trimseqscommand.cpp

   1 /*
   2  *  trimseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/6/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "trimseqscommand.h"
  11 #include "needlemanoverlap.hpp"
  12 #include "trimoligos.h"
  13
  14
  15 //**********************************************************************************************************************
  16 vector<string> TrimSeqsCommand::setParameters(){
  17         try {
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  19                 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(poligos);
  20                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
  21                 CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
  22         CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
  23                 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  24                 CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
  25                 CommandParameter pmaxhomop("maxhomop", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxhomop);
  26                 CommandParameter pminlength("minlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pminlength);
  27                 CommandParameter pmaxlength("maxlength", "Number", "", "0", "", "", "",false,false); parameters.push_back(pmaxlength);
  28                 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ppdiffs);
  29                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pbdiffs);
  30         CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(pldiffs);
  31                 CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(psdiffs);
  32         CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "",false,false); parameters.push_back(ptdiffs);
  33                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  34                 CommandParameter pallfiles("allfiles", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pallfiles);
  35                 CommandParameter pkeepforward("keepforward", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pkeepforward);
  36                 CommandParameter pqtrim("qtrim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqtrim);
  37                 CommandParameter pqthreshold("qthreshold", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqthreshold);
  38                 CommandParameter pqaverage("qaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqaverage);
  39                 CommandParameter prollaverage("rollaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(prollaverage);
  40                 CommandParameter pqwindowaverage("qwindowaverage", "Number", "", "0", "", "", "",false,false); parameters.push_back(pqwindowaverage);
  41                 CommandParameter pqstepsize("qstepsize", "Number", "", "1", "", "", "",false,false); parameters.push_back(pqstepsize);
  42                 CommandParameter pqwindowsize("qwindowsize", "Number", "", "50", "", "", "",false,false); parameters.push_back(pqwindowsize);
  43                 CommandParameter pkeepfirst("keepfirst", "Number", "", "0", "", "", "",false,false); parameters.push_back(pkeepfirst);
  44                 CommandParameter premovelast("removelast", "Number", "", "0", "", "", "",false,false); parameters.push_back(premovelast);
  45                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  46                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  47
  48                 vector<string> myArray;
  49                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  50                 return myArray;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "TrimSeqsCommand", "setParameters");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 string TrimSeqsCommand::getHelpString(){
  59         try {
  60                 string helpString = "";
  61                 helpString += "The trim.seqs command reads a fastaFile and creates 2 new fasta files, .trim.fasta and scrap.fasta, as well as group files if you provide and oligos file.\n";
  62                 helpString += "The .trim.fasta contains sequences that meet your requirements, and the .scrap.fasta contains those which don't.\n";
  63                 helpString += "The trim.seqs command parameters are fasta, name, count, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim, keepfirst, removelast and allfiles.\n";
  64                 helpString += "The fasta parameter is required.\n";
  65                 helpString += "The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n";
  66                 helpString += "The oligos parameter allows you to provide an oligos file.\n";
  67                 helpString += "The name parameter allows you to provide a names file with your fasta file.\n";
  68         helpString += "The count parameter allows you to provide a count file with your fasta file.\n";
  69                 helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
  70                 helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
  71                 helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
  72                 helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
  73                 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";
  74                 helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
  75                 helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
  76         helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
  77                 helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
  78                 helpString += "The qfile parameter allows you to provide a quality file.\n";
  79                 helpString += "The qthreshold parameter allows you to set a minimum quality score allowed. \n";
  80                 helpString += "The qaverage parameter allows you to set a minimum average quality score allowed. \n";
  81                 helpString += "The qwindowsize parameter allows you to set a number of bases in a window. Default=50.\n";
  82                 helpString += "The qwindowaverage parameter allows you to set a minimum average quality score allowed over a window. \n";
  83                 helpString += "The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. \n";
  84                 helpString += "The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.\n";
  85                 helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n";
  86                 helpString += "The keepforward parameter allows you to indicate whether you want the forward primer removed or not. The default is F, meaning remove the forward primer.\n";
  87                 helpString += "The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.\n";
  88                 helpString += "The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. \n";
  89                 helpString += "The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.\n";
  90                 helpString += "The trim.seqs command should be in the following format: \n";
  91                 helpString += "trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n";
  92                 helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n";
  93                 helpString += "Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
  94                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  95                 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n";
  96                 return helpString;
  97         }
  98         catch(exception& e) {
  99                 m->errorOut(e, "TrimSeqsCommand", "getHelpString");
 100                 exit(1);
 101         }
 102 }
 103 //**********************************************************************************************************************
 104 string TrimSeqsCommand::getOutputFileNameTag(string type, string inputName=""){
 105         try {
 106         string outputFileName = "";
 107                 map<string, vector<string> >::iterator it;
 108
 109         //is this a type this command creates
 110         it = outputTypes.find(type);
 111         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
 112         else {
 113             if (type == "qfile")            {   outputFileName =  "qual";   }
 114             else if (type == "fasta")            {   outputFileName =  "fasta";   }
 115             else if (type == "group")            {   outputFileName =  "groups";   }
 116             else if (type == "name")            {   outputFileName =  "names";   }
 117             else if (type == "count")            {   outputFileName =  "count_table";   }
 118             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
 119         }
 120         return outputFileName;
 121         }
 122         catch(exception& e) {
 123                 m->errorOut(e, "TrimSeqsCommand", "getOutputFileNameTag");
 124                 exit(1);
 125         }
 126 }
 127
 128
 129 //**********************************************************************************************************************
 130
 131 TrimSeqsCommand::TrimSeqsCommand(){
 132         try {
 133                 abort = true; calledHelp = true;
 134                 setParameters();
 135                 vector<string> tempOutNames;
 136                 outputTypes["fasta"] = tempOutNames;
 137                 outputTypes["qfile"] = tempOutNames;
 138                 outputTypes["group"] = tempOutNames;
 139                 outputTypes["name"] = tempOutNames;
 140         outputTypes["count"] = tempOutNames;
 141         }
 142         catch(exception& e) {
 143                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 144                 exit(1);
 145         }
 146 }
 147 //***************************************************************************************************************
 148
 149 TrimSeqsCommand::TrimSeqsCommand(string option)  {
 150         try {
 151
 152                 abort = false; calledHelp = false;
 153                 comboStarts = 0;
 154
 155                 //allow user to run help
 156                 if(option == "help") { help(); abort = true; calledHelp = true; }
 157                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 158
 159                 else {
 160                         vector<string> myArray = setParameters();
 161
 162                         OptionParser parser(option);
 163                         map<string,string> parameters = parser.getParameters();
 164
 165                         ValidParameters validParameter;
 166                         map<string,string>::iterator it;
 167
 168                         //check to make sure all parameters are valid for command
 169                         for (it = parameters.begin(); it != parameters.end(); it++) {
 170                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 171                         }
 172
 173                         //initialize outputTypes
 174                         vector<string> tempOutNames;
 175                         outputTypes["fasta"] = tempOutNames;
 176                         outputTypes["qfile"] = tempOutNames;
 177                         outputTypes["group"] = tempOutNames;
 178                         outputTypes["name"] = tempOutNames;
 179             outputTypes["count"] = tempOutNames;
 180
 181                         //if the user changes the input directory command factory will send this info to us in the output parameter
 182                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 183                         if (inputDir == "not found"){   inputDir = "";          }
 184                         else {
 185                                 string path;
 186                                 it = parameters.find("fasta");
 187                                 //user has given a template file
 188                                 if(it != parameters.end()){
 189                                         path = m->hasPath(it->second);
 190                                         //if the user has not given a path then, add inputdir. else leave path alone.
 191                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 192                                 }
 193
 194                                 it = parameters.find("oligos");
 195                                 //user has given a template file
 196                                 if(it != parameters.end()){
 197                                         path = m->hasPath(it->second);
 198                                         //if the user has not given a path then, add inputdir. else leave path alone.
 199                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 200                                 }
 201
 202                                 it = parameters.find("qfile");
 203                                 //user has given a template file
 204                                 if(it != parameters.end()){
 205                                         path = m->hasPath(it->second);
 206                                         //if the user has not given a path then, add inputdir. else leave path alone.
 207                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 208                                 }
 209
 210                                 it = parameters.find("name");
 211                                 //user has given a template file
 212                                 if(it != parameters.end()){
 213                                         path = m->hasPath(it->second);
 214                                         //if the user has not given a path then, add inputdir. else leave path alone.
 215                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 216                                 }
 217
 218                 it = parameters.find("count");
 219                                 //user has given a template file
 220                                 if(it != parameters.end()){
 221                                         path = m->hasPath(it->second);
 222                                         //if the user has not given a path then, add inputdir. else leave path alone.
 223                                         if (path == "") {       parameters["count"] = inputDir + it->second;            }
 224                                 }
 225
 226                         }
 227
 228
 229                         //check for required parameters
 230                         fastaFile = validParameter.validFile(parameters, "fasta", true);
 231                         if (fastaFile == "not found") {
 232                                 fastaFile = m->getFastaFile();
 233                                 if (fastaFile != "") { m->mothurOut("Using " + fastaFile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 234                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 235                         }else if (fastaFile == "not open") { abort = true; }
 236                         else { m->setFastaFile(fastaFile); }
 237
 238                         //if the user changes the output directory command factory will send this info to us in the output parameter
 239                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 240                                 outputDir = "";
 241                                 outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
 242                         }
 243
 244
 245                         //check for optional parameter and set defaults
 246                         // ...at some point should added some additional type checking...
 247                         string temp;
 248                         temp = validParameter.validFile(parameters, "flip", false);
 249                         if (temp == "not found")    {   flip = 0;       }
 250                         else {  flip = m->isTrue(temp);         }
 251
 252                         temp = validParameter.validFile(parameters, "oligos", true);
 253                         if (temp == "not found"){       oligoFile = "";         }
 254                         else if(temp == "not open"){    abort = true;   }
 255                         else                                    {       oligoFile = temp; m->setOligosFile(oligoFile);          }
 256
 257
 258                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 259                         m->mothurConvert(temp, maxAmbig);
 260
 261                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
 262                         m->mothurConvert(temp, maxHomoP);
 263
 264                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
 265                         m->mothurConvert(temp, minLength);
 266
 267                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
 268                         m->mothurConvert(temp, maxLength);
 269
 270                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
 271                         m->mothurConvert(temp, bdiffs);
 272
 273                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 274                         m->mothurConvert(temp, pdiffs);
 275
 276             temp = validParameter.validFile(parameters, "ldiffs", false);               if (temp == "not found") { temp = "0"; }
 277                         m->mothurConvert(temp, ldiffs);
 278
 279             temp = validParameter.validFile(parameters, "sdiffs", false);               if (temp == "not found") { temp = "0"; }
 280                         m->mothurConvert(temp, sdiffs);
 281
 282                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs;  temp = toString(tempTotal); }
 283                         m->mothurConvert(temp, tdiffs);
 284
 285                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs + ldiffs + sdiffs;     }
 286
 287                         temp = validParameter.validFile(parameters, "qfile", true);
 288                         if (temp == "not found")        {       qFileName = "";         }
 289                         else if(temp == "not open")     {       abort = true;           }
 290                         else                                            {       qFileName = temp;       m->setQualFile(qFileName); }
 291
 292                         temp = validParameter.validFile(parameters, "name", true);
 293                         if (temp == "not found")        {       nameFile = "";          }
 294                         else if(temp == "not open")     {       nameFile = "";  abort = true;           }
 295                         else                                            {       nameFile = temp;        m->setNameFile(nameFile); }
 296
 297             countfile = validParameter.validFile(parameters, "count", true);
 298                         if (countfile == "not open") { abort = true; countfile = ""; }
 299                         else if (countfile == "not found") { countfile = ""; }
 300                         else { m->setCountTableFile(countfile); }
 301
 302             if ((countfile != "") && (nameFile != "")) { m->mothurOut("You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; }
 303
 304                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 305                         m->mothurConvert(temp, qThreshold);
 306
 307                         temp = validParameter.validFile(parameters, "qtrim", false);            if (temp == "not found") { temp = "t"; }
 308                         qtrim = m->isTrue(temp);
 309
 310                         temp = validParameter.validFile(parameters, "rollaverage", false);      if (temp == "not found") { temp = "0"; }
 311                         convert(temp, qRollAverage);
 312
 313                         temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
 314                         convert(temp, qWindowAverage);
 315
 316                         temp = validParameter.validFile(parameters, "qwindowsize", false);      if (temp == "not found") { temp = "50"; }
 317                         convert(temp, qWindowSize);
 318
 319                         temp = validParameter.validFile(parameters, "qstepsize", false);        if (temp == "not found") { temp = "1"; }
 320                         convert(temp, qWindowStep);
 321
 322                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 323                         convert(temp, qAverage);
 324
 325                         temp = validParameter.validFile(parameters, "keepfirst", false);        if (temp == "not found") { temp = "0"; }
 326                         convert(temp, keepFirst);
 327
 328                         temp = validParameter.validFile(parameters, "removelast", false);       if (temp == "not found") { temp = "0"; }
 329                         convert(temp, removeLast);
 330
 331                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 332                         allFiles = m->isTrue(temp);
 333
 334             temp = validParameter.validFile(parameters, "keepforward", false);          if (temp == "not found") { temp = "F"; }
 335                         keepforward = m->isTrue(temp);
 336
 337                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 338                         m->setProcessors(temp);
 339                         m->mothurConvert(temp, processors);
 340
 341
 342                         if(allFiles && (oligoFile == "")){
 343                                 m->mothurOut("You selected allfiles, but didn't enter an oligos.  Ignoring the allfiles request."); m->mothurOutEndLine();
 344                         }
 345                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 346                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 347                                 qAverage=0;
 348                                 qThreshold=0;
 349                         }
 350                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 351                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 352                                 abort = true;
 353                         }
 354
 355             if (countfile == "") {
 356                 if (nameFile == "") {
 357                     vector<string> files; files.push_back(fastaFile);
 358                     parser.getNameFile(files);
 359                 }
 360             }
 361                 }
 362
 363         }
 364         catch(exception& e) {
 365                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 366                 exit(1);
 367         }
 368 }
 369 //***************************************************************************************************************
 370
 371 int TrimSeqsCommand::execute(){
 372         try{
 373
 374                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 375
 376                 numFPrimers = 0;  //this needs to be initialized
 377                 numRPrimers = 0;
 378         numSpacers = 0;
 379         numLinkers = 0;
 380                 createGroup = false;
 381                 vector<vector<string> > fastaFileNames;
 382                 vector<vector<string> > qualFileNames;
 383                 vector<vector<string> > nameFileNames;
 384
 385                 string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("fasta");
 386                 outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
 387
 388                 string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("fasta");
 389                 outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
 390
 391                 string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim." + getOutputFileNameTag("qfile");
 392                 string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap." + getOutputFileNameTag("qfile");
 393
 394                 if (qFileName != "") {
 395                         outputNames.push_back(trimQualFile);
 396                         outputNames.push_back(scrapQualFile);
 397                         outputTypes["qfile"].push_back(trimQualFile);
 398                         outputTypes["qfile"].push_back(scrapQualFile);
 399                 }
 400
 401                 string trimNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "trim." + getOutputFileNameTag("name");
 402                 string scrapNameFile = outputDir + m->getRootName(m->getSimpleName(nameFile)) + "scrap." + getOutputFileNameTag("name");
 403
 404                 if (nameFile != "") {
 405                         m->readNames(nameFile, nameMap);
 406                         outputNames.push_back(trimNameFile);
 407                         outputNames.push_back(scrapNameFile);
 408                         outputTypes["name"].push_back(trimNameFile);
 409                         outputTypes["name"].push_back(scrapNameFile);
 410                 }
 411
 412         string trimCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "trim." + getOutputFileNameTag("count");
 413                 string scrapCountFile = outputDir + m->getRootName(m->getSimpleName(countfile)) + "scrap." + getOutputFileNameTag("count");
 414
 415                 if (countfile != "") {
 416             CountTable ct;
 417             ct.readTable(countfile);
 418             nameCount = ct.getNameMap();
 419                         outputNames.push_back(trimCountFile);
 420                         outputNames.push_back(scrapCountFile);
 421                         outputTypes["count"].push_back(trimCountFile);
 422                         outputTypes["count"].push_back(scrapCountFile);
 423                 }
 424
 425
 426                 if (m->control_pressed) { return 0; }
 427
 428                 string outputGroupFileName;
 429                 if(oligoFile != ""){
 430                         createGroup = getOligos(fastaFileNames, qualFileNames, nameFileNames);
 431                         if ((createGroup) && (countfile == "")){
 432                                 outputGroupFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + getOutputFileNameTag("group");
 433                                 outputNames.push_back(outputGroupFileName); outputTypes["group"].push_back(outputGroupFileName);
 434                         }
 435                 }
 436
 437         //fills lines and qlines
 438                 setLines(fastaFile, qFileName);
 439
 440         if(processors == 1){
 441             driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, trimCountFile, scrapCountFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
 442         }else{
 443             createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, trimNameFile, scrapNameFile, trimCountFile, scrapCountFile, outputGroupFileName, fastaFileNames, qualFileNames, nameFileNames);
 444         }
 445
 446
 447                 if (m->control_pressed) {  return 0; }
 448
 449                 if(allFiles){
 450                         map<string, string> uniqueFastaNames;// so we don't add the same groupfile multiple times
 451                         map<string, string>::iterator it;
 452                         set<string> namesToRemove;
 453                         for(int i=0;i<fastaFileNames.size();i++){
 454                                 for(int j=0;j<fastaFileNames[0].size();j++){
 455                                         if (fastaFileNames[i][j] != "") {
 456                                                 if (namesToRemove.count(fastaFileNames[i][j]) == 0) {
 457                                                         if(m->isBlank(fastaFileNames[i][j])){
 458                                                                 m->mothurRemove(fastaFileNames[i][j]);
 459                                                                 namesToRemove.insert(fastaFileNames[i][j]);
 460
 461                                                                 if(qFileName != ""){
 462                                                                         m->mothurRemove(qualFileNames[i][j]);
 463                                                                         namesToRemove.insert(qualFileNames[i][j]);
 464                                                                 }
 465
 466                                                                 if(nameFile != ""){
 467                                                                         m->mothurRemove(nameFileNames[i][j]);
 468                                                                         namesToRemove.insert(nameFileNames[i][j]);
 469                                                                 }
 470                                                         }else{
 471                                                                 it = uniqueFastaNames.find(fastaFileNames[i][j]);
 472                                                                 if (it == uniqueFastaNames.end()) {
 473                                                                         uniqueFastaNames[fastaFileNames[i][j]] = barcodeNameVector[i];
 474                                                                 }
 475                                                         }
 476                                                 }
 477                                         }
 478                                 }
 479                         }
 480
 481                         //remove names for outputFileNames, just cleans up the output
 482                         vector<string> outputNames2;
 483                         for(int i = 0; i < outputNames.size(); i++) { if (namesToRemove.count(outputNames[i]) == 0) { outputNames2.push_back(outputNames[i]); } }
 484                         outputNames = outputNames2;
 485
 486             for (it = uniqueFastaNames.begin(); it != uniqueFastaNames.end(); it++) {
 487                 ifstream in;
 488                 m->openInputFile(it->first, in);
 489
 490                 ofstream out;
 491                 string thisGroupName = outputDir + m->getRootName(m->getSimpleName(it->first));
 492                 if (countfile == "") { thisGroupName += getOutputFileNameTag("group"); outputNames.push_back(thisGroupName); outputTypes["group"].push_back(thisGroupName); }
 493                 else {  thisGroupName += getOutputFileNameTag("count"); outputNames.push_back(thisGroupName); outputTypes["count"].push_back(thisGroupName);  }
 494                 m->openOutputFile(thisGroupName, out);
 495
 496                 if (countfile != "") {  out << "Representative_Sequence\ttotal\t" << it->second << endl;  }
 497
 498                 while (!in.eof()){
 499                     if (m->control_pressed) { break; }
 500
 501                     Sequence currSeq(in); m->gobble(in);
 502                     if (countfile == "") {
 503                         out << currSeq.getName() << '\t' << it->second << endl;
 504
 505                         if (nameFile != "") {
 506                             map<string, string>::iterator itName = nameMap.find(currSeq.getName());
 507                             if (itName != nameMap.end()) {
 508                                 vector<string> thisSeqsNames;
 509                                 m->splitAtChar(itName->second, thisSeqsNames, ',');
 510                                 for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
 511                                     out << thisSeqsNames[k] << '\t' << it->second << endl;
 512                                 }
 513                             }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
 514                         }
 515                     }else {
 516                         map<string, int>::iterator itTotalReps = nameCount.find(currSeq.getName());
 517                         if (itTotalReps != nameCount.end()) { out << currSeq.getName() << '\t' << itTotalReps->second << '\t' << itTotalReps->second << endl; }
 518                         else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
 519                     }
 520                 }
 521                 in.close();
 522                 out.close();
 523             }
 524
 525             if (countfile != "") { //create countfile with group info included
 526                 CountTable* ct = new CountTable();
 527                 ct->readTable(trimCountFile);
 528                 map<string, int> justTrimmedNames = ct->getNameMap();
 529                 delete ct;
 530
 531                 CountTable newCt;
 532                 for (map<string, int>::iterator itCount = groupCounts.begin(); itCount != groupCounts.end(); itCount++) { newCt.addGroup(itCount->first); }
 533                 vector<int> tempCounts; tempCounts.resize(groupCounts.size(), 0);
 534                 for (map<string, int>::iterator itNames = justTrimmedNames.begin(); itNames != justTrimmedNames.end(); itNames++) {
 535                     newCt.push_back(itNames->first, tempCounts); //add it to the table with no abundance so we can set the groups abundance
 536                     map<string, string>::iterator it2 = groupMap.find(itNames->first);
 537                     if (it2 != groupMap.end()) { newCt.setAbund(itNames->first, it2->second, itNames->second); }
 538                     else { m->mothurOut("[ERROR]: missing group info for " + itNames->first + "."); m->mothurOutEndLine(); m->control_pressed = true; }
 539                 }
 540                 newCt.printTable(trimCountFile);
 541             }
 542                 }
 543
 544                 if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 545
 546                 //output group counts
 547                 m->mothurOutEndLine();
 548                 int total = 0;
 549                 if (groupCounts.size() != 0) {  m->mothurOut("Group count: \n");  }
 550                 for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 551                          total += it->second; m->mothurOut(it->first + "\t" + toString(it->second)); m->mothurOutEndLine();
 552                 }
 553                 if (total != 0) { m->mothurOut("Total of all groups is " + toString(total)); m->mothurOutEndLine(); }
 554
 555                 if (m->control_pressed) {       for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;    }
 556
 557                 //set fasta file as new current fastafile
 558                 string current = "";
 559                 itTypes = outputTypes.find("fasta");
 560                 if (itTypes != outputTypes.end()) {
 561                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 562                 }
 563
 564                 itTypes = outputTypes.find("name");
 565                 if (itTypes != outputTypes.end()) {
 566                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 567                 }
 568
 569                 itTypes = outputTypes.find("qfile");
 570                 if (itTypes != outputTypes.end()) {
 571                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 572                 }
 573
 574                 itTypes = outputTypes.find("group");
 575                 if (itTypes != outputTypes.end()) {
 576                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 577                 }
 578
 579         itTypes = outputTypes.find("count");
 580                 if (itTypes != outputTypes.end()) {
 581                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
 582                 }
 583
 584                 m->mothurOutEndLine();
 585                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 586                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 587                 m->mothurOutEndLine();
 588
 589                 return 0;
 590
 591         }
 592         catch(exception& e) {
 593                 m->errorOut(e, "TrimSeqsCommand", "execute");
 594                 exit(1);
 595         }
 596 }
 597
 598 /**************************************************************************************/
 599 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFileName, string scrapFileName, string trimQFileName, string scrapQFileName, string trimNFileName, string scrapNFileName, string trimCFileName, string scrapCFileName, string groupFileName, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames, linePair line, linePair qline) {
 600
 601         try {
 602
 603                 ofstream trimFASTAFile;
 604                 m->openOutputFile(trimFileName, trimFASTAFile);
 605
 606                 ofstream scrapFASTAFile;
 607                 m->openOutputFile(scrapFileName, scrapFASTAFile);
 608
 609                 ofstream trimQualFile;
 610                 ofstream scrapQualFile;
 611                 if(qFileName != ""){
 612                         m->openOutputFile(trimQFileName, trimQualFile);
 613                         m->openOutputFile(scrapQFileName, scrapQualFile);
 614                 }
 615
 616                 ofstream trimNameFile;
 617                 ofstream scrapNameFile;
 618                 if(nameFile != ""){
 619                         m->openOutputFile(trimNFileName, trimNameFile);
 620                         m->openOutputFile(scrapNFileName, scrapNameFile);
 621                 }
 622
 623         ofstream trimCountFile;
 624                 ofstream scrapCountFile;
 625                 if(countfile != ""){
 626                         m->openOutputFile(trimCFileName, trimCountFile);
 627                         m->openOutputFile(scrapCFileName, scrapCountFile);
 628             if (line.start == 0) { trimCountFile << "Representative_Sequence\ttotal" << endl; scrapCountFile << "Representative_Sequence\ttotal" << endl; }
 629                 }
 630
 631                 ofstream outGroupsFile;
 632                 if ((createGroup) && (countfile == "")){        m->openOutputFile(groupFileName, outGroupsFile);   }
 633                 if(allFiles){
 634                         for (int i = 0; i < fastaFileNames.size(); i++) { //clears old file
 635                                 for (int j = 0; j < fastaFileNames[i].size(); j++) { //clears old file
 636                                         if (fastaFileNames[i][j] != "") {
 637                                                 ofstream temp;
 638                                                 m->openOutputFile(fastaFileNames[i][j], temp);                  temp.close();
 639                                                 if(qFileName != ""){
 640                                                         m->openOutputFile(qualFileNames[i][j], temp);                   temp.close();
 641                                                 }
 642
 643                                                 if(nameFile != ""){
 644                                                         m->openOutputFile(nameFileNames[i][j], temp);                   temp.close();
 645                                                 }
 646                                         }
 647                                 }
 648                         }
 649                 }
 650
 651                 ifstream inFASTA;
 652                 m->openInputFile(filename, inFASTA);
 653                 inFASTA.seekg(line.start);
 654
 655                 ifstream qFile;
 656                 if(qFileName != "")     {
 657                         m->openInputFile(qFileName, qFile);
 658                         qFile.seekg(qline.start);
 659                 }
 660
 661                 int count = 0;
 662                 bool moreSeqs = 1;
 663                 TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
 664
 665                 while (moreSeqs) {
 666
 667                         if (m->control_pressed) {
 668                                 inFASTA.close(); trimFASTAFile.close(); scrapFASTAFile.close();
 669                                 if ((createGroup) && (countfile == "")) {        outGroupsFile.close();   }
 670                 if(qFileName != "")     {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
 671                 if(nameFile != "")      {       scrapNameFile.close(); trimNameFile.close();    }
 672                 if(countfile != "")     {       scrapCountFile.close(); trimCountFile.close();  }
 673                                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurRemove(outputNames[i]); } return 0;
 674                         }
 675
 676                         int success = 1;
 677                         string trashCode = "";
 678                         int currentSeqsDiffs = 0;
 679
 680                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 681                         //cout << currSeq.getName() << '\t' << currSeq.getUnaligned().length() << endl;
 682
 683                         QualityScores currQual;
 684                         if(qFileName != ""){
 685                                 currQual = QualityScores(qFile);  m->gobble(qFile);
 686                 //cout << currQual.getName() << endl;
 687                         }
 688
 689                         string origSeq = currSeq.getUnaligned();
 690                         if (origSeq != "") {
 691
 692                                 int barcodeIndex = 0;
 693                                 int primerIndex = 0;
 694
 695                 if(numLinkers != 0){
 696                                         success = trimOligos.stripLinker(currSeq, currQual);
 697                                         if(success > ldiffs)            {       trashCode += 'k';       }
 698                                         else{ currentSeqsDiffs += success;  }
 699
 700                                 }
 701
 702                                 if(barcodes.size() != 0){
 703                                         success = trimOligos.stripBarcode(currSeq, currQual, barcodeIndex);
 704                                         if(success > bdiffs)            {       trashCode += 'b';       }
 705                                         else{ currentSeqsDiffs += success;  }
 706                                 }
 707
 708                 if(numSpacers != 0){
 709                                         success = trimOligos.stripSpacer(currSeq, currQual);
 710                                         if(success > sdiffs)            {       trashCode += 's';       }
 711                                         else{ currentSeqsDiffs += success;  }
 712
 713                                 }
 714
 715                                 if(numFPrimers != 0){
 716                                         success = trimOligos.stripForward(currSeq, currQual, primerIndex, keepforward);
 717                                         if(success > pdiffs)            {       trashCode += 'f';       }
 718                                         else{ currentSeqsDiffs += success;  }
 719                                 }
 720
 721                                 if (currentSeqsDiffs > tdiffs)  {       trashCode += 't';   }
 722
 723                                 if(numRPrimers != 0){
 724                                         success = trimOligos.stripReverse(currSeq, currQual);
 725                                         if(!success)                            {       trashCode += 'r';       }
 726                                 }
 727
 728                                 if(keepFirst != 0){
 729                                         success = keepFirstTrim(currSeq, currQual);
 730                                 }
 731
 732                                 if(removeLast != 0){
 733                                         success = removeLastTrim(currSeq, currQual);
 734                                         if(!success)                            {       trashCode += 'l';       }
 735                                 }
 736
 737
 738                                 if(qFileName != ""){
 739                                         int origLength = currSeq.getNumBases();
 740
 741                                         if(qThreshold != 0)                     {       success = currQual.stripQualThreshold(currSeq, qThreshold);                     }
 742                                         else if(qAverage != 0)          {       success = currQual.cullQualAverage(currSeq, qAverage);                          }
 743                                         else if(qRollAverage != 0)      {       success = currQual.stripQualRollingAverage(currSeq, qRollAverage);      }
 744                                         else if(qWindowAverage != 0){   success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);   }
 745                                         else                                            {       success = 1;                            }
 746
 747                                         //you don't want to trim, if it fails above then scrap it
 748                                         if ((!qtrim) && (origLength != currSeq.getNumBases())) {  success = 0; }
 749
 750                                         if(!success)                            {       trashCode += 'q';       }
 751                                 }
 752
 753                                 if(minLength > 0 || maxLength > 0){
 754                                         success = cullLength(currSeq);
 755                                         if(!success)                            {       trashCode += 'l';       }
 756                                 }
 757                                 if(maxHomoP > 0){
 758                                         success = cullHomoP(currSeq);
 759                                         if(!success)                            {       trashCode += 'h';       }
 760                                 }
 761                                 if(maxAmbig != -1){
 762                                         success = cullAmbigs(currSeq);
 763                                         if(!success)                            {       trashCode += 'n';       }
 764                                 }
 765
 766                                 if(flip){               // should go last
 767                                         currSeq.reverseComplement();
 768                                         if(qFileName != ""){
 769                                                 currQual.flipQScores();
 770                                         }
 771                                 }
 772
 773                 if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + ", trashcode= " + trashCode); if (trashCode.length() != 0) { m->mothurOutEndLine(); } }
 774
 775                                 if(trashCode.length() == 0){
 776                                         currSeq.setAligned(currSeq.getUnaligned());
 777                                         currSeq.printSequence(trimFASTAFile);
 778
 779                                         if(qFileName != ""){
 780                                                 currQual.printQScores(trimQualFile);
 781                                         }
 782
 783
 784                                         if(nameFile != ""){
 785                                                 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
 786                                                 if (itName != nameMap.end()) {  trimNameFile << itName->first << '\t' << itName->second << endl; }
 787                                                 else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
 788                                         }
 789
 790                     int numRedundants = 0;
 791                     if (countfile != "") {
 792                         map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
 793                         if (itCount != nameCount.end()) {
 794                             trimCountFile << itCount->first << '\t' << itCount->second << endl;
 795                             numRedundants = itCount->second-1;
 796                         }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
 797                     }
 798
 799                                         if (createGroup) {
 800                                                 if(barcodes.size() != 0){
 801                                                         string thisGroup = barcodeNameVector[barcodeIndex];
 802                                                         if (primers.size() != 0) {
 803                                                                 if (primerNameVector[primerIndex] != "") {
 804                                                                         if(thisGroup != "") {
 805                                                                                 thisGroup += "." + primerNameVector[primerIndex];
 806                                                                         }else {
 807                                                                                 thisGroup = primerNameVector[primerIndex];
 808                                                                         }
 809                                                                 }
 810                                                         }
 811
 812                             if (m->debug) { m->mothurOut(", group= " + thisGroup + "\n"); }
 813
 814                                                         if (countfile == "") { outGroupsFile << currSeq.getName() << '\t' << thisGroup << endl; }
 815                             else {   groupMap[currSeq.getName()] = thisGroup; }
 816
 817                                                         if (nameFile != "") {
 818                                                                 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
 819                                                                 if (itName != nameMap.end()) {
 820                                                                         vector<string> thisSeqsNames;
 821                                                                         m->splitAtChar(itName->second, thisSeqsNames, ',');
 822                                     numRedundants = thisSeqsNames.size()-1; //we already include ourselves below
 823                                                                         for (int k = 1; k < thisSeqsNames.size(); k++) { //start at 1 to skip self
 824                                                                                 outGroupsFile << thisSeqsNames[k] << '\t' << thisGroup << endl;
 825                                                                         }
 826                                                                 }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
 827                                                         }
 828
 829                                                         map<string, int>::iterator it = groupCounts.find(thisGroup);
 830                                                         if (it == groupCounts.end()) {  groupCounts[thisGroup] = 1 + numRedundants; }
 831                                                         else { groupCounts[it->first] += (1 + numRedundants); }
 832
 833                                                 }
 834                                         }
 835
 836                                         if(allFiles){
 837                                                 ofstream output;
 838                                                 m->openOutputFileAppend(fastaFileNames[barcodeIndex][primerIndex], output);
 839                                                 currSeq.printSequence(output);
 840                                                 output.close();
 841
 842                                                 if(qFileName != ""){
 843                                                         m->openOutputFileAppend(qualFileNames[barcodeIndex][primerIndex], output);
 844                                                         currQual.printQScores(output);
 845                                                         output.close();
 846                                                 }
 847
 848                                                 if(nameFile != ""){
 849                                                         map<string, string>::iterator itName = nameMap.find(currSeq.getName());
 850                                                         if (itName != nameMap.end()) {
 851                                                                 m->openOutputFileAppend(nameFileNames[barcodeIndex][primerIndex], output);
 852                                                                 output << itName->first << '\t' << itName->second << endl;
 853                                                                 output.close();
 854                                                         }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
 855                                                 }
 856                                         }
 857                                 }
 858                                 else{
 859                                         if(nameFile != ""){ //needs to be before the currSeq name is changed
 860                                                 map<string, string>::iterator itName = nameMap.find(currSeq.getName());
 861                                                 if (itName != nameMap.end()) {  scrapNameFile << itName->first << '\t' << itName->second << endl; }
 862                                                 else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); }
 863                                         }
 864                     if (countfile != "") {
 865                         map<string, int>::iterator itCount = nameCount.find(currSeq.getName());
 866                         if (itCount != nameCount.end()) {
 867                             trimCountFile << itCount->first << '\t' << itCount->second << endl;
 868                         }else { m->mothurOut("[ERROR]: " + currSeq.getName() + " is not in your count file, please correct."); m->mothurOutEndLine(); }
 869                     }
 870
 871                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 872                                         currSeq.setUnaligned(origSeq);
 873                                         currSeq.setAligned(origSeq);
 874                                         currSeq.printSequence(scrapFASTAFile);
 875                                         if(qFileName != ""){
 876                                                 currQual.printQScores(scrapQualFile);
 877                                         }
 878                                 }
 879                                 count++;
 880                         }
 881
 882                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 883                                 unsigned long long pos = inFASTA.tellg();
 884                                 if ((pos == -1) || (pos >= line.end)) { break; }
 885
 886                         #else
 887                                 if (inFASTA.eof()) { break; }
 888                         #endif
 889
 890                         //report progress
 891                         if((count) % 1000 == 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 892
 893                 }
 894                 //report progress
 895                 if((count) % 1000 != 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 896
 897
 898                 inFASTA.close();
 899                 trimFASTAFile.close();
 900                 scrapFASTAFile.close();
 901                 if (createGroup) {       outGroupsFile.close();   }
 902                 if(qFileName != "")     {       qFile.close();  scrapQualFile.close(); trimQualFile.close();    }
 903                 if(nameFile != "")      {       scrapNameFile.close(); trimNameFile.close();    }
 904         if(countfile != "")     {       scrapCountFile.close(); trimCountFile.close();  }
 905
 906                 return count;
 907         }
 908         catch(exception& e) {
 909                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 910                 exit(1);
 911         }
 912 }
 913
 914 /**************************************************************************************************/
 915
 916 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFASTAFileName, string scrapFASTAFileName, string trimQualFileName, string scrapQualFileName, string trimNameFileName, string scrapNameFileName, string trimCountFileName, string scrapCountFileName, string groupFile, vector<vector<string> > fastaFileNames, vector<vector<string> > qualFileNames, vector<vector<string> > nameFileNames) {
 917         try {
 918
 919         int process = 1;
 920                 int exitCommand = 1;
 921                 processIDS.clear();
 922
 923 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 924                                 //loop through and create all the processes you want
 925                 while (process != processors) {
 926                         int pid = fork();
 927
 928                         if (pid > 0) {
 929                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 930                                 process++;
 931                         }else if (pid == 0){
 932
 933                                 vector<vector<string> > tempFASTAFileNames = fastaFileNames;
 934                                 vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
 935                                 vector<vector<string> > tempNameFileNames = nameFileNames;
 936
 937                                 if(allFiles){
 938                                         ofstream temp;
 939
 940                                         for(int i=0;i<tempFASTAFileNames.size();i++){
 941                                                 for(int j=0;j<tempFASTAFileNames[i].size();j++){
 942                                                         if (tempFASTAFileNames[i][j] != "") {
 943                                                                 tempFASTAFileNames[i][j] += toString(getpid()) + ".temp";
 944                                                                 m->openOutputFile(tempFASTAFileNames[i][j], temp);                      temp.close();
 945
 946                                                                 if(qFileName != ""){
 947                                                                         tempPrimerQualFileNames[i][j] += toString(getpid()) + ".temp";
 948                                                                         m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
 949                                                                 }
 950                                                                 if(nameFile != ""){
 951                                                                         tempNameFileNames[i][j] += toString(getpid()) + ".temp";
 952                                                                         m->openOutputFile(tempNameFileNames[i][j], temp);               temp.close();
 953                                                                 }
 954                                                         }
 955                                                 }
 956                                         }
 957                                 }
 958
 959                                 driverCreateTrim(filename,
 960                                                                  qFileName,
 961                                                                  (trimFASTAFileName + toString(getpid()) + ".temp"),
 962                                                                  (scrapFASTAFileName + toString(getpid()) + ".temp"),
 963                                                                  (trimQualFileName + toString(getpid()) + ".temp"),
 964                                                                  (scrapQualFileName + toString(getpid()) + ".temp"),
 965                                                                  (trimNameFileName + toString(getpid()) + ".temp"),
 966                                                                  (scrapNameFileName + toString(getpid()) + ".temp"),
 967                                  (trimCountFileName + toString(getpid()) + ".temp"),
 968                                                                  (scrapCountFileName + toString(getpid()) + ".temp"),
 969                                                                  (groupFile + toString(getpid()) + ".temp"),
 970                                                                  tempFASTAFileNames,
 971                                                                  tempPrimerQualFileNames,
 972                                                                  tempNameFileNames,
 973                                                                  lines[process],
 974                                                                  qLines[process]);
 975
 976                 if (m->debug) { m->mothurOut("[DEBUG]: " + toString(lines[process].start) + '\t' + toString(qLines[process].start) + '\t' + toString(getpid()) + '\n'); }
 977
 978                                 //pass groupCounts to parent
 979                                 if(createGroup){
 980                                         ofstream out;
 981                                         string tempFile = filename + toString(getpid()) + ".num.temp";
 982                                         m->openOutputFile(tempFile, out);
 983
 984                                         out << groupCounts.size() << endl;
 985
 986                                         for (map<string, int>::iterator it = groupCounts.begin(); it != groupCounts.end(); it++) {
 987                                                 out << it->first << '\t' << it->second << endl;
 988                                         }
 989
 990                     out << groupMap.size() << endl;
 991                     for (map<string, string>::iterator it = groupMap.begin(); it != groupMap.end(); it++) {
 992                                                 out << it->first << '\t' << it->second << endl;
 993                                         }
 994                                         out.close();
 995                                 }
 996                                 exit(0);
 997                         }else {
 998                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 999                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1000                                 exit(0);
1001                         }
1002                 }
1003
1004                 //parent do my part
1005                 ofstream temp;
1006                 m->openOutputFile(trimFASTAFileName, temp);             temp.close();
1007                 m->openOutputFile(scrapFASTAFileName, temp);    temp.close();
1008                 if(qFileName != ""){
1009                         m->openOutputFile(trimQualFileName, temp);              temp.close();
1010                         m->openOutputFile(scrapQualFileName, temp);             temp.close();
1011                 }
1012                 if (nameFile != "") {
1013                         m->openOutputFile(trimNameFileName, temp);              temp.close();
1014                         m->openOutputFile(scrapNameFileName, temp);             temp.close();
1015                 }
1016         if (countfile != "") {
1017                         m->openOutputFile(trimCountFileName, temp);             temp.close();
1018                         m->openOutputFile(scrapCountFileName, temp);            temp.close();
1019                 }
1020
1021                 driverCreateTrim(filename, qFileName, trimFASTAFileName, scrapFASTAFileName, trimQualFileName, scrapQualFileName, trimNameFileName, scrapNameFileName, trimCountFileName, scrapCountFileName, groupFile, fastaFileNames, qualFileNames, nameFileNames, lines[0], qLines[0]);
1022
1023                 //force parent to wait until all the processes are done
1024                 for (int i=0;i<processIDS.size();i++) {
1025                         int temp = processIDS[i];
1026                         wait(&temp);
1027                 }
1028 #else
1029         //////////////////////////////////////////////////////////////////////////////////////////////////////
1030                 //Windows version shared memory, so be careful when passing variables through the trimData struct.
1031                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1032                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1033
1034                 vector<trimData*> pDataArray;
1035                 DWORD   dwThreadIdArray[processors-1];
1036                 HANDLE  hThreadArray[processors-1];
1037
1038                 //Create processor worker threads.
1039                 for( int i=0; i<processors-1; i++){
1040
1041             string extension = "";
1042                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
1043             vector<vector<string> > tempFASTAFileNames = fastaFileNames;
1044             vector<vector<string> > tempPrimerQualFileNames = qualFileNames;
1045             vector<vector<string> > tempNameFileNames = nameFileNames;
1046
1047             if(allFiles){
1048                 ofstream temp;
1049
1050                 for(int i=0;i<tempFASTAFileNames.size();i++){
1051                     for(int j=0;j<tempFASTAFileNames[i].size();j++){
1052                         if (tempFASTAFileNames[i][j] != "") {
1053                             tempFASTAFileNames[i][j] += extension;
1054                             m->openOutputFile(tempFASTAFileNames[i][j], temp);                  temp.close();
1055
1056                             if(qFileName != ""){
1057                                 tempPrimerQualFileNames[i][j] += extension;
1058                                 m->openOutputFile(tempPrimerQualFileNames[i][j], temp);         temp.close();
1059                             }
1060                             if(nameFile != ""){
1061                                 tempNameFileNames[i][j] += extension;
1062                                 m->openOutputFile(tempNameFileNames[i][j], temp);               temp.close();
1063                             }
1064                         }
1065                     }
1066                 }
1067             }
1068
1069
1070                         trimData* tempTrim = new trimData(filename,
1071                                               qFileName, nameFile, countfile,
1072                                               (trimFASTAFileName+extension),
1073                                               (scrapFASTAFileName+extension),
1074                                               (trimQualFileName+extension),
1075                                               (scrapQualFileName+extension),
1076                                               (trimNameFileName+extension),
1077                                               (scrapNameFileName+extension),
1078                                               (trimCountFileName+extension),
1079                                               (scrapCountFileName+extension),
1080                                               (groupFile+extension),
1081                                               tempFASTAFileNames,
1082                                               tempPrimerQualFileNames,
1083                                               tempNameFileNames,
1084                                               lines[i].start, lines[i].end, qLines[i].start, qLines[i].end, m,
1085                                               pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer,
1086                                              primerNameVector, barcodeNameVector, createGroup, allFiles, keepforward, keepFirst, removeLast,
1087                                               qWindowStep, qWindowSize, qWindowAverage, qtrim, qThreshold, qAverage, qRollAverage,
1088                                              minLength, maxAmbig, maxHomoP, maxLength, flip, nameMap, nameCount);
1089                         pDataArray.push_back(tempTrim);
1090
1091                         hThreadArray[i] = CreateThread(NULL, 0, MyTrimThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1092                 }
1093
1094         //parent do my part
1095                 ofstream temp;
1096                 m->openOutputFile(trimFASTAFileName, temp);             temp.close();
1097                 m->openOutputFile(scrapFASTAFileName, temp);    temp.close();
1098                 if(qFileName != ""){
1099                         m->openOutputFile(trimQualFileName, temp);              temp.close();
1100                         m->openOutputFile(scrapQualFileName, temp);             temp.close();
1101                 }
1102                 if (nameFile != "") {
1103                         m->openOutputFile(trimNameFileName, temp);              temp.close();
1104                         m->openOutputFile(scrapNameFileName, temp);             temp.close();
1105                 }
1106
1107                 driverCreateTrim(filename, qFileName, (trimFASTAFileName + toString(processors-1) + ".temp"), (scrapFASTAFileName + toString(processors-1) + ".temp"), (trimQualFileName + toString(processors-1) + ".temp"), (scrapQualFileName + toString(processors-1) + ".temp"), (trimNameFileName + toString(processors-1) + ".temp"), (scrapNameFileName + toString(processors-1) + ".temp"), (trimCountFileName + toString(processors-1) + ".temp"), (scrapCountFileName + toString(processors-1) + ".temp"), (groupFile + toString(processors-1) + ".temp"), fastaFileNames, qualFileNames, nameFileNames, lines[processors-1], qLines[processors-1]);
1108         processIDS.push_back(processors-1);
1109
1110
1111                 //Wait until all threads have terminated.
1112                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1113
1114                 //Close all thread handles and free memory allocations.
1115                 for(int i=0; i < pDataArray.size(); i++){
1116                         for (map<string, int>::iterator it = pDataArray[i]->groupCounts.begin(); it != pDataArray[i]->groupCounts.end(); it++) {
1117                 map<string, int>::iterator it2 = groupCounts.find(it->first);
1118                 if (it2 == groupCounts.end()) { groupCounts[it->first] = it->second; }
1119                 else { groupCounts[it->first] += it->second; }
1120             }
1121             for (map<string, string>::iterator it = pDataArray[i]->groupMap.begin(); it != pDataArray[i]->groupMap.end(); it++) {
1122                 map<string, string>::iterator it2 = groupMap.find(it->first);
1123                 if (it2 == groupMap.end()) {    groupMap[it->first] = it->second; }
1124                 else { m->mothurOut("[ERROR]: " + it->first + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
1125             }
1126             CloseHandle(hThreadArray[i]);
1127                         delete pDataArray[i];
1128                 }
1129
1130 #endif
1131
1132
1133         //append files
1134                 for(int i=0;i<processIDS.size();i++){
1135
1136                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
1137
1138                         m->appendFiles((trimFASTAFileName + toString(processIDS[i]) + ".temp"), trimFASTAFileName);
1139                         m->mothurRemove((trimFASTAFileName + toString(processIDS[i]) + ".temp"));
1140                         m->appendFiles((scrapFASTAFileName + toString(processIDS[i]) + ".temp"), scrapFASTAFileName);
1141                         m->mothurRemove((scrapFASTAFileName + toString(processIDS[i]) + ".temp"));
1142
1143                         if(qFileName != ""){
1144                                 m->appendFiles((trimQualFileName + toString(processIDS[i]) + ".temp"), trimQualFileName);
1145                                 m->mothurRemove((trimQualFileName + toString(processIDS[i]) + ".temp"));
1146                                 m->appendFiles((scrapQualFileName + toString(processIDS[i]) + ".temp"), scrapQualFileName);
1147                                 m->mothurRemove((scrapQualFileName + toString(processIDS[i]) + ".temp"));
1148                         }
1149
1150                         if(nameFile != ""){
1151                                 m->appendFiles((trimNameFileName + toString(processIDS[i]) + ".temp"), trimNameFileName);
1152                                 m->mothurRemove((trimNameFileName + toString(processIDS[i]) + ".temp"));
1153                                 m->appendFiles((scrapNameFileName + toString(processIDS[i]) + ".temp"), scrapNameFileName);
1154                                 m->mothurRemove((scrapNameFileName + toString(processIDS[i]) + ".temp"));
1155                         }
1156
1157             if(countfile != ""){
1158                                 m->appendFiles((trimCountFileName + toString(processIDS[i]) + ".temp"), trimCountFileName);
1159                                 m->mothurRemove((trimCountFileName + toString(processIDS[i]) + ".temp"));
1160                                 m->appendFiles((scrapCountFileName + toString(processIDS[i]) + ".temp"), scrapCountFileName);
1161                                 m->mothurRemove((scrapCountFileName + toString(processIDS[i]) + ".temp"));
1162                         }
1163
1164                         if((createGroup)&&(countfile == "")){
1165                                 m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
1166                                 m->mothurRemove((groupFile + toString(processIDS[i]) + ".temp"));
1167                         }
1168
1169
1170                         if(allFiles){
1171                                 for(int j=0;j<fastaFileNames.size();j++){
1172                                         for(int k=0;k<fastaFileNames[j].size();k++){
1173                                                 if (fastaFileNames[j][k] != "") {
1174                                                         m->appendFiles((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"), fastaFileNames[j][k]);
1175                                                         m->mothurRemove((fastaFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1176
1177                                                         if(qFileName != ""){
1178                                                                 m->appendFiles((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"), qualFileNames[j][k]);
1179                                                                 m->mothurRemove((qualFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1180                                                         }
1181
1182                                                         if(nameFile != ""){
1183                                                                 m->appendFiles((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"), nameFileNames[j][k]);
1184                                                                 m->mothurRemove((nameFileNames[j][k] + toString(processIDS[i]) + ".temp"));
1185                                                         }
1186                                                 }
1187                                         }
1188                                 }
1189                         }
1190
1191             #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1192                         if(createGroup){
1193                                 ifstream in;
1194                                 string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1195                                 m->openInputFile(tempFile, in);
1196                                 int tempNum;
1197                                 string group;
1198
1199                                 in >> tempNum; m->gobble(in);
1200
1201                                 if (tempNum != 0) {
1202                                         for (int i = 0; i < tempNum; i++) {
1203                         int groupNum;
1204                                                 in >> group >> groupNum; m->gobble(in);
1205
1206                                                 map<string, int>::iterator it = groupCounts.find(group);
1207                                                 if (it == groupCounts.end()) {  groupCounts[group] = groupNum; }
1208                                                 else { groupCounts[it->first] += groupNum; }
1209                                         }
1210                                 }
1211                 in >> tempNum; m->gobble(in);
1212                 if (tempNum != 0) {
1213                                         for (int i = 0; i < tempNum; i++) {
1214                         string group, seqName;
1215                                                 in >> seqName >> group; m->gobble(in);
1216
1217                                                 map<string, string>::iterator it = groupMap.find(seqName);
1218                                                 if (it == groupMap.end()) {     groupMap[seqName] = group; }
1219                                                 else { m->mothurOut("[ERROR]: " + seqName + " is in your fasta file more than once. Sequence names must be unique. please correct.\n");  }
1220                                         }
1221                                 }
1222
1223                                 in.close(); m->mothurRemove(tempFile);
1224                         }
1225             #endif
1226                 }
1227
1228         return exitCommand;
1229         }
1230         catch(exception& e) {
1231                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
1232                 exit(1);
1233         }
1234 }
1235
1236 /**************************************************************************************************/
1237
1238 int TrimSeqsCommand::setLines(string filename, string qfilename) {
1239         try {
1240
1241         vector<unsigned long long> fastaFilePos;
1242                 vector<unsigned long long> qfileFilePos;
1243
1244                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1245                 //set file positions for fasta file
1246                 fastaFilePos = m->divideFile(filename, processors);
1247
1248                 //get name of first sequence in each chunk
1249                 map<string, int> firstSeqNames;
1250                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
1251                         ifstream in;
1252                         m->openInputFile(filename, in);
1253                         in.seekg(fastaFilePos[i]);
1254
1255                         Sequence temp(in);
1256                         firstSeqNames[temp.getName()] = i;
1257
1258                         in.close();
1259                 }
1260
1261                 if(qfilename != "")     {
1262             //seach for filePos of each first name in the qfile and save in qfileFilePos
1263             ifstream inQual;
1264             m->openInputFile(qfilename, inQual);
1265
1266             string input;
1267             while(!inQual.eof()){
1268                 input = m->getline(inQual);
1269
1270                 if (input.length() != 0) {
1271                     if(input[0] == '>'){ //this is a sequence name line
1272                         istringstream nameStream(input);
1273
1274                         string sname = "";  nameStream >> sname;
1275                         sname = sname.substr(1);
1276
1277                         map<string, int>::iterator it = firstSeqNames.find(sname);
1278
1279                         if(it != firstSeqNames.end()) { //this is the start of a new chunk
1280                             unsigned long long pos = inQual.tellg();
1281                             qfileFilePos.push_back(pos - input.length() - 1);
1282                             firstSeqNames.erase(it);
1283                         }
1284                     }
1285                 }
1286
1287                 if (firstSeqNames.size() == 0) { break; }
1288             }
1289             inQual.close();
1290
1291
1292             if (firstSeqNames.size() != 0) {
1293                 for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
1294                     m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
1295                 }
1296                 qFileName = "";
1297                 return processors;
1298             }
1299
1300             //get last file position of qfile
1301             FILE * pFile;
1302             unsigned long long size;
1303
1304             //get num bytes in file
1305             pFile = fopen (qfilename.c_str(),"rb");
1306             if (pFile==NULL) perror ("Error opening file");
1307             else{
1308                 fseek (pFile, 0, SEEK_END);
1309                 size=ftell (pFile);
1310                 fclose (pFile);
1311             }
1312
1313             qfileFilePos.push_back(size);
1314         }
1315
1316         for (int i = 0; i < (fastaFilePos.size()-1); i++) {
1317             if (m->debug) { m->mothurOut("[DEBUG]: " + toString(i) +'\t' + toString(fastaFilePos[i]) + '\t' + toString(fastaFilePos[i+1]) + '\n'); }
1318                         lines.push_back(linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
1319                         if (qfilename != "") {  qLines.push_back(linePair(qfileFilePos[i], qfileFilePos[(i+1)]));  }
1320                 }
1321                 if(qfilename == "")     {       qLines = lines; } //files with duds
1322
1323                 return processors;
1324
1325                 #else
1326
1327         if (processors == 1) { //save time
1328                         //fastaFilePos.push_back(0); qfileFilePos.push_back(0);
1329                         //fastaFilePos.push_back(1000); qfileFilePos.push_back(1000);
1330             lines.push_back(linePair(0, 1000));
1331             if (qfilename != "") {  qLines.push_back(linePair(0, 1000)); }
1332         }else{
1333             int numFastaSeqs = 0;
1334             fastaFilePos = m->setFilePosFasta(filename, numFastaSeqs);
1335             if (fastaFilePos.size() < processors) { processors = fastaFilePos.size(); }
1336
1337             if (qfilename != "") {
1338                 int numQualSeqs = 0;
1339                 qfileFilePos = m->setFilePosFasta(qfilename, numQualSeqs);
1340
1341                 if (numFastaSeqs != numQualSeqs) {
1342                     m->mothurOut("[ERROR]: You have " + toString(numFastaSeqs) + " sequences in your fasta file, but " + toString(numQualSeqs) + " sequences in your quality file."); m->mothurOutEndLine(); m->control_pressed = true;
1343                 }
1344             }
1345
1346             //figure out how many sequences you have to process
1347             int numSeqsPerProcessor = numFastaSeqs / processors;
1348             for (int i = 0; i < processors; i++) {
1349                 int startIndex =  i * numSeqsPerProcessor;
1350                 if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
1351                 lines.push_back(linePair(fastaFilePos[startIndex], numSeqsPerProcessor));
1352                 if (qfilename != "") {  qLines.push_back(linePair(qfileFilePos[startIndex], numSeqsPerProcessor)); }
1353             }
1354         }
1355             if(qfilename == "") {       qLines = lines; } //files with duds
1356                         return 1;
1357
1358                 #endif
1359         }
1360         catch(exception& e) {
1361                 m->errorOut(e, "TrimSeqsCommand", "setLines");
1362                 exit(1);
1363         }
1364 }
1365
1366 //***************************************************************************************************************
1367
1368 bool TrimSeqsCommand::getOligos(vector<vector<string> >& fastaFileNames, vector<vector<string> >& qualFileNames, vector<vector<string> >& nameFileNames){
1369         try {
1370                 ifstream inOligos;
1371                 m->openInputFile(oligoFile, inOligos);
1372
1373                 ofstream test;
1374
1375                 string type, oligo, group;
1376
1377                 int indexPrimer = 0;
1378                 int indexBarcode = 0;
1379
1380                 while(!inOligos.eof()){
1381
1382                         inOligos >> type;
1383
1384                         if (m->debug) { m->mothurOut("[DEBUG]: reading type - " + type + ".\n"); }
1385
1386                         if(type[0] == '#'){
1387                                 while (!inOligos.eof()) {       char c = inOligos.get();  if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
1388                                 m->gobble(inOligos);
1389                         }
1390                         else{
1391                                 m->gobble(inOligos);
1392                                 //make type case insensitive
1393                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
1394
1395                                 inOligos >> oligo;
1396
1397                 if (m->debug) { m->mothurOut("[DEBUG]: reading - " + oligo + ".\n"); }
1398
1399                                 for(int i=0;i<oligo.length();i++){
1400                                         oligo[i] = toupper(oligo[i]);
1401                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
1402                                 }
1403
1404                                 if(type == "FORWARD"){
1405                                         group = "";
1406
1407                                         // get rest of line in case there is a primer name
1408                                         while (!inOligos.eof()) {
1409                                                 char c = inOligos.get();
1410                                                 if (c == 10 || c == 13){        break;  }
1411                                                 else if (c == 32 || c == 9){;} //space or tab
1412                                                 else {  group += c;  }
1413                                         }
1414
1415                                         //check for repeat barcodes
1416                                         map<string, int>::iterator itPrime = primers.find(oligo);
1417                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
1418
1419                     if (m->debug) {  if (group != "") { m->mothurOut("[DEBUG]: reading group " + group + ".\n"); }else{ m->mothurOut("[DEBUG]: no group for primer " + oligo + ".\n"); }  }
1420
1421                                         primers[oligo]=indexPrimer; indexPrimer++;
1422                                         primerNameVector.push_back(group);
1423                                 }
1424                                 else if(type == "REVERSE"){
1425                                         //Sequence oligoRC("reverse", oligo);
1426                                         //oligoRC.reverseComplement();
1427                     string oligoRC = reverseOligo(oligo);
1428                                         revPrimer.push_back(oligoRC);
1429                                 }
1430                                 else if(type == "BARCODE"){
1431                                         inOligos >> group;
1432
1433                                         //check for repeat barcodes
1434                                         map<string, int>::iterator itBar = barcodes.find(oligo);
1435                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
1436
1437                                         barcodes[oligo]=indexBarcode; indexBarcode++;
1438                                         barcodeNameVector.push_back(group);
1439                                 }else if(type == "LINKER"){
1440                                         linker.push_back(oligo);
1441                                 }else if(type == "SPACER"){
1442                                         spacer.push_back(oligo);
1443                                 }
1444                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
1445                         }
1446                         m->gobble(inOligos);
1447                 }
1448                 inOligos.close();
1449
1450                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
1451
1452                 //add in potential combos
1453                 if(barcodeNameVector.size() == 0){
1454                         barcodes[""] = 0;
1455                         barcodeNameVector.push_back("");
1456                 }
1457
1458                 if(primerNameVector.size() == 0){
1459                         primers[""] = 0;
1460                         primerNameVector.push_back("");
1461                 }
1462
1463                 fastaFileNames.resize(barcodeNameVector.size());
1464                 for(int i=0;i<fastaFileNames.size();i++){
1465                         fastaFileNames[i].assign(primerNameVector.size(), "");
1466                 }
1467                 if(qFileName != "")     {       qualFileNames = fastaFileNames; }
1468                 if(nameFile != "")      {       nameFileNames = fastaFileNames; }
1469
1470                 if(allFiles){
1471                         set<string> uniqueNames; //used to cleanup outputFileNames
1472                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1473                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1474
1475                                         string primerName = primerNameVector[itPrimer->second];
1476                                         string barcodeName = barcodeNameVector[itBar->second];
1477
1478                                         string comboGroupName = "";
1479                                         string fastaFileName = "";
1480                                         string qualFileName = "";
1481                                         string nameFileName = "";
1482                     string countFileName = "";
1483
1484                                         if(primerName == ""){
1485                                                 comboGroupName = barcodeNameVector[itBar->second];
1486                                         }
1487                                         else{
1488                                                 if(barcodeName == ""){
1489                                                         comboGroupName = primerNameVector[itPrimer->second];
1490                                                 }
1491                                                 else{
1492                                                         comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
1493                                                 }
1494                                         }
1495
1496
1497                                         ofstream temp;
1498                                         fastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + comboGroupName + ".fasta";
1499                                         if (uniqueNames.count(fastaFileName) == 0) {
1500                                                 outputNames.push_back(fastaFileName);
1501                                                 outputTypes["fasta"].push_back(fastaFileName);
1502                                                 uniqueNames.insert(fastaFileName);
1503                                         }
1504
1505                                         fastaFileNames[itBar->second][itPrimer->second] = fastaFileName;
1506                                         m->openOutputFile(fastaFileName, temp);         temp.close();
1507
1508                                         if(qFileName != ""){
1509                                                 qualFileName = outputDir + m->getRootName(m->getSimpleName(qFileName)) + comboGroupName + ".qual";
1510                                                 if (uniqueNames.count(qualFileName) == 0) {
1511                                                         outputNames.push_back(qualFileName);
1512                                                         outputTypes["qfile"].push_back(qualFileName);
1513                                                 }
1514
1515                                                 qualFileNames[itBar->second][itPrimer->second] = qualFileName;
1516                                                 m->openOutputFile(qualFileName, temp);          temp.close();
1517                                         }
1518
1519                                         if(nameFile != ""){
1520                                                 nameFileName = outputDir + m->getRootName(m->getSimpleName(nameFile)) + comboGroupName + ".names";
1521                                                 if (uniqueNames.count(nameFileName) == 0) {
1522                                                         outputNames.push_back(nameFileName);
1523                                                         outputTypes["name"].push_back(nameFileName);
1524                                                 }
1525
1526                                                 nameFileNames[itBar->second][itPrimer->second] = nameFileName;
1527                                                 m->openOutputFile(nameFileName, temp);          temp.close();
1528                                         }
1529                                 }
1530                         }
1531                 }
1532                 numFPrimers = primers.size();
1533                 numRPrimers = revPrimer.size();
1534         numLinkers = linker.size();
1535         numSpacers = spacer.size();
1536
1537                 bool allBlank = true;
1538                 for (int i = 0; i < barcodeNameVector.size(); i++) {
1539                         if (barcodeNameVector[i] != "") {
1540                                 allBlank = false;
1541                                 break;
1542                         }
1543                 }
1544                 for (int i = 0; i < primerNameVector.size(); i++) {
1545                         if (primerNameVector[i] != "") {
1546                                 allBlank = false;
1547                                 break;
1548                         }
1549                 }
1550
1551                 if (allBlank) {
1552                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a groupfile."); m->mothurOutEndLine();
1553                         allFiles = false;
1554                         return false;
1555                 }
1556
1557                 return true;
1558
1559         }
1560         catch(exception& e) {
1561                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
1562                 exit(1);
1563         }
1564 }
1565 //***************************************************************************************************************
1566
1567 bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
1568         try {
1569                 bool success = 1;
1570                 if(qscores.getName() != ""){
1571                         qscores.trimQScores(-1, keepFirst);
1572                 }
1573                 sequence.trim(keepFirst);
1574                 return success;
1575         }
1576         catch(exception& e) {
1577                 m->errorOut(e, "keepFirstTrim", "countDiffs");
1578                 exit(1);
1579         }
1580
1581 }
1582
1583 //***************************************************************************************************************
1584
1585 bool TrimSeqsCommand::removeLastTrim(Sequence& sequence, QualityScores& qscores){
1586         try {
1587                 bool success = 0;
1588
1589                 int length = sequence.getNumBases() - removeLast;
1590
1591                 if(length > 0){
1592                         if(qscores.getName() != ""){
1593                                 qscores.trimQScores(-1, length);
1594                         }
1595                         sequence.trim(length);
1596                         success = 1;
1597                 }
1598                 else{
1599                         success = 0;
1600                 }
1601
1602                 return success;
1603         }
1604         catch(exception& e) {
1605                 m->errorOut(e, "removeLastTrim", "countDiffs");
1606                 exit(1);
1607         }
1608
1609 }
1610
1611 //***************************************************************************************************************
1612
1613 bool TrimSeqsCommand::cullLength(Sequence& seq){
1614         try {
1615
1616                 int length = seq.getNumBases();
1617                 bool success = 0;       //guilty until proven innocent
1618
1619                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
1620                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
1621                 else                                                                                            {       success = 0;    }
1622
1623                 return success;
1624
1625         }
1626         catch(exception& e) {
1627                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1628                 exit(1);
1629         }
1630
1631 }
1632
1633 //***************************************************************************************************************
1634
1635 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1636         try {
1637                 int longHomoP = seq.getLongHomoPolymer();
1638                 bool success = 0;       //guilty until proven innocent
1639
1640                 if(longHomoP <= maxHomoP){      success = 1;    }
1641                 else                                    {       success = 0;    }
1642
1643                 return success;
1644         }
1645         catch(exception& e) {
1646                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1647                 exit(1);
1648         }
1649
1650 }
1651 //********************************************************************/
1652 string TrimSeqsCommand::reverseOligo(string oligo){
1653         try {
1654         string reverse = "";
1655
1656         for(int i=oligo.length()-1;i>=0;i--){
1657
1658             if(oligo[i] == 'A')         {       reverse += 'T'; }
1659             else if(oligo[i] == 'T'){   reverse += 'A'; }
1660             else if(oligo[i] == 'U'){   reverse += 'A'; }
1661
1662             else if(oligo[i] == 'G'){   reverse += 'C'; }
1663             else if(oligo[i] == 'C'){   reverse += 'G'; }
1664
1665             else if(oligo[i] == 'R'){   reverse += 'Y'; }
1666             else if(oligo[i] == 'Y'){   reverse += 'R'; }
1667
1668             else if(oligo[i] == 'M'){   reverse += 'K'; }
1669             else if(oligo[i] == 'K'){   reverse += 'M'; }
1670
1671             else if(oligo[i] == 'W'){   reverse += 'W'; }
1672             else if(oligo[i] == 'S'){   reverse += 'S'; }
1673
1674             else if(oligo[i] == 'B'){   reverse += 'V'; }
1675             else if(oligo[i] == 'V'){   reverse += 'B'; }
1676
1677             else if(oligo[i] == 'D'){   reverse += 'H'; }
1678             else if(oligo[i] == 'H'){   reverse += 'D'; }
1679
1680             else                                                {       reverse += 'N'; }
1681         }
1682
1683
1684         return reverse;
1685     }
1686         catch(exception& e) {
1687                 m->errorOut(e, "TrimSeqsCommand", "reverseOligo");
1688                 exit(1);
1689         }
1690 }
1691
1692 //***************************************************************************************************************
1693
1694 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1695         try {
1696                 int numNs = seq.getAmbigBases();
1697                 bool success = 0;       //guilty until proven innocent
1698
1699                 if(numNs <= maxAmbig)   {       success = 1;    }
1700                 else                                    {       success = 0;    }
1701
1702                 return success;
1703         }
1704         catch(exception& e) {
1705                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1706                 exit(1);
1707         }
1708
1709 }
1710 //***************************************************************************************************************