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 pthreshold("threshold", "Number", "", "40", "", "", "",false,false); parameters.push_back(pthreshold);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "MakeContigsCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string MakeContigsCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The make.contigs command reads a forward fastq file and a reverse fastq file and outputs new fasta and quality files.\n";
  40                 helpString += "The make.contigs command parameters are ffastq, rfastq, align, match, mismatch, gapopen, gapextend and processors.\n";
  41                 helpString += "The ffastq and rfastq parameter is required.\n";
  42                 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";
  43                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  44                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  45                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  46                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  47         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";
  48         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  49         helpString += "The make.contigs command should be in the following format: \n";
  50                 helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "MakeContigsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59
  60 //**********************************************************************************************************************
  61 MakeContigsCommand::MakeContigsCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["fasta"] = tempOutNames;
  67                 outputTypes["qfile"] = tempOutNames;
  68         outputTypes["mismatch"] = tempOutNames;
  69         }
  70         catch(exception& e) {
  71                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
  72                 exit(1);
  73         }
  74 }
  75 //**********************************************************************************************************************
  76 MakeContigsCommand::MakeContigsCommand(string option)  {
  77         try {
  78                 abort = false; calledHelp = false;
  79
  80                 //allow user to run help
  81                 if(option == "help") { help(); abort = true; calledHelp = true; }
  82                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  83
  84                 else {
  85                         vector<string> myArray = setParameters();
  86
  87                         OptionParser parser(option);
  88                         map<string, string> parameters = parser.getParameters();
  89
  90                         ValidParameters validParameter("pairwise.seqs");
  91                         map<string, string>::iterator it;
  92
  93                         //check to make sure all parameters are valid for command
  94                         for (it = parameters.begin(); it != parameters.end(); it++) {
  95                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  96                         }
  97
  98                         //initialize outputTypes
  99                         vector<string> tempOutNames;
 100                         outputTypes["fasta"] = tempOutNames;
 101                         outputTypes["qfile"] = tempOutNames;
 102             outputTypes["mismatch"] = tempOutNames;
 103
 104
 105                         //if the user changes the input directory command factory will send this info to us in the output parameter
 106                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 107                         if (inputDir == "not found"){   inputDir = "";          }
 108                         else {
 109                                 string path;
 110                 it = parameters.find("ffastq");
 111                                 //user has given a template file
 112                                 if(it != parameters.end()){
 113                                         path = m->hasPath(it->second);
 114                                         //if the user has not given a path then, add inputdir. else leave path alone.
 115                                         if (path == "") {       parameters["ffastq"] = inputDir + it->second;           }
 116                                 }
 117
 118                 it = parameters.find("rfastq");
 119                                 //user has given a template file
 120                                 if(it != parameters.end()){
 121                                         path = m->hasPath(it->second);
 122                                         //if the user has not given a path then, add inputdir. else leave path alone.
 123                                         if (path == "") {       parameters["rfastq"] = inputDir + it->second;           }
 124                                 }
 125             }
 126
 127             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
 128                         if (ffastqfile == "not open") { ffastqfile = ""; abort = true; }
 129                         else if (ffastqfile == "not found") { ffastqfile = ""; abort=true;  m->mothurOut("The ffastq parameter is required.\n"); }
 130
 131                         rfastqfile = validParameter.validFile(parameters, "rfastq", true);
 132                         if (rfastqfile == "not open") { rfastqfile = ""; abort = true; }
 133                         else if (rfastqfile == "not found") { rfastqfile = ""; abort=true;  m->mothurOut("The rfastq parameter is required.\n"); }
 134
 135             //if the user changes the output directory command factory will send this info to us in the output parameter
 136                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(ffastqfile);             }
 137
 138
 139                         //check for optional parameter and set defaults
 140                         // ...at some point should added some additional type checking...
 141                         string temp;
 142                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 143                         m->mothurConvert(temp, match);
 144
 145                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 146                         m->mothurConvert(temp, misMatch);
 147             if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 148
 149                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 150                         m->mothurConvert(temp, gapOpen);
 151             if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 152
 153                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 154                         m->mothurConvert(temp, gapExtend);
 155             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 156
 157             temp = validParameter.validFile(parameters, "threshold", false);    if (temp == "not found"){       temp = "40";                    }
 158                         m->mothurConvert(temp, threshold);
 159             if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
 160
 161                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 162                         m->setProcessors(temp);
 163                         m->mothurConvert(temp, processors);
 164
 165                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 166                         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"; }
 167         }
 168
 169         }
 170         catch(exception& e) {
 171                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 172                 exit(1);
 173         }
 174 }
 175 //**********************************************************************************************************************
 176 int MakeContigsCommand::execute(){
 177         try {
 178                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 179
 180         //read ffastq and rfastq files creating fasta and qual files.
 181         //this function will create a forward and reverse, fasta and qual files for each processor.
 182         //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual
 183         int numReads = 0;
 184         int start = time(NULL);
 185         longestBase = 1000;
 186         m->mothurOut("Reading fastq data...\n");
 187         vector< vector<string> > files = readFastqFiles(numReads);
 188         m->mothurOut("Done.\n");
 189
 190         if (m->control_pressed) { return 0; }
 191
 192         string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.fasta";
 193         string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.qual";
 194         string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + "contigs.mismatches";
 195         outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 196         outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
 197         outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
 198
 199         m->mothurOut("Making contigs...\n");
 200         createProcesses(files, outFastaFile, outQualFile, outMisMatchFile);
 201         m->mothurOut("Done.\n");
 202
 203         //remove temp fasta and qual files
 204         for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }  }
 205
 206         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 207
 208         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 209
 210         string currentFasta = "";
 211                 itTypes = outputTypes.find("fasta");
 212                 if (itTypes != outputTypes.end()) {
 213                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 214                 }
 215
 216         string currentQual = "";
 217                 itTypes = outputTypes.find("qfile");
 218                 if (itTypes != outputTypes.end()) {
 219                         if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
 220                 }
 221
 222         //output files created by command
 223                 m->mothurOutEndLine();
 224                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 225                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 226                 m->mothurOutEndLine();
 227
 228
 229         return 0;
 230     }
 231         catch(exception& e) {
 232                 m->errorOut(e, "MakeContigsCommand", "execute");
 233                 exit(1);
 234         }
 235 }
 236 //**********************************************************************************************************************
 237 int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputMisMatches) {
 238         try {
 239                 int num = 0;
 240                 vector<int> processIDS;
 241 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 242                 int process = 0;
 243
 244                 //loop through and create all the processes you want
 245                 while (process != processors-1) {
 246                         int pid = fork();
 247
 248                         if (pid > 0) {
 249                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 250                                 process++;
 251                         }else if (pid == 0){
 252                                 num = driver(files[process], outputFasta + toString(getpid()) + ".temp", outputQual + toString(getpid()) + ".temp", outputMisMatches + toString(getpid()) + ".temp");
 253
 254                                 //pass numSeqs to parent
 255                                 ofstream out;
 256                                 string tempFile = outputFasta + toString(getpid()) + ".num.temp";
 257                                 m->openOutputFile(tempFile, out);
 258                                 out << num << endl;
 259                                 out.close();
 260
 261                                 exit(0);
 262                         }else {
 263                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 264                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 265                                 exit(0);
 266                         }
 267                 }
 268
 269                 //do my part
 270                 num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
 271
 272                 //force parent to wait until all the processes are done
 273                 for (int i=0;i<processIDS.size();i++) {
 274                         int temp = processIDS[i];
 275                         wait(&temp);
 276                 }
 277
 278                 for (int i = 0; i < processIDS.size(); i++) {
 279                         ifstream in;
 280                         string tempFile =  outputFasta + toString(processIDS[i]) + ".num.temp";
 281                         m->openInputFile(tempFile, in);
 282                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 283                         in.close(); m->mothurRemove(tempFile);
 284         }
 285     #else
 286
 287         //////////////////////////////////////////////////////////////////////////////////////////////////////
 288                 //Windows version shared memory, so be careful when passing variables through the contigsData struct.
 289                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 290                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 291
 292                 vector<contigsData*> pDataArray;
 293                 DWORD   dwThreadIdArray[processors-1];
 294                 HANDLE  hThreadArray[processors-1];
 295
 296                 //Create processor worker threads.
 297                 for( int i=0; i<processors-1; i++ ){
 298                         string extension = toString(i) + ".temp";
 299
 300                         contigsData* tempcontig = new contigsData(files[i], (outputFasta + extension), (outputQual + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, i);
 301                         pDataArray.push_back(tempcontig);
 302                         processIDS.push_back(i);
 303
 304                         hThreadArray[i] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 305                 }
 306
 307         num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
 308
 309                 //Wait until all threads have terminated.
 310                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 311
 312                 //Close all thread handles and free memory allocations.
 313                 for(int i=0; i < pDataArray.size(); i++){
 314                         num += pDataArray[i]->count;
 315             CloseHandle(hThreadArray[i]);
 316                         delete pDataArray[i];
 317         }
 318
 319     #endif
 320
 321         for (int i = 0; i < processIDS.size(); i++) {
 322                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 323                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 324
 325                         m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
 326                         m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
 327
 328             m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 329                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 330                 }
 331
 332                 return num;
 333         }
 334         catch(exception& e) {
 335                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 336                 exit(1);
 337         }
 338 }
 339 //**********************************************************************************************************************
 340 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputMisMatches){
 341     try {
 342
 343         Alignment* alignment;
 344         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 345                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 346
 347         int num = 0;
 348         string thisffastafile = files[0];
 349         string thisfqualfile = files[1];
 350         string thisrfastafile = files[2];
 351         string thisrqualfile = files[3];
 352
 353         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 354
 355         ifstream inFFasta, inRFasta, inFQual, inRQual;
 356         m->openInputFile(thisffastafile, inFFasta);
 357         m->openInputFile(thisfqualfile, inFQual);
 358         m->openInputFile(thisrfastafile, inRFasta);
 359         m->openInputFile(thisrqualfile, inRQual);
 360
 361         ofstream outFasta, outQual, outMisMatch;
 362         m->openOutputFile(outputFasta, outFasta);
 363         m->openOutputFile(outputQual, outQual);
 364         m->openOutputFile(outputMisMatches, outMisMatch);
 365         outMisMatch << "Name\tLength\tMisMatches\n";
 366
 367         while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
 368
 369             if (m->control_pressed) { break; }
 370
 371             //read seqs and quality info
 372             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 373             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 374             QualityScores fQual(inFQual); m->gobble(inFQual);
 375             QualityScores rQual(inRQual); m->gobble(inRQual);
 376
 377             //flip the reverse reads
 378             rSeq.reverseComplement();
 379             rQual.flipQScores();
 380
 381             //pairwise align
 382             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 383             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 384             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 385             fSeq.setAligned(alignment->getSeqAAln());
 386             rSeq.setAligned(alignment->getSeqBAln());
 387             int length = fSeq.getAligned().length();
 388
 389             //traverse alignments merging into one contiguous seq
 390             string contig = "";
 391             vector<int> contigScores;
 392             int numMismatches = 0;
 393             string seq1 = fSeq.getAligned();
 394             string seq2 = rSeq.getAligned();
 395             vector<int> scores1 = fQual.getQualityScores();
 396             vector<int> scores2 = rQual.getQualityScores();
 397
 398            // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
 399             int overlapStart = fSeq.getStartPos();
 400             int seq2Start = rSeq.getStartPos();
 401             //bigger of the 2 starting positions is the location of the overlapping start
 402             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 403                 overlapStart = seq2Start;
 404                 for (int i = 0; i < overlapStart; i++) {
 405                     contig += seq1[i];
 406                     contigScores.push_back(scores1[ABaseMap[i]]);
 407                 }
 408             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 409                 for (int i = 0; i < overlapStart; i++) {
 410                     contig += seq2[i];
 411                     contigScores.push_back(scores2[BBaseMap[i]]);
 412                 }
 413             }
 414
 415             int seq1End = fSeq.getEndPos();
 416             int seq2End = rSeq.getEndPos();
 417             int overlapEnd = seq1End;
 418             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 419
 420             for (int i = overlapStart; i < overlapEnd; i++) {
 421                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 422                     contig += seq1[i];
 423                     contigScores.push_back(scores1[ABaseMap[i]]);
 424                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
 425                 }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
 426                     if (scores2[BBaseMap[i]] < threshold) { } //
 427                     else {
 428                         contig += seq2[i];
 429                         contigScores.push_back(scores2[BBaseMap[i]]);
 430                     }
 431                 }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
 432                     if (scores1[ABaseMap[i]] < threshold) { } //
 433                     else {
 434                         contig += seq1[i];
 435                         contigScores.push_back(scores1[ABaseMap[i]]);
 436                     }
 437                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 438                     char c = seq1[i];
 439                     contigScores.push_back(scores1[ABaseMap[i]]);
 440                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
 441                     contig += c;
 442                     numMismatches++;
 443                 }else { //should never get here
 444                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
 445                 }
 446             }
 447
 448             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
 449                 for (int i = overlapEnd; i < length; i++) {
 450                     contig += seq2[i];
 451                     contigScores.push_back(scores2[BBaseMap[i]]);
 452                 }
 453             }else { //seq2 ends before seq1 so take from overlap to length from seq1
 454                 for (int i = overlapEnd; i < length; i++) {
 455                     contig += seq1[i];
 456                     contigScores.push_back(scores1[ABaseMap[i]]);
 457                 }
 458
 459             }
 460             //if (num < 5) { cout << overlapStart << '\t' << overlapEnd << endl << seq1 << endl << seq2 << endl<< contig << endl; }
 461             //output
 462             outFasta << ">" << fSeq.getName() << endl << contig << endl;
 463             outQual << ">" << fSeq.getName() << endl;
 464             for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
 465             outQual << endl;
 466             outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
 467
 468             num++;
 469
 470                         //report progress
 471                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 472                 }
 473
 474                 //report progress
 475                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 476
 477         inFFasta.close();
 478         inFQual.close();
 479         inRFasta.close();
 480         inRQual.close();
 481         outFasta.close();
 482         outQual.close();
 483         outMisMatch.close();
 484         delete alignment;
 485
 486         if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta);  m->mothurRemove(outputMisMatches);}
 487
 488         return num;
 489     }
 490         catch(exception& e) {
 491                 m->errorOut(e, "MakeContigsCommand", "driver");
 492                 exit(1);
 493         }
 494 }
 495 //**********************************************************************************************************************
 496 vector< vector<string> > MakeContigsCommand::readFastqFiles(int& count){
 497     try {
 498         vector< vector<string> > files;
 499
 500         //maps processors number to file pointer
 501         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
 502         map<int, vector<ofstream*> >::iterator it;
 503
 504         //create files to write to
 505         for (int i = 0; i < processors; i++) {
 506             vector<ofstream*> temp;
 507             ofstream* outFF = new ofstream;     temp.push_back(outFF);
 508             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
 509             ofstream* outRF = new ofstream;     temp.push_back(outRF);
 510             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
 511             tempfiles[i] = temp;
 512
 513             vector<string> names;
 514             string ffastafilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "ffasta.temp";
 515             string rfastafilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rfasta.temp";
 516             string fqualfilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "fqual.temp";
 517             string rqualfilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rqual.temp";
 518             names.push_back(ffastafilename); names.push_back(fqualfilename);
 519             names.push_back(rfastafilename); names.push_back(rqualfilename);
 520             files.push_back(names);
 521
 522             m->openOutputFile(ffastafilename, *outFF);
 523             m->openOutputFile(rfastafilename, *outRF);
 524             m->openOutputFile(fqualfilename, *outFQ);
 525             m->openOutputFile(rqualfilename, *outRQ);
 526         }
 527
 528         if (m->control_pressed) {
 529             //close files, delete ofstreams
 530             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]; } }
 531             //remove files
 532             for (int i = 0; i < files.size(); i++) {
 533                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
 534             }
 535         }
 536
 537         ifstream inForward;
 538         m->openInputFile(ffastqfile, inForward);
 539
 540         ifstream inReverse;
 541         m->openInputFile(rfastqfile, inReverse);
 542
 543         count = 0;
 544         while ((!inForward.eof()) && (!inReverse.eof())) {
 545
 546             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; }
 547
 548             //get a read from forward and reverse fastq files
 549             fastqRead fread = readFastq(inForward);
 550             fastqRead rread = readFastq(inReverse);
 551             checkReads(fread, rread);
 552
 553             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; }
 554
 555             //if the reads are okay write to output files
 556             int process = count % processors;
 557
 558             *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
 559             *(tempfiles[process][1]) << ">" << fread.name << endl;
 560             for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
 561             *(tempfiles[process][1]) << endl;
 562             *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
 563             *(tempfiles[process][3]) << ">" << rread.name << endl;
 564             for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
 565             *(tempfiles[process][3]) << endl;
 566
 567             count++;
 568
 569             //report progress
 570                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 571
 572                 }
 573                 //report progress
 574                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 575
 576
 577
 578         //close files, delete ofstreams
 579         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]; } }
 580         inForward.close();
 581         inReverse.close();
 582
 583         //adjust for really large processors or really small files
 584         if (count < processors) {
 585             for (int i = count; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 586             files.resize(count);
 587             processors = count;
 588         }
 589
 590         return files;
 591     }
 592     catch(exception& e) {
 593         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
 594         exit(1);
 595     }
 596 }
 597 //**********************************************************************************************************************
 598 fastqRead MakeContigsCommand::readFastq(ifstream& in){
 599     try {
 600         fastqRead read;
 601
 602         //read sequence name
 603         string name = m->getline(in); m->gobble(in);
 604         if (name == "") {  m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 605         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; }
 606         else { name = name.substr(1); }
 607
 608         //read sequence
 609         string sequence = m->getline(in); m->gobble(in);
 610         if (sequence == "") {  m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 611
 612         //read sequence name
 613         string name2 = m->getline(in); m->gobble(in);
 614         if (name2 == "") {  m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 615         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; }
 616         else { name2 = name2.substr(1);  }
 617
 618         //read quality scores
 619         string quality = m->getline(in); m->gobble(in);
 620         if (quality == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 621
 622         //sanity check sequence length and number of quality scores match
 623         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; } }
 624         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; }
 625
 626         vector<int> qualScores;
 627                 int controlChar = int('@');
 628                 for (int i = 0; i < quality.length(); i++) {
 629                         int temp = int(quality[i]);
 630                         temp -= controlChar;
 631
 632                         qualScores.push_back(temp);
 633                 }
 634
 635         read.name = name;
 636         read.sequence = sequence;
 637         read.scores = qualScores;
 638
 639         return read;
 640     }
 641     catch(exception& e) {
 642         m->errorOut(e, "MakeContigsCommand", "readFastq");
 643         exit(1);
 644     }
 645 }
 646 //**********************************************************************************************************************
 647 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){
 648     try {
 649         bool good = true;
 650
 651         //fix names
 652         if ((forward.name.length() > 2) && (reverse.name.length() > 2)) {
 653             forward.name = forward.name.substr(0, forward.name.length()-2);
 654             reverse.name = reverse.name.substr(0, reverse.name.length()-2);
 655         }else { good = false; m->control_pressed = true; }
 656
 657         //do names match
 658         if (forward.name != reverse.name) {
 659             m->mothurOut("[ERROR]: read " + forward.name + " from " + ffastqfile + ", but read " + reverse.name + " from " + rfastqfile + ".\n");
 660             good = false; m->control_pressed = true;
 661         }
 662
 663         //do sequence lengths match
 664         if (forward.sequence.length() != reverse.sequence.length()) {
 665             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");
 666             good = false; m->control_pressed = true;
 667         }
 668
 669         //do number of qual scores match
 670         if (forward.scores.size() != reverse.scores.size()) {
 671             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");
 672             good = false; m->control_pressed = true;
 673         }
 674
 675         return good;
 676     }
 677     catch(exception& e) {
 678         m->errorOut(e, "MakeContigsCommand", "readFastq");
 679         exit(1);
 680     }
 681 }
 682 //**********************************************************************************************************************
 683
 684
 685
 686