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","",false,false,true); parameters.push_back(pfqual);
  19         CommandParameter prqual("rqfile", "InputTypes", "", "", "none", "none", "qfileGroup","",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 ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
  25
  26         CommandParameter palign("align", "Multiple", "needleman-gotoh", "needleman", "", "", "","",false,false); parameters.push_back(palign);
  27         CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pallfiles);
  28         CommandParameter ptrimoverlap("trimoverlap", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptrimoverlap);
  29                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "","",false,false); parameters.push_back(pmatch);
  30                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch);
  31                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen);
  32                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend);
  33         CommandParameter pthreshold("insert", "Number", "", "20", "", "", "","",false,false); parameters.push_back(pthreshold);
  34         CommandParameter pdeltaq("deltaq", "Number", "", "6", "", "", "","",false,false); parameters.push_back(pdeltaq);
  35                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  36         CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat);
  37                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  38                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  39
  40                 vector<string> myArray;
  41                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  42                 return myArray;
  43         }
  44         catch(exception& e) {
  45                 m->errorOut(e, "MakeContigsCommand", "setParameters");
  46                 exit(1);
  47         }
  48 }
  49 //**********************************************************************************************************************
  50 string MakeContigsCommand::getHelpString(){
  51         try {
  52                 string helpString = "";
  53                 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";
  54         helpString += "If an oligos file is provided barcodes and primers will be trimmed, and a group file will be created.\n";
  55                 helpString += "The make.contigs command parameters are file, ffastq, rfastq, ffasta, rfasta, fqfile, rqfile, oligos, format, tdiffs, bdiffs, pdiffs, align, match, mismatch, gapopen, gapextend, insert, deltaq, allfiles and processors.\n";
  56                 helpString += "The ffastq and rfastq, file, or ffasta and rfasta parameters are required.\n";
  57         helpString += "The file parameter is 2 or 3 column file containing the forward fastq files in the first column and their matching reverse fastq files in the second column, or a groupName then forward fastq file and reverse fastq file.  Mothur will process each pair and create a combined fasta and report file with all the sequences.\n";
  58         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";
  59         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";
  60         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";
  61                 helpString += "The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=illumina1.8+.\n";
  62         helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh and needleman. The default is needleman.\n";
  63         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";
  64                 helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
  65                 helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
  66         //helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
  67                 //helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
  68                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n";
  69                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n";
  70         helpString += "The deltaq parameter allows you to specify the delta allowed between quality scores of a mismatched base.  For example in the overlap, if deltaq=5 and in the alignment seqA, pos 200 has a quality score of 30 and the same position in seqB has a quality score of 20, you take the base from seqA (30-20 >= 5).  If the quality score in seqB is 28 then the base in the consensus will be an N (30-28<5) The default is 6.\n";
  71                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n";
  72                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n";
  73         helpString += "The insert 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 equal to or below the threshold we eliminate it. Default=20.\n";
  74         helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  75         helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
  76         helpString += "The trimoverlap parameter allows you to trim the sequences to only the overlapping section. The default is F.\n";
  77         helpString += "The make.contigs command should be in the following format: \n";
  78                 helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
  79                 helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
  80                 return helpString;
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "MakeContigsCommand", "getHelpString");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88 string MakeContigsCommand::getOutputPattern(string type) {
  89     try {
  90         string pattern = "";
  91
  92         if (type == "fasta") {  pattern = "[filename],[tag],contigs.fasta"; }
  93         else if (type == "group") {  pattern = "[filename],[tag],contigs.groups"; }
  94         else if (type == "report") {  pattern = "[filename],[tag],contigs.report"; }
  95         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  96
  97         return pattern;
  98     }
  99     catch(exception& e) {
 100         m->errorOut(e, "MakeContigsCommand", "getOutputPattern");
 101         exit(1);
 102     }
 103 }
 104 //**********************************************************************************************************************
 105 MakeContigsCommand::MakeContigsCommand(){
 106         try {
 107                 abort = true; calledHelp = true;
 108                 setParameters();
 109                 vector<string> tempOutNames;
 110                 outputTypes["fasta"] = tempOutNames;
 111         outputTypes["group"] = tempOutNames;
 112         outputTypes["report"] = tempOutNames;
 113         }
 114         catch(exception& e) {
 115                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 116                 exit(1);
 117         }
 118 }
 119 //**********************************************************************************************************************
 120 MakeContigsCommand::MakeContigsCommand(string option)  {
 121         try {
 122                 abort = false; calledHelp = false;
 123         createFileGroup = false; createOligosGroup = false;
 124
 125                 //allow user to run help
 126                 if(option == "help") { help(); abort = true; calledHelp = true; }
 127                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 128
 129                 else {
 130                         vector<string> myArray = setParameters();
 131
 132                         OptionParser parser(option);
 133                         map<string, string> parameters = parser.getParameters();
 134
 135                         ValidParameters validParameter("pairwise.seqs");
 136                         map<string, string>::iterator it;
 137
 138                         //check to make sure all parameters are valid for command
 139                         for (it = parameters.begin(); it != parameters.end(); it++) {
 140                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 141                         }
 142
 143                         //initialize outputTypes
 144                         vector<string> tempOutNames;
 145                         outputTypes["fasta"] = tempOutNames;
 146             outputTypes["report"] = tempOutNames;
 147             outputTypes["group"] = tempOutNames;
 148
 149
 150                         //if the user changes the input directory command factory will send this info to us in the output parameter
 151                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 152                         if (inputDir == "not found"){   inputDir = "";          }
 153                         else {
 154                                 string path;
 155                 it = parameters.find("ffastq");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["ffastq"] = inputDir + it->second;           }
 161                                 }
 162
 163                 it = parameters.find("rfastq");
 164                                 //user has given a template file
 165                                 if(it != parameters.end()){
 166                                         path = m->hasPath(it->second);
 167                                         //if the user has not given a path then, add inputdir. else leave path alone.
 168                                         if (path == "") {       parameters["rfastq"] = inputDir + it->second;           }
 169                                 }
 170
 171                 it = parameters.find("ffasta");
 172                                 //user has given a template file
 173                                 if(it != parameters.end()){
 174                                         path = m->hasPath(it->second);
 175                                         //if the user has not given a path then, add inputdir. else leave path alone.
 176                                         if (path == "") {       parameters["ffasta"] = inputDir + it->second;           }
 177                                 }
 178
 179                 it = parameters.find("rfasta");
 180                                 //user has given a template file
 181                                 if(it != parameters.end()){
 182                                         path = m->hasPath(it->second);
 183                                         //if the user has not given a path then, add inputdir. else leave path alone.
 184                                         if (path == "") {       parameters["rfasta"] = inputDir + it->second;           }
 185                                 }
 186
 187                 it = parameters.find("fqfile");
 188                                 //user has given a template file
 189                                 if(it != parameters.end()){
 190                                         path = m->hasPath(it->second);
 191                                         //if the user has not given a path then, add inputdir. else leave path alone.
 192                                         if (path == "") {       parameters["fqfile"] = inputDir + it->second;           }
 193                                 }
 194
 195                 it = parameters.find("rqfile");
 196                                 //user has given a template file
 197                                 if(it != parameters.end()){
 198                                         path = m->hasPath(it->second);
 199                                         //if the user has not given a path then, add inputdir. else leave path alone.
 200                                         if (path == "") {       parameters["rqfile"] = inputDir + it->second;           }
 201                                 }
 202
 203                 it = parameters.find("file");
 204                                 //user has given a template file
 205                                 if(it != parameters.end()){
 206                                         path = m->hasPath(it->second);
 207                                         //if the user has not given a path then, add inputdir. else leave path alone.
 208                                         if (path == "") {       parameters["file"] = inputDir + it->second;             }
 209                                 }
 210
 211                 it = parameters.find("oligos");
 212                                 //user has given a template file
 213                                 if(it != parameters.end()){
 214                                         path = m->hasPath(it->second);
 215                                         //if the user has not given a path then, add inputdir. else leave path alone.
 216                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 217                                 }
 218             }
 219
 220             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
 221                         if (ffastqfile == "not open") {  abort = true; }
 222                         else if (ffastqfile == "not found") { ffastqfile = ""; }
 223
 224                         rfastqfile = validParameter.validFile(parameters, "rfastq", true);
 225                         if (rfastqfile == "not open") {  abort = true; }
 226                         else if (rfastqfile == "not found") { rfastqfile = "";  }
 227
 228             ffastafile = validParameter.validFile(parameters, "ffasta", true);
 229                         if (ffastafile == "not open") {  abort = true; }
 230                         else if (ffastafile == "not found") { ffastafile = ""; }
 231
 232                         rfastafile = validParameter.validFile(parameters, "rfasta", true);
 233                         if (rfastafile == "not open") {  abort = true; }
 234                         else if (rfastafile == "not found") { rfastafile = "";  }
 235
 236             fqualfile = validParameter.validFile(parameters, "fqfile", true);
 237                         if (fqualfile == "not open") {  abort = true; }
 238                         else if (fqualfile == "not found") { fqualfile = ""; }
 239
 240                         rqualfile = validParameter.validFile(parameters, "rqfile", true);
 241                         if (rqualfile == "not open") {  abort = true; }
 242                         else if (rqualfile == "not found") { rqualfile = "";  }
 243
 244             file = validParameter.validFile(parameters, "file", true);
 245                         if (file == "not open") {  abort = true; }
 246                         else if (file == "not found") { file = "";  }
 247
 248             //provide at least
 249             if ((file == "") && (ffastafile == "") && (ffastqfile == "")) { abort = true; m->mothurOut("[ERROR]: The file, ffastq and rfastq or ffasta and rfasta parameters are required.\n"); }
 250             if ((file != "") && ((ffastafile != "") || (ffastqfile != ""))) { abort = true; m->mothurOut("[ERROR]: The file, ffastq and rfastq or ffasta and rfasta parameters are required.\n"); }
 251             if ((ffastqfile != "") && (rfastqfile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the ffastq, you must provide a rfastq file.\n"); }
 252             if ((ffastqfile == "") && (rfastqfile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rfastq, you must provide a ffastq file.\n"); }
 253             if ((ffastafile != "") && (rfastafile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the ffasta, you must provide a rfasta file.\n"); }
 254             if ((ffastafile == "") && (rfastafile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rfasta, you must provide a ffasta file.\n"); }
 255             if ((fqualfile != "") && (rqualfile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the fqfile, you must provide a rqfile file.\n"); }
 256             if ((fqualfile == "") && (rqualfile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rqfile, you must provide a fqfile file.\n"); }
 257             if (((fqualfile != "") || (rqualfile != "")) && ((ffastafile == "") || (rfastafile == ""))) {
 258                 abort = true; m->mothurOut("[ERROR]: If you provide use the rqfile or fqfile file, you must provide the ffasta and rfasta parameters.\n");
 259             }
 260
 261             oligosfile = validParameter.validFile(parameters, "oligos", true);
 262                         if (oligosfile == "not found")      {   oligosfile = "";        }
 263                         else if(oligosfile == "not open")   {   abort = true;       }
 264                         else {   m->setOligosFile(oligosfile);          }
 265
 266             //if the user changes the output directory command factory will send this info to us in the output parameter
 267                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 268                  outputDir = "";
 269             }
 270
 271
 272                         //check for optional parameter and set defaults
 273                         // ...at some point should added some additional type checking...
 274                         string temp;
 275                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 276                         m->mothurConvert(temp, match);
 277
 278                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 279                         m->mothurConvert(temp, misMatch);
 280             if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 281
 282                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 283                         m->mothurConvert(temp, gapOpen);
 284             if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 285
 286                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 287                         m->mothurConvert(temp, gapExtend);
 288             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 289
 290             temp = validParameter.validFile(parameters, "insert", false);       if (temp == "not found"){       temp = "20";                    }
 291                         m->mothurConvert(temp, insert);
 292             if ((insert < 0) || (insert > 40)) { m->mothurOut("[ERROR]: insert must be between 0 and 40.\n"); abort=true; }
 293
 294             temp = validParameter.validFile(parameters, "deltaq", false);       if (temp == "not found"){       temp = "6";                     }
 295                         m->mothurConvert(temp, deltaq);
 296
 297                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 298                         m->setProcessors(temp);
 299                         m->mothurConvert(temp, processors);
 300
 301             temp = validParameter.validFile(parameters, "bdiffs", false);               if (temp == "not found") { temp = "0"; }
 302                         m->mothurConvert(temp, bdiffs);
 303
 304                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 305                         m->mothurConvert(temp, pdiffs);
 306
 307   //          temp = validParameter.validFile(parameters, "ldiffs", false);             if (temp == "not found") { temp = "0"; }
 308 //                      m->mothurConvert(temp, ldiffs);
 309             ldiffs = 0;
 310
 311  //           temp = validParameter.validFile(parameters, "sdiffs", false);             if (temp == "not found") { temp = "0"; }
 312  //           m->mothurConvert(temp, sdiffs);
 313             sdiffs = 0;
 314
 315                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 316                         m->mothurConvert(temp, tdiffs);
 317
 318                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }  //+ ldiffs + sdiffs;
 319
 320             temp = validParameter.validFile(parameters, "allfiles", false);             if (temp == "not found") { temp = "F"; }
 321                         allFiles = m->isTrue(temp);
 322
 323             temp = validParameter.validFile(parameters, "trimoverlap", false);          if (temp == "not found") { temp = "F"; }
 324                         trimOverlap = m->isTrue(temp);
 325
 326                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 327                         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"; }
 328
 329             format = validParameter.validFile(parameters, "format", false);             if (format == "not found"){     format = "illumina1.8+";        }
 330
 331             if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+") && (format != "solexa"))  {
 332                                 m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
 333                                 abort=true;
 334                         }
 335
 336             //fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
 337             for (int i = -64; i < 65; i++) {
 338                 char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
 339                 convertTable.push_back(temp);
 340             }
 341         }
 342
 343         }
 344         catch(exception& e) {
 345                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 346                 exit(1);
 347         }
 348 }
 349 //**********************************************************************************************************************
 350 int MakeContigsCommand::execute(){
 351         try {
 352                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 353
 354         //read ffastq and rfastq files creating fasta and qual files.
 355         //this function will create a forward and reverse, fasta and qual files for each processor.
 356         //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.
 357         unsigned long int numReads = 0;
 358         int start = time(NULL);
 359         longestBase = 1000;
 360         m->mothurOut("Reading fastq data...\n");
 361         vector < vector< vector<string> > > filesToProcess = preProcessData(numReads);
 362         m->mothurOut("Done.\n");
 363
 364         if (m->control_pressed) { return 0; }
 365
 366         map<string, string> cvars;
 367         string compOutputDir = outputDir;
 368         if (outputDir == "") { compOutputDir = m->hasPath(file); }
 369         cvars["[filename]"] = compOutputDir + m->getRootName(m->getSimpleName(file));
 370         cvars["[tag]"] = "";
 371         string compositeGroupFile = getOutputFileName("group",cvars);
 372         cvars["[tag]"] = "trim";
 373         string compositeFastaFile = getOutputFileName("fasta",cvars);
 374         cvars["[tag]"] = "scrap";
 375         string compositeScrapFastaFile = getOutputFileName("fasta",cvars);
 376         cvars["[tag]"] = "";
 377         string compositeMisMatchFile = getOutputFileName("report",cvars);
 378
 379         if (filesToProcess.size() > 1) { //clear files for append below
 380             ofstream outCTFasta, outCTQual, outCSFasta, outCSQual, outCMisMatch;
 381             m->openOutputFile(compositeFastaFile, outCTFasta); outCTFasta.close();
 382             m->openOutputFile(compositeScrapFastaFile, outCSFasta); outCSFasta.close();
 383             m->openOutputFile(compositeMisMatchFile, outCMisMatch); outCMisMatch.close();
 384             outputNames.push_back(compositeFastaFile); outputTypes["fasta"].push_back(compositeFastaFile);
 385             outputNames.push_back(compositeMisMatchFile); outputTypes["report"].push_back(compositeMisMatchFile);
 386             outputNames.push_back(compositeScrapFastaFile); outputTypes["fasta"].push_back(compositeScrapFastaFile);
 387         }
 388
 389         for (int l = 0; l < filesToProcess.size(); l++) {
 390
 391             m->mothurOut("\n>>>>>\tProcessing " + filesToProcess[l][0][0] + " (file " + toString(l+1) + " of " + toString(filesToProcess.size()) + ")\t<<<<<\n");
 392
 393             vector<vector<string> > fastaFileNames;
 394             createOligosGroup = false;
 395             string outputGroupFileName;
 396             map<string, string> variables;
 397             string thisOutputDir = outputDir;
 398             if (outputDir == "") {  thisOutputDir = m->hasPath(filesToProcess[l][0][0]); }
 399             variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(filesToProcess[l][0][0]));
 400             variables["[tag]"] = "";
 401             if(oligosfile != ""){  createOligosGroup = getOligos(fastaFileNames, variables["[filename]"]);  }
 402             if (createOligosGroup || createFileGroup) {
 403                 outputGroupFileName = getOutputFileName("group",variables);
 404             }
 405
 406             //give group in file file precedence
 407             if (createFileGroup) {  createOligosGroup = false; }
 408
 409             variables["[tag]"] = "trim";
 410             string outFastaFile = getOutputFileName("fasta",variables);
 411             variables["[tag]"] = "scrap";
 412             string outScrapFastaFile = getOutputFileName("fasta",variables);
 413             variables["[tag]"] = "";
 414             string outMisMatchFile = getOutputFileName("report",variables);
 415
 416             m->mothurOut("Making contigs...\n");
 417             createProcesses(filesToProcess[l], outFastaFile, outScrapFastaFile, outMisMatchFile, fastaFileNames, l);
 418             m->mothurOut("Done.\n");
 419
 420             //remove temp fasta and qual files
 421             for (int i = 0; i < processors; i++) { for(int j = 0; j < filesToProcess[l][i].size(); j++) { m->mothurRemove(filesToProcess[l][i][j]); }  }
 422
 423             if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); }  return 0; }
 424
 425             if(allFiles){
 426                 map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
 427                 map<string, string>::iterator it;
 428                 set<string> namesToRemove;
 429                 for(int i=0;i<fastaFileNames.size();i++){
 430                     for(int j=0;j<fastaFileNames[0].size();j++){
 431                         if (fastaFileNames[i][j] != "") {
 432                             if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
 433                                 if(m->isBlank(fastaFileNames[i][j])){
 434                                     m->mothurRemove(fastaFileNames[i][j]);
 435                                     namesToRemove.insert(fastaFileNames[i][j]);
 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 (createFileGroup || createOligosGroup) {
 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 (createFileGroup || createOligosGroup) {
 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                     if (!allFiles) { m->mothurRemove(outputGroupFileName);  }
 490                     else { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
 491                 }
 492                 if (l == 0) {  m->appendFiles(outMisMatchFile, compositeMisMatchFile);  }
 493                 else {  m->appendFilesWithoutHeaders(outMisMatchFile, compositeMisMatchFile);  }
 494                 m->appendFiles(outFastaFile, compositeFastaFile);
 495                 m->appendFiles(outScrapFastaFile, compositeScrapFastaFile);
 496                 if (!allFiles) {
 497                     m->mothurRemove(outMisMatchFile);
 498                     m->mothurRemove(outFastaFile);
 499                     m->mothurRemove(outScrapFastaFile);
 500                 }else {
 501                     outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 502                     outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
 503                     outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
 504                 }
 505             }else {
 506                 outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 507                 outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
 508                 outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
 509                 if (createFileGroup || createOligosGroup) { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
 510             }
 511         }
 512         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 513
 514         if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 515
 516                 //output group counts
 517                 m->mothurOutEndLine();
 518                 int total = 0;
 519                 if (groupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
 520                 for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 521             total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
 522                 }
 523                 if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
 524
 525                 if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 526
 527         string currentFasta = "";
 528                 itTypes = outputTypes.find("fasta");
 529                 if (itTypes != outputTypes.end()) {
 530                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 531                 }
 532
 533         string currentGroup = "";
 534                 itTypes = outputTypes.find("group");
 535                 if (itTypes != outputTypes.end()) {
 536                         if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); }
 537                 }
 538
 539         //output files created by command
 540                 m->mothurOutEndLine();
 541                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 542                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 543                 m->mothurOutEndLine();
 544
 545         return 0;
 546     }
 547         catch(exception& e) {
 548                 m->errorOut(e, "MakeContigsCommand", "execute");
 549                 exit(1);
 550         }
 551 }
 552 //**********************************************************************************************************************
 553 vector< vector< vector<string> > > MakeContigsCommand::preProcessData(unsigned long int& numReads) {
 554         try {
 555         vector< vector< vector<string> > > filesToProcess;
 556
 557         if (ffastqfile != "") { //reading one file
 558             vector< vector<string> > files = readFastqFiles(numReads, ffastqfile, rfastqfile);
 559             //adjust for really large processors or really small files
 560             if (numReads == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
 561             if (numReads < processors) {
 562                 for (int i = numReads; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 563                 files.resize(numReads);
 564                 processors = numReads;
 565             }
 566             filesToProcess.push_back(files);
 567         }else if (file != "") { //reading multiple files
 568             //return only valid pairs
 569             vector< vector<string> > filePairsToProcess = readFileNames(file);
 570
 571             if (m->control_pressed) { return filesToProcess; }
 572
 573             if (filePairsToProcess.size() != 0) {
 574                 for (int i = 0; i < filePairsToProcess.size(); i++) {
 575
 576                     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; } }
 577
 578                     unsigned long int thisFilesReads;
 579                     vector< vector<string> > files = readFastqFiles(thisFilesReads, filePairsToProcess[i][0], filePairsToProcess[i][1]);
 580
 581                     //adjust for really large processors or really small files
 582                     if (thisFilesReads < processors) {
 583                         m->mothurOut("[ERROR]: " + filePairsToProcess[i][0] + " has less than " + toString(processors) + " good reads, skipping\n");
 584                         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(); }
 585                     }else {
 586                         filesToProcess.push_back(files);
 587                         numReads += thisFilesReads;
 588                     }
 589                 }
 590                 //all files are bad
 591                 if (numReads == 0) {  m->control_pressed = true; }
 592             }
 593         }else if (ffastafile != "") {
 594             vector< vector<string> > files = readFastaFiles(numReads, ffastafile, rfastafile);
 595             //adjust for really large processors or really small files
 596             if (numReads == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
 597             if (numReads < processors) {
 598                 for (int i = numReads; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 599                 files.resize(numReads);
 600                 processors = numReads;
 601             }
 602             filesToProcess.push_back(files);
 603         }else { m->control_pressed = true; } //should not get here
 604
 605         return filesToProcess;
 606     }
 607         catch(exception& e) {
 608                 m->errorOut(e, "MakeContigsCommand", "preProcessData");
 609                 exit(1);
 610         }
 611 }
 612 //**********************************************************************************************************************
 613 int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int index) {
 614         try {
 615                 int num = 0;
 616                 vector<int> processIDS;
 617         string group = "";
 618         map<int, string>::iterator it = file2Group.find(index);
 619         if (it != file2Group.end()) { group = it->second; }
 620
 621 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 622                 int process = 0;
 623
 624                 //loop through and create all the processes you want
 625                 while (process != processors-1) {
 626                         int pid = fork();
 627
 628                         if (pid > 0) {
 629                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 630                                 process++;
 631                         }else if (pid == 0){
 632                 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 633
 634                                 if(allFiles){
 635                                         ofstream temp;
 636
 637                                         for(int i=0;i<tempFASTAFileNames.size();i++){
 638                                                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 639                                                         if (tempFASTAFileNames[i][j] != "") {
 640                                                                 tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
 641                                                                 m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 642                                                         }
 643                                                 }
 644                                         }
 645                                 }
 646
 647                                 num = driver(files[process],
 648                              outputFasta + toString(getpid()) + ".temp",
 649                              outputScrapFasta + toString(getpid()) + ".temp",
 650                              outputMisMatches + toString(getpid()) + ".temp",
 651                              tempFASTAFileNames, process, group);
 652
 653                                 //pass groupCounts to parent
 654                 ofstream out;
 655                 string tempFile = toString(getpid()) + ".num.temp";
 656                 m->openOutputFile(tempFile, out);
 657                 out << num << endl;
 658                                 if (createFileGroup || createOligosGroup) {
 659                                         out << groupCounts.size() << endl;
 660
 661                                         for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 662                                                 out << it->first << '\t' << it->second << endl;
 663                                         }
 664
 665                     out << groupMap.size() << endl;
 666                     for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
 667                                                 out << it->first << '\t' << it->second << endl;
 668                                         }
 669                                 }
 670                 out.close();
 671
 672                                 exit(0);
 673                         }else {
 674                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 675                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 676                                 exit(0);
 677                         }
 678                 }
 679
 680         ofstream temp;
 681                 m->openOutputFile(outputFasta, temp);           temp.close();
 682         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 683
 684                 //do my part
 685                 num = driver(files[processors-1], outputFasta, outputScrapFasta,  outputMisMatches, fastaFileNames, processors-1, group);
 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 (createFileGroup || createOligosGroup) {
 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
 745             if(allFiles){
 746                 ofstream temp;
 747
 748                 for(int i=0;i<tempFASTAFileNames.size();i++){
 749                     for(int j=0;j<tempFASTAFileNames[i].size();j++){
 750                         if (tempFASTAFileNames[i][j] != "") {
 751                             tempFASTAFileNames[i][j] += extension;
 752                             m->openOutputFile(tempFASTAFileNames[i][j], temp);                  temp.close();
 753                         }
 754                     }
 755                 }
 756             }
 757
 758
 759                         contigsData* tempcontig = new contigsData(group, files[h], (outputFasta + extension), (outputScrapFasta + extension), (outputMisMatches + extension), align, m, match, misMatch, gapOpen, gapExtend, insert, deltaq, barcodes, primers, tempFASTAFileNames, barcodeNameVector, primerNameVector, pdiffs, bdiffs, tdiffs, createOligosGroup, createFileGroup, allFiles, trimOverlap, h);
 760                         pDataArray.push_back(tempcontig);
 761
 762                         hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
 763                 }
 764
 765         vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 766
 767         if(allFiles){
 768             ofstream temp;
 769             string extension = toString(processors-1) + ".temp";
 770
 771             for(int i=0;i<tempFASTAFileNames.size();i++){
 772                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 773                     if (tempFASTAFileNames[i][j] != "") {
 774                         tempFASTAFileNames[i][j] += extension;
 775                         m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 776                     }
 777                 }
 778             }
 779         }
 780
 781                 //parent do my part
 782                 ofstream temp;
 783                 m->openOutputFile(outputFasta, temp);           temp.close();
 784         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 785
 786         //do my part
 787         processIDS.push_back(processors-1);
 788                 num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"),  (outputScrapFasta+ toString(processors-1) + ".temp"),  (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, processors-1, group);
 789
 790                 //Wait until all threads have terminated.
 791                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 792
 793                 //Close all thread handles and free memory allocations.
 794                 for(int i=0; i < pDataArray.size(); i++){
 795                         num += pDataArray[i]->count;
 796             if (!pDataArray[i]->done) {
 797                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of sequences assigned to it, quitting. \n"); m->control_pressed = true;
 798             }
 799             for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
 800                 map<string, int>::iterator it2 = groupCounts.find(it->first);
 801                 if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
 802                 else { groupCounts[it->first] += it->second; }
 803             }
 804             for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
 805                 map<string, string>::iterator it2 = groupMap.find(it->first);
 806                 if (it2 == groupMap.end()) {    groupMap[it->first] = it->second; }
 807                 else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 808             }
 809             CloseHandle(hThreadArray[i]);
 810                         delete pDataArray[i];
 811         }
 812
 813     #endif
 814
 815         for (int i = 0; i < processIDS.size(); i++) {
 816                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 817                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 818
 819                         m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
 820                         m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp"));
 821
 822             m->appendFilesWithoutHeaders((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 823                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 824
 825             if(allFiles){
 826                                 for(int j=0;j<fastaFileNames.size();j++){
 827                                         for(int k=0;k<fastaFileNames[j].size();k++){
 828                                                 if (fastaFileNames[j][k] != "") {
 829                                                         m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
 830                                                         m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 831                                                 }
 832                                         }
 833                                 }
 834                         }
 835                 }
 836
 837                 return num;
 838         }
 839         catch(exception& e) {
 840                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 841                 exit(1);
 842         }
 843 }
 844 //**********************************************************************************************************************
 845 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int process, string group){
 846     try {
 847
 848         Alignment* alignment;
 849         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 850                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 851
 852         int num = 0;
 853         string thisffastafile = files[0];
 854         string thisfqualfile = files[1];
 855         string thisrfastafile = files[2];
 856         string thisrqualfile = files[3];
 857
 858         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 859
 860         ifstream inFFasta, inRFasta, inFQual, inRQual;
 861         ofstream outFasta, outMisMatch, outScrapFasta;
 862         m->openInputFile(thisffastafile, inFFasta);
 863         m->openInputFile(thisrfastafile, inRFasta);
 864         if (thisfqualfile != "") {
 865             m->openInputFile(thisfqualfile, inFQual);
 866             m->openInputFile(thisrqualfile, inRQual);
 867         }
 868         m->openOutputFile(outputFasta, outFasta);
 869         m->openOutputFile(outputScrapFasta, outScrapFasta);
 870         m->openOutputFile(outputMisMatches, outMisMatch);
 871         outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n";
 872
 873         TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
 874
 875         while ((!inFFasta.eof()) && (!inRFasta.eof())) {
 876
 877             if (m->control_pressed) { break; }
 878
 879             int success = 1;
 880             string trashCode = "";
 881             int currentSeqsDiffs = 0;
 882
 883             //read seqs and quality info
 884             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 885             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 886             QualityScores* fQual = NULL; QualityScores* rQual = NULL;
 887             if (thisfqualfile != "") {
 888                 fQual = new QualityScores(inFQual); m->gobble(inFQual);
 889                 rQual = new QualityScores(inRQual); m->gobble(inRQual);
 890             }
 891
 892             int barcodeIndex = 0;
 893             int primerIndex = 0;
 894
 895             if(barcodes.size() != 0){
 896                 if (thisfqualfile != "") {
 897                     success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
 898                 }else {
 899                     success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
 900                 }
 901                 if(success > bdiffs)            {       trashCode += 'b';       }
 902                 else{ currentSeqsDiffs += success;  }
 903             }
 904
 905             if(primers.size() != 0){
 906                 if (thisfqualfile != "") {
 907                     success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
 908                 }else {
 909                     success = trimOligos.stripForward(fSeq, rSeq, primerIndex);
 910                 }
 911                 if(success > pdiffs)            {       trashCode += 'f';       }
 912                 else{ currentSeqsDiffs += success;  }
 913             }
 914
 915             if (currentSeqsDiffs > tdiffs)      {       trashCode += 't';   }
 916
 917             //flip the reverse reads
 918             rSeq.reverseComplement();
 919             if (thisfqualfile != "") { rQual->flipQScores(); }
 920
 921             //pairwise align
 922             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 923             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 924             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 925             fSeq.setAligned(alignment->getSeqAAln());
 926             rSeq.setAligned(alignment->getSeqBAln());
 927             int length = fSeq.getAligned().length();
 928
 929             //traverse alignments merging into one contiguous seq
 930             string contig = "";
 931             int numMismatches = 0;
 932             string seq1 = fSeq.getAligned();
 933             string seq2 = rSeq.getAligned();
 934             vector<int> scores1, scores2;
 935             if (thisfqualfile != "") {
 936                 scores1 = fQual->getQualityScores();
 937                 scores2 = rQual->getQualityScores();
 938                 delete fQual; delete rQual;
 939             }
 940
 941             // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
 942             int overlapStart = fSeq.getStartPos();
 943             int seq2Start = rSeq.getStartPos();
 944
 945             //bigger of the 2 starting positions is the location of the overlapping start
 946             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 947                 overlapStart = seq2Start;
 948                 for (int i = 0; i < overlapStart; i++) { contig += seq1[i];  }
 949             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 950                 for (int i = 0; i < overlapStart; i++) {  contig += seq2[i]; }
 951             }
 952
 953             int seq1End = fSeq.getEndPos();
 954             int seq2End = rSeq.getEndPos();
 955             int overlapEnd = seq1End;
 956             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 957
 958             int oStart = contig.length();
 959             for (int i = overlapStart; i < overlapEnd; i++) {
 960                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 961                     contig += seq1[i];
 962                 }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 insert. In that case eliminate base
 963                     if (thisfqualfile != "") {
 964                         if (scores2[BBaseMap[i]] <= insert) { } //
 965                         else { contig += seq2[i];  }
 966                     }else { contig += seq2[i]; } //with no quality info, then we keep it?
 967                 }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 insert. In that case eliminate base
 968                     if (thisfqualfile != "") {
 969                         if (scores1[ABaseMap[i]] <= insert) { } //
 970                         else { contig += seq1[i];  }
 971                     }else { contig += seq1[i]; } //with no quality info, then we keep it?
 972                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 973                     if (thisfqualfile != "") {
 974                         if (abs(scores1[ABaseMap[i]] - scores2[BBaseMap[i]]) >= deltaq) { //is the difference in qual scores >= deltaq, if yes choose base with higher score
 975                             char c = seq1[i];
 976                             if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { c = seq2[i]; }
 977                             contig += c;
 978                         }else { //if no, base becomes n
 979                             contig += 'N';
 980                         }
 981                         numMismatches++;
 982                     }else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
 983                 }else { //should never get here
 984                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
 985                 }
 986             }
 987             int oend = contig.length();
 988             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
 989                 for (int i = overlapEnd; i < length; i++) { contig += seq2[i];  }
 990             }else { //seq2 ends before seq1 so take from overlap to length from seq1
 991                 for (int i = overlapEnd; i < length; i++) {  contig += seq1[i]; }
 992             }
 993
 994             if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart);  if (contig.length() == 0) { trashCode += "l"; } }
 995
 996             if(trashCode.length() == 0){
 997                 bool ignore = false;
 998
 999                 if (m->debug) { m->mothurOut(fSeq.getName()); }
1000
1001                 if (createOligosGroup) {
1002                     if(barcodes.size() != 0){
1003                         string thisGroup = barcodeNameVector[barcodeIndex];
1004                         if (primers.size() != 0) {
1005                             if (primerNameVector[primerIndex] != "") {
1006                                 if(thisGroup != "") {
1007                                     thisGroup += "." + primerNameVector[primerIndex];
1008                                 }else {
1009                                     thisGroup = primerNameVector[primerIndex];
1010                                 }
1011                             }
1012                         }
1013
1014                         if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
1015
1016                         int pos = thisGroup.find("ignore");
1017                         if (pos == string::npos) {
1018                             groupMap[fSeq.getName()] = thisGroup;
1019
1020                             map<string, int>::iterator it = groupCounts.find(thisGroup);
1021                             if (it == groupCounts.end()) {      groupCounts[thisGroup] = 1; }
1022                             else { groupCounts[it->first] ++; }
1023                         }else { ignore = true; }
1024
1025                     }
1026                 }else if (createFileGroup) {
1027                     int pos = group.find("ignore");
1028                     if (pos == string::npos) {
1029                         groupMap[fSeq.getName()] = group;
1030
1031                         map<string, int>::iterator it = groupCounts.find(group);
1032                         if (it == groupCounts.end()) {  groupCounts[group] = 1; }
1033                         else { groupCounts[it->first] ++; }
1034                     }else { ignore = true; }
1035                 }
1036                 if (m->debug) { m->mothurOut("\n"); }
1037
1038                 if(allFiles && !ignore){
1039                     ofstream output;
1040                     m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
1041                     output << ">" << fSeq.getName() << endl << contig << endl;
1042                     output.close();
1043                 }
1044
1045                 //output
1046                 outFasta << ">" << fSeq.getName() << endl << contig << endl;
1047                 int numNs = 0;
1048                 for (int i = 0; i < contig.length(); i++) { if (contig[i] == 'N') { numNs++; }  }
1049                 outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << (oend-oStart) << '\t' << oStart << '\t' << oend << '\t' << numMismatches << '\t' << numNs << endl;
1050             }else {
1051                 //output
1052                 outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
1053             }
1054             num++;
1055
1056                         //report progress
1057                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
1058                 }
1059
1060                 //report progress
1061                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
1062
1063         inFFasta.close();
1064         inRFasta.close();
1065         outFasta.close();
1066         outScrapFasta.close();
1067         outMisMatch.close();
1068         if (thisfqualfile != "") {
1069             inFQual.close();
1070             inRQual.close();
1071         }
1072         delete alignment;
1073
1074         if (m->control_pressed) {  m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches);  }
1075
1076         return num;
1077     }
1078         catch(exception& e) {
1079                 m->errorOut(e, "MakeContigsCommand", "driver");
1080                 exit(1);
1081         }
1082 }
1083 //**********************************************************************************************************************
1084 vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& count, string ffastq, string rfastq){
1085     try {
1086         vector< vector<string> > files;
1087         //maps processors number to file pointer
1088         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
1089         map<int, vector<ofstream*> >::iterator it;
1090
1091         //create files to write to
1092         for (int i = 0; i < processors; i++) {
1093             vector<ofstream*> temp;
1094             ofstream* outFF = new ofstream;     temp.push_back(outFF);
1095             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
1096             ofstream* outRF = new ofstream;     temp.push_back(outRF);
1097             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
1098             tempfiles[i] = temp;
1099
1100             vector<string> names;
1101             string thisOutputDir = outputDir;
1102             if (outputDir == "") { thisOutputDir = m->hasPath(ffastq); }
1103             string ffastafilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "ffastatemp";
1104             string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rfastatemp";
1105             string fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "fqualtemp";
1106             string rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rqualtemp";
1107             names.push_back(ffastafilename); names.push_back(fqualfilename);
1108             names.push_back(rfastafilename); names.push_back(rqualfilename);
1109             files.push_back(names);
1110
1111             m->openOutputFile(ffastafilename, *outFF);
1112             m->openOutputFile(rfastafilename, *outRF);
1113             m->openOutputFile(fqualfilename, *outFQ);
1114             m->openOutputFile(rqualfilename, *outRQ);
1115         }
1116
1117         if (m->control_pressed) {
1118             //close files, delete ofstreams
1119             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]; } }
1120             //remove files
1121             for (int i = 0; i < files.size(); i++) {
1122                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
1123             }
1124         }
1125
1126         ifstream inForward;
1127         m->openInputFile(ffastq, inForward);
1128
1129         ifstream inReverse;
1130         m->openInputFile(rfastq, inReverse);
1131
1132         count = 0;
1133         map<string, fastqRead> uniques;
1134         map<string, fastqRead>::iterator itUniques;
1135         while ((!inForward.eof()) || (!inReverse.eof())) {
1136
1137             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; }
1138
1139             //get a read from forward and reverse fastq files
1140             bool ignoref, ignorer;
1141             fastqRead thisFread, thisRread;
1142             if (!inForward.eof()) {  thisFread = readFastq(inForward, ignoref); }
1143             else { ignoref = true; }
1144             if (!inReverse.eof()) { thisRread = readFastq(inReverse, ignorer);  }
1145             else { ignorer = true; }
1146
1147             vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
1148
1149             for (int i = 0; i < reads.size(); i++) {
1150                 fastqRead fread = reads[i].forward;
1151                 fastqRead rread = reads[i].reverse;
1152
1153                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
1154
1155                 //if (checkReads(fread, rread, ffastq, rfastq)) {
1156                     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; }
1157
1158                     //if the reads are okay write to output files
1159                     int process = count % processors;
1160
1161                     *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
1162                     *(tempfiles[process][1]) << ">" << fread.name << endl;
1163                     for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
1164                     *(tempfiles[process][1]) << endl;
1165                     *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
1166                     *(tempfiles[process][3]) << ">" << rread.name << endl;
1167                     for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
1168                     *(tempfiles[process][3]) << endl;
1169
1170                     count++;
1171
1172                     //report progress
1173                     if((count) % 10000 == 0){   m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1174                 //}
1175             }
1176                 }
1177                 //report progress
1178                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1179
1180         if (uniques.size() != 0) {
1181             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
1182                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
1183             }
1184             m->mothurOutEndLine();
1185         }
1186
1187         //close files, delete ofstreams
1188         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]; } }
1189         inForward.close();
1190         inReverse.close();
1191
1192         return files;
1193     }
1194     catch(exception& e) {
1195         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1196         exit(1);
1197     }
1198 }
1199 //**********************************************************************************************************************
1200 vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& count, string ffasta, string rfasta){
1201     try {
1202         vector< vector<string> > files;
1203         //maps processors number to file pointer
1204         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
1205         map<int, vector<ofstream*> >::iterator it;
1206
1207         //create files to write to
1208         for (int i = 0; i < processors; i++) {
1209             vector<ofstream*> temp;
1210             ofstream* outFF = new ofstream;     temp.push_back(outFF);
1211             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
1212             ofstream* outRF = new ofstream;     temp.push_back(outRF);
1213             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
1214             tempfiles[i] = temp;
1215
1216             vector<string> names;
1217             string thisOutputDir = outputDir;
1218             if (outputDir == "") { thisOutputDir = m->hasPath(ffasta); }
1219             string ffastafilename = thisOutputDir + m->getRootName(m->getSimpleName(ffasta)) + toString(i) + "ffastatemp";
1220             string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfasta)) + toString(i) + "rfastatemp";
1221             string fqualfilename = "";
1222             if (fqualfile != "") { fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(fqualfile)) + toString(i) + "fqual.temp";  m->openOutputFile(fqualfilename, *outFQ); }
1223             string rqualfilename = "";
1224             if (rqualfile != "") { rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rqualfile)) + toString(i) + "rqual.temp"; m->openOutputFile(rqualfilename, *outRQ); }
1225             names.push_back(ffastafilename); names.push_back(fqualfilename);
1226             names.push_back(rfastafilename); names.push_back(rqualfilename);
1227             files.push_back(names);
1228
1229             m->openOutputFile(ffastafilename, *outFF);
1230             m->openOutputFile(rfastafilename, *outRF);
1231         }
1232
1233         if (m->control_pressed) {
1234             //close files, delete ofstreams
1235             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]; } }
1236             //remove files
1237             for (int i = 0; i < files.size(); i++) {
1238                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
1239             }
1240         }
1241
1242         ifstream inForwardFasta;
1243         m->openInputFile(ffasta, inForwardFasta);
1244
1245         ifstream inReverseFasta;
1246         m->openInputFile(rfasta, inReverseFasta);
1247
1248         ifstream inForwardQual, inReverseQual;
1249         if (fqualfile != "") { m->openInputFile(fqualfile, inForwardQual); m->openInputFile(rqualfile, inReverseQual); }
1250
1251         count = 0;
1252         map<string, fastqRead> uniques;
1253         map<string, fastqRead>::iterator itUniques;
1254         while ((!inForwardFasta.eof()) || (!inReverseFasta.eof())) {
1255
1256             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; }
1257
1258             //get a reads from forward and reverse fasta files
1259             bool ignoref, ignorer;
1260             fastqRead thisFread, thisRread;
1261             if (!inForwardFasta.eof()) {
1262                 ignoref = false;
1263                 Sequence temp(inForwardFasta); m->gobble(inForwardFasta);
1264                 thisFread.name = temp.getName();
1265                 thisFread.sequence = temp.getUnaligned();
1266             }else { ignoref = true; }
1267             if (!inReverseFasta.eof()) {
1268                 ignorer = false;
1269                 Sequence temp(inReverseFasta); m->gobble(inReverseFasta);
1270                 thisRread.name = temp.getName();
1271                 thisRread.sequence = temp.getUnaligned();
1272             }else { ignorer = true; }
1273
1274             //get qual reads if given
1275             if (fqualfile != "") {
1276                 if (!inForwardQual.eof() && !ignoref) {
1277                     QualityScores temp(inForwardQual); m->gobble(inForwardQual);
1278                     //if forward files dont match ignore read
1279                     if (thisFread.name != temp.getName()) { ignoref = true; }
1280                     else { thisFread.scores = temp.getQualityScores(); }
1281                 }else { ignoref = true; }
1282                 if (!inReverseQual.eof() && !ignorer) {
1283                     QualityScores temp(inReverseQual); m->gobble(inReverseQual);
1284                     //if reverse files dont match ignore read
1285                     if (thisRread.name != temp.getName()) { ignorer = true; }
1286                     else { thisRread.scores = temp.getQualityScores(); }
1287                 }else { ignorer = true; }
1288             }
1289
1290             vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
1291
1292             for (int i = 0; i < reads.size(); i++) {
1293                 fastqRead fread = reads[i].forward;
1294                 fastqRead rread = reads[i].reverse;
1295
1296                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
1297
1298                // if (checkReads(fread, rread, ffasta, rfasta)) {
1299                     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; }
1300
1301                     //if the reads are okay write to output files
1302                     int process = count % processors;
1303
1304                     *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
1305                     *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
1306                     if (fqualfile != "") { //if you have quality info, print it
1307                         *(tempfiles[process][1]) << ">" << fread.name << endl;
1308                         for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
1309                         *(tempfiles[process][1]) << endl;
1310                         *(tempfiles[process][3]) << ">" << rread.name << endl;
1311                         for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
1312                         *(tempfiles[process][3]) << endl;
1313                     }
1314                     count++;
1315
1316                     //report progress
1317                     if((count) % 10000 == 0){   m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1318                 //}
1319             }
1320                 }
1321                 //report progress
1322                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1323
1324         if (uniques.size() != 0) {
1325             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
1326                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
1327             }
1328             m->mothurOutEndLine();
1329         }
1330
1331         //close files, delete ofstreams
1332         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]; } }
1333         inReverseFasta.close();
1334         inForwardFasta.close();
1335         if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); }
1336
1337         return files;
1338     }
1339     catch(exception& e) {
1340         m->errorOut(e, "MakeContigsCommand", "readFastaFiles");
1341         exit(1);
1342     }
1343 }
1344 //**********************************************************************************************************************
1345 vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques){
1346     try {
1347         vector<pairFastqRead> reads;
1348         map<string, fastqRead>::iterator itUniques;
1349
1350         if (!ignoref && !ignorer) {
1351             if (forward.name == reverse.name) {
1352                 pairFastqRead temp(forward, reverse);
1353                 reads.push_back(temp);
1354             }else {
1355                 bool match = false;
1356                 //if no match are the names only different by 1 and 2?
1357                 string tempFRead = forward.name.substr(0, forward.name.length()-1);
1358                 string tempRRead = reverse.name.substr(0, reverse.name.length()-1);
1359                 if (tempFRead == tempRRead) {
1360                     if ((forward.name[forward.name.length()-1] == '1') && (reverse.name[reverse.name.length()-1] == '2')) {
1361                         forward.name = tempFRead;
1362                         reverse.name = tempRRead;
1363                         pairFastqRead temp(forward, reverse);
1364                         reads.push_back(temp);
1365                         match = true;
1366                     }
1367                 }
1368
1369                 if (!match) {
1370                     //look for forward pair
1371                     itUniques = uniques.find(forward.name);
1372                     if (itUniques != uniques.end()) {  //we have the pair for this read
1373                         pairFastqRead temp(forward, itUniques->second);
1374                         reads.push_back(temp);
1375                         uniques.erase(itUniques);
1376                     }else { //save this read for later
1377                         uniques[forward.name] = forward;
1378                     }
1379
1380                     //look for reverse pair
1381                     itUniques = uniques.find(reverse.name);
1382                     if (itUniques != uniques.end()) {  //we have the pair for this read
1383                         pairFastqRead temp(itUniques->second, reverse);
1384                         reads.push_back(temp);
1385                         uniques.erase(itUniques);
1386                     }else { //save this read for later
1387                         uniques[reverse.name] = reverse;
1388                     }
1389                 }
1390
1391             }
1392         }else if (!ignoref && ignorer) { //ignore reverse keep forward
1393             //look for forward pair
1394             itUniques = uniques.find(forward.name);
1395             if (itUniques != uniques.end()) {  //we have the pair for this read
1396                 pairFastqRead temp(forward, itUniques->second);
1397                 reads.push_back(temp);
1398                 uniques.erase(itUniques);
1399             }else { //save this read for later
1400                 uniques[forward.name] = forward;
1401             }
1402
1403         }else if (ignoref && !ignorer) { //ignore forward keep reverse
1404             //look for reverse pair
1405             itUniques = uniques.find(reverse.name);
1406             if (itUniques != uniques.end()) {  //we have the pair for this read
1407                 pairFastqRead temp(itUniques->second, reverse);
1408                 reads.push_back(temp);
1409                 uniques.erase(itUniques);
1410             }else { //save this read for later
1411                 uniques[reverse.name] = reverse;
1412             }
1413         }//else ignore both and do nothing
1414
1415         return reads;
1416     }
1417     catch(exception& e) {
1418         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1419         exit(1);
1420     }
1421 }
1422 //**********************************************************************************************************************
1423 fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
1424     try {
1425         fastqRead read;
1426
1427         ignore = false;
1428
1429         //read sequence name
1430         string line = m->getline(in); m->gobble(in);
1431         vector<string> pieces = m->splitWhiteSpace(line);
1432         string name = "";  if (pieces.size() != 0) { name = pieces[0]; }
1433         if (name == "") {  m->mothurOut("[WARNING]: Blank fasta name, ignoring read."); m->mothurOutEndLine(); ignore=true;  }
1434         else if (name[0] != '@') { m->mothurOut("[WARNING]: reading " + name + " expected a name with @ as a leading character, ignoring read."); m->mothurOutEndLine(); ignore=true; }
1435         else { name = name.substr(1); }
1436
1437         //read sequence
1438         string sequence = m->getline(in); m->gobble(in);
1439         if (sequence == "") {  m->mothurOut("[WARNING]: missing sequence for " + name + ", ignoring."); ignore=true; }
1440
1441         //read sequence name
1442         line = m->getline(in); m->gobble(in);
1443         pieces = m->splitWhiteSpace(line);
1444         string name2 = "";  if (pieces.size() != 0) { name2 = pieces[0]; }
1445         if (name2 == "") {  m->mothurOut("[WARNING]: expected a name with + as a leading character, ignoring."); ignore=true; }
1446         else if (name2[0] != '+') { m->mothurOut("[WARNING]: reading " + name2 + " expected a name with + as a leading character, ignoring."); ignore=true; }
1447         else { name2 = name2.substr(1); if (name2 == "") { name2 = name; } }
1448
1449         //read quality scores
1450         string quality = m->getline(in); m->gobble(in);
1451         if (quality == "") {  m->mothurOut("[WARNING]: missing quality for " + name2 + ", ignoring."); ignore=true; }
1452
1453         //sanity check sequence length and number of quality scores match
1454         if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } }
1455         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; }
1456
1457         vector<int> qualScores = convertQual(quality);
1458
1459         read.name = name;
1460         read.sequence = sequence;
1461         read.scores = qualScores;
1462
1463         return read;
1464     }
1465     catch(exception& e) {
1466         m->errorOut(e, "MakeContigsCommand", "readFastq");
1467         exit(1);
1468     }
1469 }
1470 /**********************************************************************************************************************
1471 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse, string ffile, string rfile){
1472     try {
1473         bool good = true;
1474
1475         //do sequence lengths match
1476         if (forward.sequence.length() != reverse.sequence.length()) {
1477             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");
1478             good = false;
1479         }
1480
1481         //do number of qual scores match
1482         if (forward.scores.size() != reverse.scores.size()) {
1483             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");
1484             good = false;
1485         }
1486
1487         return good;
1488     }
1489     catch(exception& e) {
1490         m->errorOut(e, "MakeContigsCommand", "checkReads");
1491         exit(1);
1492     }
1493 }*/
1494 //***************************************************************************************************************
1495 vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
1496         try {
1497         vector< vector<string> > files;
1498         string forward, reverse;
1499
1500         ifstream in;
1501         m->openInputFile(filename, in);
1502
1503         while(!in.eof()) {
1504
1505             if (m->control_pressed) { return files; }
1506
1507             in >> forward; m->gobble(in);
1508             in >> reverse;
1509
1510             string group = "";
1511             while (!in.eof())   { //do we have a group assigned to this pair
1512                 char c = in.get();
1513                 if (c == 10 || c == 13 || c == -1){     break;  }
1514                 else if (c == 32 || c == 9){;} //space or tab
1515                 else {  group += c;  }
1516             }
1517
1518             if (group != "") {
1519                 //line in file look like: group forward reverse
1520                 string temp = forward;
1521                 forward = reverse;
1522                 reverse = group;
1523                 group = temp;
1524                 createFileGroup = true;
1525             }
1526             m->gobble(in);
1527
1528
1529             //check to make sure both are able to be opened
1530             ifstream in2;
1531             int openForward = m->openInputFile(forward, in2, "noerror");
1532
1533             //if you can't open it, try default location
1534             if (openForward == 1) {
1535                 if (m->getDefaultPath() != "") { //default path is set
1536                     string tryPath = m->getDefaultPath() + m->getSimpleName(forward);
1537                     m->mothurOut("Unable to open " + forward + ". Trying default " + tryPath); m->mothurOutEndLine();
1538                     ifstream in3;
1539                     openForward = m->openInputFile(tryPath, in3, "noerror");
1540                     in3.close();
1541                     forward = tryPath;
1542                 }
1543             }
1544
1545             //if you can't open it, try output location
1546             if (openForward == 1) {
1547                 if (m->getOutputDir() != "") { //default path is set
1548                     string tryPath = m->getOutputDir() + m->getSimpleName(forward);
1549                     m->mothurOut("Unable to open " + forward + ". Trying output directory " + tryPath); m->mothurOutEndLine();
1550                     ifstream in4;
1551                     openForward = m->openInputFile(tryPath, in4, "noerror");
1552                     forward = tryPath;
1553                     in4.close();
1554                 }
1555             }
1556
1557             if (openForward == 1) { //can't find it
1558                 m->mothurOut("[WARNING]: can't find " + forward + ", ignoring pair.\n");
1559             }else{  in2.close();  }
1560
1561             ifstream in3;
1562             int openReverse = m->openInputFile(reverse, in3, "noerror");
1563
1564             //if you can't open it, try default location
1565             if (openReverse == 1) {
1566                 if (m->getDefaultPath() != "") { //default path is set
1567                     string tryPath = m->getDefaultPath() + m->getSimpleName(reverse);
1568                     m->mothurOut("Unable to open " + reverse + ". Trying default " + tryPath); m->mothurOutEndLine();
1569                     ifstream in3;
1570                     openReverse = m->openInputFile(tryPath, in3, "noerror");
1571                     in3.close();
1572                     reverse = tryPath;
1573                 }
1574             }
1575
1576             //if you can't open it, try output location
1577             if (openReverse == 1) {
1578                 if (m->getOutputDir() != "") { //default path is set
1579                     string tryPath = m->getOutputDir() + m->getSimpleName(reverse);
1580                     m->mothurOut("Unable to open " + reverse + ". Trying output directory " + tryPath); m->mothurOutEndLine();
1581                     ifstream in4;
1582                     openReverse = m->openInputFile(tryPath, in4, "noerror");
1583                     reverse = tryPath;
1584                     in4.close();
1585                 }
1586             }
1587
1588             if (openReverse == 1) { //can't find it
1589                 m->mothurOut("[WARNING]: can't find " + reverse + ", ignoring pair.\n");
1590             }else{  in3.close();  }
1591
1592             if ((openForward != 1) && (openReverse != 1)) { //good pair
1593                 file2Group[files.size()] = group;
1594                 vector<string> pair;
1595                 pair.push_back(forward);
1596                 pair.push_back(reverse);
1597                 files.push_back(pair);
1598             }
1599         }
1600         in.close();
1601
1602         return files;
1603     }
1604     catch(exception& e) {
1605         m->errorOut(e, "MakeContigsCommand", "checkReads");
1606         exit(1);
1607     }
1608 }
1609 //***************************************************************************************************************
1610 //illumina data requires paired forward and reverse data
1611 //BARCODE   atgcatgc   atgcatgc    groupName
1612 //PRIMER   atgcatgc   atgcatgc    groupName
1613 //PRIMER   atgcatgc   atgcatgc
1614 bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, string rootname){
1615         try {
1616                 ifstream in;
1617                 m->openInputFile(oligosfile, in);
1618
1619                 ofstream test;
1620
1621                 string type, foligo, roligo, group;
1622
1623                 int indexPrimer = 0;
1624                 int indexBarcode = 0;
1625         set<string> uniquePrimers;
1626         set<string> uniqueBarcodes;
1627
1628                 while(!in.eof()){
1629
1630                         in >> type;
1631
1632                         if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
1633
1634                         if(type[0] == '#'){
1635                                 while (!in.eof())       {       char c = in.get();  if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
1636                                 m->gobble(in);
1637                         }
1638                         else{
1639                                 m->gobble(in);
1640                                 //make type case insensitive
1641                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
1642
1643                                 in >> foligo;
1644
1645                 if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); }
1646
1647                                 for(int i=0;i<foligo.length();i++){
1648                                         foligo[i] = toupper(foligo[i]);
1649                                         if(foligo[i] == 'U')    {       foligo[i] = 'T';        }
1650                                 }
1651
1652                                 if(type == "PRIMER"){
1653                                         m->gobble(in);
1654
1655                     in >> roligo;
1656
1657                     for(int i=0;i<roligo.length();i++){
1658                         roligo[i] = toupper(roligo[i]);
1659                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1660                     }
1661                     //roligo = reverseOligo(roligo);
1662
1663                     group = "";
1664
1665                                         // get rest of line in case there is a primer name
1666                                         while (!in.eof())       {
1667                                                 char c = in.get();
1668                                                 if (c == 10 || c == 13){        break;  }
1669                                                 else if (c == 32 || c == 9){;} //space or tab
1670                                                 else {  group += c;  }
1671                                         }
1672
1673                     oligosPair newPrimer(foligo, roligo);
1674
1675                                         //check for repeat barcodes
1676                     string tempPair = foligo+roligo;
1677                     if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine();  }
1678                     else { uniquePrimers.insert(tempPair); }
1679
1680                     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"); }  }
1681
1682                                         primers[indexPrimer]=newPrimer; indexPrimer++;
1683                                         primerNameVector.push_back(group);
1684                                 }else if(type == "BARCODE"){
1685                                         m->gobble(in);
1686
1687                     in >> roligo;
1688
1689                     for(int i=0;i<roligo.length();i++){
1690                         roligo[i] = toupper(roligo[i]);
1691                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1692                     }
1693                     //roligo = reverseOligo(roligo);
1694
1695                     oligosPair newPair(foligo, roligo);
1696
1697                     group = "";
1698                     while (!in.eof())   {
1699                                                 char c = in.get();
1700                                                 if (c == 10 || c == 13){        break;  }
1701                                                 else if (c == 32 || c == 9){;} //space or tab
1702                                                 else {  group += c;  }
1703                                         }
1704
1705                     if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
1706
1707                     //check for repeat barcodes
1708                     string tempPair = foligo+roligo;
1709                     if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse +  " is in your oligos file already, disregarding."); m->mothurOutEndLine();  }
1710                     else { uniqueBarcodes.insert(tempPair); }
1711
1712                     barcodes[indexBarcode]=newPair; indexBarcode++;
1713                                         barcodeNameVector.push_back(group);
1714                                 }else if(type == "LINKER"){
1715                                         linker.push_back(foligo);
1716                     m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");
1717                                 }else if(type == "SPACER"){
1718                                         spacer.push_back(foligo);
1719                     m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n");
1720                                 }
1721                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); }
1722                         }
1723                         m->gobble(in);
1724                 }
1725                 in.close();
1726
1727                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
1728
1729                 //add in potential combos
1730                 if(barcodeNameVector.size() == 0){
1731             oligosPair temp("", "");
1732                         barcodes[0] = temp;
1733                         barcodeNameVector.push_back("");
1734                 }
1735
1736                 if(primerNameVector.size() == 0){
1737             oligosPair temp("", "");
1738                         primers[0] = temp;
1739                         primerNameVector.push_back("");
1740                 }
1741
1742                 fastaFileNames.resize(barcodeNameVector.size());
1743                 for(int i=0;i<fastaFileNames.size();i++){
1744                         fastaFileNames[i].assign(primerNameVector.size(), "");
1745                 }
1746
1747                 if(allFiles){
1748                         set<string> uniqueNames; //used to cleanup outputFileNames
1749                         for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1750                                 for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1751
1752                                         string primerName = primerNameVector[itPrimer->first];
1753                                         string barcodeName = barcodeNameVector[itBar->first];
1754
1755                     if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
1756                                         else {
1757                         string comboGroupName = "";
1758                         string fastaFileName = "";
1759                         string qualFileName = "";
1760                         string nameFileName = "";
1761                         string countFileName = "";
1762
1763                         if(primerName == ""){
1764                             comboGroupName = barcodeNameVector[itBar->first];
1765                         }
1766                         else{
1767                             if(barcodeName == ""){
1768                                 comboGroupName = primerNameVector[itPrimer->first];
1769                             }
1770                             else{
1771                                 comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
1772                             }
1773                         }
1774
1775
1776                         ofstream temp;
1777                         fastaFileName = rootname + comboGroupName + ".fasta";
1778                         if (uniqueNames.count(fastaFileName) == 0) {
1779                             outputNames.push_back(fastaFileName);
1780                             outputTypes["fasta"].push_back(fastaFileName);
1781                             uniqueNames.insert(fastaFileName);
1782                         }
1783
1784                         fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
1785                         m->openOutputFile(fastaFileName, temp);         temp.close();
1786                     }
1787                                 }
1788                         }
1789                 }
1790
1791                 bool allBlank = true;
1792                 for (int i = 0; i < barcodeNameVector.size(); i++) {
1793                         if (barcodeNameVector[i] != "") {
1794                                 allBlank = false;
1795                                 break;
1796                         }
1797                 }
1798                 for (int i = 0; i < primerNameVector.size(); i++) {
1799                         if (primerNameVector[i] != "") {
1800                                 allBlank = false;
1801                                 break;
1802                         }
1803                 }
1804
1805                 if (allBlank) {
1806                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
1807                         allFiles = false;
1808                         return false;
1809                 }
1810
1811                 return true;
1812
1813         }
1814         catch(exception& e) {
1815                 m->errorOut(e, "MakeContigsCommand", "getOligos");
1816                 exit(1);
1817         }
1818 }
1819 //********************************************************************/
1820 string MakeContigsCommand::reverseOligo(string oligo){
1821         try {
1822         string reverse = "";
1823
1824         for(int i=oligo.length()-1;i>=0;i--){
1825
1826             if(oligo[i] == 'A')         {       reverse += 'T'; }
1827             else if(oligo[i] == 'T'){   reverse += 'A'; }
1828             else if(oligo[i] == 'U'){   reverse += 'A'; }
1829
1830             else if(oligo[i] == 'G'){   reverse += 'C'; }
1831             else if(oligo[i] == 'C'){   reverse += 'G'; }
1832
1833             else if(oligo[i] == 'R'){   reverse += 'Y'; }
1834             else if(oligo[i] == 'Y'){   reverse += 'R'; }
1835
1836             else if(oligo[i] == 'M'){   reverse += 'K'; }
1837             else if(oligo[i] == 'K'){   reverse += 'M'; }
1838
1839             else if(oligo[i] == 'W'){   reverse += 'W'; }
1840             else if(oligo[i] == 'S'){   reverse += 'S'; }
1841
1842             else if(oligo[i] == 'B'){   reverse += 'V'; }
1843             else if(oligo[i] == 'V'){   reverse += 'B'; }
1844
1845             else if(oligo[i] == 'D'){   reverse += 'H'; }
1846             else if(oligo[i] == 'H'){   reverse += 'D'; }
1847
1848             else                                                {       reverse += 'N'; }
1849         }
1850
1851
1852         return reverse;
1853     }
1854         catch(exception& e) {
1855                 m->errorOut(e, "MakeContigsCommand", "reverseOligo");
1856                 exit(1);
1857         }
1858 }
1859 //**********************************************************************************************************************
1860 vector<int> MakeContigsCommand::convertQual(string qual) {
1861         try {
1862                 vector<int> qualScores;
1863         bool negativeScores = false;
1864
1865                 for (int i = 0; i < qual.length(); i++) {
1866
1867             int temp = 0;
1868             temp = int(qual[i]);
1869             if (format == "illumina") {
1870                 temp -= 64; //char '@'
1871             }else if (format == "illumina1.8+") {
1872                     temp -= int('!'); //char '!'
1873             }else if (format == "solexa") {
1874                 temp = int(convertTable[temp]); //convert to sanger
1875                 temp -= int('!'); //char '!'
1876             }else {
1877                 temp -= int('!'); //char '!'
1878             }
1879
1880             if (temp < -5) { negativeScores = true; }
1881                         qualScores.push_back(temp);
1882                 }
1883
1884         if (negativeScores) { m->mothurOut("[ERROR]: finding negative quality scores, do you have the right format selected? http://en.wikipedia.org/wiki/FASTQ_format#Encoding \n");  m->control_pressed = true;  }
1885
1886                 return qualScores;
1887         }
1888         catch(exception& e) {
1889                 m->errorOut(e, "MakeContigsCommand", "convertQual");
1890                 exit(1);
1891         }
1892 }
1893
1894 //**********************************************************************************************************************
1895
1896
1897
1898