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 parameters are required.\n";
  42                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh and needleman. 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 string MakeContigsCommand::getOutputFileNameTag(string type, string inputName=""){
  61         try {
  62         string outputFileName = "";
  63                 map<string, vector<string> >::iterator it;
  64
  65         //is this a type this command creates
  66         it = outputTypes.find(type);
  67         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  68         else {
  69             if (type == "fasta")             {   outputFileName =  "contigs.fasta";         }
  70             else if (type == "qfile")        {   outputFileName =  "contigs.qual";          }
  71             else if (type == "mismatch")     {   outputFileName =  "contigs.mismatch";      }
  72             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  73         }
  74         return outputFileName;
  75         }
  76         catch(exception& e) {
  77                 m->errorOut(e, "MakeContigsCommand", "getOutputFileNameTag");
  78                 exit(1);
  79         }
  80 }
  81 //**********************************************************************************************************************
  82 MakeContigsCommand::MakeContigsCommand(){
  83         try {
  84                 abort = true; calledHelp = true;
  85                 setParameters();
  86                 vector<string> tempOutNames;
  87                 outputTypes["fasta"] = tempOutNames;
  88                 outputTypes["qfile"] = tempOutNames;
  89         outputTypes["mismatch"] = tempOutNames;
  90         }
  91         catch(exception& e) {
  92                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
  93                 exit(1);
  94         }
  95 }
  96 //**********************************************************************************************************************
  97 MakeContigsCommand::MakeContigsCommand(string option)  {
  98         try {
  99                 abort = false; calledHelp = false;
 100
 101                 //allow user to run help
 102                 if(option == "help") { help(); abort = true; calledHelp = true; }
 103                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 104
 105                 else {
 106                         vector<string> myArray = setParameters();
 107
 108                         OptionParser parser(option);
 109                         map<string, string> parameters = parser.getParameters();
 110
 111                         ValidParameters validParameter("pairwise.seqs");
 112                         map<string, string>::iterator it;
 113
 114                         //check to make sure all parameters are valid for command
 115                         for (it = parameters.begin(); it != parameters.end(); it++) {
 116                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 117                         }
 118
 119                         //initialize outputTypes
 120                         vector<string> tempOutNames;
 121                         outputTypes["fasta"] = tempOutNames;
 122                         outputTypes["qfile"] = tempOutNames;
 123             outputTypes["mismatch"] = tempOutNames;
 124
 125
 126                         //if the user changes the input directory command factory will send this info to us in the output parameter
 127                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 128                         if (inputDir == "not found"){   inputDir = "";          }
 129                         else {
 130                                 string path;
 131                 it = parameters.find("ffastq");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["ffastq"] = inputDir + it->second;           }
 137                                 }
 138
 139                 it = parameters.find("rfastq");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["rfastq"] = inputDir + it->second;           }
 145                                 }
 146             }
 147
 148             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
 149                         if (ffastqfile == "not open") { ffastqfile = ""; abort = true; }
 150                         else if (ffastqfile == "not found") { ffastqfile = ""; abort=true;  m->mothurOut("The ffastq parameter is required.\n"); }
 151
 152                         rfastqfile = validParameter.validFile(parameters, "rfastq", true);
 153                         if (rfastqfile == "not open") { rfastqfile = ""; abort = true; }
 154                         else if (rfastqfile == "not found") { rfastqfile = ""; abort=true;  m->mothurOut("The rfastq parameter is required.\n"); }
 155
 156             //if the user changes the output directory command factory will send this info to us in the output parameter
 157                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(ffastqfile);             }
 158
 159
 160                         //check for optional parameter and set defaults
 161                         // ...at some point should added some additional type checking...
 162                         string temp;
 163                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 164                         m->mothurConvert(temp, match);
 165
 166                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 167                         m->mothurConvert(temp, misMatch);
 168             if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 169
 170                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 171                         m->mothurConvert(temp, gapOpen);
 172             if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 173
 174                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 175                         m->mothurConvert(temp, gapExtend);
 176             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 177
 178             temp = validParameter.validFile(parameters, "threshold", false);    if (temp == "not found"){       temp = "40";                    }
 179                         m->mothurConvert(temp, threshold);
 180             if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
 181
 182                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 183                         m->setProcessors(temp);
 184                         m->mothurConvert(temp, processors);
 185
 186                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 187                         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"; }
 188         }
 189
 190         }
 191         catch(exception& e) {
 192                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 193                 exit(1);
 194         }
 195 }
 196 //**********************************************************************************************************************
 197 int MakeContigsCommand::execute(){
 198         try {
 199                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 200
 201         //read ffastq and rfastq files creating fasta and qual files.
 202         //this function will create a forward and reverse, fasta and qual files for each processor.
 203         //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual
 204         int numReads = 0;
 205         int start = time(NULL);
 206         longestBase = 1000;
 207         m->mothurOut("Reading fastq data...\n");
 208         vector< vector<string> > files = readFastqFiles(numReads);
 209         m->mothurOut("Done.\n");
 210
 211         if (m->control_pressed) { return 0; }
 212
 213         string outFastaFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("fasta");
 214         string outQualFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("qfile");
 215         string outMisMatchFile = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + getOutputFileNameTag("mismatch");
 216         outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 217         outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
 218         outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
 219
 220         m->mothurOut("Making contigs...\n");
 221         createProcesses(files, outFastaFile, outQualFile, outMisMatchFile);
 222         m->mothurOut("Done.\n");
 223
 224         //remove temp fasta and qual files
 225         for (int i = 0; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }  }
 226
 227         if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]); }  return 0; }
 228
 229         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 230
 231         string currentFasta = "";
 232                 itTypes = outputTypes.find("fasta");
 233                 if (itTypes != outputTypes.end()) {
 234                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 235                 }
 236
 237         string currentQual = "";
 238                 itTypes = outputTypes.find("qfile");
 239                 if (itTypes != outputTypes.end()) {
 240                         if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
 241                 }
 242
 243         //output files created by command
 244                 m->mothurOutEndLine();
 245                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 246                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 247                 m->mothurOutEndLine();
 248
 249
 250         return 0;
 251     }
 252         catch(exception& e) {
 253                 m->errorOut(e, "MakeContigsCommand", "execute");
 254                 exit(1);
 255         }
 256 }
 257 //**********************************************************************************************************************
 258 int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputMisMatches) {
 259         try {
 260                 int num = 0;
 261                 vector<int> processIDS;
 262 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 263                 int process = 0;
 264
 265                 //loop through and create all the processes you want
 266                 while (process != processors-1) {
 267                         int pid = fork();
 268
 269                         if (pid > 0) {
 270                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 271                                 process++;
 272                         }else if (pid == 0){
 273                                 num = driver(files[process], outputFasta + toString(getpid()) + ".temp", outputQual + toString(getpid()) + ".temp", outputMisMatches + toString(getpid()) + ".temp");
 274
 275                                 //pass numSeqs to parent
 276                                 ofstream out;
 277                                 string tempFile = outputFasta + toString(getpid()) + ".num.temp";
 278                                 m->openOutputFile(tempFile, out);
 279                                 out << num << endl;
 280                                 out.close();
 281
 282                                 exit(0);
 283                         }else {
 284                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 285                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 286                                 exit(0);
 287                         }
 288                 }
 289
 290                 //do my part
 291                 num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
 292
 293                 //force parent to wait until all the processes are done
 294                 for (int i=0;i<processIDS.size();i++) {
 295                         int temp = processIDS[i];
 296                         wait(&temp);
 297                 }
 298
 299                 for (int i = 0; i < processIDS.size(); i++) {
 300                         ifstream in;
 301                         string tempFile =  outputFasta + toString(processIDS[i]) + ".num.temp";
 302                         m->openInputFile(tempFile, in);
 303                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 304                         in.close(); m->mothurRemove(tempFile);
 305         }
 306     #else
 307
 308         //////////////////////////////////////////////////////////////////////////////////////////////////////
 309                 //Windows version shared memory, so be careful when passing variables through the contigsData struct.
 310                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 311                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 312
 313                 vector<contigsData*> pDataArray;
 314                 DWORD   dwThreadIdArray[processors-1];
 315                 HANDLE  hThreadArray[processors-1];
 316
 317                 //Create processor worker threads.
 318                 for( int i=0; i<processors-1; i++ ){
 319                         string extension = toString(i) + ".temp";
 320
 321                         contigsData* tempcontig = new contigsData(files[i], (outputFasta + extension), (outputQual + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, i);
 322                         pDataArray.push_back(tempcontig);
 323                         processIDS.push_back(i);
 324
 325                         hThreadArray[i] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 326                 }
 327
 328         num = driver(files[processors-1], outputFasta, outputQual, outputMisMatches);
 329
 330                 //Wait until all threads have terminated.
 331                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 332
 333                 //Close all thread handles and free memory allocations.
 334                 for(int i=0; i < pDataArray.size(); i++){
 335                         num += pDataArray[i]->count;
 336             CloseHandle(hThreadArray[i]);
 337                         delete pDataArray[i];
 338         }
 339
 340     #endif
 341
 342         for (int i = 0; i < processIDS.size(); i++) {
 343                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 344                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 345
 346                         m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
 347                         m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
 348
 349             m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 350                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 351                 }
 352
 353                 return num;
 354         }
 355         catch(exception& e) {
 356                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 357                 exit(1);
 358         }
 359 }
 360 //**********************************************************************************************************************
 361 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputMisMatches){
 362     try {
 363
 364         Alignment* alignment;
 365         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 366                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 367
 368         int num = 0;
 369         string thisffastafile = files[0];
 370         string thisfqualfile = files[1];
 371         string thisrfastafile = files[2];
 372         string thisrqualfile = files[3];
 373
 374         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 375
 376         ifstream inFFasta, inRFasta, inFQual, inRQual;
 377         m->openInputFile(thisffastafile, inFFasta);
 378         m->openInputFile(thisfqualfile, inFQual);
 379         m->openInputFile(thisrfastafile, inRFasta);
 380         m->openInputFile(thisrqualfile, inRQual);
 381
 382         ofstream outFasta, outQual, outMisMatch;
 383         m->openOutputFile(outputFasta, outFasta);
 384         m->openOutputFile(outputQual, outQual);
 385         m->openOutputFile(outputMisMatches, outMisMatch);
 386         outMisMatch << "Name\tLength\tMisMatches\n";
 387
 388         while ((!inFQual.eof()) && (!inFFasta.eof()) && (!inRFasta.eof()) && (!inRQual.eof())) {
 389
 390             if (m->control_pressed) { break; }
 391
 392             //read seqs and quality info
 393             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 394             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 395             QualityScores fQual(inFQual); m->gobble(inFQual);
 396             QualityScores rQual(inRQual); m->gobble(inRQual);
 397
 398             //flip the reverse reads
 399             rSeq.reverseComplement();
 400             rQual.flipQScores();
 401
 402             //pairwise align
 403             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 404             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 405             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 406             fSeq.setAligned(alignment->getSeqAAln());
 407             rSeq.setAligned(alignment->getSeqBAln());
 408             int length = fSeq.getAligned().length();
 409
 410             //traverse alignments merging into one contiguous seq
 411             string contig = "";
 412             vector<int> contigScores;
 413             int numMismatches = 0;
 414             string seq1 = fSeq.getAligned();
 415             string seq2 = rSeq.getAligned();
 416             vector<int> scores1 = fQual.getQualityScores();
 417             vector<int> scores2 = rQual.getQualityScores();
 418
 419            // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
 420             int overlapStart = fSeq.getStartPos();
 421             int seq2Start = rSeq.getStartPos();
 422             //bigger of the 2 starting positions is the location of the overlapping start
 423             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 424                 overlapStart = seq2Start;
 425                 for (int i = 0; i < overlapStart; i++) {
 426                     contig += seq1[i];
 427                     contigScores.push_back(scores1[ABaseMap[i]]);
 428                 }
 429             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 430                 for (int i = 0; i < overlapStart; i++) {
 431                     contig += seq2[i];
 432                     contigScores.push_back(scores2[BBaseMap[i]]);
 433                 }
 434             }
 435
 436             int seq1End = fSeq.getEndPos();
 437             int seq2End = rSeq.getEndPos();
 438             int overlapEnd = seq1End;
 439             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 440
 441             for (int i = overlapStart; i < overlapEnd; i++) {
 442                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 443                     contig += seq1[i];
 444                     contigScores.push_back(scores1[ABaseMap[i]]);
 445                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
 446                 }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
 447                     if (scores2[BBaseMap[i]] < threshold) { } //
 448                     else {
 449                         contig += seq2[i];
 450                         contigScores.push_back(scores2[BBaseMap[i]]);
 451                     }
 452                 }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
 453                     if (scores1[ABaseMap[i]] < threshold) { } //
 454                     else {
 455                         contig += seq1[i];
 456                         contigScores.push_back(scores1[ABaseMap[i]]);
 457                     }
 458                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 459                     char c = seq1[i];
 460                     contigScores.push_back(scores1[ABaseMap[i]]);
 461                     if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
 462                     contig += c;
 463                     numMismatches++;
 464                 }else { //should never get here
 465                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
 466                 }
 467             }
 468
 469             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
 470                 for (int i = overlapEnd; i < length; i++) {
 471                     contig += seq2[i];
 472                     contigScores.push_back(scores2[BBaseMap[i]]);
 473                 }
 474             }else { //seq2 ends before seq1 so take from overlap to length from seq1
 475                 for (int i = overlapEnd; i < length; i++) {
 476                     contig += seq1[i];
 477                     contigScores.push_back(scores1[ABaseMap[i]]);
 478                 }
 479
 480             }
 481             //if (num < 5) { cout << overlapStart << '\t' << overlapEnd << endl << seq1 << endl << seq2 << endl<< contig << endl; }
 482             //output
 483             outFasta << ">" << fSeq.getName() << endl << contig << endl;
 484             outQual << ">" << fSeq.getName() << endl;
 485             for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
 486             outQual << endl;
 487             outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
 488
 489             num++;
 490
 491                         //report progress
 492                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 493                 }
 494
 495                 //report progress
 496                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
 497
 498         inFFasta.close();
 499         inFQual.close();
 500         inRFasta.close();
 501         inRQual.close();
 502         outFasta.close();
 503         outQual.close();
 504         outMisMatch.close();
 505         delete alignment;
 506
 507         if (m->control_pressed) { m->mothurRemove(outputQual); m->mothurRemove(outputFasta);  m->mothurRemove(outputMisMatches);}
 508
 509         return num;
 510     }
 511         catch(exception& e) {
 512                 m->errorOut(e, "MakeContigsCommand", "driver");
 513                 exit(1);
 514         }
 515 }
 516 //**********************************************************************************************************************
 517 vector< vector<string> > MakeContigsCommand::readFastqFiles(int& count){
 518     try {
 519         vector< vector<string> > files;
 520
 521         //maps processors number to file pointer
 522         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
 523         map<int, vector<ofstream*> >::iterator it;
 524
 525         //create files to write to
 526         for (int i = 0; i < processors; i++) {
 527             vector<ofstream*> temp;
 528             ofstream* outFF = new ofstream;     temp.push_back(outFF);
 529             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
 530             ofstream* outRF = new ofstream;     temp.push_back(outRF);
 531             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
 532             tempfiles[i] = temp;
 533
 534             vector<string> names;
 535             string ffastafilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "ffasta.temp";
 536             string rfastafilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rfasta.temp";
 537             string fqualfilename = outputDir + m->getRootName(m->getSimpleName(ffastqfile)) + toString(i) + "fqual.temp";
 538             string rqualfilename = outputDir + m->getRootName(m->getSimpleName(rfastqfile)) + toString(i) + "rqual.temp";
 539             names.push_back(ffastafilename); names.push_back(fqualfilename);
 540             names.push_back(rfastafilename); names.push_back(rqualfilename);
 541             files.push_back(names);
 542
 543             m->openOutputFile(ffastafilename, *outFF);
 544             m->openOutputFile(rfastafilename, *outRF);
 545             m->openOutputFile(fqualfilename, *outFQ);
 546             m->openOutputFile(rqualfilename, *outRQ);
 547         }
 548
 549         if (m->control_pressed) {
 550             //close files, delete ofstreams
 551             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]; } }
 552             //remove files
 553             for (int i = 0; i < files.size(); i++) {
 554                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
 555             }
 556         }
 557
 558         ifstream inForward;
 559         m->openInputFile(ffastqfile, inForward);
 560
 561         ifstream inReverse;
 562         m->openInputFile(rfastqfile, inReverse);
 563
 564         count = 0;
 565         while ((!inForward.eof()) && (!inReverse.eof())) {
 566
 567             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; }
 568
 569             //get a read from forward and reverse fastq files
 570             fastqRead fread = readFastq(inForward);
 571             fastqRead rread = readFastq(inReverse);
 572             checkReads(fread, rread);
 573
 574             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; }
 575
 576             //if the reads are okay write to output files
 577             int process = count % processors;
 578
 579             *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
 580             *(tempfiles[process][1]) << ">" << fread.name << endl;
 581             for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
 582             *(tempfiles[process][1]) << endl;
 583             *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
 584             *(tempfiles[process][3]) << ">" << rread.name << endl;
 585             for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
 586             *(tempfiles[process][3]) << endl;
 587
 588             count++;
 589
 590             //report progress
 591                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 592
 593                 }
 594                 //report progress
 595                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 596
 597
 598
 599         //close files, delete ofstreams
 600         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]; } }
 601         inForward.close();
 602         inReverse.close();
 603
 604         //adjust for really large processors or really small files
 605         if (count < processors) {
 606             for (int i = count; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 607             files.resize(count);
 608             processors = count;
 609         }
 610
 611         return files;
 612     }
 613     catch(exception& e) {
 614         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
 615         exit(1);
 616     }
 617 }
 618 //**********************************************************************************************************************
 619 fastqRead MakeContigsCommand::readFastq(ifstream& in){
 620     try {
 621         fastqRead read;
 622
 623         //read sequence name
 624         string name = m->getline(in); m->gobble(in);
 625         if (name == "") {  m->mothurOut("[ERROR]: Blank fasta name."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 626         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; }
 627         else { name = name.substr(1); }
 628
 629         //read sequence
 630         string sequence = m->getline(in); m->gobble(in);
 631         if (sequence == "") {  m->mothurOut("[ERROR]: missing sequence for " + name); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 632
 633         //read sequence name
 634         string name2 = m->getline(in); m->gobble(in);
 635         if (name2 == "") {  m->mothurOut("[ERROR]: Blank quality name."); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 636         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; }
 637         else { name2 = name2.substr(1);  }
 638
 639         //read quality scores
 640         string quality = m->getline(in); m->gobble(in);
 641         if (quality == "") {  m->mothurOut("[ERROR]: missing quality for " + name2); m->mothurOutEndLine(); m->control_pressed = true; return read; }
 642
 643         //sanity check sequence length and number of quality scores match
 644         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; } }
 645         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; }
 646
 647         vector<int> qualScores;
 648                 int controlChar = int('@');
 649                 for (int i = 0; i < quality.length(); i++) {
 650                         int temp = int(quality[i]);
 651                         temp -= controlChar;
 652
 653                         qualScores.push_back(temp);
 654                 }
 655
 656         read.name = name;
 657         read.sequence = sequence;
 658         read.scores = qualScores;
 659
 660         return read;
 661     }
 662     catch(exception& e) {
 663         m->errorOut(e, "MakeContigsCommand", "readFastq");
 664         exit(1);
 665     }
 666 }
 667 //**********************************************************************************************************************
 668 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse){
 669     try {
 670         bool good = true;
 671
 672         //fix names
 673         if ((forward.name.length() > 2) && (reverse.name.length() > 2)) {
 674             forward.name = forward.name.substr(0, forward.name.length()-2);
 675             reverse.name = reverse.name.substr(0, reverse.name.length()-2);
 676         }else { good = false; m->control_pressed = true; }
 677
 678         //do names match
 679         if (forward.name != reverse.name) {
 680             m->mothurOut("[ERROR]: read " + forward.name + " from " + ffastqfile + ", but read " + reverse.name + " from " + rfastqfile + ".\n");
 681             good = false; m->control_pressed = true;
 682         }
 683
 684         //do sequence lengths match
 685         if (forward.sequence.length() != reverse.sequence.length()) {
 686             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");
 687             good = false; m->control_pressed = true;
 688         }
 689
 690         //do number of qual scores match
 691         if (forward.scores.size() != reverse.scores.size()) {
 692             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");
 693             good = false; m->control_pressed = true;
 694         }
 695
 696         return good;
 697     }
 698     catch(exception& e) {
 699         m->errorOut(e, "MakeContigsCommand", "readFastq");
 700         exit(1);
 701     }
 702 }
 703 //**********************************************************************************************************************
 704
 705
 706
 707