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 palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "",false,false); parameters.push_back(palign);
  17                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  18                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  19                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  20                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  21                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  22                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  23                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  24
  25                 vector<string> myArray;
  26                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  27                 return myArray;
  28         }
  29         catch(exception& e) {
  30                 m->errorOut(e, "MakeContigsCommand", "setParameters");
  31                 exit(1);
  32         }
  33 }
  34 //**********************************************************************************************************************
  35 string MakeContigsCommand::getHelpString(){
  36         try {
  37                 string helpString = "";
  38                 helpString += "The make.contigs command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.\n";
  39                 helpString += "The make.contigs command parameters are ffastq, rfastq, align, match, mismatch, gapopen, gapextend and processors.\n";
  40                 helpString += "The ffastq and rfastq parameter is required.\n";
  41                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n";
  42                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  43                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  44                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  45                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  46         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  47         helpString += "The make.contigs command should be in the following format: \n";
  48                 helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
  49                 helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "MakeContigsCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57
  58 //**********************************************************************************************************************
  59 MakeContigsCommand::MakeContigsCommand(){
  60         try {
  61                 abort = true; calledHelp = true;
  62                 setParameters();
  63                 vector<string> tempOutNames;
  64                 outputTypes["fasta"] = tempOutNames;
  65                 outputTypes["qfile"] = tempOutNames;
  66         outputTypes["mismatch"] = tempOutNames;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74 MakeContigsCommand::MakeContigsCommand(string option)  {
  75         try {
  76                 abort = false; calledHelp = false;
  77
  78                 //allow user to run help
  79                 if(option == "help") { help(); abort = true; calledHelp = true; }
  80                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  81
  82                 else {
  83                         vector<string> myArray = setParameters();
  84
  85                         OptionParser parser(option);
  86                         map<string, string> parameters = parser.getParameters();
  87
  88                         ValidParameters validParameter("pairwise.seqs");
  89                         map<string, string>::iterator it;
  90
  91                         //check to make sure all parameters are valid for command
  92                         for (it = parameters.begin(); it != parameters.end(); it++) {
  93                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  94                         }
  95
  96                         //initialize outputTypes
  97                         vector<string> tempOutNames;
  98                         outputTypes["fasta"] = tempOutNames;
  99                         outputTypes["qfile"] = tempOutNames;
 100             outputTypes["mismatch"] = tempOutNames;
 101
 102
 103                         //if the user changes the input directory command factory will send this info to us in the output parameter
 104                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 105                         if (inputDir == "not found"){   inputDir = "";          }
 106                         else {
 107                                 string path;
 108                 it = parameters.find("ffastq");
 109                                 //user has given a template file
 110                                 if(it != parameters.end()){
 111                                         path = m->hasPath(it->second);
 112                                         //if the user has not given a path then, add inputdir. else leave path alone.
 113                                         if (path == "") {       parameters["ffastq"] = inputDir + it->second;           }
 114                                 }
 115
 116                 it = parameters.find("rfastq");
 117                                 //user has given a template file
 118                                 if(it != parameters.end()){
 119                                         path = m->hasPath(it->second);
 120                                         //if the user has not given a path then, add inputdir. else leave path alone.
 121                                         if (path == "") {       parameters["rfastq"] = inputDir + it->second;           }
 122                                 }
 123             }
 124
 125             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
 126                         if (ffastqfile == "not open") { ffastqfile = ""; abort = true; }
 127                         else if (ffastqfile == "not found") { ffastqfile = ""; abort=true;  m->mothurOut("The ffastq parameter is required.\n"); }
 128
 129                         rfastqfile = validParameter.validFile(parameters, "rfastq", true);
 130                         if (rfastqfile == "not open") { rfastqfile = ""; abort = true; }
 131                         else if (rfastqfile == "not found") { rfastqfile = ""; abort=true;  m->mothurOut("The rfastq parameter is required.\n"); }
 132
 133             //if the user changes the output directory command factory will send this info to us in the output parameter
 134                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(ffastqfile);             }
 135
 136
 137                         //check for optional parameter and set defaults
 138                         // ...at some point should added some additional type checking...
 139                         string temp;
 140                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 141                         m->mothurConvert(temp, match);
 142
 143                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 144                         m->mothurConvert(temp, misMatch);
 145             if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 146
 147                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 148                         m->mothurConvert(temp, gapOpen);
 149             if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 150
 151                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 152                         m->mothurConvert(temp, gapExtend);
 153             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 154
 155                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 156                         m->setProcessors(temp);
 157                         m->mothurConvert(temp, processors);
 158
 159                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 160                         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"; }
 161         }
 162
 163         }
 164         catch(exception& e) {
 165                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 166                 exit(1);
 167         }
 168 }
 169 //**********************************************************************************************************************
 170 int MakeContigsCommand::execute(){
 171         try {
 172                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 173
 174         //read ffastq and rfastq files creating fasta and qual files.
 175         //this function will create a forward and reverse, fasta and qual files for each processor.
 176         //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual
 177         int numReads = 0;
 178         int start = time(NULL);
 179         longestBase = 1000;
 180         m->mothurOut("Reading fastq data...\n");
 181         vector< vector<string> > files = readFastqFiles(numReads);
 182         m->mothurOut("Done.\n");
 183
 184         if (m->control_pressed) { return 0; }
 185
 186         string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.fasta";
 187         string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.qual";
 188         string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.mismatches";
 189         outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 190         outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
 191         outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
 192
 193         m->mothurOut("Making contigs...\n");
 194         createProcesses(files, outFastaFile, outQualFile, outMisMatchFile);
 195         m->mothurOut("Done.\n");
 196
 197         //remove temp fasta and qual files
 198         for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }  }
 199
 200         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 201
 202         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 203
 204         string currentFasta = "";
 205                 itTypes = outputTypes.find("fasta");
 206                 if (itTypes != outputTypes.end()) {
 207                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 208                 }
 209
 210         string currentQual = "";
 211                 itTypes = outputTypes.find("qfile");
 212                 if (itTypes != outputTypes.end()) {
 213                         if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
 214                 }
 215
 216         //output files created by command
 217                 m->mothurOutEndLine();
 218                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 219                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 220                 m->mothurOutEndLine();
 221
 222
 223         return 0;
 224     }
 225         catch(exception& e) {
 226                 m->errorOut(e, "MakeContigsCommand", "execute");
 227                 exit(1);
 228         }
 229 }
 230 //**********************************************************************************************************************
 231 int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputMisMatches) {
 232         try {
 233                 int num = 0;
 234                 vector<int> processIDS;
 235 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 236                 int process = 0;
 237
 238                 //loop through and create all the processes you want
 239                 while (process != processors-1) {
 240                         int pid = fork();
 241
 242                         if (pid > 0) {
 243                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 244                                 process++;
 245                         }else if (pid == 0){
 246                                 num = driver(files[process], outputFasta + toString(getpid()) + ".temp", outputQual + toString(getpid()) + ".temp", outputMisMatches + toString(getpid()) + ".temp");
 247
 248                                 //pass numSeqs to parent
 249                                 ofstream out;
 250                                 string tempFile = outputFasta + toString(getpid()) + ".num.temp";
 251                                 m->openOutputFile(tempFile, out);
 252                                 out << num << endl;
 253                                 out.close();
 254
 255                                 exit(0);
 256                         }else {
 257                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 258                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 259                                 exit(0);
 260                         }
 261                 }
 262
 263                 //do my part
 264                 num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
 265
 266                 //force parent to wait until all the processes are done
 267                 for (int i=0;i<processIDS.size();i++) {
 268                         int temp = processIDS[i];
 269                         wait(&temp);
 270                 }
 271
 272                 for (int i = 0; i < processIDS.size(); i++) {
 273                         ifstream in;
 274                         string tempFile =  outputFasta + toString(processIDS[i]) + ".num.temp";
 275                         m->openInputFile(tempFile, in);
 276                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 277                         in.close(); m->mothurRemove(tempFile);
 278         }
 279     #else
 280
 281         //////////////////////////////////////////////////////////////////////////////////////////////////////
 282                 //Windows version shared memory, so be careful when passing variables through the contigsData struct.
 283                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 284                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 285
 286                 vector<contigsData*> pDataArray;
 287                 DWORD   dwThreadIdArray[processors-1];
 288                 HANDLE  hThreadArray[processors-1];
 289
 290                 //Create processor worker threads.
 291                 for( int i=0; i<processors-1; i++ ){
 292                         string extension = toString(i) + ".temp";
 293
 294                         contigsData* tempcontig = new contigsData(files[i], (outputFasta + extension), (outputQual + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, i);
 295                         pDataArray.push_back(tempcontig);
 296                         processIDS.push_back(i);
 297
 298                         hThreadArray[i] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 299                 }
 300
 301         num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
 302
 303                 //Wait until all threads have terminated.
 304                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 305
 306                 //Close all thread handles and free memory allocations.
 307                 for(int i=0; i < pDataArray.size(); i++){
 308                         num += pDataArray[i]->count;
 309             CloseHandle(hThreadArray[i]);
 310                         delete pDataArray[i];
 311         }
 312
 313     #endif
 314
 315         for (int i = 0; i < processIDS.size(); i++) {
 316                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 317                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 318
 319                         m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
 320                         m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
 321
 322             m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 323                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 324                 }
 325
 326                 return num;
 327         }
 328         catch(exception& e) {
 329                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 330                 exit(1);
 331         }
 332 }
 333 //**********************************************************************************************************************
 334 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputMisMatches){
 335     try {
 336
 337         Alignment* alignment;
 338         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 339                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 340
 341         int num = 0;
 342         string thisffastafile = files[0];
 343         string thisfqualfile = files[1];
 344         string thisrfastafile = files[2];
 345         string thisrqualfile = files[3];
 346
 347         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 348
 349         ifstream inFFasta, inRFasta, inFQual, inRQual;
 350         m->openInputFile(thisffastafile, inFFasta);
 351         m->openInputFile(thisfqualfile, inFQual);
 352         m->openInputFile(thisrfastafile, inRFasta);
 353         m->openInputFile(thisrqualfile, inRQual);
 354
 355         ofstream outFasta, outQual, outMisMatch;
 356         m->openOutputFile(outputFasta, outFasta);
 357         m->openOutputFile(outputQual, outQual);
 358         m->openOutputFile(outputMisMatches, outMisMatch);
 359         outMisMatch << "Name\tLength\tMisMatches\n";
 360
 361         while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
 362
 363             if (m->control_pressed) { break; }
 364
 365             //read seqs and quality info
 366             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 367             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 368             QualityScores fQual(inFQual); m->gobble(inFQual);
 369             QualityScores rQual(inRQual); m->gobble(inRQual);
 370
 371             //flip the reverse reads
 372             rSeq.reverseComplement();
 373             rQual.flipQScores();
 374
 375             //pairwise align
 376             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 377             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 378             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 379             fSeq.setAligned(alignment->getSeqAAln());
 380             rSeq.setAligned(alignment->getSeqBAln());
 381             int length = fSeq.getAligned().length();
 382
 383             //traverse alignments merging into one contiguous seq
 384             string contig = "";
 385             vector<int> contigScores;
 386             int numMismatches = 0;
 387             string seq1 = fSeq.getAligned();
 388             string seq2 = rSeq.getAligned();
 389
 390             vector<int> scores1 = fQual.getQualityScores();
 391             vector<int> scores2 = rQual.getQualityScores();
 392
 393             for (int i = 0; i < length; i++) {
 394                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 395                     contig += seq1[i];
 396                     contigScores.push_back(scores1[ABaseMap[i]]);
 397                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; }
 398                 }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2
 399                     contig += seq2[i];
 400                     contigScores.push_back(scores2[BBaseMap[i]]);
 401                 }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1
 402                     contig += seq1[i];
 403                     contigScores.push_back(scores1[ABaseMap[i]]);
 404                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 405                     char c = seq1[i];
 406                     contigScores.push_back(scores1[ABaseMap[i]]);
 407                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[i] = scores2[BBaseMap[i]]; c = seq2[i]; }
 408                     contig += c;
 409                     numMismatches++;
 410                 }else { //should never get here
 411                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
 412                 }
 413             }
 414
 415             //output
 416             outFasta << ">" << fSeq.getName() << endl << contig << endl;
 417             outQual << ">" << fSeq.getName() << endl;
 418             for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
 419             outQual << endl;
 420             outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
 421
 422             num++;
 423
 424                         //report progress
 425                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 426                 }
 427
 428                 //report progress
 429                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 430
 431         inFFasta.close();
 432         inFQual.close();
 433         inRFasta.close();
 434         inRQual.close();
 435         outFasta.close();
 436         outQual.close();
 437         outMisMatch.close();
 438         delete alignment;
 439
 440         if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta);  m->mothurRemove(outputMisMatches);}
 441
 442         return num;
 443     }
 444         catch(exception& e) {
 445                 m->errorOut(e, "MakeContigsCommand", "driver");
 446                 exit(1);
 447         }
 448 }
 449 //**********************************************************************************************************************
 450 vector< vector<string> > MakeContigsCommand::readFastqFiles(int& count){
 451     try {
 452         vector< vector<string> > files;
 453
 454         //maps processors number to file pointer
 455         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
 456         map<int, vector<ofstream*> >::iterator it;
 457
 458         //create files to write to
 459         for (int i = 0; i < processors; i++) {
 460             vector<ofstream*> temp;
 461             ofstream* outFF = new ofstream;     temp.push_back(outFF);
 462             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
 463             ofstream* outRF = new ofstream;     temp.push_back(outRF);
 464             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
 465             tempfiles[i] = temp;
 466
 467             vector<string> names;
 468             string ffastafilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "ffasta.temp";
 469             string rfastafilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rfasta.temp";
 470             string fqualfilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "fqual.temp";
 471             string rqualfilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rqual.temp";
 472             names.push_back(ffastafilename); names.push_back(fqualfilename);
 473             names.push_back(rfastafilename); names.push_back(rqualfilename);
 474             files.push_back(names);
 475
 476             m->openOutputFile(ffastafilename, *outFF);
 477             m->openOutputFile(rfastafilename, *outRF);
 478             m->openOutputFile(fqualfilename, *outFQ);
 479             m->openOutputFile(rqualfilename, *outRQ);
 480         }
 481
 482         if (m->control_pressed) {
 483             //close files, delete ofstreams
 484             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]; } }
 485             //remove files
 486             for (int i = 0; i < files.size(); i++) {
 487                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
 488             }
 489         }
 490
 491         ifstream inForward;
 492         m->openInputFile(ffastqfile, inForward);
 493
 494         ifstream inReverse;
 495         m->openInputFile(rfastqfile, inReverse);
 496
 497         count = 0;
 498         while ((!inForward.eof()) && (!inReverse.eof())) {
 499
 500             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; }
 501
 502             //get a read from forward and reverse fastq files
 503             fastqRead fread = readFastq(inForward);
 504             fastqRead rread = readFastq(inReverse);
 505             checkReads(fread, rread);
 506
 507             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; }
 508
 509             //if the reads are okay write to output files
 510             int process = count % processors;
 511
 512             *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
 513             *(tempfiles[process][1]) << ">" << fread.name << endl;
 514             for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
 515             *(tempfiles[process][1]) << endl;
 516             *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
 517             *(tempfiles[process][3]) << ">" << rread.name << endl;
 518             for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
 519             *(tempfiles[process][3]) << endl;
 520
 521             count++;
 522
 523             //report progress
 524                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 525
 526                 }
 527                 //report progress
 528                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 529
 530
 531
 532         //close files, delete ofstreams
 533         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]; } }
 534         inForward.close();
 535         inReverse.close();
 536
 537         //adjust for really large processors or really small files
 538         if (count < processors) {
 539             for (int i = count; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 540             files.resize(count);
 541             processors = count;
 542         }
 543
 544         return files;
 545     }
 546     catch(exception& e) {
 547         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
 548         exit(1);
 549     }
 550 }
 551 //**********************************************************************************************************************
 552 fastqRead MakeContigsCommand::readFastq(ifstream& in){
 553     try {
 554         fastqRead read;
 555
 556         //read sequence name
 557         string name = m->getline(in); m->gobble(in);
 558         if (name == "") {  m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 559         else if (name[0] != '@') { m->mothurOut("[ERROR]: reading " + name + " expected a name with @ as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 560         else { name = name.substr(1); }
 561
 562         //read sequence
 563         string sequence = m->getline(in); m->gobble(in);
 564         if (sequence == "") {  m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 565
 566         //read sequence name
 567         string name2 = m->getline(in); m->gobble(in);
 568         if (name2 == "") {  m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 569         else if (name2[0] != '+') { m->mothurOut("[ERROR]: reading " + name2 + " expected a name with + as a leading character."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 570         else { name2 = name2.substr(1);  }
 571
 572         //read quality scores
 573         string quality = m->getline(in); m->gobble(in);
 574         if (quality == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 575
 576         //sanity check sequence length and number of quality scores match
 577         if (name2 != "") { if (name != name2) { m->mothurOut("[ERROR]: names do not match. read " + name + " for fasta and " + name2 + " for quality."); m->mothurOutEndLine(); m->control_pressed = true; return read; } }
 578         if (quality.length() != sequence.length()) { m->mothurOut("[ERROR]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 579
 580         vector<int> qualScores;
 581                 int controlChar = int('@');
 582                 for (int i = 0; i < quality.length(); i++) {
 583                         int temp = int(quality[i]);
 584                         temp -= controlChar;
 585
 586                         qualScores.push_back(temp);
 587                 }
 588
 589         read.name = name;
 590         read.sequence = sequence;
 591         read.scores = qualScores;
 592
 593         return read;
 594     }
 595     catch(exception& e) {
 596         m->errorOut(e, "MakeContigsCommand", "readFastq");
 597         exit(1);
 598     }
 599 }
 600 //**********************************************************************************************************************
 601 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){
 602     try {
 603         bool good = true;
 604
 605         //fix names
 606         if ((forward.name.length() > 2) && (reverse.name.length() > 2)) {
 607             forward.name = forward.name.substr(0, forward.name.length()-2);
 608             reverse.name = reverse.name.substr(0, reverse.name.length()-2);
 609         }else { good = false; m->control_pressed = true; }
 610
 611         //do names match
 612         if (forward.name != reverse.name) {
 613             m->mothurOut("[ERROR]: read " + forward.name + " from " + ffastqfile + ", but read " + reverse.name + " from " + rfastqfile + ".\n");
 614             good = false; m->control_pressed = true;
 615         }
 616
 617         //do sequence lengths match
 618         if (forward.sequence.length() != reverse.sequence.length()) {
 619             m->mothurOut("[ERROR]: For sequence " + forward.name + " I read a sequence of length " + toString(forward.sequence.length()) + " from " + ffastqfile + ", but read a sequence of length " + toString(reverse.sequence.length()) + " from " + rfastqfile + ".\n");
 620             good = false; m->control_pressed = true;
 621         }
 622
 623         //do number of qual scores match
 624         if (forward.scores.size() != reverse.scores.size()) {
 625             m->mothurOut("[ERROR]: For sequence " + forward.name + " I read " + toString(forward.scores.size()) + " quality scores from " + ffastqfile + ", but read  " + toString(reverse.scores.size()) + " quality scores from " + rfastqfile + ".\n");
 626             good = false; m->control_pressed = true;
 627         }
 628
 629         return good;
 630     }
 631     catch(exception& e) {
 632         m->errorOut(e, "MakeContigsCommand", "readFastq");
 633         exit(1);
 634     }
 635 }
 636 //**********************************************************************************************************************
 637
 638
 639
 640