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
  77         helpString += "The trimoverlap parameter allows you to trim the sequences to only the overlapping section. The default is F.\n";
  78         helpString += "The make.contigs command should be in the following format: \n";
  79                 helpString += "make.contigs(ffastq=yourForwardFastqFile, rfastq=yourReverseFastqFile, align=yourAlignmentMethod) \n";
  80                 helpString += "Note: No spaces between parameter labels (i.e. ffastq), '=' and parameters (i.e.yourForwardFastqFile).\n";
  81                 return helpString;
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "MakeContigsCommand", "getHelpString");
  85                 exit(1);
  86         }
  87 }
  88 //**********************************************************************************************************************
  89 string MakeContigsCommand::getOutputPattern(string type) {
  90     try {
  91         string pattern = "";
  92
  93         if (type == "fasta") {  pattern = "[filename],[tag],contigs.fasta"; }
  94         else if (type == "group") {  pattern = "[filename],[tag],contigs.groups"; }
  95         else if (type == "report") {  pattern = "[filename],[tag],contigs.report"; }
  96         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  97
  98         return pattern;
  99     }
 100     catch(exception& e) {
 101         m->errorOut(e, "MakeContigsCommand", "getOutputPattern");
 102         exit(1);
 103     }
 104 }
 105 //**********************************************************************************************************************
 106 MakeContigsCommand::MakeContigsCommand(){
 107         try {
 108                 abort = true; calledHelp = true;
 109                 setParameters();
 110                 vector<string> tempOutNames;
 111                 outputTypes["fasta"] = tempOutNames;
 112         outputTypes["group"] = tempOutNames;
 113         outputTypes["report"] = tempOutNames;
 114     }
 115         catch(exception& e) {
 116                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 117                 exit(1);
 118         }
 119 }
 120 //**********************************************************************************************************************
 121 MakeContigsCommand::MakeContigsCommand(string option)  {
 122         try {
 123                 abort = false; calledHelp = false;
 124         createFileGroup = false; createOligosGroup = false;
 125
 126                 //allow user to run help
 127                 if(option == "help") { help(); abort = true; calledHelp = true; }
 128                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 129
 130                 else {
 131                         vector<string> myArray = setParameters();
 132
 133                         OptionParser parser(option);
 134                         map<string, string> parameters = parser.getParameters();
 135
 136                         ValidParameters validParameter("pairwise.seqs");
 137                         map<string, string>::iterator it;
 138
 139                         //check to make sure all parameters are valid for command
 140                         for (it = parameters.begin(); it != parameters.end(); it++) {
 141                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 142                         }
 143
 144                         //initialize outputTypes
 145                         vector<string> tempOutNames;
 146                         outputTypes["fasta"] = tempOutNames;
 147             outputTypes["report"] = tempOutNames;
 148             outputTypes["group"] = tempOutNames;
 149
 150
 151                         //if the user changes the input directory command factory will send this info to us in the output parameter
 152                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 153                         if (inputDir == "not found"){   inputDir = "";          }
 154                         else {
 155                                 string path;
 156                 it = parameters.find("ffastq");
 157                                 //user has given a template file
 158                                 if(it != parameters.end()){
 159                                         path = m->hasPath(it->second);
 160                                         //if the user has not given a path then, add inputdir. else leave path alone.
 161                                         if (path == "") {       parameters["ffastq"] = inputDir + it->second;           }
 162                                 }
 163
 164                 it = parameters.find("rfastq");
 165                                 //user has given a template file
 166                                 if(it != parameters.end()){
 167                                         path = m->hasPath(it->second);
 168                                         //if the user has not given a path then, add inputdir. else leave path alone.
 169                                         if (path == "") {       parameters["rfastq"] = inputDir + it->second;           }
 170                                 }
 171
 172                 it = parameters.find("ffasta");
 173                                 //user has given a template file
 174                                 if(it != parameters.end()){
 175                                         path = m->hasPath(it->second);
 176                                         //if the user has not given a path then, add inputdir. else leave path alone.
 177                                         if (path == "") {       parameters["ffasta"] = inputDir + it->second;           }
 178                                 }
 179
 180                 it = parameters.find("rfasta");
 181                                 //user has given a template file
 182                                 if(it != parameters.end()){
 183                                         path = m->hasPath(it->second);
 184                                         //if the user has not given a path then, add inputdir. else leave path alone.
 185                                         if (path == "") {       parameters["rfasta"] = inputDir + it->second;           }
 186                                 }
 187
 188                 it = parameters.find("fqfile");
 189                                 //user has given a template file
 190                                 if(it != parameters.end()){
 191                                         path = m->hasPath(it->second);
 192                                         //if the user has not given a path then, add inputdir. else leave path alone.
 193                                         if (path == "") {       parameters["fqfile"] = inputDir + it->second;           }
 194                                 }
 195
 196                 it = parameters.find("rqfile");
 197                                 //user has given a template file
 198                                 if(it != parameters.end()){
 199                                         path = m->hasPath(it->second);
 200                                         //if the user has not given a path then, add inputdir. else leave path alone.
 201                                         if (path == "") {       parameters["rqfile"] = inputDir + it->second;           }
 202                                 }
 203
 204                 it = parameters.find("file");
 205                                 //user has given a template file
 206                                 if(it != parameters.end()){
 207                                         path = m->hasPath(it->second);
 208                                         //if the user has not given a path then, add inputdir. else leave path alone.
 209                                         if (path == "") {       parameters["file"] = inputDir + it->second;             }
 210                                 }
 211
 212                 it = parameters.find("oligos");
 213                                 //user has given a template file
 214                                 if(it != parameters.end()){
 215                                         path = m->hasPath(it->second);
 216                                         //if the user has not given a path then, add inputdir. else leave path alone.
 217                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 218                                 }
 219             }
 220
 221             ffastqfile = validParameter.validFile(parameters, "ffastq", true);
 222                         if (ffastqfile == "not open") {  abort = true; }
 223                         else if (ffastqfile == "not found") { ffastqfile = ""; }
 224
 225                         rfastqfile = validParameter.validFile(parameters, "rfastq", true);
 226                         if (rfastqfile == "not open") {  abort = true; }
 227                         else if (rfastqfile == "not found") { rfastqfile = "";  }
 228
 229             ffastafile = validParameter.validFile(parameters, "ffasta", true);
 230                         if (ffastafile == "not open") {  abort = true; }
 231                         else if (ffastafile == "not found") { ffastafile = ""; }
 232
 233                         rfastafile = validParameter.validFile(parameters, "rfasta", true);
 234                         if (rfastafile == "not open") {  abort = true; }
 235                         else if (rfastafile == "not found") { rfastafile = "";  }
 236
 237             fqualfile = validParameter.validFile(parameters, "fqfile", true);
 238                         if (fqualfile == "not open") {  abort = true; }
 239                         else if (fqualfile == "not found") { fqualfile = ""; }
 240
 241                         rqualfile = validParameter.validFile(parameters, "rqfile", true);
 242                         if (rqualfile == "not open") {  abort = true; }
 243                         else if (rqualfile == "not found") { rqualfile = "";  }
 244
 245             file = validParameter.validFile(parameters, "file", true);
 246                         if (file == "not open") {  abort = true; }
 247                         else if (file == "not found") { file = "";  }
 248
 249             //provide at least
 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 ((file != "") && ((ffastafile != "") || (ffastqfile != ""))) { abort = true; m->mothurOut("[ERROR]: The file, ffastq and rfastq or ffasta and rfasta parameters are required.\n"); }
 252             if ((ffastqfile != "") && (rfastqfile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the ffastq, you must provide a rfastq file.\n"); }
 253             if ((ffastqfile == "") && (rfastqfile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rfastq, you must provide a ffastq file.\n"); }
 254             if ((ffastafile != "") && (rfastafile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the ffasta, you must provide a rfasta file.\n"); }
 255             if ((ffastafile == "") && (rfastafile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rfasta, you must provide a ffasta file.\n"); }
 256             if ((fqualfile != "") && (rqualfile == "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the fqfile, you must provide a rqfile file.\n"); }
 257             if ((fqualfile == "") && (rqualfile != "")) {  abort = true; m->mothurOut("[ERROR]: If you provide use the rqfile, you must provide a fqfile file.\n"); }
 258             if (((fqualfile != "") || (rqualfile != "")) && ((ffastafile == "") || (rfastafile == ""))) {
 259                 abort = true; m->mothurOut("[ERROR]: If you provide use the rqfile or fqfile file, you must provide the ffasta and rfasta parameters.\n");
 260             }
 261
 262             oligosfile = validParameter.validFile(parameters, "oligos", true);
 263                         if (oligosfile == "not found")      {   oligosfile = "";        }
 264                         else if(oligosfile == "not open")   {   abort = true;       }
 265                         else {   m->setOligosFile(oligosfile);          }
 266
 267             //if the user changes the output directory command factory will send this info to us in the output parameter
 268                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 269                  outputDir = "";
 270             }
 271
 272
 273                         //check for optional parameter and set defaults
 274                         // ...at some point should added some additional type checking...
 275                         string temp;
 276                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 277                         m->mothurConvert(temp, match);
 278
 279                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 280                         m->mothurConvert(temp, misMatch);
 281             if (misMatch > 0) { m->mothurOut("[ERROR]: mismatch must be negative.\n"); abort=true; }
 282
 283                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 284                         m->mothurConvert(temp, gapOpen);
 285             if (gapOpen > 0) { m->mothurOut("[ERROR]: gapopen must be negative.\n"); abort=true; }
 286
 287                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 288                         m->mothurConvert(temp, gapExtend);
 289             if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; }
 290
 291             temp = validParameter.validFile(parameters, "insert", false);       if (temp == "not found"){       temp = "20";                    }
 292                         m->mothurConvert(temp, insert);
 293             if ((insert < 0) || (insert > 40)) { m->mothurOut("[ERROR]: insert must be between 0 and 40.\n"); abort=true; }
 294
 295             temp = validParameter.validFile(parameters, "deltaq", false);       if (temp == "not found"){       temp = "6";                     }
 296                         m->mothurConvert(temp, deltaq);
 297
 298                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 299                         m->setProcessors(temp);
 300                         m->mothurConvert(temp, processors);
 301
 302             temp = validParameter.validFile(parameters, "bdiffs", false);               if (temp == "not found") { temp = "0"; }
 303                         m->mothurConvert(temp, bdiffs);
 304
 305                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 306                         m->mothurConvert(temp, pdiffs);
 307
 308   //          temp = validParameter.validFile(parameters, "ldiffs", false);             if (temp == "not found") { temp = "0"; }
 309 //                      m->mothurConvert(temp, ldiffs);
 310             ldiffs = 0;
 311
 312  //           temp = validParameter.validFile(parameters, "sdiffs", false);             if (temp == "not found") { temp = "0"; }
 313  //           m->mothurConvert(temp, sdiffs);
 314             sdiffs = 0;
 315
 316                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 317                         m->mothurConvert(temp, tdiffs);
 318
 319                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }  //+ ldiffs + sdiffs;
 320
 321             temp = validParameter.validFile(parameters, "allfiles", false);             if (temp == "not found") { temp = "F"; }
 322                         allFiles = m->isTrue(temp);
 323
 324
 325             temp = validParameter.validFile(parameters, "trimoverlap", false);          if (temp == "not found") { temp = "F"; }
 326                         trimOverlap = m->isTrue(temp);
 327
 328                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 329                         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"; }
 330
 331             format = validParameter.validFile(parameters, "format", false);             if (format == "not found"){     format = "illumina1.8+";        }
 332
 333             if ((format != "sanger") && (format != "illumina") && (format != "illumina1.8+") && (format != "solexa"))  {
 334                                 m->mothurOut(format + " is not a valid format. Your format choices are sanger, solexa, illumina1.8+ and illumina, aborting." ); m->mothurOutEndLine();
 335                                 abort=true;
 336                         }
 337
 338             //fill convert table - goes from solexa to sanger. Used fq_all2std.pl as a reference.
 339             for (int i = -64; i < 65; i++) {
 340                 char temp = (char) ((int)(33 + 10*log(1+pow(10,(i/10.0)))/log(10)+0.499));
 341                 convertTable.push_back(temp);
 342             }
 343         }
 344
 345         }
 346         catch(exception& e) {
 347                 m->errorOut(e, "MakeContigsCommand", "MakeContigsCommand");
 348                 exit(1);
 349         }
 350 }
 351 //**********************************************************************************************************************
 352 int MakeContigsCommand::execute(){
 353         try {
 354                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 355
 356         //read ffastq and rfastq files creating fasta and qual files.
 357         //this function will create a forward and reverse, fasta and qual files for each processor.
 358         //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.
 359         unsigned long int numReads = 0;
 360         int start = time(NULL);
 361         longestBase = 1000;
 362         m->mothurOut("Reading fastq data...\n");
 363         vector < vector< vector<string> > > filesToProcess = preProcessData(numReads);
 364         m->mothurOut("Done.\n");
 365
 366         if (m->control_pressed) { return 0; }
 367
 368         map<string, string> cvars;
 369         string compOutputDir = outputDir;
 370         if (outputDir == "") { compOutputDir = m->hasPath(file); }
 371         cvars["[filename]"] = compOutputDir + m->getRootName(m->getSimpleName(file));
 372         cvars["[tag]"] = "";
 373         string compositeGroupFile = getOutputFileName("group",cvars);
 374         cvars["[tag]"] = "trim";
 375         string compositeFastaFile = getOutputFileName("fasta",cvars);
 376         cvars["[tag]"] = "scrap";
 377         string compositeScrapFastaFile = getOutputFileName("fasta",cvars);
 378         cvars["[tag]"] = "";
 379         string compositeMisMatchFile = getOutputFileName("report",cvars);
 380
 381         if (filesToProcess.size() > 1) { //clear files for append below
 382             ofstream outCTFasta, outCTQual, outCSFasta, outCSQual, outCMisMatch;
 383             m->openOutputFile(compositeFastaFile, outCTFasta); outCTFasta.close();
 384             m->openOutputFile(compositeScrapFastaFile, outCSFasta); outCSFasta.close();
 385             m->openOutputFile(compositeMisMatchFile, outCMisMatch); outCMisMatch.close();
 386             outputNames.push_back(compositeFastaFile); outputTypes["fasta"].push_back(compositeFastaFile);
 387             outputNames.push_back(compositeMisMatchFile); outputTypes["report"].push_back(compositeMisMatchFile);
 388             outputNames.push_back(compositeScrapFastaFile); outputTypes["fasta"].push_back(compositeScrapFastaFile);
 389         }
 390
 391         map<string, int> totalGroupCounts;
 392
 393         for (int l = 0; l < filesToProcess.size(); l++) {
 394
 395             m->mothurOut("\n>>>>>\tProcessing " + filesToProcess[l][0][0] + " (file " + toString(l+1) + " of " + toString(filesToProcess.size()) + ")\t<<<<<\n");
 396
 397             groupCounts.clear();
 398             groupMap.clear();
 399             vector<vector<string> > fastaFileNames;
 400             createOligosGroup = false;
 401             string outputGroupFileName;
 402             map<string, string> variables;
 403             string thisOutputDir = outputDir;
 404             if (outputDir == "") {  thisOutputDir = m->hasPath(filesToProcess[l][0][0]); }
 405             variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(filesToProcess[l][0][0]));
 406             variables["[tag]"] = "";
 407             if(oligosfile != ""){  createOligosGroup = getOligos(fastaFileNames, variables["[filename]"]);  }
 408             if (createOligosGroup || createFileGroup) {
 409                 outputGroupFileName = getOutputFileName("group",variables);
 410             }
 411
 412             //give group in file file precedence
 413             if (createFileGroup) {  createOligosGroup = false; }
 414
 415             variables["[tag]"] = "trim";
 416             string outFastaFile = getOutputFileName("fasta",variables);
 417             variables["[tag]"] = "scrap";
 418             string outScrapFastaFile = getOutputFileName("fasta",variables);
 419             variables["[tag]"] = "";
 420             string outMisMatchFile = getOutputFileName("report",variables);
 421
 422             m->mothurOut("Making contigs...\n");
 423             createProcesses(filesToProcess[l], outFastaFile, outScrapFastaFile, outMisMatchFile, fastaFileNames, l);
 424              m->mothurOut("Here...\n");
 425
 426             //remove temp fasta and qual files
 427             for (int i = 0; i < processors; i++) { for(int j = 0; j < filesToProcess[l][i].size(); j++) { m->mothurRemove(filesToProcess[l][i][j]); }  }
 428
 429             if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {    m->mothurRemove(outputNames[i]); }  return 0; }
 430
 431             if(allFiles){
 432                 map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
 433                 map<string, string>::iterator it;
 434                 set<string> namesToRemove;
 435                 for(int i=0;i<fastaFileNames.size();i++){
 436                     for(int j=0;j<fastaFileNames[0].size();j++){
 437                         if (fastaFileNames[i][j] != "") {
 438                             if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
 439                                 if(m->isBlank(fastaFileNames[i][j])){
 440                                     m->mothurRemove(fastaFileNames[i][j]);
 441                                     namesToRemove.insert(fastaFileNames[i][j]);
 442                                 }else{
 443                                     it = uniqueFastaNames.find(fastaFileNames[i][j]);
 444                                     if (it == uniqueFastaNames.end()) {
 445                                         uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
 446                                     }
 447                                 }
 448                             }
 449                         }
 450                     }
 451                 }
 452
 453                 //remove names for outputFileNames, just cleans up the output
 454                 vector<string> outputNames2;
 455                 for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
 456                 outputNames = outputNames2;
 457
 458                 for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
 459                     ifstream in;
 460                     m->openInputFile(it->first, in);
 461
 462                     ofstream out;
 463                     string thisGroupName = thisOutputDir + m->getRootName(m->getSimpleName(it->first));
 464                     thisGroupName += getOutputFileName("group",variables); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName);
 465                     m->openOutputFile(thisGroupName, out);
 466
 467                     while (!in.eof()){
 468                         if (m->control_pressed) { break; }
 469
 470                         Sequence currSeq(in); m->gobble(in);
 471                         out << currSeq.getName() << '\t' << it->second << endl;
 472                     }
 473                     out.close();
 474                     in.close();
 475                 }
 476             }
 477
 478             if (createFileGroup || createOligosGroup) {
 479                 ofstream outGroup;
 480                 m->openOutputFile(outputGroupFileName, outGroup);
 481                 for (map<string, string>::iterator itGroup = groupMap.begin(); itGroup != groupMap.end(); itGroup++) {
 482                     outGroup << itGroup->first << '\t' << itGroup->second << endl;
 483                 }
 484                 outGroup.close();
 485             }
 486
 487             if (filesToProcess.size() > 1) { //merge into large combo files
 488                 if (createFileGroup || createOligosGroup) {
 489                     if (l == 0) {
 490                         ofstream outCGroup;
 491                         m->openOutputFile(compositeGroupFile, outCGroup); outCGroup.close();
 492                         outputNames.push_back(compositeGroupFile); outputTypes["group"].push_back(compositeGroupFile);
 493                     }
 494                     m->appendFiles(outputGroupFileName, compositeGroupFile);
 495                     if (!allFiles) { m->mothurRemove(outputGroupFileName);  }
 496                     else { outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName); }
 497
 498                     for (map<string, int>::iterator itGroups = groupCounts.begin(); itGroups != groupCounts.end(); itGroups++) {
 499                         map<string, int>::iterator itTemp = totalGroupCounts.find(itGroups->first);
 500                         if (itTemp == totalGroupCounts.end()) { totalGroupCounts[itGroups->first] = itGroups->second; } //new group create it in totalGroups
 501                         else { itTemp->second += itGroups->second; } //existing group, update total
 502                     }
 503                 }
 504                 if (l == 0) {  m->appendFiles(outMisMatchFile, compositeMisMatchFile);  }
 505                 else {  m->appendFilesWithoutHeaders(outMisMatchFile, compositeMisMatchFile);  }
 506                 m->appendFiles(outFastaFile, compositeFastaFile);
 507                 m->appendFiles(outScrapFastaFile, compositeScrapFastaFile);
 508                 if (!allFiles) {
 509                     m->mothurRemove(outMisMatchFile);
 510                     m->mothurRemove(outFastaFile);
 511                     m->mothurRemove(outScrapFastaFile);
 512                 }else {
 513                     outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 514                     outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
 515                     outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
 516                 }
 517             }else {
 518                 totalGroupCounts = groupCounts;
 519                 outputNames.push_back(outFastaFile); outputTypes["fasta"].push_back(outFastaFile);
 520                 outputNames.push_back(outScrapFastaFile); outputTypes["fasta"].push_back(outScrapFastaFile);
 521                 outputNames.push_back(outMisMatchFile); outputTypes["report"].push_back(outMisMatchFile);
 522                 if (createFileGroup || createOligosGroup) {
 523                      outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
 524                 }
 525             }
 526             m->mothurOut("Done.\n");
 527         }
 528
 529         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to process " + toString(numReads) + " sequences.\n");
 530
 531         if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 532
 533                 //output group counts
 534                 m->mothurOutEndLine();
 535                 int total = 0;
 536                 if (totalGroupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
 537                 for (map<string, int>::iterator it = totalGroupCounts.begin(); it != totalGroupCounts.end(); it++) {
 538             total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
 539                 }
 540                 if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
 541
 542                 if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 543
 544         string currentFasta = "";
 545                 itTypes = outputTypes.find("fasta");
 546                 if (itTypes != outputTypes.end()) {
 547                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 548                 }
 549
 550         string currentGroup = "";
 551                 itTypes = outputTypes.find("group");
 552                 if (itTypes != outputTypes.end()) {
 553                         if ((itTypes->second).size() != 0) { currentGroup = (itTypes->second)[0]; m->setGroupFile(currentGroup); }
 554                 }
 555
 556         //output files created by command
 557                 m->mothurOutEndLine();
 558                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 559                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 560                 m->mothurOutEndLine();
 561
 562         return 0;
 563     }
 564         catch(exception& e) {
 565                 m->errorOut(e, "MakeContigsCommand", "execute");
 566                 exit(1);
 567         }
 568 }
 569 //**********************************************************************************************************************
 570 vector< vector< vector<string> > > MakeContigsCommand::preProcessData(unsigned long int& numReads) {
 571         try {
 572         vector< vector< vector<string> > > filesToProcess;
 573
 574         if (ffastqfile != "") { //reading one file
 575             vector< vector<string> > files = readFastqFiles(numReads, ffastqfile, rfastqfile);
 576             //adjust for really large processors or really small files
 577             if (numReads == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
 578             if (numReads < processors) {
 579                 for (int i = numReads; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 580                 files.resize(numReads);
 581                 processors = numReads;
 582             }
 583             filesToProcess.push_back(files);
 584         }else if (file != "") { //reading multiple files
 585             //return only valid pairs
 586             vector< vector<string> > filePairsToProcess = readFileNames(file);
 587
 588             if (m->control_pressed) { return filesToProcess; }
 589
 590             if (filePairsToProcess.size() != 0) {
 591                 for (int i = 0; i < filePairsToProcess.size(); i++) {
 592
 593                     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; } }
 594
 595                     unsigned long int thisFilesReads;
 596                     vector< vector<string> > files = readFastqFiles(thisFilesReads, filePairsToProcess[i][0], filePairsToProcess[i][1]);
 597
 598                     //adjust for really large processors or really small files
 599                     if (thisFilesReads < processors) {
 600                         m->mothurOut("[ERROR]: " + filePairsToProcess[i][0] + " has less than " + toString(processors) + " good reads, skipping\n");
 601                         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(); }
 602                     }else {
 603                         filesToProcess.push_back(files);
 604                         numReads += thisFilesReads;
 605                     }
 606                 }
 607                 //all files are bad
 608                 if (numReads == 0) {  m->control_pressed = true; }
 609             }
 610         }else if (ffastafile != "") {
 611             vector< vector<string> > files = readFastaFiles(numReads, ffastafile, rfastafile);
 612             //adjust for really large processors or really small files
 613             if (numReads == 0) {  m->mothurOut("[ERROR]: no good reads.\n"); m->control_pressed = true; }
 614             if (numReads < processors) {
 615                 for (int i = numReads; i < processors; i++) { for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); } files[i].clear(); }
 616                 files.resize(numReads);
 617                 processors = numReads;
 618             }
 619             filesToProcess.push_back(files);
 620         }else { m->control_pressed = true; } //should not get here
 621
 622         return filesToProcess;
 623     }
 624         catch(exception& e) {
 625                 m->errorOut(e, "MakeContigsCommand", "preProcessData");
 626                 exit(1);
 627         }
 628 }
 629 //**********************************************************************************************************************
 630 int MakeContigsCommand::createProcesses(vector< vector<string> > files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int index) {
 631         try {
 632                 int num = 0;
 633                 vector<int> processIDS;
 634         string group = "";
 635         map<int, string>::iterator it = file2Group.find(index);
 636         if (it != file2Group.end()) { group = it->second; }
 637
 638 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 639                 int process = 0;
 640
 641                 //loop through and create all the processes you want
 642                 while (process != processors-1) {
 643                         int pid = fork();
 644
 645                         if (pid > 0) {
 646                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 647                                 process++;
 648                         }else if (pid == 0){
 649                 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 650
 651                                 if(allFiles){
 652                                         ofstream temp;
 653
 654                                         for(int i=0;i<tempFASTAFileNames.size();i++){
 655                                                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 656                                                         if (tempFASTAFileNames[i][j] != "") {
 657                                                                 tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
 658                                                                 m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 659                                                         }
 660                                                 }
 661                                         }
 662                                 }
 663
 664                                 num = driver(files[process],
 665                              outputFasta + toString(getpid()) + ".temp",
 666                              outputScrapFasta + toString(getpid()) + ".temp",
 667                              outputMisMatches + toString(getpid()) + ".temp",
 668                              tempFASTAFileNames, process, group);
 669
 670                                 //pass groupCounts to parent
 671                 ofstream out;
 672                 string tempFile = toString(getpid()) + ".num.temp";
 673                 m->openOutputFile(tempFile, out);
 674                 out << num << endl;
 675                                 if (createFileGroup || createOligosGroup) {
 676                                         out << groupCounts.size() << endl;
 677
 678                                         for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 679                                                 out << it->first << '\t' << it->second << endl;
 680                                         }
 681
 682                     out << groupMap.size() << endl;
 683                     for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
 684                                                 out << it->first << '\t' << it->second << endl;
 685                                         }
 686                                 }
 687                 out.close();
 688
 689                                 exit(0);
 690                         }else {
 691                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 692                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 693                                 exit(0);
 694                         }
 695                 }
 696
 697         ofstream temp;
 698                 m->openOutputFile(outputFasta, temp);           temp.close();
 699         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 700
 701                 //do my part
 702                 num = driver(files[processors-1], outputFasta, outputScrapFasta,  outputMisMatches, fastaFileNames, processors-1, group);
 703
 704                 //force parent to wait until all the processes are done
 705                 for (int i=0;i<processIDS.size();i++) {
 706                         int temp = processIDS[i];
 707                         wait(&temp);
 708                 }
 709
 710                 for (int i = 0; i < processIDS.size(); i++) {
 711             ifstream in;
 712             string tempFile = toString(processIDS[i]) + ".num.temp";
 713             m->openInputFile(tempFile, in);
 714             int tempNum;
 715             in >> tempNum; num += tempNum; m->gobble(in);
 716
 717                         if (createFileGroup || createOligosGroup) {
 718                                 string group;
 719                                 in >> tempNum; m->gobble(in);
 720
 721                                 if (tempNum != 0) {
 722                                         for (int j = 0; j < tempNum; j++) {
 723                         int groupNum;
 724                                                 in >> group >> groupNum; m->gobble(in);
 725
 726                                                 map<string, int>::iterator it = groupCounts.find(group);
 727                                                 if (it == groupCounts.end()) {  groupCounts[group] = groupNum; }
 728                                                 else { groupCounts[it->first] += groupNum; }
 729                                         }
 730                                 }
 731                 in >> tempNum; m->gobble(in);
 732                 if (tempNum != 0) {
 733                                         for (int j = 0; j < tempNum; j++) {
 734                         string group, seqName;
 735                                                 in >> seqName >> group; m->gobble(in);
 736
 737                                                 map<string, string>::iterator it = groupMap.find(seqName);
 738                                                 if (it == groupMap.end()) {     groupMap[seqName] = group; }
 739                                                 else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 740                                         }
 741                                 }
 742                         }
 743             in.close(); m->mothurRemove(tempFile);
 744         }
 745     #else
 746
 747         //////////////////////////////////////////////////////////////////////////////////////////////////////
 748                 //Windows version shared memory, so be careful when passing variables through the contigsData struct.
 749                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 750                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 751
 752                 vector<contigsData*> pDataArray;
 753                 DWORD   dwThreadIdArray[processors-1];
 754                 HANDLE  hThreadArray[processors-1];
 755
 756                 //Create processor worker threads.
 757                 for( int h=0; h<processors-1; h++ ){
 758                         string extension = "";
 759                         if (h != 0) { extension = toString(h) + ".temp"; processIDS.push_back(h); }
 760             vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 761
 762             if(allFiles){
 763                 ofstream temp;
 764
 765                 for(int i=0;i<tempFASTAFileNames.size();i++){
 766                     for(int j=0;j<tempFASTAFileNames[i].size();j++){
 767                         if (tempFASTAFileNames[i][j] != "") {
 768                             tempFASTAFileNames[i][j] += extension;
 769                             m->openOutputFile(tempFASTAFileNames[i][j], temp);                  temp.close();
 770                         }
 771                     }
 772                 }
 773             }
 774
 775                         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);
 776                         pDataArray.push_back(tempcontig);
 777
 778                         hThreadArray[h] = CreateThread(NULL, 0, MyContigsThreadFunction, pDataArray[h], 0, &dwThreadIdArray[h]);
 779                 }
 780
 781         vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 782
 783         if(allFiles){
 784             ofstream temp;
 785             string extension = toString(processors-1) + ".temp";
 786
 787             for(int i=0;i<tempFASTAFileNames.size();i++){
 788                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 789                     if (tempFASTAFileNames[i][j] != "") {
 790                         tempFASTAFileNames[i][j] += extension;
 791                         m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 792                     }
 793                 }
 794             }
 795         }
 796
 797                 //parent do my part
 798                 ofstream temp;
 799                 m->openOutputFile(outputFasta, temp);           temp.close();
 800         m->openOutputFile(outputScrapFasta, temp);              temp.close();
 801
 802         //do my part
 803         processIDS.push_back(processors-1);
 804                 num = driver(files[processors-1], (outputFasta+ toString(processors-1) + ".temp"),  (outputScrapFasta+ toString(processors-1) + ".temp"),  (outputMisMatches+ toString(processors-1) + ".temp"), tempFASTAFileNames, processors-1, group);
 805
 806                 //Wait until all threads have terminated.
 807                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 808
 809                 //Close all thread handles and free memory allocations.
 810                 for(int i=0; i < pDataArray.size(); i++){
 811                         num += pDataArray[i]->count;
 812             if (!pDataArray[i]->done) {
 813                 m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of sequences assigned to it, quitting. \n"); m->control_pressed = true;
 814             }
 815             for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
 816                 map<string, int>::iterator it2 = groupCounts.find(it->first);
 817                 if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
 818                 else { groupCounts[it->first] += it->second; }
 819             }
 820             for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
 821                 map<string, string>::iterator it2 = groupMap.find(it->first);
 822                 if (it2 == groupMap.end()) {    groupMap[it->first] = it->second; }
 823                 else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
 824             }
 825             CloseHandle(hThreadArray[i]);
 826                         delete pDataArray[i];
 827         }
 828
 829     #endif
 830
 831         for (int i = 0; i < processIDS.size(); i++) {
 832                         m->appendFiles((outputFasta + toString(processIDS[i]) + ".temp"), outputFasta);
 833                         m->mothurRemove((outputFasta + toString(processIDS[i]) + ".temp"));
 834
 835                         m->appendFiles((outputScrapFasta + toString(processIDS[i]) + ".temp"), outputScrapFasta);
 836                         m->mothurRemove((outputScrapFasta + toString(processIDS[i]) + ".temp"));
 837
 838             m->appendFilesWithoutHeaders((outputMisMatches + toString(processIDS[i]) + ".temp"), outputMisMatches);
 839                         m->mothurRemove((outputMisMatches + toString(processIDS[i]) + ".temp"));
 840
 841             if(allFiles){
 842                                 for(int j=0;j<fastaFileNames.size();j++){
 843                                         for(int k=0;k<fastaFileNames[j].size();k++){
 844                                                 if (fastaFileNames[j][k] != "") {
 845                                                         m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
 846                                                         m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 847                                                 }
 848                                         }
 849                                 }
 850                         }
 851                 }
 852
 853                 return num;
 854         }
 855         catch(exception& e) {
 856                 m->errorOut(e, "MakeContigsCommand", "createProcesses");
 857                 exit(1);
 858         }
 859 }
 860 //**********************************************************************************************************************
 861 int MakeContigsCommand::driver(vector<string> files, string outputFasta, string outputScrapFasta, string outputMisMatches, vector<vector<string> > fastaFileNames, int process, string group){
 862     try {
 863
 864         Alignment* alignment;
 865         if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 866                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 867
 868         int num = 0;
 869         string thisffastafile = files[0];
 870         string thisfqualfile = files[1];
 871         string thisrfastafile = files[2];
 872         string thisrqualfile = files[3];
 873
 874         if (m->debug) {  m->mothurOut("[DEBUG]: ffasta = " + thisffastafile + ".\n[DEBUG]: fqual = " + thisfqualfile + ".\n[DEBUG]: rfasta = " + thisrfastafile + ".\n[DEBUG]: rqual = " + thisrqualfile + ".\n"); }
 875
 876         ifstream inFFasta, inRFasta, inFQual, inRQual;
 877         ofstream outFasta, outMisMatch, outScrapFasta;
 878         m->openInputFile(thisffastafile, inFFasta);
 879         m->openInputFile(thisrfastafile, inRFasta);
 880         if (thisfqualfile != "") {
 881             m->openInputFile(thisfqualfile, inFQual);
 882             m->openInputFile(thisrqualfile, inRQual);
 883         }
 884         m->openOutputFile(outputFasta, outFasta);
 885         m->openOutputFile(outputScrapFasta, outScrapFasta);
 886         m->openOutputFile(outputMisMatches, outMisMatch);
 887         outMisMatch << "Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns\n";
 888
 889         TrimOligos trimOligos(pdiffs, bdiffs, 0, 0, primers, barcodes);
 890
 891         while ((!inFFasta.eof()) && (!inRFasta.eof())) {
 892
 893             if (m->control_pressed) { break; }
 894
 895             int success = 1;
 896             string trashCode = "";
 897             int currentSeqsDiffs = 0;
 898
 899             //read seqs and quality info
 900             Sequence fSeq(inFFasta); m->gobble(inFFasta);
 901             Sequence rSeq(inRFasta); m->gobble(inRFasta);
 902             QualityScores* fQual = NULL; QualityScores* rQual = NULL;
 903             if (thisfqualfile != "") {
 904                 fQual = new QualityScores(inFQual); m->gobble(inFQual);
 905                 rQual = new QualityScores(inRQual); m->gobble(inRQual);
 906             }
 907
 908             int barcodeIndex = 0;
 909             int primerIndex = 0;
 910
 911             if(barcodes.size() != 0){
 912                 if (thisfqualfile != "") {
 913                     success = trimOligos.stripBarcode(fSeq, rSeq, *fQual, *rQual, barcodeIndex);
 914                 }else {
 915                     success = trimOligos.stripBarcode(fSeq, rSeq, barcodeIndex);
 916                 }
 917                 if(success > bdiffs)            {       trashCode += 'b';       }
 918                 else{ currentSeqsDiffs += success;  }
 919             }
 920
 921             if(primers.size() != 0){
 922                 if (thisfqualfile != "") {
 923                     success = trimOligos.stripForward(fSeq, rSeq, *fQual, *rQual, primerIndex);
 924                 }else {
 925                     success = trimOligos.stripForward(fSeq, rSeq, primerIndex);
 926                 }
 927                 if(success > pdiffs)            {       trashCode += 'f';       }
 928                 else{ currentSeqsDiffs += success;  }
 929             }
 930
 931             if (currentSeqsDiffs > tdiffs)      {       trashCode += 't';   }
 932
 933             //flip the reverse reads
 934             rSeq.reverseComplement();
 935             if (thisfqualfile != "") { rQual->flipQScores(); }
 936
 937             //pairwise align
 938             alignment->align(fSeq.getUnaligned(), rSeq.getUnaligned());
 939             map<int, int> ABaseMap = alignment->getSeqAAlnBaseMap();
 940             map<int, int> BBaseMap = alignment->getSeqBAlnBaseMap();
 941             fSeq.setAligned(alignment->getSeqAAln());
 942             rSeq.setAligned(alignment->getSeqBAln());
 943             int length = fSeq.getAligned().length();
 944
 945             //traverse alignments merging into one contiguous seq
 946             string contig = "";
 947             int numMismatches = 0;
 948             string seq1 = fSeq.getAligned();
 949             string seq2 = rSeq.getAligned();
 950             vector<int> scores1, scores2;
 951             if (thisfqualfile != "") {
 952                 scores1 = fQual->getQualityScores();
 953                 scores2 = rQual->getQualityScores();
 954                 delete fQual; delete rQual;
 955             }
 956
 957             // if (num < 5) {  cout << fSeq.getStartPos() << '\t' << fSeq.getEndPos() << '\t' << rSeq.getStartPos() << '\t' << rSeq.getEndPos() << endl; }
 958             int overlapStart = fSeq.getStartPos();
 959             int seq2Start = rSeq.getStartPos();
 960
 961             //bigger of the 2 starting positions is the location of the overlapping start
 962             if (overlapStart < seq2Start) { //seq2 starts later so take from 0 to seq2Start from seq1
 963                 overlapStart = seq2Start;
 964                 for (int i = 0; i < overlapStart; i++) { contig += seq1[i];  }
 965             }else { //seq1 starts later so take from 0 to overlapStart from seq2
 966                 for (int i = 0; i < overlapStart; i++) {  contig += seq2[i]; }
 967             }
 968
 969             int seq1End = fSeq.getEndPos();
 970             int seq2End = rSeq.getEndPos();
 971             int overlapEnd = seq1End;
 972             if (seq2End < overlapEnd) { overlapEnd = seq2End; }  //smallest end position is where overlapping ends
 973
 974             int oStart = contig.length();
 975             for (int i = overlapStart; i < overlapEnd; i++) {
 976                 if (seq1[i] == seq2[i]) { //match, add base and choose highest score
 977                     contig += seq1[i];
 978                 }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
 979                     if (thisfqualfile != "") {
 980                         if (scores2[BBaseMap[i]] <= insert) { } //
 981                         else { contig += seq2[i];  }
 982                     }else { contig += seq2[i]; } //with no quality info, then we keep it?
 983                 }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
 984                     if (thisfqualfile != "") {
 985                         if (scores1[ABaseMap[i]] <= insert) { } //
 986                         else { contig += seq1[i];  }
 987                     }else { contig += seq1[i]; } //with no quality info, then we keep it?
 988                 }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality
 989                     if (thisfqualfile != "") {
 990                         if (abs(scores1[ABaseMap[i]] - scores2[BBaseMap[i]]) >= deltaq) { //is the difference in qual scores >= deltaq, if yes choose base with higher score
 991                             char c = seq1[i];
 992                             if (scores1[ABaseMap[i]] < scores2[BBaseMap[i]]) { c = seq2[i]; }
 993                             contig += c;
 994                         }else { //if no, base becomes n
 995                             contig += 'N';
 996                         }
 997                         numMismatches++;
 998                     }else { numMismatches++; } //cant decide, so eliminate and mark as mismatch
 999                 }else { //should never get here
1000                     m->mothurOut("[ERROR]: case I didn't think of seq1 = " + toString(seq1[i]) + " and seq2 = " + toString(seq2[i]) + "\n");
1001                 }
1002             }
1003             int oend = contig.length();
1004             if (seq1End < seq2End) { //seq1 ends before seq2 so take from overlap to length from seq2
1005                 for (int i = overlapEnd; i < length; i++) { contig += seq2[i];  }
1006             }else { //seq2 ends before seq1 so take from overlap to length from seq1
1007                 for (int i = overlapEnd; i < length; i++) {  contig += seq1[i]; }
1008             }
1009
1010             if (trimOverlap) { contig = contig.substr(overlapStart-1, oend-oStart);  if (contig.length() == 0) { trashCode += "l"; } }
1011
1012             if(trashCode.length() == 0){
1013                 bool ignore = false;
1014
1015                 if (m->debug) { m->mothurOut(fSeq.getName()); }
1016
1017                 if (createOligosGroup) {
1018                     if(barcodes.size() != 0){
1019                         string thisGroup = barcodeNameVector[barcodeIndex];
1020                         if (primers.size() != 0) {
1021                             if (primerNameVector[primerIndex] != "") {
1022                                 if(thisGroup != "") {
1023                                     thisGroup += "." + primerNameVector[primerIndex];
1024                                 }else {
1025                                     thisGroup = primerNameVector[primerIndex];
1026                                 }
1027                             }
1028                         }
1029
1030                         if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
1031
1032                         int pos = thisGroup.find("ignore");
1033                         if (pos == string::npos) {
1034                             groupMap[fSeq.getName()] = thisGroup;
1035
1036                             map<string, int>::iterator it = groupCounts.find(thisGroup);
1037                             if (it == groupCounts.end()) {      groupCounts[thisGroup] = 1; }
1038                             else { groupCounts[it->first] ++; }
1039                         }else { ignore = true; }
1040
1041                     }
1042                 }else if (createFileGroup) {
1043                     int pos = group.find("ignore");
1044                     if (pos == string::npos) {
1045                         groupMap[fSeq.getName()] = group;
1046
1047                         map<string, int>::iterator it = groupCounts.find(group);
1048                         if (it == groupCounts.end()) {  groupCounts[group] = 1; }
1049                         else { groupCounts[it->first] ++; }
1050                     }else { ignore = true; }
1051                 }
1052                 if (m->debug) { m->mothurOut("\n"); }
1053
1054                 if(allFiles && !ignore){
1055                     ofstream output;
1056                     m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
1057                     output << ">" << fSeq.getName() << endl << contig << endl;
1058                     output.close();
1059                 }
1060
1061                 //output
1062                 outFasta << ">" << fSeq.getName() << endl << contig << endl;
1063                 int numNs = 0;
1064                 for (int i = 0; i < contig.length(); i++) { if (contig[i] == 'N') { numNs++; }  }
1065                 outMisMatch << fSeq.getName() << '\t' << contig.length() << '\t' << (oend-oStart) << '\t' << oStart << '\t' << oend << '\t' << numMismatches << '\t' << numNs << endl;
1066             }else {
1067                 //output
1068                 outScrapFasta << ">" << fSeq.getName() << " | " << trashCode << endl << contig << endl;
1069             }
1070             num++;
1071
1072                         //report progress
1073                         if((num) % 1000 == 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
1074                 }
1075
1076                 //report progress
1077                 if((num) % 1000 != 0){  m->mothurOut(toString(num)); m->mothurOutEndLine();             }
1078
1079         inFFasta.close();
1080         inRFasta.close();
1081         outFasta.close();
1082         outScrapFasta.close();
1083         outMisMatch.close();
1084         if (thisfqualfile != "") {
1085             inFQual.close();
1086             inRQual.close();
1087         }
1088         delete alignment;
1089
1090         if (m->control_pressed) {  m->mothurRemove(outputFasta); m->mothurRemove(outputScrapFasta);m->mothurRemove(outputMisMatches);  }
1091
1092         return num;
1093     }
1094         catch(exception& e) {
1095                 m->errorOut(e, "MakeContigsCommand", "driver");
1096                 exit(1);
1097         }
1098 }
1099 //**********************************************************************************************************************
1100 vector< vector<string> > MakeContigsCommand::readFastqFiles(unsigned long int& count, string ffastq, string rfastq){
1101     try {
1102         vector< vector<string> > files;
1103         //maps processors number to file pointer
1104         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
1105         map<int, vector<ofstream*> >::iterator it;
1106
1107         //create files to write to
1108         for (int i = 0; i < processors; i++) {
1109             vector<ofstream*> temp;
1110             ofstream* outFF = new ofstream;     temp.push_back(outFF);
1111             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
1112             ofstream* outRF = new ofstream;     temp.push_back(outRF);
1113             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
1114             tempfiles[i] = temp;
1115
1116             vector<string> names;
1117             string thisOutputDir = outputDir;
1118             if (outputDir == "") { thisOutputDir = m->hasPath(ffastq); }
1119             string ffastafilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "ffastatemp";
1120             string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rfastatemp";
1121             string fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(ffastq)) + toString(i) + "fqualtemp";
1122             string rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rfastq)) + toString(i) + "rqualtemp";
1123             names.push_back(ffastafilename); names.push_back(fqualfilename);
1124             names.push_back(rfastafilename); names.push_back(rqualfilename);
1125             files.push_back(names);
1126
1127             m->openOutputFile(ffastafilename, *outFF);
1128             m->openOutputFile(rfastafilename, *outRF);
1129             m->openOutputFile(fqualfilename, *outFQ);
1130             m->openOutputFile(rqualfilename, *outRQ);
1131         }
1132
1133         if (m->control_pressed) {
1134             //close files, delete ofstreams
1135             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]; } }
1136             //remove files
1137             for (int i = 0; i < files.size(); i++) {
1138                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
1139             }
1140         }
1141
1142         ifstream inForward;
1143         m->openInputFile(ffastq, inForward);
1144
1145         ifstream inReverse;
1146         m->openInputFile(rfastq, inReverse);
1147
1148         count = 0;
1149         map<string, fastqRead> uniques;
1150         map<string, fastqRead>::iterator itUniques;
1151         while ((!inForward.eof()) || (!inReverse.eof())) {
1152
1153             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; }
1154
1155             //get a read from forward and reverse fastq files
1156             bool ignoref, ignorer;
1157             fastqRead thisFread, thisRread;
1158             if (!inForward.eof()) {  thisFread = readFastq(inForward, ignoref); }
1159             else { ignoref = true; }
1160             if (!inReverse.eof()) { thisRread = readFastq(inReverse, ignorer);  }
1161             else { ignorer = true; }
1162
1163             vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
1164
1165             for (int i = 0; i < reads.size(); i++) {
1166                 fastqRead fread = reads[i].forward;
1167                 fastqRead rread = reads[i].reverse;
1168
1169                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
1170
1171                 //if (checkReads(fread, rread, ffastq, rfastq)) {
1172                     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; }
1173
1174                     //if the reads are okay write to output files
1175                     int process = count % processors;
1176
1177                     *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
1178                     *(tempfiles[process][1]) << ">" << fread.name << endl;
1179                     for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
1180                     *(tempfiles[process][1]) << endl;
1181                     *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
1182                     *(tempfiles[process][3]) << ">" << rread.name << endl;
1183                     for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
1184                     *(tempfiles[process][3]) << endl;
1185
1186                     count++;
1187
1188                     //report progress
1189                     if((count) % 10000 == 0){   m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1190                 //}
1191             }
1192                 }
1193                 //report progress
1194                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1195
1196         if (uniques.size() != 0) {
1197             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
1198                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
1199             }
1200             m->mothurOutEndLine();
1201         }
1202
1203         //close files, delete ofstreams
1204         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]; } }
1205         inForward.close();
1206         inReverse.close();
1207
1208         return files;
1209     }
1210     catch(exception& e) {
1211         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1212         exit(1);
1213     }
1214 }
1215 //**********************************************************************************************************************
1216 vector< vector<string> > MakeContigsCommand::readFastaFiles(unsigned long int& count, string ffasta, string rfasta){
1217     try {
1218         vector< vector<string> > files;
1219         //maps processors number to file pointer
1220         map<int, vector<ofstream*> > tempfiles;  //tempfiles[0] = forwardFasta, [1] = forwardQual, [2] = reverseFasta, [3] = reverseQual
1221         map<int, vector<ofstream*> >::iterator it;
1222
1223         //create files to write to
1224         for (int i = 0; i < processors; i++) {
1225             vector<ofstream*> temp;
1226             ofstream* outFF = new ofstream;     temp.push_back(outFF);
1227             ofstream* outFQ = new ofstream;     temp.push_back(outFQ);
1228             ofstream* outRF = new ofstream;     temp.push_back(outRF);
1229             ofstream* outRQ = new ofstream;     temp.push_back(outRQ);
1230             tempfiles[i] = temp;
1231
1232             vector<string> names;
1233             string thisOutputDir = outputDir;
1234             if (outputDir == "") { thisOutputDir = m->hasPath(ffasta); }
1235             string ffastafilename = thisOutputDir + m->getRootName(m->getSimpleName(ffasta)) + toString(i) + "ffastatemp";
1236             string rfastafilename = thisOutputDir + m->getRootName(m->getSimpleName(rfasta)) + toString(i) + "rfastatemp";
1237             string fqualfilename = "";
1238             if (fqualfile != "") { fqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(fqualfile)) + toString(i) + "fqual.temp";  m->openOutputFile(fqualfilename, *outFQ); }
1239             string rqualfilename = "";
1240             if (rqualfile != "") { rqualfilename = thisOutputDir + m->getRootName(m->getSimpleName(rqualfile)) + toString(i) + "rqual.temp"; m->openOutputFile(rqualfilename, *outRQ); }
1241             names.push_back(ffastafilename); names.push_back(fqualfilename);
1242             names.push_back(rfastafilename); names.push_back(rqualfilename);
1243             files.push_back(names);
1244
1245             m->openOutputFile(ffastafilename, *outFF);
1246             m->openOutputFile(rfastafilename, *outRF);
1247         }
1248
1249         if (m->control_pressed) {
1250             //close files, delete ofstreams
1251             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]; } }
1252             //remove files
1253             for (int i = 0; i < files.size(); i++) {
1254                 for(int j = 0; j < files[i].size(); j++) { m->mothurRemove(files[i][j]); }
1255             }
1256         }
1257
1258         ifstream inForwardFasta;
1259         m->openInputFile(ffasta, inForwardFasta);
1260
1261         ifstream inReverseFasta;
1262         m->openInputFile(rfasta, inReverseFasta);
1263
1264         ifstream inForwardQual, inReverseQual;
1265         if (fqualfile != "") { m->openInputFile(fqualfile, inForwardQual); m->openInputFile(rqualfile, inReverseQual); }
1266
1267         count = 0;
1268         map<string, fastqRead> uniques;
1269         map<string, fastqRead>::iterator itUniques;
1270         while ((!inForwardFasta.eof()) || (!inReverseFasta.eof())) {
1271
1272             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; }
1273
1274             //get a reads from forward and reverse fasta files
1275             bool ignoref, ignorer;
1276             fastqRead thisFread, thisRread;
1277             if (!inForwardFasta.eof()) {
1278                 ignoref = false;
1279                 Sequence temp(inForwardFasta); m->gobble(inForwardFasta);
1280                 thisFread.name = temp.getName();
1281                 thisFread.sequence = temp.getUnaligned();
1282             }else { ignoref = true; }
1283             if (!inReverseFasta.eof()) {
1284                 ignorer = false;
1285                 Sequence temp(inReverseFasta); m->gobble(inReverseFasta);
1286                 thisRread.name = temp.getName();
1287                 thisRread.sequence = temp.getUnaligned();
1288             }else { ignorer = true; }
1289
1290             //get qual reads if given
1291             if (fqualfile != "") {
1292                 if (!inForwardQual.eof() && !ignoref) {
1293                     QualityScores temp(inForwardQual); m->gobble(inForwardQual);
1294                     //if forward files dont match ignore read
1295                     if (thisFread.name != temp.getName()) { ignoref = true; }
1296                     else { thisFread.scores = temp.getQualityScores(); }
1297                 }else { ignoref = true; }
1298                 if (!inReverseQual.eof() && !ignorer) {
1299                     QualityScores temp(inReverseQual); m->gobble(inReverseQual);
1300                     //if reverse files dont match ignore read
1301                     if (thisRread.name != temp.getName()) { ignorer = true; }
1302                     else { thisRread.scores = temp.getQualityScores(); }
1303                 }else { ignorer = true; }
1304             }
1305
1306             vector<pairFastqRead> reads = getReads(ignoref, ignorer, thisFread, thisRread, uniques);
1307
1308             for (int i = 0; i < reads.size(); i++) {
1309                 fastqRead fread = reads[i].forward;
1310                 fastqRead rread = reads[i].reverse;
1311
1312                 if (m->debug) { m->mothurOut(toString(count) + '\t' + fread.name + '\t' + rread.name + '\n'); }
1313
1314                // if (checkReads(fread, rread, ffasta, rfasta)) {
1315                     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; }
1316
1317                     //if the reads are okay write to output files
1318                     int process = count % processors;
1319
1320                     *(tempfiles[process][0]) << ">" << fread.name << endl << fread.sequence << endl;
1321                     *(tempfiles[process][2]) << ">" << rread.name << endl << rread.sequence << endl;
1322                     if (fqualfile != "") { //if you have quality info, print it
1323                         *(tempfiles[process][1]) << ">" << fread.name << endl;
1324                         for (int i = 0; i < fread.scores.size(); i++) { *(tempfiles[process][1]) << fread.scores[i] << " "; }
1325                         *(tempfiles[process][1]) << endl;
1326                         *(tempfiles[process][3]) << ">" << rread.name << endl;
1327                         for (int i = 0; i < rread.scores.size(); i++) { *(tempfiles[process][3]) << rread.scores[i] << " "; }
1328                         *(tempfiles[process][3]) << endl;
1329                     }
1330                     count++;
1331
1332                     //report progress
1333                     if((count) % 10000 == 0){   m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1334                 //}
1335             }
1336                 }
1337                 //report progress
1338                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1339
1340         if (uniques.size() != 0) {
1341             for (itUniques = uniques.begin(); itUniques != uniques.end(); itUniques++) {
1342                 m->mothurOut("[WARNING]: did not find paired read for " + itUniques->first + ", ignoring.\n");
1343             }
1344             m->mothurOutEndLine();
1345         }
1346
1347         //close files, delete ofstreams
1348         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]; } }
1349         inReverseFasta.close();
1350         inForwardFasta.close();
1351         if (fqualfile != "") { inReverseQual.close(); inReverseQual.close(); }
1352
1353         return files;
1354     }
1355     catch(exception& e) {
1356         m->errorOut(e, "MakeContigsCommand", "readFastaFiles");
1357         exit(1);
1358     }
1359 }
1360 //**********************************************************************************************************************
1361 vector<pairFastqRead> MakeContigsCommand::getReads(bool ignoref, bool ignorer, fastqRead forward, fastqRead reverse, map<string, fastqRead>& uniques){
1362     try {
1363         vector<pairFastqRead> reads;
1364         map<string, fastqRead>::iterator itUniques;
1365
1366         if (!ignoref && !ignorer) {
1367             if (forward.name == reverse.name) {
1368                 pairFastqRead temp(forward, reverse);
1369                 reads.push_back(temp);
1370             }else {
1371                 bool match = false;
1372                 //if no match are the names only different by 1 and 2?
1373                 string tempFRead = forward.name.substr(0, forward.name.length()-1);
1374                 string tempRRead = reverse.name.substr(0, reverse.name.length()-1);
1375                 if (tempFRead == tempRRead) {
1376                     if ((forward.name[forward.name.length()-1] == '1') && (reverse.name[reverse.name.length()-1] == '2')) {
1377                         forward.name = tempFRead;
1378                         reverse.name = tempRRead;
1379                         pairFastqRead temp(forward, reverse);
1380                         reads.push_back(temp);
1381                         match = true;
1382                     }
1383                 }
1384
1385                 if (!match) {
1386                     //look for forward pair
1387                     itUniques = uniques.find(forward.name);
1388                     if (itUniques != uniques.end()) {  //we have the pair for this read
1389                         pairFastqRead temp(forward, itUniques->second);
1390                         reads.push_back(temp);
1391                         uniques.erase(itUniques);
1392                     }else { //save this read for later
1393                         uniques[forward.name] = forward;
1394                     }
1395
1396                     //look for reverse pair
1397                     itUniques = uniques.find(reverse.name);
1398                     if (itUniques != uniques.end()) {  //we have the pair for this read
1399                         pairFastqRead temp(itUniques->second, reverse);
1400                         reads.push_back(temp);
1401                         uniques.erase(itUniques);
1402                     }else { //save this read for later
1403                         uniques[reverse.name] = reverse;
1404                     }
1405                 }
1406
1407             }
1408         }else if (!ignoref && ignorer) { //ignore reverse keep forward
1409             //look for forward pair
1410             itUniques = uniques.find(forward.name);
1411             if (itUniques != uniques.end()) {  //we have the pair for this read
1412                 pairFastqRead temp(forward, itUniques->second);
1413                 reads.push_back(temp);
1414                 uniques.erase(itUniques);
1415             }else { //save this read for later
1416                 uniques[forward.name] = forward;
1417             }
1418
1419         }else if (ignoref && !ignorer) { //ignore forward keep reverse
1420             //look for reverse pair
1421             itUniques = uniques.find(reverse.name);
1422             if (itUniques != uniques.end()) {  //we have the pair for this read
1423                 pairFastqRead temp(itUniques->second, reverse);
1424                 reads.push_back(temp);
1425                 uniques.erase(itUniques);
1426             }else { //save this read for later
1427                 uniques[reverse.name] = reverse;
1428             }
1429         }//else ignore both and do nothing
1430
1431         return reads;
1432     }
1433     catch(exception& e) {
1434         m->errorOut(e, "MakeContigsCommand", "readFastqFiles");
1435         exit(1);
1436     }
1437 }
1438 //**********************************************************************************************************************
1439 fastqRead MakeContigsCommand::readFastq(ifstream& in, bool& ignore){
1440     try {
1441         fastqRead read;
1442
1443         ignore = false;
1444
1445         //read sequence name
1446         string line = m->getline(in); m->gobble(in);
1447         vector<string> pieces = m->splitWhiteSpace(line);
1448         string name = "";  if (pieces.size() != 0) { name = pieces[0]; }
1449         if (name == "") {  m->mothurOut("[WARNING]: Blank fasta name, ignoring read."); m->mothurOutEndLine(); ignore=true;  }
1450         else if (name[0] != '@') { m->mothurOut("[WARNING]: reading " + name + " expected a name with @ as a leading character, ignoring read."); m->mothurOutEndLine(); ignore=true; }
1451         else { name = name.substr(1); }
1452
1453         //read sequence
1454         string sequence = m->getline(in); m->gobble(in);
1455         if (sequence == "") {  m->mothurOut("[WARNING]: missing sequence for " + name + ", ignoring."); ignore=true; }
1456
1457         //read sequence name
1458         line = m->getline(in); m->gobble(in);
1459         pieces = m->splitWhiteSpace(line);
1460         string name2 = "";  if (pieces.size() != 0) { name2 = pieces[0]; }
1461         if (name2 == "") {  m->mothurOut("[WARNING]: expected a name with + as a leading character, ignoring."); ignore=true; }
1462         else if (name2[0] != '+') { m->mothurOut("[WARNING]: reading " + name2 + " expected a name with + as a leading character, ignoring."); ignore=true; }
1463         else { name2 = name2.substr(1); if (name2 == "") { name2 = name; } }
1464
1465         //read quality scores
1466         string quality = m->getline(in); m->gobble(in);
1467         if (quality == "") {  m->mothurOut("[WARNING]: missing quality for " + name2 + ", ignoring."); ignore=true; }
1468
1469         //sanity check sequence length and number of quality scores match
1470         if (name2 != "") { if (name != name2) { m->mothurOut("[WARNING]: names do not match. read " + name + " for fasta and " + name2 + " for quality, ignoring."); ignore=true; } }
1471         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; }
1472
1473         vector<int> qualScores = convertQual(quality);
1474
1475         read.name = name;
1476         read.sequence = sequence;
1477         read.scores = qualScores;
1478
1479         return read;
1480     }
1481     catch(exception& e) {
1482         m->errorOut(e, "MakeContigsCommand", "readFastq");
1483         exit(1);
1484     }
1485 }
1486 /**********************************************************************************************************************
1487 bool MakeContigsCommand::checkReads(fastqRead& forward, fastqRead& reverse, string ffile, string rfile){
1488     try {
1489         bool good = true;
1490
1491         //do sequence lengths match
1492         if (forward.sequence.length() != reverse.sequence.length()) {
1493             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");
1494             good = false;
1495         }
1496
1497         //do number of qual scores match
1498         if (forward.scores.size() != reverse.scores.size()) {
1499             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");
1500             good = false;
1501         }
1502
1503         return good;
1504     }
1505     catch(exception& e) {
1506         m->errorOut(e, "MakeContigsCommand", "checkReads");
1507         exit(1);
1508     }
1509 }*/
1510 //***************************************************************************************************************
1511 vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
1512         try {
1513         vector< vector<string> > files;
1514         string forward, reverse;
1515
1516         ifstream in;
1517         m->openInputFile(filename, in);
1518
1519         while(!in.eof()) {
1520
1521             if (m->control_pressed) { return files; }
1522
1523             in >> forward; m->gobble(in);
1524             in >> reverse;
1525
1526             string group = "";
1527             while (!in.eof())   { //do we have a group assigned to this pair
1528                 char c = in.get();
1529                 if (c == 10 || c == 13 || c == -1){     break;  }
1530                 else if (c == 32 || c == 9){;} //space or tab
1531                 else {  group += c;  }
1532             }
1533
1534             if (group != "") {
1535                 //line in file look like: group forward reverse
1536                 string temp = forward;
1537                 forward = reverse;
1538                 reverse = group;
1539                 group = temp;
1540                 createFileGroup = true;
1541             }
1542             m->gobble(in);
1543
1544
1545             //check to make sure both are able to be opened
1546             ifstream in2;
1547             int openForward = m->openInputFile(forward, in2, "noerror");
1548
1549             //if you can't open it, try default location
1550             if (openForward == 1) {
1551                 if (m->getDefaultPath() != "") { //default path is set
1552                     string tryPath = m->getDefaultPath() + m->getSimpleName(forward);
1553                     m->mothurOut("Unable to open " + forward + ". Trying default " + tryPath); m->mothurOutEndLine();
1554                     ifstream in3;
1555                     openForward = m->openInputFile(tryPath, in3, "noerror");
1556                     in3.close();
1557                     forward = tryPath;
1558                 }
1559             }
1560
1561             //if you can't open it, try output location
1562             if (openForward == 1) {
1563                 if (m->getOutputDir() != "") { //default path is set
1564                     string tryPath = m->getOutputDir() + m->getSimpleName(forward);
1565                     m->mothurOut("Unable to open " + forward + ". Trying output directory " + tryPath); m->mothurOutEndLine();
1566                     ifstream in4;
1567                     openForward = m->openInputFile(tryPath, in4, "noerror");
1568                     forward = tryPath;
1569                     in4.close();
1570                 }
1571             }
1572
1573             if (openForward == 1) { //can't find it
1574                 m->mothurOut("[WARNING]: can't find " + forward + ", ignoring pair.\n");
1575             }else{  in2.close();  }
1576
1577             ifstream in3;
1578             int openReverse = m->openInputFile(reverse, in3, "noerror");
1579
1580             //if you can't open it, try default location
1581             if (openReverse == 1) {
1582                 if (m->getDefaultPath() != "") { //default path is set
1583                     string tryPath = m->getDefaultPath() + m->getSimpleName(reverse);
1584                     m->mothurOut("Unable to open " + reverse + ". Trying default " + tryPath); m->mothurOutEndLine();
1585                     ifstream in3;
1586                     openReverse = m->openInputFile(tryPath, in3, "noerror");
1587                     in3.close();
1588                     reverse = tryPath;
1589                 }
1590             }
1591
1592             //if you can't open it, try output location
1593             if (openReverse == 1) {
1594                 if (m->getOutputDir() != "") { //default path is set
1595                     string tryPath = m->getOutputDir() + m->getSimpleName(reverse);
1596                     m->mothurOut("Unable to open " + reverse + ". Trying output directory " + tryPath); m->mothurOutEndLine();
1597                     ifstream in4;
1598                     openReverse = m->openInputFile(tryPath, in4, "noerror");
1599                     reverse = tryPath;
1600                     in4.close();
1601                 }
1602             }
1603
1604             if (openReverse == 1) { //can't find it
1605                 m->mothurOut("[WARNING]: can't find " + reverse + ", ignoring pair.\n");
1606             }else{  in3.close();  }
1607
1608             if ((openForward != 1) && (openReverse != 1)) { //good pair
1609                 file2Group[files.size()] = group;
1610                 vector<string> pair;
1611                 pair.push_back(forward);
1612                 pair.push_back(reverse);
1613                 files.push_back(pair);
1614             }
1615         }
1616         in.close();
1617
1618         return files;
1619     }
1620     catch(exception& e) {
1621         m->errorOut(e, "MakeContigsCommand", "checkReads");
1622         exit(1);
1623     }
1624 }
1625 //***************************************************************************************************************
1626 //illumina data requires paired forward and reverse data
1627 //BARCODE   atgcatgc   atgcatgc    groupName
1628 //PRIMER   atgcatgc   atgcatgc    groupName
1629 //PRIMER   atgcatgc   atgcatgc
1630 bool MakeContigsCommand::getOligos(vector<vector<string> >& fastaFileNames, string rootname){
1631         try {
1632                 ifstream in;
1633                 m->openInputFile(oligosfile, in);
1634
1635                 ofstream test;
1636
1637                 string type, foligo, roligo, group;
1638
1639                 int indexPrimer = 0;
1640                 int indexBarcode = 0;
1641         set<string> uniquePrimers;
1642         set<string> uniqueBarcodes;
1643
1644                 while(!in.eof()){
1645
1646                         in >> type;
1647
1648                         if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
1649
1650                         if(type[0] == '#'){
1651                                 while (!in.eof())       {       char c = in.get();  if (c == 10 || c == 13){    break;  }       } // get rest of line if there's any crap there
1652                                 m->gobble(in);
1653                         }
1654                         else{
1655                                 m->gobble(in);
1656                                 //make type case insensitive
1657                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
1658
1659                                 in >> foligo;
1660
1661                 if (m->debug) { m->mothurOut("[DEBUG]: reading - " + foligo + ".\n"); }
1662
1663                                 for(int i=0;i<foligo.length();i++){
1664                                         foligo[i] = toupper(foligo[i]);
1665                                         if(foligo[i] == 'U')    {       foligo[i] = 'T';        }
1666                                 }
1667
1668                                 if(type == "PRIMER"){
1669                                         m->gobble(in);
1670
1671                     in >> roligo;
1672
1673                     for(int i=0;i<roligo.length();i++){
1674                         roligo[i] = toupper(roligo[i]);
1675                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1676                     }
1677                     //roligo = reverseOligo(roligo);
1678
1679                     group = "";
1680
1681                                         // get rest of line in case there is a primer name
1682                                         while (!in.eof())       {
1683                                                 char c = in.get();
1684                                                 if (c == 10 || c == 13 || c == -1){     break;  }
1685                                                 else if (c == 32 || c == 9){;} //space or tab
1686                                                 else {  group += c;  }
1687                                         }
1688
1689                     oligosPair newPrimer(foligo, roligo);
1690
1691                                         //check for repeat barcodes
1692                     string tempPair = foligo+roligo;
1693                     if (uniquePrimers.count(tempPair) != 0) { m->mothurOut("primer pair " + newPrimer.forward + " " + newPrimer.reverse + " is in your oligos file already."); m->mothurOutEndLine();  }
1694                     else { uniquePrimers.insert(tempPair); }
1695
1696                     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"); }  }
1697
1698                                         primers[indexPrimer]=newPrimer; indexPrimer++;
1699                                         primerNameVector.push_back(group);
1700                                 }else if(type == "BARCODE"){
1701                                         m->gobble(in);
1702
1703                     in >> roligo;
1704
1705                     for(int i=0;i<roligo.length();i++){
1706                         roligo[i] = toupper(roligo[i]);
1707                         if(roligo[i] == 'U')    {       roligo[i] = 'T';        }
1708                     }
1709                     //roligo = reverseOligo(roligo);
1710
1711                     oligosPair newPair(foligo, roligo);
1712
1713                     group = "";
1714                     while (!in.eof())   {
1715                                                 char c = in.get();
1716                                                 if (c == 10 || c == 13 || c == -1){     break;  }
1717                                                 else if (c == 32 || c == 9){;} //space or tab
1718                                                 else {  group += c;  }
1719                                         }
1720
1721                     if (m->debug) { m->mothurOut("[DEBUG]: barcode pair " + newPair.forward + " " + newPair.reverse + ", and group = " + group + ".\n"); }
1722
1723                     //check for repeat barcodes
1724                     string tempPair = foligo+roligo;
1725                     if (uniqueBarcodes.count(tempPair) != 0) { m->mothurOut("barcode pair " + newPair.forward + " " + newPair.reverse +  " is in your oligos file already, disregarding."); m->mothurOutEndLine();  }
1726                     else { uniqueBarcodes.insert(tempPair); }
1727
1728                     barcodes[indexBarcode]=newPair; indexBarcode++;
1729                                         barcodeNameVector.push_back(group);
1730                                 }else if(type == "LINKER"){
1731                                         linker.push_back(foligo);
1732                     m->mothurOut("[WARNING]: make.contigs is not setup to remove linkers, ignoring.\n");
1733                                 }else if(type == "SPACER"){
1734                                         spacer.push_back(foligo);
1735                     m->mothurOut("[WARNING]: make.contigs is not setup to remove spacers, ignoring.\n");
1736                                 }
1737                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are primer, barcode, linker and spacer. Ignoring " + foligo + "."); m->mothurOutEndLine(); }
1738                         }
1739                         m->gobble(in);
1740                 }
1741                 in.close();
1742
1743                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
1744
1745                 //add in potential combos
1746                 if(barcodeNameVector.size() == 0){
1747             oligosPair temp("", "");
1748                         barcodes[0] = temp;
1749                         barcodeNameVector.push_back("");
1750                 }
1751
1752                 if(primerNameVector.size() == 0){
1753             oligosPair temp("", "");
1754                         primers[0] = temp;
1755                         primerNameVector.push_back("");
1756                 }
1757
1758                 fastaFileNames.resize(barcodeNameVector.size());
1759                 for(int i=0;i<fastaFileNames.size();i++){
1760                         fastaFileNames[i].assign(primerNameVector.size(), "");
1761                 }
1762
1763                 if(allFiles){
1764                         set<string> uniqueNames; //used to cleanup outputFileNames
1765                         for(map<int, oligosPair>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1766                                 for(map<int, oligosPair>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1767
1768                                         string primerName = primerNameVector[itPrimer->first];
1769                                         string barcodeName = barcodeNameVector[itBar->first];
1770
1771                     if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
1772                                         else {
1773                         string comboGroupName = "";
1774                         string fastaFileName = "";
1775                         string qualFileName = "";
1776                         string nameFileName = "";
1777                         string countFileName = "";
1778
1779                         if(primerName == ""){
1780                             comboGroupName = barcodeNameVector[itBar->first];
1781                         }
1782                         else{
1783                             if(barcodeName == ""){
1784                                 comboGroupName = primerNameVector[itPrimer->first];
1785                             }
1786                             else{
1787                                 comboGroupName = barcodeNameVector[itBar->first] + "." + primerNameVector[itPrimer->first];
1788                             }
1789                         }
1790
1791
1792                         ofstream temp;
1793                         fastaFileName = rootname + comboGroupName + ".fasta";
1794                         if (uniqueNames.count(fastaFileName) == 0) {
1795                             outputNames.push_back(fastaFileName);
1796                             outputTypes["fasta"].push_back(fastaFileName);
1797                             uniqueNames.insert(fastaFileName);
1798                         }
1799
1800                         fastaFileNames[itBar->first][itPrimer->first] = fastaFileName;
1801                         m->openOutputFile(fastaFileName, temp);         temp.close();
1802                     }
1803                                 }
1804                         }
1805                 }
1806
1807                 bool allBlank = true;
1808                 for (int i = 0; i < barcodeNameVector.size(); i++) {
1809                         if (barcodeNameVector[i] != "") {
1810                                 allBlank = false;
1811                                 break;
1812                         }
1813                 }
1814                 for (int i = 0; i < primerNameVector.size(); i++) {
1815                         if (primerNameVector[i] != "") {
1816                                 allBlank = false;
1817                                 break;
1818                         }
1819                 }
1820
1821                 if (allBlank) {
1822                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
1823                         allFiles = false;
1824                         return false;
1825                 }
1826
1827                 return true;
1828
1829         }
1830         catch(exception& e) {
1831                 m->errorOut(e, "MakeContigsCommand", "getOligos");
1832                 exit(1);
1833         }
1834 }
1835 //********************************************************************/
1836 string MakeContigsCommand::reverseOligo(string oligo){
1837         try {
1838         string reverse = "";
1839
1840         for(int i=oligo.length()-1;i>=0;i--){
1841
1842             if(oligo[i] == 'A')         {       reverse += 'T'; }
1843             else if(oligo[i] == 'T'){   reverse += 'A'; }
1844             else if(oligo[i] == 'U'){   reverse += 'A'; }
1845
1846             else if(oligo[i] == 'G'){   reverse += 'C'; }
1847             else if(oligo[i] == 'C'){   reverse += 'G'; }
1848
1849             else if(oligo[i] == 'R'){   reverse += 'Y'; }
1850             else if(oligo[i] == 'Y'){   reverse += 'R'; }
1851
1852             else if(oligo[i] == 'M'){   reverse += 'K'; }
1853             else if(oligo[i] == 'K'){   reverse += 'M'; }
1854
1855             else if(oligo[i] == 'W'){   reverse += 'W'; }
1856             else if(oligo[i] == 'S'){   reverse += 'S'; }
1857
1858             else if(oligo[i] == 'B'){   reverse += 'V'; }
1859             else if(oligo[i] == 'V'){   reverse += 'B'; }
1860
1861             else if(oligo[i] == 'D'){   reverse += 'H'; }
1862             else if(oligo[i] == 'H'){   reverse += 'D'; }
1863
1864             else                                                {       reverse += 'N'; }
1865         }
1866
1867
1868         return reverse;
1869     }
1870         catch(exception& e) {
1871                 m->errorOut(e, "MakeContigsCommand", "reverseOligo");
1872                 exit(1);
1873         }
1874 }
1875 //**********************************************************************************************************************
1876 vector<int> MakeContigsCommand::convertQual(string qual) {
1877         try {
1878                 vector<int> qualScores;
1879         bool negativeScores = false;
1880
1881                 for (int i = 0; i < qual.length(); i++) {
1882
1883             int temp = 0;
1884             temp = int(qual[i]);
1885             if (format == "illumina") {
1886                 temp -= 64; //char '@'
1887             }else if (format == "illumina1.8+") {
1888                     temp -= int('!'); //char '!'
1889             }else if (format == "solexa") {
1890                 temp = int(convertTable[temp]); //convert to sanger
1891                 temp -= int('!'); //char '!'
1892             }else {
1893                 temp -= int('!'); //char '!'
1894             }
1895
1896             if (temp < -5) { negativeScores = true; }
1897                         qualScores.push_back(temp);
1898                 }
1899
1900         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;  }
1901
1902                 return qualScores;
1903         }
1904         catch(exception& e) {
1905                 m->errorOut(e, "MakeContigsCommand", "convertQual");
1906                 exit(1);
1907         }
1908 }
1909
1910 //**********************************************************************************************************************
1911
1912
1913
1914