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