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