 vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 419
 420                                 if(allFiles){
 421                                         ofstream temp;
 422
 423                                         for(int i=0;i<tempFASTAFileNames.size();i++){
 424                                                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 425                                                         if (tempFASTAFileNames[i][j] != "") {
 426                                                                 tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
 427                                                                 m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 428
 429                                 tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
 430                                 m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
 431                                                         }
 432                                                 }
 433                                         }
 434                                 }
 435
 436                                 num = driver(files[process],
 437                              outputFasta + toString(getpid()) + ".temp",
 438                              outputQual + toString(getpid()) + ".temp",
 439                              outputScrapFasta + toString(getpid()) + ".temp",
 440                              outputScrapQual + toString(getpid()) + ".temp",
 441                              outputMisMatches + toString(getpid()) + ".temp",
 442                              tempFASTAFileNames,
 443                              tempPrimerQualFileNames);
 444
 445                                 //pass groupCounts to parent
 446                 ofstream out;
 447                 string tempFile = toString(getpid()) + ".num.temp";
 448                 m->openOutputFile(tempFile, out);
 449                 out << num << endl;
 450                                 if(createGroup){
 451                                         out << groupCounts.size() << endl;
 452
 453                                         for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 454                                                 out << it->first << '\t' << it->second << endl;
 455                                         }
 456
 457                     out << groupMap.size() << endl;
 458                     for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
 459                                                 out << it->first << '\t' << it->second << endl;
 460                                         }
 461                                 }
 462                 out.close();
 463
 464                                 exit(0);
 465                         }else {
 466                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 467                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 468                                 exit(0);
 469                         }
 470                 }
 471
 472         ofstream temp;
 473                 m->openOutputFile(outputFasta, temp);           temp.close();
 474                 m->openOutputFile(outputQual, temp);    temp.close();
 475         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 476         m->openOutputFile(outputScrapQual, temp);               temp.close();
 477
 478                 //do my part
 479                 num = driver(files[processors-1], outputFasta, outputQual, outputScrapFasta, outputScrapQual, outputMisMatches, fastaFileNames, qualFileNames);
 480
 481                 //force parent to wait until all the processes are done
 482                 for (int i=0;i<processIDS.size();i++) {
 483                         int temp = processIDS[i];
 484                         wait(&temp);
 485                 }
 486
 487                 for (int i = 0; i < processIDS.size(); i++) {
 488             ifstream in;
 489             string tempFile = toString(processIDS[i]) + ".num.temp";
 490             m->openInputFile(tempFile, in);
 491             int tempNum;
 492             in >> tempNum; num += tempNum; m->gobble(in);
 493
 494                         if(createGroup){
 495                                 string group;
 496                                 in >> tempNum; m->gobble(in);
 497
 498                                 if (tempNum != 0) {
 499                                         for (int j = 0; j < tempNum; j++) {
 500                         int groupNum;
 501                                                 in >> group >> groupNum; m->gobble(in);
 502
 503                                                 map<string, int>::iterator it = groupCounts.find(group);
 504                                                 if (it == groupCounts.end()) {  groupCounts[group] = groupNum; }
 505                                                 else { groupCounts[it->first] += groupNum; }
 506                                         }
 507                                 }
 508                 in >> tempNum; m->gobble(in);
 509                 if (tempNum != 0) {
 510                                         for (int j = 0; j < tempNum; j++) {
 511                         string group, seqName;
 512                                                 in >> seqName >> group; m->gobble(in);
 513
 514                                                 map<string, string>::iterator it = groupMap.find(seqName);
 515                                                 if (it == groupMap.end()) {     groupMap[seqName] = group; }
 516                                                 else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 517                                         }
 518                                 }
 519                         }
 520             in.close(); m->mothurRemove(tempFile);
 521         }
 522     #else
 523
 524         //////////////////////////////////////////////////////////////////////////////////////////////////////
 525                 //Windows version shared memory, so be careful when passing variables through the contigsData struct.
 526                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 527                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 528
 529                 vector<contigsData*> pDataArray;
 530                 DWORD   dwThreadIdArray[processors-1];
 531                 HANDLE  hThreadArray[processors-1];
 532
 533                 //Create processor worker threads.
 534                 for( int h=0; h<processors-1; h++ ){
 535                         string extension = "";
 536                         if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
 537             vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 538             vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 539
 540             if(allFiles){
 541                 ofstream temp;
 542
 543                 for(int i=0;i<tempFASTAFileNames.size();i++){
 544                     for(int j=0;j<tempFASTAFileNames[i].size();j++){
 545                         if (tempFASTAFileNames[i][j] != "") {
 546                             tempFASTAFileNames[i][j] += extension;
 547                             m->openOutputFile(tempFASTAFileNames[i][j], temp);                  temp.close();
 548
 549
 550                             tempPrimerQualFileNames[i][j] += extension;
 551                             m->openOutputFile(tempPrimerQualFileNames[i][j], temp);             temp.close();
 552                         }
 553                     }
 554                 }
 555             }
 556
 557
 558                         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);
 559                         pDataArray.push_back(tempcontig);
 560
 561                         hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
 562                 }
 563
 564         vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 565         vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 566
 567         if(allFiles){
 568             ofstream temp;
 569             string extension = toString(processors-1) + ".temp";
 570
 571             for(int i=0;i<tempFASTAFileNames.size();i++){
 572                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 573                     if (tempFASTAFileNames[i][j] != "") {
 574                         tempFASTAFileNames[i][j] += extension;
 575                         m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 576
 577
 578                         tempPrimerQualFileNames[i][j] += extension;
 579                         m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
 580                     }
 581                 }
 582             }
 583         }
 584
 585                 //parent do my part
 586                 ofstream temp;
 587                 m->openOutputFile(outputFasta, temp);           temp.close();
 588                 m->openOutputFile(outputQual, temp);    temp.close();
 589         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 590         m->openOutputFile(outputScrapQual, temp);               temp.close();
 591
 592
 593         //do my part
 594                 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);
 595
 596                 //Wait until all threads have terminated.
 597                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 598
 599                 //Close all thread handles and free memory allocations.
 600                 for(int i=0; i < pDataArray.size(); i++){
 601                         num += pDataArray[i]->count;
 602             for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
 603                 map<string, int>::iterator it2 = groupCounts.find(it->first);
 604                 if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
 605                 else { groupCounts[it->first] += it->second; }
 606             }
 607             for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
 608                 map<string, string>::iterator it2 = groupMap.find(it->first);
 609                 if (it2 == groupMap.end()) {    groupMap[it->first] = it->second; }
 610                 else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 611             }
 612             CloseHandle(hThreadArray[i]);
 613                         delete pDataArray[i];
 614         }
 615
 616     #endif
 617
 618         for (int i = 0; i < processIDS.size(); i++) {
 619                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 620                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 621
 622                         m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
 623                         m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
 624
 625             m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
 626                         m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp"));
 627
 628                         m->appendFiles((outputScrapQual + toString(processIDS[i]) + ".temp"), outputScrapQual);
 629                         m->mothurRemove((outputScrapQual + toString(processIDS[i]) + ".temp"));
 630
 631             m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 632                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 633
 634             if(allFiles){
 635                                 for(int j=0;j<fastaFileNames.size();j++){
 636                                         for(int k=0;k<fastaFileNames[j].size();k++){
 637                                                 if (fastaFileNames[j][k] != "") {
 638                                                         m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
 639                                                         m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 640
 641                             m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
 642                             m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 643                                                 }
 644                                         }
 645                                 }
 646                         }
 647                 }
 648
 649                 return num;
 650         }
 651         catch(exception& e) {
 652                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 653                 exit(1);
 654         }
 655 }
 656 //**********************************************************************************************************************
 657 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames){
 658     try {
 659
 660         Alignment* alignment;
 661         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 662                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 663
 664         int num = 0;
 665         string thisffastafile = files[0];
 666         string thisfqualfile = files[1];
 667         string thisrfastafile = files[2];
 668         string thisrqualfile = files[3];
 669
 670         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 671
 672         ifstream inFFasta, inRFasta, inFQual, inRQual;
 673         m->openInputFile(thisffastafile, inFFasta);
 674         m->openInputFile(thisfqualfile, inFQual);
 675         m->openInputFile(thisrfastafile, inRFasta);
 676         m->openInputFile(thisrqualfile, inRQual);
 677
 678         ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
 679         m->openOutputFile(outputFasta, outFasta);
 680         m->openOutputFile(outputQual, outQual);
 681         m->openOutputFile(outputScrapFasta, outScrapFasta);
 682         m->openOutputFile(outputScrapQual, outScrapQual);
 683         m->openOutputFile(outputMisMatches, outMisMatch);
 684         outMisMatch << "Name\tLength\tMisMatches\n";
 685
 686         TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
 687
 688         while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
 689
 690             if (m->control_pressed) { break; }
 691
 692             int success = 1;
 693             string trashCode = "";
 694             int currentSeqsDiffs = 0;
 695
 696             //read seqs and quality info
 697             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 698             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 699             QualityScores fQual(inFQual); m->gobble(inFQual);
 700             QualityScores rQual(inRQual); m->gobble(inRQual);
 701
 702             int barcodeIndex = 0;
 703             int primerIndex = 0;
 704
 705             if(barcodes.size() != 0){
 706                 success = trimOligos.stripBarcode(fSeq, rSeq, fQual, rQual, barcodeIndex);
 707                 if(success > bdiffs)            {       trashCode += 'b';       }
 708                 else{ currentSeqsDiffs += success;  }
 709             }
 710
 711             if(primers.size() != 0){
 712                 success = trimOligos.stripForward(fSeq, rSeq, fQual, rQual, primerIndex);
 713                 if(success > pdiffs)            {       trashCode += 'f';       }
 714                 else{ currentSeqsDiffs += success;  }
 715             }
 716
 717             if (currentSeqsDiffs > tdiffs)      {       trashCode += 't';   }
 718
 719             //flip the reverse reads
 720             rSeq.reverseComplement();
 721             rQual.flipQScores();
 722
 723             //pairwise align
 724             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 725             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 726             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 727             fSeq.setAligned(alignment->getSeqAAln());
 728             rSeq.setAligned(alignment->getSeqBAln());
 729             int length = fSeq.getAligned().length();
 730
 731             //traverse alignments merging into one contiguous seq
 732             string contig = "";
 733             vector<int> contigScores;
 734             int numMismatches = 0;
 735             string seq1 = fSeq.getAligned();
 736             string seq2 = rSeq.getAligned();
 737             vector<int> scores1 = fQual.getQualityScores();
 738             vector<int> scores2 = rQual.getQualityScores();
 739
 740             // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
 741             int overlapStart = fSeq.getStartPos();
 742             int seq2Start = rSeq.getStartPos();
 743             //bigger of the 2 starting positions is the location of the overlapping start
 744             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 745                 overlapStart = seq2Start;
 746                 for (int i = 0; i < overlapStart; i++) {
 747                     contig += seq1[i];
 748                     contigScores.push_back(scores1[ABaseMap[i]]);
 749                 }
 750             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 751                 for (int i = 0; i < overlapStart; i++) {
 752                     contig += seq2[i];
 753                     contigScores.push_back(scores2[BBaseMap[i]]);
 754                 }
 755             }
 756
 757             int seq1End = fSeq.getEndPos();
 758             int seq2End = rSeq.getEndPos();
 759             int overlapEnd = seq1End;
 760             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 761
 762             for (int i = overlapStart; i < overlapEnd; i++) {
 763                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 764                     contig += seq1[i];
 765                     contigScores.push_back(scores1[ABaseMap[i]]);
 766                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
 767                 }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
 768                     if (scores2[BBaseMap[i]] < threshold) { } //
 769                     else {
 770                         contig += seq2[i];
 771                         contigScores.push_back(scores2[BBaseMap[i]]);
 772                     }
 773                 }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
 774                     if (scores1[ABaseMap[i]] < threshold) { } //
 775                     else {
 776                         contig += seq1[i];
 777                         contigScores.push_back(scores1[ABaseMap[i]]);
 778                     }
 779                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 780                     char c = seq1[i];
 781                     contigScores.push_back(scores1[ABaseMap[i]]);
 782                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
 783                     contig += c;
 784                     numMismatches++;
 785                 }else { //should never get here
 786                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
 787                 }
 788             }
 789
 790             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
 791                 for (int i = overlapEnd; i < length; i++) {
 792                     contig += seq2[i];
 793                     contigScores.push_back(scores2[BBaseMap[i]]);
 794                 }
 795             }else { //seq2 ends before seq1 so take from overlap to length from seq1
 796                 for (int i = overlapEnd; i < length; i++) {
 797                     contig += seq1[i];
 798                     contigScores.push_back(scores1[ABaseMap[i]]);
 799                 }
 800
 801             }
 802
 803             if(trashCode.length() == 0){
 804                 if (createGroup) {
 805                     if(barcodes.size() != 0){
 806                         string thisGroup = barcodeNameVector[barcodeIndex];
 807                         if (primers.size() != 0) {
 808                             if (primerNameVector[primerIndex] != "") {
 809                                 if(thisGroup != "") {
 810                                     thisGroup += "." + primerNameVector[primerIndex];
 811                                 }else {
 812                                     thisGroup = primerNameVector[primerIndex];
 813                                 }
 814                             }
 815                         }
 816
 817                         if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
 818
 819                         groupMap[fSeq.getName()] = thisGroup;
 820
 821                         map<string, int>::iterator it = groupCounts.find(thisGroup);
 822                         if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1; }
 823                         else { groupCounts[it->first] ++; }
 824
 825                     }
 826                 }
 827
 828                 if(allFiles){
 829                     ofstream output;
 830                     m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
 831                     output << ">" << fSeq.getName() << endl << contig << endl;
 832                     output.close();
 833
 834                     m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
 835                     output << ">" << fSeq.getName() << endl;
 836                     for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
 837                     output << endl;
 838                     output.close();
 839                 }
 840
 841                 //output
 842                 outFasta << ">" << fSeq.getName() << endl << contig << endl;
 843                 outQual << ">" << fSeq.getName() << endl;
 844                 for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
 845                 outQual << endl;
 846                 outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
 847             }else {
 848                 //output
 849                 outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
 850                 outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
 851                 for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
 852                 outScrapQual << endl;
 853             }
 854             num++;
 855
 856                         //report progress
 857                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 858                 }
 859
 860                 //report progress
 861                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 862
 863         inFFasta.close();
 864         inFQual.close();
 865         inRFasta.close();
 866         inRQual.close();
 867         outFasta.close();
 868         outQual.close();
 869         outScrapFasta.close();
 870         outScrapQual.close();
 871         outMisMatch.close();
 872         delete alignment;
 873
 874         if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta);   m->mothurRemove(outputScrapQual); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches);}
 875
 876         return num;
 877     }
 878         catch(exception& e) {
 879                 m->errorOut(e, "MakeContigsCommand", "driver");
 880                 exit(1);
 881         }
 882 }
 883 //**********************************************************************************************************************
 884 vector< vector<string> > MakeContigsCommand::readFastqFiles(int& count){
 885     try {
 886         vector< vector<string> > files;
 887
 888         //maps processors number to file pointer
 889         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
 890         map<int, vector<ofstream*> >::iterator it;
 891
 892         //create files to write to
 893         for (int i = 0; i < processors; i++) {
 894             vector<ofstream*> temp;
 895             ofstream* outFF = new ofstream;     temp.push_back(outFF);
 896             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
 897             ofstream* outRF = new ofstream;     temp.push_back(outRF);
 898             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
 899             tempfiles[i] = temp;
 900
 901             vector<string> names;
 902             string ffastafilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "ffasta.temp";
 903             string rfastafilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rfasta.temp";
 904             string fqualfilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "fqual.temp";
 905             string rqualfilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rqual.temp";
 906             names.push_back(ffastafilename); names.push_back(fqualfilename);
 907             names.push_back(rfastafilename); names.push_back(rqualfilename);
 908             files.push_back(names);
 909
 910             m->openOutputFile(ffastafilename, *outFF);
 911             m->openOutputFile(rfastafilename, *outRF);
 912             m->openOutputFile(fqualfilename, *outFQ);
 913             m->openOutputFile(rqualfilename, *outRQ);
 914         }
 915
 916         if (m->control_pressed) {
 917             //close files, delete ofstreams
 918             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]; } }
 919             //remove files
 920             for (int i = 0; i < files.size(); i++) {
 921                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
 922             }
 923         }
 924
 925         ifstream inForward;
 926         m->openInputFile(ffastqfile, inForward);
 927
 928         ifstream inReverse;
 929         m->openInputFile(rfastqfile, inReverse);
 930
 931         count = 0;
 932         map<string, fastqRead> uniques;
 933         map<string, fastqRead>::iterator itUniques;
 934         while ((!inForward.eof()) || (!inReverse.eof())) {
 935
 936             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; }
 937
 938             //get a read from forward and reverse fastq files
 939             bool ignoref, ignorer;
 940             fastqRead thisFread, thisRread;
 941             if (!inForward.eof()) {  thisFread = readFastq(inForward, ignoref); }
 942             else { ignoref = true; }
 943             if (!inReverse.eof()) { thisRread = readFastq(inReverse, ignorer);  }
 944             else { ignorer = true; }
 945
 946             vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
 947
 948             for (int i = 0; i < reads.size(); i++) {
 949                 fastqRead fread = reads[i].forward;
 950                 fastqRead rread = reads[i].reverse;
 951
 952                 if (checkReads(fread, rread)) {
 953                     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; }
 954
 955                     //if the reads are okay write to output files
 956                     int process = count % processors;
 957
 958                     *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
 959                     *(tempfiles[process][1]) << ">" << fread.name << endl;
 960                     for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
 961                     *(tempfiles[process][1]) << endl;
 962                     *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
 963                     *(tempfiles[process][3]) << ">" << rread.name << endl;
 964                     for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
 965                     *(tempfiles[process][3]) << endl;
 966
 967                     count++;
 968
 969                     //report progress
 970                     if((count) % 10000 == 0){   m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 971                 }
 972             }
 973                 }
 974                 //report progress
 975                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 976
 977         if (uniques.size() != 0) {
 978             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
 979                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
 980             }
 981             m->mothurOutEndLine();
 982         }
 983
 984         //close files, delete ofstreams
 985         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]; } }
 986         inForward.close();
 987         inReverse.close();
 988
 989         //adjust for really large processors or really small files
 990         if (count == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
 991         if (count < processors) {
 992             for (int i = count; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 993             files.resize(count);
 994             processors = count;
 995         }
 996
 997         return files;
 998     }
 999     catch(exception& e) {
1000         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1001         exit(1);
1002     }
1003 }
1004 //**********************************************************************************************************************
1005 vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques){
1006     try {
1007         vector<pairFastqRead> reads;
1008         map<string, fastqRead>::iterator itUniques;
1009
1010         if (!ignoref && !ignorer) {
1011             if (forward.name == reverse.name) {
1012                 pairFastqRead temp(forward, reverse);
1013                 reads.push_back(temp);
1014             }else {
1015                 //look for forward pair
1016                 itUniques = uniques.find(forward.name);
1017                 if (itUniques != uniques.end()) {  //we have the pair for this read
1018                     pairFastqRead temp(forward, itUniques->second);
1019                     reads.push_back(temp);
1020                     uniques.erase(itUniques);
1021                 }else { //save this read for later
1022                     uniques[forward.name] = forward;
1023                 }
1024
1025                 //look for reverse pair
1026                 itUniques = uniques.find(reverse.name);
1027                 if (itUniques != uniques.end()) {  //we have the pair for this read
1028                     pairFastqRead temp(itUniques->second, reverse);
1029                     reads.push_back(temp);
1030                     uniques.erase(itUniques);
1031                 }else { //save this read for later
1032                     uniques[reverse.name] = reverse;
1033                 }
1034             }
1035         }else if (!ignoref && ignorer) { //ignore reverse keep forward
1036             //look for forward pair
1037             itUniques = uniques.find(forward.name);
1038             if (itUniques != uniques.end()) {  //we have the pair for this read
1039                 pairFastqRead temp(forward, itUniques->second);
1040                 reads.push_back(temp);
1041                 uniques.erase(itUniques);
1042             }else { //save this read for later
1043                 uniques[forward.name] = forward;
1044             }
1045
1046         }else if (ignoref && !ignorer) { //ignore forward keep reverse
1047             //look for reverse pair
1048             itUniques = uniques.find(reverse.name);
1049             if (itUniques != uniques.end()) {  //we have the pair for this read
1050                 pairFastqRead temp(itUniques->second, reverse);
1051                 reads.push_back(temp);
1052                 uniques.erase(itUniques);
1053             }else { //save this read for later
1054                 uniques[reverse.name] = reverse;
1055             }
1056         }//else ignore both and do nothing
1057
1058         return reads;
1059     }
1060     catch(exception& e) {
1061         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1062         exit(1);
1063     }
1064 }
1065 //**********************************************************************************************************************
1066 fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
1067     try {
1068         fastqRead read;
1069
1070         ignore = false;
1071
1072         //read sequence name
1073         string line = m->getline(in); m->gobble(in);
1074         vector<string> pieces = m->splitWhiteSpace(line);
1075         string name = "";  if (pieces.size() != 0) { name = pieces[0]; }
1076         if (name == "") {  m->mothurOut("[WARNING]: Blank fasta name, ignoring read."); m->mothurOutEndLine(); ignore=true;  }
1077         else if (name[0] != '@') { m->mothurOut("[WARNING]: reading " + name + " expected a name with @ as a leading character, ignoring read."); m->mothurOutEndLine(); ignore=true; }
1078         else { name = name.substr(1); }
1079
1080         //read sequence
1081         string sequence = m->getline(in); m->gobble(in);
1082         if (sequence == "") {  m->mothurOut("[WARNING]: missing sequence for " + name + ", ignoring."); ignore=true; }
1083
1084         //read sequence name
1085         line = m->getline(in); m->gobble(in);
1086         pieces = m->splitWhiteSpace(line);
1087         string name2 = "";  if (pieces.size() != 0) { name2 = pieces[0]; }
1088         if (name2 == "") {  m->mothurOut("[WARNING]: expected a name with + as a leading character, ignoring."); ignore=true; }
1089         else if (name2[0] != '+') { m->mothurOut("[WARNING]: reading " + name2 + " expected a name with + as a leading character, ignoring."); ignore=true; }
1090         else { name2 = name2.substr(1); if (name2 == "") { name2 = name; } }
1091
1092         //read quality scores
1093         string quality = m->getline(in); m->gobble(in);
1094         if (quality == "") {  m->mothurOut("[WARNING]: missing quality for " + name2 + ", ignoring."); ignore=true; }
1095
1096         //sanity check sequence length and number of quality scores match
1097         if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } }
1098         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; }
1099
1100         vector<int> qualScores;
1101                 int controlChar = int('!');
1102                 for (int i = 0; i < quality.length(); i++) {
1103                         int temp = int(quality[i]);
1104                         temp -= controlChar;
1105
1106                         qualScores.push_back(temp);
1107                 }
1108
1109         read.name = name;
1110         read.sequence = sequence;
1111         read.scores = qualScores;
1112
1113         return read;
1114     }
1115     catch(exception& e) {
1116         m->errorOut(e, "MakeContigsCommand", "readFastq");
1117         exit(1);
1118     }
1119 }
1120 //**********************************************************************************************************************
1121 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){
1122     try {
1123         bool good = true;
1124
1125         //do sequence lengths match
1126         if (forward.sequence.length() != reverse.sequence.length()) {
1127             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");
1128             good = false;
1129         }
1130
1131         //do number of qual scores match
1132         if (forward.scores.size() != reverse.scores.size()) {
1133             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");
1134             good = false;
1135         }
1136
1137         return good;
1138     }
1139     catch(exception& e) {
1140         m->errorOut(e, "MakeContigsCommand", "checkReads");
1141         exit(1);
1142     }
1143 }
1144 //***************************************************************************************************************
1145 //illumina data requires paired forward and reverse data
1146 //BARCODE   atgcatgc   atgcatgc    groupName
1147 //PRIMER   atgcatgc   atgcatgc    groupName
1148 //PRIMER   atgcatgc   atgcatgc
1149 bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames){
1150         try {
1151                 ifstream in;
1152                 m->openInputFile(oligosfile, in);
1153
1154                 ofstream test;
1155
1156                 string type, foligo, roligo, group;
1157
1158                 int indexPrimer = 0;
1159                 int indexBarcode = 0;
1160         set<string> uniquePrimers;
1161         set<string> uniqueBarcodes;
1162
1163                 while(!in.eof()){
1164
1165                         in >> type;
1166
1167                         if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
1168
1169                         if(type[0] == '#'){
1170                                 while (!in.eof())       {       char c = in.get();  if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
1171                                 m->gobble(in);
1172                         }
1173                         else{
1174                                 m->gobble(in);
1175                                 //make type case insensitive
1176                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
1177
1178                                 in >> foligo;
1179
1180                 if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); }
1181
1182                                 for(int i=0;i<foligo.length();i++){
1183                                         foligo[i] = toupper(foligo[i]);
1184                                         if(foligo[i] == 'U')    {       foligo[i] = 'T';        }
1185                                 }
1186
1187                                 if(type == "FORWARD"){
1188                                         m->gobble(in);
1189
1190                     in >> roligo;
1191
1192                     for(int i=0;i<roligo.length();i++){
1193                         roligo[i] = toupper(roligo[i]);
1194                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1195                     }
1196                     //roligo = reverseOligo(roligo);
1197
1198                     group = "";
1199
1200                                         // get rest of line in case there is a primer name
1201                                         while (!in.eof())       {
1202                                                 char c = in.get();
1203                                                 if (c == 10 || c == 13){        break;  }
1204                                                 else if (c == 32 || c == 9){;} //space or tab
1205                                                 else {  group += c;  }
1206                                         }
1207
1208                     oligosPair newPrimer(foligo, roligo);
1209
1210                                         //check for repeat barcodes
1211                     string tempPair = foligo+roligo;
1212                     if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine();  }
1213                     else { uniquePrimers.insert(tempPair); }
1214
1215                     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"); }  }
1216
1217                                         primers[indexPrimer]=newPrimer; indexPrimer++;
1218                                         primerNameVector.push_back(group);
1219                                 }else if(type == "BARCODE"){
1220                                         m->gobble(in);
1221
1222                     in >> roligo;
1223
1224                     for(int i=0;i<roligo.length();i++){
1225                         roligo[i] = toupper(roligo[i]);
1226                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1227                     }
1228                     //roligo = reverseOligo(roligo);
1229
1230                     oligosPair newPair(foligo, roligo);
1231
1232                     group = "";
1233                     while (!in.eof())   {
1234                                                 char c = in.get();
1235                                                 if (c == 10 || c == 13){        break;  }
1236                                                 else if (c == 32 || c == 9){;} //space or tab
1237                                                 else {  group += c;  }
1238                                         }
1239
1240                     if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
1241
1242                     //check for repeat barcodes
1243                     string tempPair = foligo+roligo;
1244                     if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse +  " is in your oligos file already, disregarding."); m->mothurOutEndLine();  }
1245                     else { uniqueBarcodes.insert(tempPair); }
1246
1247                     barcodes[indexBarcode]=newPair; indexBarcode++;
1248                                         barcodeNameVector.push_back(group);
1249                                 }else if(type == "LINKER"){
1250                                         linker.push_back(foligo);
1251                     m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");
1252                                 }else if(type == "SPACER"){
1253                                         spacer.push_back(foligo);
1254                     m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n");
1255                                 }
1256                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); }
1257                         }
1258                         m->gobble(in);
1259                 }
1260                 in.close();
1261
1262                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
1263
1264                 //add in potential combos
1265                 if(barcodeNameVector.size() == 0){
1266             oligosPair temp("", "");
1267                         barcodes[0] = temp;
1268                         barcodeNameVector.push_back("");
1269                 }
1270
1271                 if(primerNameVector.size() == 0){
1272             oligosPair temp("", "");
1273                         primers[0] = temp;
1274                         primerNameVector.push_back("");
1275                 }
1276
1277                 fastaFileNames.resize(barcodeNameVector.size());
1278                 for(int i=0;i<fastaFileNames.size();i++){
1279                         fastaFileNames[i].assign(primerNameVector.size(), "");
1280                 }
1281                 qualFileNames = fastaFileNames;
1282
1283                 if(allFiles){
1284                         set<string> uniqueNames; //used to cleanup outputFileNames
1285                         for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1286                                 for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1287
1288                                         string primerName = primerNameVector[itPrimer->first];
1289                                         string barcodeName = barcodeNameVector[itBar->first];
1290
1291                                         string comboGroupName = "";
1292                                         string fastaFileName = "";
1293                                         string qualFileName = "";
1294                                         string nameFileName = "";
1295                     string countFileName = "";
1296
1297                                         if(primerName == ""){
1298                                                 comboGroupName = barcodeNameVector[itBar->first];
1299                                         }
1300                                         else{
1301                                                 if(barcodeName == ""){
1302                                                         comboGroupName = primerNameVector[itPrimer->first];
1303                                                 }
1304                                                 else{
1305                                                         comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
1306                                                 }
1307                                         }
1308
1309
1310                                         ofstream temp;
1311                                         fastaFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".fasta";
1312                                         if (uniqueNames.count(fastaFileName) == 0) {
1313                                                 outputNames.push_back(fastaFileName);
1314                                                 outputTypes["fasta"].push_back(fastaFileName);
1315                                                 uniqueNames.insert(fastaFileName);
1316                                         }
1317
1318                                         fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
1319                                         m->openOutputFile(fastaFileName, temp);         temp.close();
1320
1321
1322                     qualFileName = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + comboGroupName + ".qual";
1323                     if (uniqueNames.count(qualFileName) == 0) {
1324                         outputNames.push_back(qualFileName);
1325                         outputTypes["qfile"].push_back(qualFileName);
1326                     }
1327
1328                     qualFileNames[itBar->first][itPrimer->first] = qualFileName;
1329                     m->openOutputFile(qualFileName, temp);              temp.close();
1330                                 }
1331                         }
1332                 }
1333
1334                 bool allBlank = true;
1335                 for (int i = 0; i < barcodeNameVector.size(); i++) {
1336                         if (barcodeNameVector[i] != "") {
1337                                 allBlank = false;
1338                                 break;
1339                         }
1340                 }
1341                 for (int i = 0; i < primerNameVector.size(); i++) {
1342                         if (primerNameVector[i] != "") {
1343                                 allBlank = false;
1344                                 break;
1345                         }
1346                 }
1347
1348                 if (allBlank) {
1349                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
1350                         allFiles = false;
1351                         return false;
1352                 }
1353
1354                 return true;
1355
1356         }
1357         catch(exception& e) {
1358                 m->errorOut(e, "MakeContigsCommand", "getOligos");
1359                 exit(1);
1360         }
1361 }
1362 //********************************************************************/
1363 string MakeContigsCommand::reverseOligo(string oligo){
1364         try {
1365         string reverse = "";
1366
1367         for(int i=oligo.length()-1;i>=0;i--){
1368
1369             if(oligo[i] == 'A')         {       reverse += 'T'; }
1370             else if(oligo[i] == 'T'){   reverse += 'A'; }
1371             else if(oligo[i] == 'U'){   reverse += 'A'; }
1372
1373             else if(oligo[i] == 'G'){   reverse += 'C'; }
1374             else if(oligo[i] == 'C'){   reverse += 'G'; }
1375
1376             else if(oligo[i] == 'R'){   reverse += 'Y'; }
1377             else if(oligo[i] == 'Y'){   reverse += 'R'; }
1378
1379             else if(oligo[i] == 'M'){   reverse += 'K'; }
1380             else if(oligo[i] == 'K'){   reverse += 'M'; }
1381
1382             else if(oligo[i] == 'W'){   reverse += 'W'; }
1383             else if(oligo[i] == 'S'){   reverse += 'S'; }
1384
1385             else if(oligo[i] == 'B'){   reverse += 'V'; }
1386             else if(oligo[i] == 'V'){   reverse += 'B'; }
1387
1388             else if(oligo[i] == 'D'){   reverse += 'H'; }
1389             else if(oligo[i] == 'H'){   reverse += 'D'; }
1390
1391             else                                                {       reverse += 'N'; }
1392         }
1393
1394
1395         return reverse;
1396     }
1397         catch(exception& e) {
1398                 m->errorOut(e, "MakeContigsCommand", "reverseOligo");
1399                 exit(1);
1400         }
1401 }
1402 //**********************************************************************************************************************
1403
1404
1405
1406