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 pfastq("ffastq", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "fastqGroup","fasta-qfile",false,false,true); parameters.push_back(pfastq);
  15         CommandParameter prfastq("rfastq", "InputTypes", "", "", "none", "none", "fastqGroup","fasta-qfile",false,false,true); parameters.push_back(prfastq);
  16         CommandParameter pfasta("ffasta", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "fastaGroup","fasta",false,false,true); parameters.push_back(pfasta);
  17         CommandParameter prfasta("rfasta", "InputTypes", "", "", "none", "none", "none","fastaGroup",false,false,true); parameters.push_back(prfasta);
  18         CommandParameter pfqual("fqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(pfqual);
  19         CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","qfile",false,false,true); parameters.push_back(prqual);
  20         CommandParameter pfile("file", "InputTypes", "", "", "FastaFastqFile", "FastaFastqFile", "none","fasta-qfile",false,false,true); parameters.push_back(pfile);
  21         CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","group",false,false,true); parameters.push_back(poligos);
  22                 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
  23                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
  24 //        CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
  25 //              CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
  26         CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
  27
  28         CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
  29         CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
  30                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
  31                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
  32                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
  33                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
  34         CommandParameter pthreshold("threshold", "Number", "", "40", "", "", "","",false,false); parameters.push_back(pthreshold);
  35                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  36                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  37                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  38
  39                 vector<string> myArray;
  40                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "MakeContigsCommand", "setParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 string MakeContigsCommand::getHelpString(){
  50         try {
  51                 string helpString = "";
  52                 helpString += "The make.contigs command reads a file, forward fastq file and a reverse fastq file or forward fasta and reverse fasta files and outputs new fasta.  It will also provide new quality files if the fastq or file parameter is used.\n";
  53         helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
  54                 helpString += "The make.contigs command parameters are ffastq, rfastq, oligos, tdiffs, bdiffs, ldiffs, sdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, allfiles and processors.\n";
  55                 helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";
  56         helpString += "The file parameter is 2 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column.  Mothur will process each pair and create a combined fasta and qual file with all the sequences.\n";
  57         helpString += "The ffastq and rfastq parameters are used to provide a forward fastq and reverse fastq file to process.  If you provide one, you must provide the other.\n";
  58         helpString += "The ffasta and rfasta parameters are used to provide a forward fasta and reverse fasta file to process.  If you provide one, you must provide the other.\n";
  59         helpString += "The fqfile and rqfile parameters are used to provide a forward quality and reverse quality files to process with the ffasta and rfasta parameters.  If you provide one, you must provide the other.\n";
  60                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh and needleman. The default is needleman.\n";
  61         helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
  62                 helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
  63                 helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
  64         helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
  65                 helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
  66                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  67                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  68                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  69                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  70         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";
  71         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  72         helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
  73         helpString += "The make.contigs command should be in the following format: \n";
  74                 helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
  75                 helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
  76                 return helpString;
  77         }
  78         catch(exception& e) {
  79                 m->errorOut(e, "MakeContigsCommand", "getHelpString");
  80                 exit(1);
  81         }
  82 }
  83 //**********************************************************************************************************************
  84 string MakeContigsCommand::getOutputPattern(string type) {
  85     try {
  86         string pattern = "";
  87
  88         if (type == "fasta") {  pattern = "[filename],[tag],contigs.fasta"; }
  89         else if (type == "qfile") {  pattern = "[filename],[tag],contigs.qual"; }
  90         else if (type == "group") {  pattern = "[filename],[tag],contigs.groups"; }
  91         else if (type == "mismatch") {  pattern = "[filename],[tag],contigs.mismatch"; }
  92         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  93
  94         return pattern;
  95     }
  96     catch(exception& e) {
  97         m->errorOut(e, "MakeContigsCommand", "getOutputPattern");
  98         exit(1);
  99     }
 100 }
 101 //**********************************************************************************************************************
 102 MakeContigsCommand::MakeContigsCommand(){
 103         try {
 104                 abort = true; calledHelp = true;
 105                 setParameters();
 106                 vector<string> tempOutNames;
 107                 outputTypes["fasta"] = tempOutNames;
 108                 outputTypes["qfile"] = tempOutNames;
 109         outputTypes["group"] = tempOutNames;
 110         outputTypes["mismatch"] = tempOutNames;
 111         }
 112         catch(exception& e) {
 113                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 114                 exit(1);
 115         }
 116 }
 117 //**********************************************************************************************************************
 118 MakeContigsCommand::MakeContigsCommand(string option)  {
 119         try {
 120                 abort = false; calledHelp = false;
 121
 122                 //allow user to run help
 123                 if(option == "help") { help(); abort = true; calledHelp = true; }
 124                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 125
 126                 else {
 127                         vector<string> myArray = setParameters();
 128
 129                         OptionParser parser(option);
 130                         map<string, string> parameters = parser.getParameters();
 131
 132                         ValidParameters validParameter("pairwise.seqs");
 133                         map<string, string>::iterator it;
 134
 135                         //check to make sure all parameters are valid for command
 136                         for (it = parameters.begin(); it != parameters.end(); it++) {
 137                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 138                         }
 139
 140                         //initialize outputTypes
 141                         vector<string> tempOutNames;
 142                         outputTypes["fasta"] = tempOutNames;
 143                         outputTypes["qfile"] = tempOutNames;
 144             outputTypes["mismatch"] = tempOutNames;
 145             outputTypes["group"] = tempOutNames;
 146
 147
 148                         //if the user changes the input directory command factory will send this info to us in the output parameter
 149                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 150                         if (inputDir == "not found"){   inputDir = "";          }
 151                         else {
 152                                 string path;
 153                 it = parameters.find("ffastq");
 154                                 //user has given a template file
 155                                 if(it != parameters.end()){
 156                                         path = m->hasPath(it->second);
 157                                         //if the user has not given a path then, add inputdir. else leave path alone.
 158                                         if (path == "") {       parameters["ffastq"] = inputDir + it->second;           }
 159                                 }
 160
 161                 it = parameters.find("rfastq");
 162                                 //user has given a template file
 163                                 if(it != parameters.end()){
 164                                         path = m->hasPath(it->second);
 165                                         //if the user has not given a path then, add inputdir. else leave path alone.
 166                                         if (path == "") {       parameters["rfastq"] = inputDir + it->second;           }
 167                                 }
 168
 169                 it = parameters.find("ffasta");
 170                                 //user has given a template file
 171                                 if(it != parameters.end()){
 172                                         path = m->hasPath(it->second);
 173                                         //if the user has not given a path then, add inputdir. else leave path alone.
 174                                         if (path == "") {       parameters["ffasta"] = inputDir + it->second;           }
 175                                 }
 176
 177                 it = parameters.find("rfasta");
 178                                 //user has given a template file
 179                                 if(it != parameters.end()){
 180                                         path = m->hasPath(it->second);
 181                                         //if the user has not given a path then, add inputdir. else leave path alone.
 182                                         if (path == "") {       parameters["rfasta"] = inputDir + it->second;           }
 183                                 }
 184
 185                 it = parameters.find("fqfile");
 186                                 //user has given a template file
 187                                 if(it != parameters.end()){
 188                                         path = m->hasPath(it->second);
 189                                         //if the user has not given a path then, add inputdir. else leave path alone.
 190                                         if (path == "") {       parameters["fqfile"] = inputDir + it->second;           }
 191                                 }
 192
 193                 it = parameters.find("rqfile");
 194                                 //user has given a template file
 195                                 if(it != parameters.end()){
 196                                         path = m->hasPath(it->second);
 197                                         //if the user has not given a path then, add inputdir. else leave path alone.
 198                                         if (path == "") {       parameters["rqfile"] = inputDir + it->second;           }
 199                                 }
 200
 201                 it = parameters.find("file");
 202                                 //user has given a template file
 203                                 if(it != parameters.end()){
 204                                         path = m->hasPath(it->second);
 205                                         //if the user has not given a path then, add inputdir. else leave path alone.
 206                                         if (path == "") {       parameters["file"] = inputDir + it->second;             }
 207                                 }
 208
 209                 it = parameters.find("oligos");
 210                                 //user has given a template file
 211                                 if(it != parameters.end()){
 212                                         path = m->hasPath(it->second);
 213                                         //if the user has not given a path then, add inputdir. else leave path alone.
 214                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 215                                 }
 216             }
 217
 218             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
 219                         if (ffastqfile == "not open") {  abort = true; }
 220                         else if (ffastqfile == "not found") { ffastqfile = ""; }
 221
 222                         rfastqfile = validParameter.validFile(parameters, "rfastq", true);
 223                         if (rfastqfile == "not open") {  abort = true; }
 224                         else if (rfastqfile == "not found") { rfastqfile = "";  }
 225
 226             ffastafile = validParameter.validFile(parameters, "ffasta", true);
 227                         if (ffastafile == "not open") {  abort = true; }
 228                         else if (ffastafile == "not found") { ffastafile = ""; }
 229
 230                         rfastafile = validParameter.validFile(parameters, "rfasta", true);
 231                         if (rfastafile == "not open") {  abort = true; }
 232                         else if (rfastafile == "not found") { rfastafile = "";  }
 233
 234             fqualfile = validParameter.validFile(parameters, "fqfile", true);
 235                         if (fqualfile == "not open") {  abort = true; }
 236                         else if (fqualfile == "not found") { fqualfile = ""; }
 237
 238                         rqualfile = validParameter.validFile(parameters, "rqfile", true);
 239                         if (rqualfile == "not open") {  abort = true; }
 240                         else if (rqualfile == "not found") { rqualfile = "";  }
 241
 242             file = validParameter.validFile(parameters, "file", true);
 243                         if (file == "not open") {  abort = true; }
 244                         else if (file == "not found") { file = "";  }
 245
 246             //provide at least
 247             if ((file == "") && (ffastafile == "") && (ffastqfile == "")) { abort = true; m->mothurOut("[ERROR]: The file, ffastq and rfastq or ffasta and rfasta parameters are required.\n"); }
 248             if ((file != "") && ((ffastafile != "") || (ffastqfile != ""))) { abort = true; m->mothurOut("[ERROR]: The file, ffastq and rfastq or ffasta and rfasta parameters are required.\n"); }
 249             if ((ffastqfile != "") && (rfastqfile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the ffastq, you must provide a rfastq file.\n"); }
 250             if ((ffastqfile == "") && (rfastqfile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rfastq, you must provide a ffastq file.\n"); }
 251             if ((ffastafile != "") && (rfastafile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the ffasta, you must provide a rfasta file.\n"); }
 252             if ((ffastafile == "") && (rfastafile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rfasta, you must provide a ffasta file.\n"); }
 253             if ((fqualfile != "") && (rqualfile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the fqfile, you must provide a rqfile file.\n"); }
 254             if ((fqualfile == "") && (rqualfile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rqfile, you must provide a fqfile file.\n"); }
 255             if (((fqualfile != "") || (rqualfile != "")) && ((ffastafile == "") || (rfastafile == ""))) {
 256                 abort = true; m->mothurOut("[ERROR]: If you provide use the rqfile or fqfile file, you must provide the ffasta and rfasta parameters.\n");
 257             }
 258
 259             oligosfile = validParameter.validFile(parameters, "oligos", true);
 260                         if (oligosfile == "not found")      {   oligosfile = "";        }
 261                         else if(oligosfile == "not open")   {   abort = true;       }
 262                         else {   m->setOligosFile(oligosfile);          }
 263
 264             //if the user changes the output directory command factory will send this info to us in the output parameter
 265                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 266                  outputDir = "";
 267             }
 268
 269
 270                         //check for optional parameter and set defaults
 271                         // ...at some point should added some additional type checking...
 272                         string temp;
 273                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 274                         m->mothurConvert(temp, match);
 275
 276                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 277                         m->mothurConvert(temp, misMatch);
 278             if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 279
 280                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 281                         m->mothurConvert(temp, gapOpen);
 282             if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 283
 284                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 285                         m->mothurConvert(temp, gapExtend);
 286             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 287
 288             temp = validParameter.validFile(parameters, "threshold", false);    if (temp == "not found"){       temp = "40";                    }
 289                         m->mothurConvert(temp, threshold);
 290             if ((threshold < 0) || (threshold > 40)) { m->mothurOut("[ERROR]: threshold must be between 0 and 40.\n"); abort=true; }
 291
 292                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 293                         m->setProcessors(temp);
 294                         m->mothurConvert(temp, processors);
 295
 296             temp = validParameter.validFile(parameters, "bdiffs", false);               if (temp == "not found") { temp = "0"; }
 297                         m->mothurConvert(temp, bdiffs);
 298
 299                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 300                         m->mothurConvert(temp, pdiffs);
 301
 302   //          temp = validParameter.validFile(parameters, "ldiffs", false);             if (temp == "not found") { temp = "0"; }
 303 //                      m->mothurConvert(temp, ldiffs);
 304             ldiffs = 0;
 305
 306  //           temp = validParameter.validFile(parameters, "sdiffs", false);             if (temp == "not found") { temp = "0"; }
 307  //           m->mothurConvert(temp, sdiffs);
 308             sdiffs = 0;
 309
 310                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 311                         m->mothurConvert(temp, tdiffs);
 312
 313                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }  //+ ldiffs + sdiffs;
 314
 315             temp = validParameter.validFile(parameters, "allfiles", false);             if (temp == "not found") { temp = "F"; }
 316                         allFiles = m->isTrue(temp);
 317
 318                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 319                         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"; }
 320         }
 321
 322         }
 323         catch(exception& e) {
 324                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 325                 exit(1);
 326         }
 327 }
 328 //**********************************************************************************************************************
 329 int MakeContigsCommand::execute(){
 330         try {
 331                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 332
 333         //read ffastq and rfastq files creating fasta and qual files.
 334         //this function will create a forward and reverse, fasta and qual files for each processor.
 335         //files has an entry for each processor. files[i][0] = forwardFasta, files[i][1] = forwardQual, files[i][2] = reverseFasta, files[i][3] = reverseQual.  filesToProcess is for each filepair in the file parameter file.  for ffastq and rfastq this will be size 1.
 336         unsigned long int numReads = 0;
 337         int start = time(NULL);
 338         longestBase = 1000;
 339         m->mothurOut("Reading fastq data...\n");
 340         vector < vector< vector<string> > > filesToProcess = preProcessData(numReads);
 341         m->mothurOut("Done.\n");
 342
 343         if (m->control_pressed) { return 0; }
 344
 345         map<string, string> cvars;
 346         string compOutputDir = outputDir;
 347         if (outputDir == "") { compOutputDir = m->hasPath(file); }
 348         cvars["[filename]"] = compOutputDir + m->getRootName(m->getSimpleName(file));
 349         cvars["[tag]"] = "";
 350         string compositeGroupFile = getOutputFileName("group",cvars);
 351         cvars["[tag]"] = "trim";
 352         string compositeFastaFile = getOutputFileName("fasta",cvars);
 353         string compositeQualFile = getOutputFileName("qfile",cvars);
 354         cvars["[tag]"] = "scrap";
 355         string compositeScrapFastaFile = getOutputFileName("fasta",cvars);
 356         string compositeScrapQualFile = getOutputFileName("qfile",cvars);
 357         cvars["[tag]"] = "";
 358         string compositeMisMatchFile = getOutputFileName("mismatch",cvars);
 359
 360         if (filesToProcess.size() > 1) { //clear files for append below
 361             ofstream outCTFasta, outCTQual, outCSFasta, outCSQual, outCMisMatch;
 362             m->openOutputFile(compositeFastaFile, outCTFasta); outCTFasta.close();
 363             m->openOutputFile(compositeScrapFastaFile, outCSFasta); outCSFasta.close();
 364             m->openOutputFile(compositeMisMatchFile, outCMisMatch); outCMisMatch.close();
 365             m->openOutputFile(compositeQualFile, outCTQual); outCTQual.close();
 366             m->openOutputFile(compositeScrapQualFile, outCSQual); outCSQual.close();
 367             outputNames.push_back(compositeFastaFile); outputTypes["fasta"].push_back(compositeFastaFile);
 368             outputNames.push_back(compositeQualFile); outputTypes["qfile"].push_back(compositeQualFile);
 369             outputNames.push_back(compositeMisMatchFile); outputTypes["mismatch"].push_back(compositeMisMatchFile);
 370             outputNames.push_back(compositeScrapFastaFile); outputTypes["fasta"].push_back(compositeScrapFastaFile);
 371             outputNames.push_back(compositeScrapQualFile); outputTypes["qfile"].push_back(compositeScrapQualFile);
 372         }
 373
 374         for (int l = 0; l < filesToProcess.size(); l++) {
 375
 376             m->mothurOut("\n>>>>>\tProcessing " + filesToProcess[l][0][0] + " (file " + toString(l+1) + " of " + toString(filesToProcess.size()) + ")\t<<<<<\n");
 377
 378             vector<vector<string> > fastaFileNames;
 379             vector<vector<string> > qualFileNames;
 380             createGroup = false;
 381             string outputGroupFileName;
 382             map<string, string> variables;
 383             string thisOutputDir = outputDir;
 384             if (outputDir == "") {  thisOutputDir = m->hasPath(filesToProcess[l][0][0]); }
 385             variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(filesToProcess[l][0][0]));
 386             variables["[tag]"] = "";
 387             if(oligosfile != ""){
 388                 createGroup = getOligos(fastaFileNames, qualFileNames, variables["[filename]"]);
 389                 if (createGroup) {
 390                     outputGroupFileName = getOutputFileName("group",variables);
 391                     outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
 392                 }
 393             }
 394
 395             variables["[tag]"] = "trim";
 396             string outFastaFile = getOutputFileName("fasta",variables);
 397             string outQualFile = getOutputFileName("qfile",variables);
 398             variables["[tag]"] = "scrap";
 399             string outScrapFastaFile = getOutputFileName("fasta",variables);
 400             string outScrapQualFile = getOutputFileName("qfile",variables);
 401             variables["[tag]"] = "";
 402             string outMisMatchFile = getOutputFileName("mismatch",variables);
 403             outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 404             outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
 405             if (filesToProcess[l][0][1] != "") {
 406                 outputNames.push_back(outQualFile); outputTypes["qfile"].push_back(outQualFile);
 407                 outputNames.push_back(outScrapQualFile); outputTypes["qfile"].push_back(outScrapQualFile);
 408             }
 409             outputNames.push_back(outMisMatchFile); outputTypes["mismatch"].push_back(outMisMatchFile);
 410
 411             m->mothurOut("Making contigs...\n");
 412             createProcesses(filesToProcess[l], outFastaFile, outQualFile, outScrapFastaFile, outScrapQualFile, outMisMatchFile, fastaFileNames, qualFileNames);
 413             m->mothurOut("Done.\n");
 414
 415             //remove temp fasta and qual files
 416             for (int i = 0; i < processors; i++) { for(int j = 0; j < filesToProcess[l][i].size(); j++) { m->mothurRemove(filesToProcess[l][i][j]); }  }
 417
 418             if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); }  return 0; }
 419
 420             if(allFiles){
 421                 map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
 422                 map<string, string>::iterator it;
 423                 set<string> namesToRemove;
 424                 for(int i=0;i<fastaFileNames.size();i++){
 425                     for(int j=0;j<fastaFileNames[0].size();j++){
 426                         if (fastaFileNames[i][j] != "") {
 427                             if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
 428                                 if(m->isBlank(fastaFileNames[i][j])){
 429                                     m->mothurRemove(fastaFileNames[i][j]);
 430                                     namesToRemove.insert(fastaFileNames[i][j]);
 431
 432                                     if (filesToProcess[l][0][1] != "") {
 433                                         m->mothurRemove(qualFileNames[i][j]);
 434                                         namesToRemove.insert(qualFileNames[i][j]);
 435                                     }
 436                                 }else{
 437                                     it = uniqueFastaNames.find(fastaFileNames[i][j]);
 438                                     if (it == uniqueFastaNames.end()) {
 439                                         uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
 440                                     }
 441                                 }
 442                             }
 443                         }
 444                     }
 445                 }
 446
 447                 //remove names for outputFileNames, just cleans up the output
 448                 vector<string> outputNames2;
 449                 for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
 450                 outputNames = outputNames2;
 451
 452                 for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
 453                     ifstream in;
 454                     m->openInputFile(it->first, in);
 455
 456                     ofstream out;
 457                     string thisGroupName = thisOutputDir + m->getRootName(m->getSimpleName(it->first));
 458                     thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
 459                     m->openOutputFile(thisGroupName, out);
 460
 461                     while (!in.eof()){
 462                         if (m->control_pressed) { break; }
 463
 464                         Sequence currSeq(in); m->gobble(in);
 465                         out << currSeq.getName() << '\t' << it->second << endl;
 466                     }
 467                     in.close();
 468                     out.close();
 469                 }
 470             }
 471
 472             if (createGroup) {
 473                 ofstream outGroup;
 474                 m->openOutputFile(outputGroupFileName, outGroup);
 475                 for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
 476                     outGroup << itGroup->first << '\t' << itGroup->second << endl;
 477                 }
 478                 outGroup.close();
 479             }
 480
 481             if (filesToProcess.size() > 1) { //merge into large combo files
 482                 if (createGroup) {
 483                     if (l == 0) {
 484                         ofstream outCGroup;
 485                         m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
 486                         outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);
 487                     }
 488                     m->appendFiles(outputGroupFileName, compositeGroupFile);
 489                 }
 490                 m->appendFiles(outMisMatchFile, compositeMisMatchFile);
 491                 m->appendFiles(outFastaFile, compositeFastaFile);
 492                 m->appendFiles(outQualFile, compositeQualFile);
 493                 m->appendFiles(outScrapFastaFile, compositeScrapFastaFile);
 494                 m->appendFiles(outScrapQualFile, compositeScrapQualFile);
 495             }
 496         }
 497         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 498
 499         if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 500
 501                 //output group counts
 502                 m->mothurOutEndLine();
 503                 int total = 0;
 504                 if (groupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
 505                 for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 506             total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
 507                 }
 508                 if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
 509
 510                 if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 511
 512         string currentFasta = "";
 513                 itTypes = outputTypes.find("fasta");
 514                 if (itTypes != outputTypes.end()) {
 515                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 516                 }
 517
 518         string currentQual = "";
 519                 itTypes = outputTypes.find("qfile");
 520                 if (itTypes != outputTypes.end()) {
 521                         if ((itTypes->second).size() != 0) { currentQual = (itTypes->second)[0]; m->setQualFile(currentQual); }
 522                 }
 523
 524         string currentGroup = "";
 525                 itTypes = outputTypes.find("group");
 526                 if (itTypes != outputTypes.end()) {
 527                         if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); }
 528                 }
 529
 530         //output files created by command
 531                 m->mothurOutEndLine();
 532                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 533                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 534                 m->mothurOutEndLine();
 535
 536         return 0;
 537     }
 538         catch(exception& e) {
 539                 m->errorOut(e, "MakeContigsCommand", "execute");
 540                 exit(1);
 541         }
 542 }
 543 //**********************************************************************************************************************
 544 vector< vector< vector<string> > > MakeContigsCommand::preProcessData(unsigned long int& numReads) {
 545         try {
 546         vector< vector< vector<string> > > filesToProcess;
 547
 548         if (ffastqfile != "") { //reading one file
 549             vector< vector<string> > files = readFastqFiles(numReads, ffastqfile, rfastqfile);
 550             //adjust for really large processors or really small files
 551             if (numReads == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
 552             if (numReads < processors) {
 553                 for (int i = numReads; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 554                 files.resize(numReads);
 555                 processors = numReads;
 556             }
 557             filesToProcess.push_back(files);
 558         }else if (file != "") { //reading multiple files
 559             //return only valid pairs
 560             vector< vector<string> > filePairsToProcess = readFileNames(file);
 561
 562             if (m->control_pressed) { return filesToProcess; }
 563
 564             if (filePairsToProcess.size() != 0) {
 565                 for (int i = 0; i < filePairsToProcess.size(); i++) {
 566
 567                     if (m->control_pressed) { for (int l = 0; l < filesToProcess.size(); l++) { for (int k = 0; k < filesToProcess[l].size(); k++) { for(int j = 0; j < filesToProcess[l][k].size(); j++) { m->mothurRemove(filesToProcess[l][k][j]); } filesToProcess[l][k].clear(); } return filesToProcess; } }
 568
 569                     unsigned long int thisFilesReads;
 570                     vector< vector<string> > files = readFastqFiles(thisFilesReads, filePairsToProcess[i][0], filePairsToProcess[i][1]);
 571
 572                     //adjust for really large processors or really small files
 573                     if (thisFilesReads < processors) {
 574                         m->mothurOut("[ERROR]: " + filePairsToProcess[i][0] + " has less than " + toString(processors) + " good reads, skipping\n");
 575                         for (int k = 0; k < files.size(); k++) { for(int j = 0; j < files[k].size(); j++) { m->mothurRemove(files[k][j]); } files[k].clear(); }
 576                     }else {
 577                         filesToProcess.push_back(files);
 578                         numReads += thisFilesReads;
 579                     }
 580                 }
 581                 //all files are bad
 582                 if (numReads == 0) {  m->control_pressed = true; }
 583             }
 584         }else if (ffastafile != "") {
 585             vector< vector<string> > files = readFastaFiles(numReads, ffastafile, rfastafile);
 586             //adjust for really large processors or really small files
 587             if (numReads == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
 588             if (numReads < processors) {
 589                 for (int i = numReads; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 590                 files.resize(numReads);
 591                 processors = numReads;
 592             }
 593             filesToProcess.push_back(files);
 594         }else { m->control_pressed = true; } //should not get here
 595
 596         return filesToProcess;
 597     }
 598         catch(exception& e) {
 599                 m->errorOut(e, "MakeContigsCommand", "preProcessData");
 600                 exit(1);
 601         }
 602 }
 603 //**********************************************************************************************************************
 604 int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames) {
 605         try {
 606                 int num = 0;
 607                 vector<int> processIDS;
 608 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 609                 int process = 0;
 610
 611                 //loop through and create all the processes you want
 612                 while (process != processors-1) {
 613                         int pid = fork();
 614
 615                         if (pid > 0) {
 616                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 617                                 process++;
 618                         }else if (pid == 0){
 619                 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 620                                 vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 621
 622                                 if(allFiles){
 623                                         ofstream temp;
 624
 625                                         for(int i=0;i<tempFASTAFileNames.size();i++){
 626                                                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 627                                                         if (tempFASTAFileNames[i][j] != "") {
 628                                                                 tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
 629                                                                 m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 630
 631                                 if (files[processors-1][1] != "") {
 632                                     tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
 633                                     m->openOutputFile(tempPrimerQualFileNames[i][j], temp);             temp.close();
 634                                 }
 635                                                         }
 636                                                 }
 637                                         }
 638                                 }
 639
 640                                 num = driver(files[process],
 641                              outputFasta + toString(getpid()) + ".temp",
 642                              outputQual + toString(getpid()) + ".temp",
 643                              outputScrapFasta + toString(getpid()) + ".temp",
 644                              outputScrapQual + toString(getpid()) + ".temp",
 645                              outputMisMatches + toString(getpid()) + ".temp",
 646                              tempFASTAFileNames,
 647                              tempPrimerQualFileNames);
 648
 649                                 //pass groupCounts to parent
 650                 ofstream out;
 651                 string tempFile = toString(getpid()) + ".num.temp";
 652                 m->openOutputFile(tempFile, out);
 653                 out << num << endl;
 654                                 if(createGroup){
 655                                         out << groupCounts.size() << endl;
 656
 657                                         for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 658                                                 out << it->first << '\t' << it->second << endl;
 659                                         }
 660
 661                     out << groupMap.size() << endl;
 662                     for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
 663                                                 out << it->first << '\t' << it->second << endl;
 664                                         }
 665                                 }
 666                 out.close();
 667
 668                                 exit(0);
 669                         }else {
 670                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 671                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 672                                 exit(0);
 673                         }
 674                 }
 675
 676         ofstream temp;
 677                 m->openOutputFile(outputFasta, temp);           temp.close();
 678         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 679         if (files[processors-1][1] != "") {
 680             m->openOutputFile(outputScrapQual, temp);           temp.close();
 681             m->openOutputFile(outputQual, temp);        temp.close();
 682         }
 683
 684                 //do my part
 685                 num = driver(files[processors-1], outputFasta, outputQual, outputScrapFasta, outputScrapQual, outputMisMatches, fastaFileNames, qualFileNames);
 686
 687                 //force parent to wait until all the processes are done
 688                 for (int i=0;i<processIDS.size();i++) {
 689                         int temp = processIDS[i];
 690                         wait(&temp);
 691                 }
 692
 693                 for (int i = 0; i < processIDS.size(); i++) {
 694             ifstream in;
 695             string tempFile = toString(processIDS[i]) + ".num.temp";
 696             m->openInputFile(tempFile, in);
 697             int tempNum;
 698             in >> tempNum; num += tempNum; m->gobble(in);
 699
 700                         if(createGroup){
 701                                 string group;
 702                                 in >> tempNum; m->gobble(in);
 703
 704                                 if (tempNum != 0) {
 705                                         for (int j = 0; j < tempNum; j++) {
 706                         int groupNum;
 707                                                 in >> group >> groupNum; m->gobble(in);
 708
 709                                                 map<string, int>::iterator it = groupCounts.find(group);
 710                                                 if (it == groupCounts.end()) {  groupCounts[group] = groupNum; }
 711                                                 else { groupCounts[it->first] += groupNum; }
 712                                         }
 713                                 }
 714                 in >> tempNum; m->gobble(in);
 715                 if (tempNum != 0) {
 716                                         for (int j = 0; j < tempNum; j++) {
 717                         string group, seqName;
 718                                                 in >> seqName >> group; m->gobble(in);
 719
 720                                                 map<string, string>::iterator it = groupMap.find(seqName);
 721                                                 if (it == groupMap.end()) {     groupMap[seqName] = group; }
 722                                                 else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 723                                         }
 724                                 }
 725                         }
 726             in.close(); m->mothurRemove(tempFile);
 727         }
 728     #else
 729
 730         //////////////////////////////////////////////////////////////////////////////////////////////////////
 731                 //Windows version shared memory, so be careful when passing variables through the contigsData struct.
 732                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 733                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 734
 735                 vector<contigsData*> pDataArray;
 736                 DWORD   dwThreadIdArray[processors-1];
 737                 HANDLE  hThreadArray[processors-1];
 738
 739                 //Create processor worker threads.
 740                 for( int h=0; h<processors-1; h++ ){
 741                         string extension = "";
 742                         if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
 743             vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 744             vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 745
 746             if(allFiles){
 747                 ofstream temp;
 748
 749                 for(int i=0;i<tempFASTAFileNames.size();i++){
 750                     for(int j=0;j<tempFASTAFileNames[i].size();j++){
 751                         if (tempFASTAFileNames[i][j] != "") {
 752                             tempFASTAFileNames[i][j] += extension;
 753                             m->openOutputFile(tempFASTAFileNames[i][j], temp);                  temp.close();
 754
 755                             if (files[processors-1][1] != "") {
 756                                 tempPrimerQualFileNames[i][j] += extension;
 757                                 m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
 758                             }
 759                         }
 760                     }
 761                 }
 762             }
 763
 764
 765                         contigsData* tempcontig = new contigsData(files[h], (outputFasta + extension), (outputQual + extension), (outputScrapFasta + extension), (outputScrapQual + extension),(outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, threshold, barcodes, primers, tempFASTAFileNames, tempPrimerQualFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createGroup, allFiles, h);
 766                         pDataArray.push_back(tempcontig);
 767
 768                         hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
 769                 }
 770
 771         vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 772         vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 773
 774         if(allFiles){
 775             ofstream temp;
 776             string extension = toString(processors-1) + ".temp";
 777
 778             for(int i=0;i<tempFASTAFileNames.size();i++){
 779                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 780                     if (tempFASTAFileNames[i][j] != "") {
 781                         tempFASTAFileNames[i][j] += extension;
 782                         m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 783
 784                         if (files[processors-1][1] != "") {
 785                             tempPrimerQualFileNames[i][j] += extension;
 786                             m->openOutputFile(tempPrimerQualFileNames[i][j], temp);             temp.close();
 787                         }
 788                     }
 789                 }
 790             }
 791         }
 792
 793                 //parent do my part
 794                 ofstream temp;
 795                 m->openOutputFile(outputFasta, temp);           temp.close();
 796         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 797         if (files[processors-1][1] != "") {
 798             m->openOutputFile(outputScrapQual, temp);           temp.close();
 799             m->openOutputFile(outputQual, temp);        temp.close();
 800                 }
 801
 802         //do my part
 803         processIDS.push_back(processors-1);
 804                 num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"), (outputQual+ toString(processors-1) + ".temp"), (outputScrapFasta+ toString(processors-1) + ".temp"), (outputScrapQual+ toString(processors-1) + ".temp"), (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, tempPrimerQualFileNames);
 805
 806                 //Wait until all threads have terminated.
 807                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 808
 809                 //Close all thread handles and free memory allocations.
 810                 for(int i=0; i < pDataArray.size(); i++){
 811                         num += pDataArray[i]->count;
 812             for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
 813                 map<string, int>::iterator it2 = groupCounts.find(it->first);
 814                 if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
 815                 else { groupCounts[it->first] += it->second; }
 816             }
 817             for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
 818                 map<string, string>::iterator it2 = groupMap.find(it->first);
 819                 if (it2 == groupMap.end()) {    groupMap[it->first] = it->second; }
 820                 else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 821             }
 822             CloseHandle(hThreadArray[i]);
 823                         delete pDataArray[i];
 824         }
 825
 826     #endif
 827
 828         for (int i = 0; i < processIDS.size(); i++) {
 829                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 830                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 831
 832                         m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
 833                         m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp"));
 834
 835             if (files[processors-1][1] != "") {
 836                 m->appendFiles((outputScrapQual + toString(processIDS[i]) + ".temp"), outputScrapQual);
 837                 m->mothurRemove((outputScrapQual + toString(processIDS[i]) + ".temp"));
 838
 839                 m->appendFiles((outputQual + toString(processIDS[i]) + ".temp"), outputQual);
 840                 m->mothurRemove((outputQual + toString(processIDS[i]) + ".temp"));
 841             }
 842
 843             m->appendFiles((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 844                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 845
 846             if(allFiles){
 847                                 for(int j=0;j<fastaFileNames.size();j++){
 848                                         for(int k=0;k<fastaFileNames[j].size();k++){
 849                                                 if (fastaFileNames[j][k] != "") {
 850                                                         m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
 851                                                         m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 852
 853                             if (files[processors-1][1] != "") {
 854                                 m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
 855                                 m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 856                             }
 857                                                 }
 858                                         }
 859                                 }
 860                         }
 861                 }
 862
 863                 return num;
 864         }
 865         catch(exception& e) {
 866                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 867                 exit(1);
 868         }
 869 }
 870 //**********************************************************************************************************************
 871 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputQual, string outputScrapFasta, string outputScrapQual, string outputMisMatches, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames){
 872     try {
 873
 874         Alignment* alignment;
 875         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 876                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 877
 878         int num = 0;
 879         string thisffastafile = files[0];
 880         string thisfqualfile = files[1];
 881         string thisrfastafile = files[2];
 882         string thisrqualfile = files[3];
 883
 884         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 885
 886         ifstream inFFasta, inRFasta, inFQual, inRQual;
 887         ofstream outFasta, outQual, outMisMatch, outScrapFasta, outScrapQual;
 888         m->openInputFile(thisffastafile, inFFasta);
 889         m->openInputFile(thisrfastafile, inRFasta);
 890         if (thisfqualfile != "") {
 891             m->openInputFile(thisfqualfile, inFQual);
 892             m->openInputFile(thisrqualfile, inRQual);
 893             m->openOutputFile(outputScrapQual, outScrapQual);
 894             m->openOutputFile(outputQual, outQual);
 895         }
 896         m->openOutputFile(outputFasta, outFasta);
 897         m->openOutputFile(outputScrapFasta, outScrapFasta);
 898         m->openOutputFile(outputMisMatches, outMisMatch);
 899         outMisMatch << "Name\tLength\tMisMatches\n";
 900
 901         TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
 902
 903         while ((!inFFasta.eof()) && (!inRFasta.eof())) {
 904
 905             if (m->control_pressed) { break; }
 906
 907             int success = 1;
 908             string trashCode = "";
 909             int currentSeqsDiffs = 0;
 910
 911             //read seqs and quality info
 912             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 913             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 914             QualityScores* fQual = NULL; QualityScores* rQual = NULL;
 915             if (thisfqualfile != "") {
 916                 fQual = new QualityScores(inFQual); m->gobble(inFQual);
 917                 rQual = new QualityScores(inRQual); m->gobble(inRQual);
 918             }
 919
 920             int barcodeIndex = 0;
 921             int primerIndex = 0;
 922
 923             if(barcodes.size() != 0){
 924                 if (thisfqualfile != "") {
 925                     success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
 926                 }else {
 927                     success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
 928                 }
 929                 if(success > bdiffs)            {       trashCode += 'b';       }
 930                 else{ currentSeqsDiffs += success;  }
 931             }
 932
 933             if(primers.size() != 0){
 934                 if (thisfqualfile != "") {
 935                     success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
 936                 }else {
 937                     success = trimOligos.stripForward(fSeq, rSeq, primerIndex);
 938                 }
 939                 if(success > pdiffs)            {       trashCode += 'f';       }
 940                 else{ currentSeqsDiffs += success;  }
 941             }
 942
 943             if (currentSeqsDiffs > tdiffs)      {       trashCode += 't';   }
 944
 945             //flip the reverse reads
 946             rSeq.reverseComplement();
 947             if (thisfqualfile != "") { rQual->flipQScores(); }
 948
 949             //pairwise align
 950             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 951             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 952             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 953             fSeq.setAligned(alignment->getSeqAAln());
 954             rSeq.setAligned(alignment->getSeqBAln());
 955             int length = fSeq.getAligned().length();
 956
 957             //traverse alignments merging into one contiguous seq
 958             string contig = "";
 959             vector<int> contigScores;
 960             int numMismatches = 0;
 961             string seq1 = fSeq.getAligned();
 962             string seq2 = rSeq.getAligned();
 963             vector<int> scores1, scores2;
 964             if (thisfqualfile != "") {
 965                 scores1 = fQual->getQualityScores();
 966                 scores2 = rQual->getQualityScores();
 967                 delete fQual; delete rQual;
 968             }
 969
 970             // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
 971             int overlapStart = fSeq.getStartPos();
 972             int seq2Start = rSeq.getStartPos();
 973             //bigger of the 2 starting positions is the location of the overlapping start
 974             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 975                 overlapStart = seq2Start;
 976                 for (int i = 0; i < overlapStart; i++) {
 977                     contig += seq1[i];
 978                     if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
 979                 }
 980             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 981                 for (int i = 0; i < overlapStart; i++) {
 982                     contig += seq2[i];
 983                     if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
 984                 }
 985             }
 986
 987             int seq1End = fSeq.getEndPos();
 988             int seq2End = rSeq.getEndPos();
 989             int overlapEnd = seq1End;
 990             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 991
 992             for (int i = overlapStart; i < overlapEnd; i++) {
 993                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 994                     contig += seq1[i];
 995                     if (thisfqualfile != "") {
 996                         contigScores.push_back(scores1[ABaseMap[i]]);
 997                         if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; }
 998                     }
 999                 }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
1000                     if (thisfqualfile != "") {
1001                         if (scores2[BBaseMap[i]] < threshold) { } //
1002                         else {
1003                             contig += seq2[i];
1004                             contigScores.push_back(scores2[BBaseMap[i]]);
1005                         }
1006                     }else { contig += seq2[i]; } //with no quality info, then we keep it?
1007                 }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
1008                     if (thisfqualfile != "") {
1009                         if (scores1[ABaseMap[i]] < threshold) { } //
1010                         else {
1011                             contig += seq1[i];
1012                             contigScores.push_back(scores1[ABaseMap[i]]);
1013                         }
1014                     }else { contig += seq1[i]; } //with no quality info, then we keep it?
1015                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
1016                     if (thisfqualfile != "") {
1017                         char c = seq1[i];
1018                         contigScores.push_back(scores1[ABaseMap[i]]);
1019                         if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { contigScores[contigScores.size()-1] = scores2[BBaseMap[i]]; c = seq2[i]; }
1020                         contig += c;
1021                         numMismatches++;
1022                     }else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
1023                 }else { //should never get here
1024                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
1025                 }
1026             }
1027
1028             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
1029                 for (int i = overlapEnd; i < length; i++) {
1030                     contig += seq2[i];
1031                     if (thisfqualfile != "") { contigScores.push_back(scores2[BBaseMap[i]]); }
1032                 }
1033             }else { //seq2 ends before seq1 so take from overlap to length from seq1
1034                 for (int i = overlapEnd; i < length; i++) {
1035                     contig += seq1[i];
1036                     if (thisfqualfile != "") { contigScores.push_back(scores1[ABaseMap[i]]); }
1037                 }
1038
1039             }
1040
1041             if(trashCode.length() == 0){
1042                 bool ignore = false;
1043
1044                 if (m->debug) { m->mothurOut(fSeq.getName()); }
1045
1046                 if (createGroup) {
1047                     if(barcodes.size() != 0){
1048                         string thisGroup = barcodeNameVector[barcodeIndex];
1049                         if (primers.size() != 0) {
1050                             if (primerNameVector[primerIndex] != "") {
1051                                 if(thisGroup != "") {
1052                                     thisGroup += "." + primerNameVector[primerIndex];
1053                                 }else {
1054                                     thisGroup = primerNameVector[primerIndex];
1055                                 }
1056                             }
1057                         }
1058
1059                         if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
1060
1061                         int pos = thisGroup.find("ignore");
1062                         if (pos == string::npos) {
1063                             groupMap[fSeq.getName()] = thisGroup;
1064
1065                             map<string, int>::iterator it = groupCounts.find(thisGroup);
1066                             if (it == groupCounts.end()) {      groupCounts[thisGroup] = 1; }
1067                             else { groupCounts[it->first] ++; }
1068                         }else { ignore = true; }
1069
1070                     }
1071                 }
1072                 if (m->debug) { m->mothurOut("\n"); }
1073
1074                 if(allFiles && !ignore){
1075                     ofstream output;
1076                     m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
1077                     output << ">" << fSeq.getName() << endl << contig << endl;
1078                     output.close();
1079
1080                     if (thisfqualfile != "") {
1081                         m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
1082                         output << ">" << fSeq.getName() << endl;
1083                         for (int i = 0; i < contigScores.size(); i++) { output << contigScores[i] << ' '; }
1084                         output << endl;
1085                         output.close();
1086                     }
1087                 }
1088
1089                 //output
1090                 outFasta << ">" << fSeq.getName() << endl << contig << endl;
1091                 if (thisfqualfile != "") {
1092                     outQual << ">" << fSeq.getName() << endl;
1093                     for (int i = 0; i < contigScores.size(); i++) { outQual << contigScores[i] << ' '; }
1094                     outQual << endl;
1095                 }
1096                 outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << numMismatches << endl;
1097             }else {
1098                 //output
1099                 outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
1100                 if (thisfqualfile != "") {
1101                     outScrapQual << ">" << fSeq.getName() << " | " << trashCode << endl;
1102                     for (int i = 0; i < contigScores.size(); i++) { outScrapQual << contigScores[i] << ' '; }
1103                     outScrapQual << endl;
1104                 }
1105             }
1106             num++;
1107
1108                         //report progress
1109                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
1110                 }
1111
1112                 //report progress
1113                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
1114
1115         inFFasta.close();
1116         inRFasta.close();
1117         outFasta.close();
1118         outScrapFasta.close();
1119         outMisMatch.close();
1120         if (thisfqualfile != "") {
1121             inFQual.close();
1122             inRQual.close();
1123             outQual.close();
1124             outScrapQual.close();
1125         }
1126         delete alignment;
1127
1128         if (m->control_pressed) {  m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches); if (thisfqualfile != "") { m->mothurRemove(outputQual); m->mothurRemove(outputScrapQual); } }
1129
1130         return num;
1131     }
1132         catch(exception& e) {
1133                 m->errorOut(e, "MakeContigsCommand", "driver");
1134                 exit(1);
1135         }
1136 }
1137 //**********************************************************************************************************************
1138 vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& count, string ffastq, string rfastq){
1139     try {
1140         vector< vector<string> > files;
1141         //maps processors number to file pointer
1142         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
1143         map<int, vector<ofstream*> >::iterator it;
1144
1145         //create files to write to
1146         for (int i = 0; i < processors; i++) {
1147             vector<ofstream*> temp;
1148             ofstream* outFF = new ofstream;     temp.push_back(outFF);
1149             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
1150             ofstream* outRF = new ofstream;     temp.push_back(outRF);
1151             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
1152             tempfiles[i] = temp;
1153
1154             vector<string> names;
1155             string thisOutputDir = outputDir;
1156             if (outputDir == "") { thisOutputDir = m->hasPath(ffastq); }
1157             string ffastafilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "ffastatemp";
1158             string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rfastatemp";
1159             string fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "fqualtemp";
1160             string rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rqualtemp";
1161             names.push_back(ffastafilename); names.push_back(fqualfilename);
1162             names.push_back(rfastafilename); names.push_back(rqualfilename);
1163             files.push_back(names);
1164
1165             m->openOutputFile(ffastafilename, *outFF);
1166             m->openOutputFile(rfastafilename, *outRF);
1167             m->openOutputFile(fqualfilename, *outFQ);
1168             m->openOutputFile(rqualfilename, *outRQ);
1169         }
1170
1171         if (m->control_pressed) {
1172             //close files, delete ofstreams
1173             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]; } }
1174             //remove files
1175             for (int i = 0; i < files.size(); i++) {
1176                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
1177             }
1178         }
1179
1180         ifstream inForward;
1181         m->openInputFile(ffastq, inForward);
1182
1183         ifstream inReverse;
1184         m->openInputFile(rfastq, inReverse);
1185
1186         count = 0;
1187         map<string, fastqRead> uniques;
1188         map<string, fastqRead>::iterator itUniques;
1189         while ((!inForward.eof()) || (!inReverse.eof())) {
1190
1191             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; }
1192
1193             //get a read from forward and reverse fastq files
1194             bool ignoref, ignorer;
1195             fastqRead thisFread, thisRread;
1196             if (!inForward.eof()) {  thisFread = readFastq(inForward, ignoref); }
1197             else { ignoref = true; }
1198             if (!inReverse.eof()) { thisRread = readFastq(inReverse, ignorer);  }
1199             else { ignorer = true; }
1200
1201             vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
1202
1203             for (int i = 0; i < reads.size(); i++) {
1204                 fastqRead fread = reads[i].forward;
1205                 fastqRead rread = reads[i].reverse;
1206
1207                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
1208
1209                 if (checkReads(fread, rread, ffastq, rfastq)) {
1210                     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; }
1211
1212                     //if the reads are okay write to output files
1213                     int process = count % processors;
1214
1215                     *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
1216                     *(tempfiles[process][1]) << ">" << fread.name << endl;
1217                     for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
1218                     *(tempfiles[process][1]) << endl;
1219                     *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
1220                     *(tempfiles[process][3]) << ">" << rread.name << endl;
1221                     for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
1222                     *(tempfiles[process][3]) << endl;
1223
1224                     count++;
1225
1226                     //report progress
1227                     if((count) % 10000 == 0){   m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1228                 }
1229             }
1230                 }
1231                 //report progress
1232                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1233
1234         if (uniques.size() != 0) {
1235             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
1236                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
1237             }
1238             m->mothurOutEndLine();
1239         }
1240
1241         //close files, delete ofstreams
1242         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]; } }
1243         inForward.close();
1244         inReverse.close();
1245
1246         return files;
1247     }
1248     catch(exception& e) {
1249         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1250         exit(1);
1251     }
1252 }
1253 //**********************************************************************************************************************
1254 vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& count, string ffasta, string rfasta){
1255     try {
1256         vector< vector<string> > files;
1257         //maps processors number to file pointer
1258         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
1259         map<int, vector<ofstream*> >::iterator it;
1260
1261         //create files to write to
1262         for (int i = 0; i < processors; i++) {
1263             vector<ofstream*> temp;
1264             ofstream* outFF = new ofstream;     temp.push_back(outFF);
1265             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
1266             ofstream* outRF = new ofstream;     temp.push_back(outRF);
1267             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
1268             tempfiles[i] = temp;
1269
1270             vector<string> names;
1271             string thisOutputDir = outputDir;
1272             if (outputDir == "") { thisOutputDir = m->hasPath(ffasta); }
1273             string ffastafilename = thisOutputDir + m->getRootName(m->getSimpleName(ffasta)) + toString(i) + "ffastatemp";
1274             string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfasta)) + toString(i) + "rfastatemp";
1275             string fqualfilename = "";
1276             if (fqualfile != "") { fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(fqualfile)) + toString(i) + "fqual.temp";  m->openOutputFile(fqualfilename, *outFQ); }
1277             string rqualfilename = "";
1278             if (rqualfile != "") { rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rqualfile)) + toString(i) + "rqual.temp"; m->openOutputFile(rqualfilename, *outRQ); }
1279             names.push_back(ffastafilename); names.push_back(fqualfilename);
1280             names.push_back(rfastafilename); names.push_back(rqualfilename);
1281             files.push_back(names);
1282
1283             m->openOutputFile(ffastafilename, *outFF);
1284             m->openOutputFile(rfastafilename, *outRF);
1285         }
1286
1287         if (m->control_pressed) {
1288             //close files, delete ofstreams
1289             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]; } }
1290             //remove files
1291             for (int i = 0; i < files.size(); i++) {
1292                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
1293             }
1294         }
1295
1296         ifstream inForwardFasta;
1297         m->openInputFile(ffasta, inForwardFasta);
1298
1299         ifstream inReverseFasta;
1300         m->openInputFile(rfasta, inReverseFasta);
1301
1302         ifstream inForwardQual, inReverseQual;
1303         if (fqualfile != "") { m->openInputFile(fqualfile, inForwardQual); m->openInputFile(rqualfile, inReverseQual); }
1304
1305         count = 0;
1306         map<string, fastqRead> uniques;
1307         map<string, fastqRead>::iterator itUniques;
1308         while ((!inForwardFasta.eof()) || (!inReverseFasta.eof())) {
1309
1310             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]); } } inReverseFasta.close(); inForwardFasta.close(); if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); } return files; }
1311
1312             //get a reads from forward and reverse fasta files
1313             bool ignoref, ignorer;
1314             fastqRead thisFread, thisRread;
1315             if (!inForwardFasta.eof()) {
1316                 ignoref = false;
1317                 Sequence temp(inForwardFasta); m->gobble(inForwardFasta);
1318                 thisFread.name = temp.getName();
1319                 thisFread.sequence = temp.getUnaligned();
1320             }else { ignoref = true; }
1321             if (!inReverseFasta.eof()) {
1322                 ignorer = false;
1323                 Sequence temp(inReverseFasta); m->gobble(inReverseFasta);
1324                 thisRread.name = temp.getName();
1325                 thisRread.sequence = temp.getUnaligned();
1326             }else { ignorer = true; }
1327
1328             //get qual reads if given
1329             if (fqualfile != "") {
1330                 if (!inForwardQual.eof() && !ignoref) {
1331                     QualityScores temp(inForwardQual); m->gobble(inForwardQual);
1332                     //if forward files dont match ignore read
1333                     if (thisFread.name != temp.getName()) { ignoref = true; }
1334                     else { thisFread.scores = temp.getQualityScores(); }
1335                 }else { ignoref = true; }
1336                 if (!inReverseQual.eof() && !ignorer) {
1337                     QualityScores temp(inReverseQual); m->gobble(inReverseQual);
1338                     //if reverse files dont match ignore read
1339                     if (thisRread.name != temp.getName()) { ignorer = true; }
1340                     else { thisRread.scores = temp.getQualityScores(); }
1341                 }else { ignorer = true; }
1342             }
1343
1344             vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
1345
1346             for (int i = 0; i < reads.size(); i++) {
1347                 fastqRead fread = reads[i].forward;
1348                 fastqRead rread = reads[i].reverse;
1349
1350                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
1351
1352                 if (checkReads(fread, rread, ffasta, rfasta)) {
1353                     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]); } } inReverseFasta.close(); inForwardFasta.close(); if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); } return files; }
1354
1355                     //if the reads are okay write to output files
1356                     int process = count % processors;
1357
1358                     *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
1359                     *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
1360                     if (fqualfile != "") { //if you have quality info, print it
1361                         *(tempfiles[process][1]) << ">" << fread.name << endl;
1362                         for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
1363                         *(tempfiles[process][1]) << endl;
1364                         *(tempfiles[process][3]) << ">" << rread.name << endl;
1365                         for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
1366                         *(tempfiles[process][3]) << endl;
1367                     }
1368                     count++;
1369
1370                     //report progress
1371                     if((count) % 10000 == 0){   m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1372                 }
1373             }
1374                 }
1375                 //report progress
1376                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1377
1378         if (uniques.size() != 0) {
1379             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
1380                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
1381             }
1382             m->mothurOutEndLine();
1383         }
1384
1385         //close files, delete ofstreams
1386         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]; } }
1387         inReverseFasta.close();
1388         inForwardFasta.close();
1389         if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); }
1390
1391         return files;
1392     }
1393     catch(exception& e) {
1394         m->errorOut(e, "MakeContigsCommand", "readFastaFiles");
1395         exit(1);
1396     }
1397 }
1398 //**********************************************************************************************************************
1399 vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques){
1400     try {
1401         vector<pairFastqRead> reads;
1402         map<string, fastqRead>::iterator itUniques;
1403
1404         if (!ignoref && !ignorer) {
1405             if (forward.name == reverse.name) {
1406                 pairFastqRead temp(forward, reverse);
1407                 reads.push_back(temp);
1408             }else {
1409                 bool match = false;
1410                 //if no match are the names only different by 1 and 2?
1411                 string tempFRead = forward.name.substr(0, forward.name.length()-1);
1412                 string tempRRead = reverse.name.substr(0, reverse.name.length()-1);
1413                 if (tempFRead == tempRRead) {
1414                     if ((forward.name[forward.name.length()-1] == '1') && (reverse.name[reverse.name.length()-1] == '2')) {
1415                         forward.name = tempFRead;
1416                         reverse.name = tempRRead;
1417                         pairFastqRead temp(forward, reverse);
1418                         reads.push_back(temp);
1419                         match = true;
1420                     }
1421                 }
1422
1423                 if (!match) {
1424                     //look for forward pair
1425                     itUniques = uniques.find(forward.name);
1426                     if (itUniques != uniques.end()) {  //we have the pair for this read
1427                         pairFastqRead temp(forward, itUniques->second);
1428                         reads.push_back(temp);
1429                         uniques.erase(itUniques);
1430                     }else { //save this read for later
1431                         uniques[forward.name] = forward;
1432                     }
1433
1434                     //look for reverse pair
1435                     itUniques = uniques.find(reverse.name);
1436                     if (itUniques != uniques.end()) {  //we have the pair for this read
1437                         pairFastqRead temp(itUniques->second, reverse);
1438                         reads.push_back(temp);
1439                         uniques.erase(itUniques);
1440                     }else { //save this read for later
1441                         uniques[reverse.name] = reverse;
1442                     }
1443                 }
1444
1445             }
1446         }else if (!ignoref && ignorer) { //ignore reverse keep forward
1447             //look for forward pair
1448             itUniques = uniques.find(forward.name);
1449             if (itUniques != uniques.end()) {  //we have the pair for this read
1450                 pairFastqRead temp(forward, itUniques->second);
1451                 reads.push_back(temp);
1452                 uniques.erase(itUniques);
1453             }else { //save this read for later
1454                 uniques[forward.name] = forward;
1455             }
1456
1457         }else if (ignoref && !ignorer) { //ignore forward keep reverse
1458             //look for reverse pair
1459             itUniques = uniques.find(reverse.name);
1460             if (itUniques != uniques.end()) {  //we have the pair for this read
1461                 pairFastqRead temp(itUniques->second, reverse);
1462                 reads.push_back(temp);
1463                 uniques.erase(itUniques);
1464             }else { //save this read for later
1465                 uniques[reverse.name] = reverse;
1466             }
1467         }//else ignore both and do nothing
1468
1469         return reads;
1470     }
1471     catch(exception& e) {
1472         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1473         exit(1);
1474     }
1475 }
1476 //**********************************************************************************************************************
1477 fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
1478     try {
1479         fastqRead read;
1480
1481         ignore = false;
1482
1483         //read sequence name
1484         string line = m->getline(in); m->gobble(in);
1485         vector<string> pieces = m->splitWhiteSpace(line);
1486         string name = "";  if (pieces.size() != 0) { name = pieces[0]; }
1487         if (name == "") {  m->mothurOut("[WARNING]: Blank fasta name, ignoring read."); m->mothurOutEndLine(); ignore=true;  }
1488         else if (name[0] != '@') { m->mothurOut("[WARNING]: reading " + name + " expected a name with @ as a leading character, ignoring read."); m->mothurOutEndLine(); ignore=true; }
1489         else { name = name.substr(1); }
1490
1491         //read sequence
1492         string sequence = m->getline(in); m->gobble(in);
1493         if (sequence == "") {  m->mothurOut("[WARNING]: missing sequence for " + name + ", ignoring."); ignore=true; }
1494
1495         //read sequence name
1496         line = m->getline(in); m->gobble(in);
1497         pieces = m->splitWhiteSpace(line);
1498         string name2 = "";  if (pieces.size() != 0) { name2 = pieces[0]; }
1499         if (name2 == "") {  m->mothurOut("[WARNING]: expected a name with + as a leading character, ignoring."); ignore=true; }
1500         else if (name2[0] != '+') { m->mothurOut("[WARNING]: reading " + name2 + " expected a name with + as a leading character, ignoring."); ignore=true; }
1501         else { name2 = name2.substr(1); if (name2 == "") { name2 = name; } }
1502
1503         //read quality scores
1504         string quality = m->getline(in); m->gobble(in);
1505         if (quality == "") {  m->mothurOut("[WARNING]: missing quality for " + name2 + ", ignoring."); ignore=true; }
1506
1507         //sanity check sequence length and number of quality scores match
1508         if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } }
1509         if (quality.length() != sequence.length()) { m->mothurOut("[WARNING]: Lengths do not match for sequence " + name + ". Read " + toString(sequence.length()) + " characters for fasta and " + toString(quality.length()) + " characters for quality scores, ignoring read."); ignore=true; }
1510
1511         vector<int> qualScores;
1512                 int controlChar = int('!');
1513                 for (int i = 0; i < quality.length(); i++) {
1514                         int temp = int(quality[i]);
1515                         temp -= controlChar;
1516
1517                         qualScores.push_back(temp);
1518                 }
1519
1520         read.name = name;
1521         read.sequence = sequence;
1522         read.scores = qualScores;
1523
1524         return read;
1525     }
1526     catch(exception& e) {
1527         m->errorOut(e, "MakeContigsCommand", "readFastq");
1528         exit(1);
1529     }
1530 }
1531 //**********************************************************************************************************************
1532 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse, string ffile, string rfile){
1533     try {
1534         bool good = true;
1535
1536         //do sequence lengths match
1537         if (forward.sequence.length() != reverse.sequence.length()) {
1538             m->mothurOut("[WARNING]: For sequence " + forward.name + " I read a sequence of length " + toString(forward.sequence.length()) + " from " + ffile + ", but read a sequence of length " + toString(reverse.sequence.length()) + " from " + rfile + ", ignoring.\n");
1539             good = false;
1540         }
1541
1542         //do number of qual scores match
1543         if (forward.scores.size() != reverse.scores.size()) {
1544             m->mothurOut("[WARNING]: For sequence " + forward.name + " I read " + toString(forward.scores.size()) + " quality scores from " + ffile + ", but read  " + toString(reverse.scores.size()) + " quality scores from " + rfile + ", ignoring.\n");
1545             good = false;
1546         }
1547
1548         return good;
1549     }
1550     catch(exception& e) {
1551         m->errorOut(e, "MakeContigsCommand", "checkReads");
1552         exit(1);
1553     }
1554 }
1555 //***************************************************************************************************************
1556 vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
1557         try {
1558         vector< vector<string> > files;
1559         string forward, reverse;
1560
1561         ifstream in;
1562         m->openInputFile(filename, in);
1563
1564         while(!in.eof()) {
1565
1566             if (m->control_pressed) { return files; }
1567
1568             in >> forward; m->gobble(in);
1569             in >> reverse; m->gobble(in);
1570
1571             //check to make sure both are able to be opened
1572             ifstream in2;
1573             int openForward = m->openInputFile(forward, in2, "noerror");
1574
1575             //if you can't open it, try default location
1576             if (openForward == 1) {
1577                 if (m->getDefaultPath() != "") { //default path is set
1578                     string tryPath = m->getDefaultPath() + m->getSimpleName(forward);
1579                     m->mothurOut("Unable to open " + forward + ". Trying default " + tryPath); m->mothurOutEndLine();
1580                     ifstream in3;
1581                     openForward = m->openInputFile(tryPath, in3, "noerror");
1582                     in3.close();
1583                     forward = tryPath;
1584                 }
1585             }
1586
1587             //if you can't open it, try output location
1588             if (openForward == 1) {
1589                 if (m->getOutputDir() != "") { //default path is set
1590                     string tryPath = m->getOutputDir() + m->getSimpleName(forward);
1591                     m->mothurOut("Unable to open " + forward + ". Trying output directory " + tryPath); m->mothurOutEndLine();
1592                     ifstream in4;
1593                     openForward = m->openInputFile(tryPath, in4, "noerror");
1594                     forward = tryPath;
1595                     in4.close();
1596                 }
1597             }
1598
1599             if (openForward == 1) { //can't find it
1600                 m->mothurOut("[WARNING]: can't find " + forward + ", ignoring pair.\n");
1601             }else{  in2.close();  }
1602
1603             ifstream in3;
1604             int openReverse = m->openInputFile(reverse, in3, "noerror");
1605
1606             //if you can't open it, try default location
1607             if (openReverse == 1) {
1608                 if (m->getDefaultPath() != "") { //default path is set
1609                     string tryPath = m->getDefaultPath() + m->getSimpleName(reverse);
1610                     m->mothurOut("Unable to open " + reverse + ". Trying default " + tryPath); m->mothurOutEndLine();
1611                     ifstream in3;
1612                     openReverse = m->openInputFile(tryPath, in3, "noerror");
1613                     in3.close();
1614                     reverse = tryPath;
1615                 }
1616             }
1617
1618             //if you can't open it, try output location
1619             if (openReverse == 1) {
1620                 if (m->getOutputDir() != "") { //default path is set
1621                     string tryPath = m->getOutputDir() + m->getSimpleName(reverse);
1622                     m->mothurOut("Unable to open " + reverse + ". Trying output directory " + tryPath); m->mothurOutEndLine();
1623                     ifstream in4;
1624                     openReverse = m->openInputFile(tryPath, in4, "noerror");
1625                     reverse = tryPath;
1626                     in4.close();
1627                 }
1628             }
1629
1630             if (openReverse == 1) { //can't find it
1631                 m->mothurOut("[WARNING]: can't find " + reverse + ", ignoring pair.\n");
1632             }else{  in3.close();  }
1633
1634             if ((openForward != 1) && (openReverse != 1)) { //good pair
1635                 vector<string> pair;
1636                 pair.push_back(forward);
1637                 pair.push_back(reverse);
1638                 files.push_back(pair);
1639             }
1640
1641         }
1642         in.close();
1643
1644         return files;
1645     }
1646     catch(exception& e) {
1647         m->errorOut(e, "MakeContigsCommand", "checkReads");
1648         exit(1);
1649     }
1650 }
1651 //***************************************************************************************************************
1652 //illumina data requires paired forward and reverse data
1653 //BARCODE   atgcatgc   atgcatgc    groupName
1654 //PRIMER   atgcatgc   atgcatgc    groupName
1655 //PRIMER   atgcatgc   atgcatgc
1656 bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, string rootname){
1657         try {
1658                 ifstream in;
1659                 m->openInputFile(oligosfile, in);
1660
1661                 ofstream test;
1662
1663                 string type, foligo, roligo, group;
1664
1665                 int indexPrimer = 0;
1666                 int indexBarcode = 0;
1667         set<string> uniquePrimers;
1668         set<string> uniqueBarcodes;
1669
1670                 while(!in.eof()){
1671
1672                         in >> type;
1673             cout << type << endl;
1674                         if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
1675
1676                         if(type[0] == '#'){
1677                                 while (!in.eof())       {       char c = in.get();  if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
1678                                 m->gobble(in);
1679                         }
1680                         else{
1681                                 m->gobble(in);
1682                                 //make type case insensitive
1683                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
1684
1685                                 in >> foligo;
1686
1687                 if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); }
1688
1689                                 for(int i=0;i<foligo.length();i++){
1690                                         foligo[i] = toupper(foligo[i]);
1691                                         if(foligo[i] == 'U')    {       foligo[i] = 'T';        }
1692                                 }
1693
1694                                 if(type == "FORWARD"){
1695                                         m->gobble(in);
1696
1697                     in >> roligo;
1698
1699                     for(int i=0;i<roligo.length();i++){
1700                         roligo[i] = toupper(roligo[i]);
1701                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1702                     }
1703                     //roligo = reverseOligo(roligo);
1704
1705                     group = "";
1706
1707                                         // get rest of line in case there is a primer name
1708                                         while (!in.eof())       {
1709                                                 char c = in.get();
1710                                                 if (c == 10 || c == 13){        break;  }
1711                                                 else if (c == 32 || c == 9){;} //space or tab
1712                                                 else {  group += c;  }
1713                                         }
1714
1715                     oligosPair newPrimer(foligo, roligo);
1716
1717                                         //check for repeat barcodes
1718                     string tempPair = foligo+roligo;
1719                     if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine();  }
1720                     else { uniquePrimers.insert(tempPair); }
1721
1722                     if (m->debug) {  if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer pair " + newPrimer.forward + " " + newPrimer.reverse + ".\n"); }  }
1723
1724                                         primers[indexPrimer]=newPrimer; indexPrimer++;
1725                                         primerNameVector.push_back(group);
1726                                 }else if(type == "BARCODE"){
1727                                         m->gobble(in);
1728
1729                     in >> roligo;
1730
1731                     for(int i=0;i<roligo.length();i++){
1732                         roligo[i] = toupper(roligo[i]);
1733                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1734                     }
1735                     //roligo = reverseOligo(roligo);
1736
1737                     oligosPair newPair(foligo, roligo);
1738
1739                     group = "";
1740                     while (!in.eof())   {
1741                                                 char c = in.get();
1742                                                 if (c == 10 || c == 13){        break;  }
1743                                                 else if (c == 32 || c == 9){;} //space or tab
1744                                                 else {  group += c;  }
1745                                         }
1746
1747                     if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
1748
1749                     //check for repeat barcodes
1750                     string tempPair = foligo+roligo;
1751                     if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse +  " is in your oligos file already, disregarding."); m->mothurOutEndLine();  }
1752                     else { uniqueBarcodes.insert(tempPair); }
1753
1754                     barcodes[indexBarcode]=newPair; indexBarcode++;
1755                                         barcodeNameVector.push_back(group);
1756                     cout << group << endl;
1757                                 }else if(type == "LINKER"){
1758                                         linker.push_back(foligo);
1759                     m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");
1760                                 }else if(type == "SPACER"){
1761                                         spacer.push_back(foligo);
1762                     m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n");
1763                                 }
1764                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); }
1765                         }
1766                         m->gobble(in);
1767                 }
1768                 in.close();
1769
1770                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
1771
1772                 //add in potential combos
1773                 if(barcodeNameVector.size() == 0){
1774             oligosPair temp("", "");
1775                         barcodes[0] = temp;
1776                         barcodeNameVector.push_back("");
1777                 }
1778
1779                 if(primerNameVector.size() == 0){
1780             oligosPair temp("", "");
1781                         primers[0] = temp;
1782                         primerNameVector.push_back("");
1783                 }
1784
1785                 fastaFileNames.resize(barcodeNameVector.size());
1786                 for(int i=0;i<fastaFileNames.size();i++){
1787                         fastaFileNames[i].assign(primerNameVector.size(), "");
1788                 }
1789                 qualFileNames = fastaFileNames;
1790
1791                 if(allFiles){
1792                         set<string> uniqueNames; //used to cleanup outputFileNames
1793                         for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1794                                 for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1795
1796                                         string primerName = primerNameVector[itPrimer->first];
1797                                         string barcodeName = barcodeNameVector[itBar->first];
1798
1799                     if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
1800                                         else {
1801                         string comboGroupName = "";
1802                         string fastaFileName = "";
1803                         string qualFileName = "";
1804                         string nameFileName = "";
1805                         string countFileName = "";
1806
1807                         if(primerName == ""){
1808                             comboGroupName = barcodeNameVector[itBar->first];
1809                         }
1810                         else{
1811                             if(barcodeName == ""){
1812                                 comboGroupName = primerNameVector[itPrimer->first];
1813                             }
1814                             else{
1815                                 comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
1816                             }
1817                         }
1818
1819
1820                         ofstream temp;
1821                         fastaFileName = rootname + comboGroupName + ".fasta";
1822                         if (uniqueNames.count(fastaFileName) == 0) {
1823                             outputNames.push_back(fastaFileName);
1824                             outputTypes["fasta"].push_back(fastaFileName);
1825                             uniqueNames.insert(fastaFileName);
1826                         }
1827
1828                         fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
1829                         m->openOutputFile(fastaFileName, temp);         temp.close();
1830
1831                         if ((fqualfile != "") || (ffastqfile != "") || (file != "")) {
1832                             qualFileName = rootname + ".qual";
1833                             if (uniqueNames.count(qualFileName) == 0) {
1834                                 outputNames.push_back(qualFileName);
1835                                 outputTypes["qfile"].push_back(qualFileName);
1836                             }
1837
1838                             qualFileNames[itBar->first][itPrimer->first] = qualFileName;
1839                             m->openOutputFile(qualFileName, temp);              temp.close();
1840                         }
1841                     }
1842                                 }
1843                         }
1844                 }
1845
1846                 bool allBlank = true;
1847                 for (int i = 0; i < barcodeNameVector.size(); i++) {
1848                         if (barcodeNameVector[i] != "") {
1849                                 allBlank = false;
1850                                 break;
1851                         }
1852                 }
1853                 for (int i = 0; i < primerNameVector.size(); i++) {
1854                         if (primerNameVector[i] != "") {
1855                                 allBlank = false;
1856                                 break;
1857                         }
1858                 }
1859
1860                 if (allBlank) {
1861                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
1862                         allFiles = false;
1863                         return false;
1864                 }
1865
1866                 return true;
1867
1868         }
1869         catch(exception& e) {
1870                 m->errorOut(e, "MakeContigsCommand", "getOligos");
1871                 exit(1);
1872         }
1873 }
1874 //********************************************************************/
1875 string MakeContigsCommand::reverseOligo(string oligo){
1876         try {
1877         string reverse = "";
1878
1879         for(int i=oligo.length()-1;i>=0;i--){
1880
1881             if(oligo[i] == 'A')         {       reverse += 'T'; }
1882             else if(oligo[i] == 'T'){   reverse += 'A'; }
1883             else if(oligo[i] == 'U'){   reverse += 'A'; }
1884
1885             else if(oligo[i] == 'G'){   reverse += 'C'; }
1886             else if(oligo[i] == 'C'){   reverse += 'G'; }
1887
1888             else if(oligo[i] == 'R'){   reverse += 'Y'; }
1889             else if(oligo[i] == 'Y'){   reverse += 'R'; }
1890
1891             else if(oligo[i] == 'M'){   reverse += 'K'; }
1892             else if(oligo[i] == 'K'){   reverse += 'M'; }
1893
1894             else if(oligo[i] == 'W'){   reverse += 'W'; }
1895             else if(oligo[i] == 'S'){   reverse += 'S'; }
1896
1897             else if(oligo[i] == 'B'){   reverse += 'V'; }
1898             else if(oligo[i] == 'V'){   reverse += 'B'; }
1899
1900             else if(oligo[i] == 'D'){   reverse += 'H'; }
1901             else if(oligo[i] == 'H'){   reverse += 'D'; }
1902
1903             else                                                {       reverse += 'N'; }
1904         }
1905
1906
1907         return reverse;
1908     }
1909         catch(exception& e) {
1910                 m->errorOut(e, "MakeContigsCommand", "reverseOligo");
1911                 exit(1);
1912         }
1913 }
1914 //**********************************************************************************************************************
1915
1916
1917
1918