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
  13 //**********************************************************************************************************************
  14 vector<string> TrimSeqsCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
  17                                                                         "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "TrimSeqsCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 TrimSeqsCommand::TrimSeqsCommand(){
  28         try {
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["fasta"] = tempOutNames;
  32                 outputTypes["qual"] = tempOutNames;
  33                 outputTypes["group"] = tempOutNames;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41 vector<string> TrimSeqsCommand::getRequiredParameters(){
  42         try {
  43                 string Array[] =  {"fasta"};
  44                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  45                 return myArray;
  46         }
  47         catch(exception& e) {
  48                 m->errorOut(e, "TrimSeqsCommand", "getRequiredParameters");
  49                 exit(1);
  50         }
  51 }
  52 //**********************************************************************************************************************
  53 vector<string> TrimSeqsCommand::getRequiredFiles(){
  54         try {
  55                 vector<string> myArray;
  56                 return myArray;
  57         }
  58         catch(exception& e) {
  59                 m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
  60                 exit(1);
  61         }
  62 }
  63 //***************************************************************************************************************
  64
  65 TrimSeqsCommand::TrimSeqsCommand(string option)  {
  66         try {
  67
  68                 abort = false;
  69                 comboStarts = 0;
  70
  71                 //allow user to run help
  72                 if(option == "help") { help(); abort = true; }
  73
  74                 else {
  75                         //valid paramters for this command
  76                         string AlignArray[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
  77                                                                         "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  78
  79                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  80
  81                         OptionParser parser(option);
  82                         map<string,string> parameters = parser.getParameters();
  83
  84                         ValidParameters validParameter;
  85                         map<string,string>::iterator it;
  86
  87                         //check to make sure all parameters are valid for command
  88                         for (it = parameters.begin(); it != parameters.end(); it++) {
  89                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  90                         }
  91
  92                         //initialize outputTypes
  93                         vector<string> tempOutNames;
  94                         outputTypes["fasta"] = tempOutNames;
  95                         outputTypes["qual"] = tempOutNames;
  96                         outputTypes["group"] = tempOutNames;
  97
  98                         //if the user changes the input directory command factory will send this info to us in the output parameter
  99                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 100                         if (inputDir == "not found"){   inputDir = "";          }
 101                         else {
 102                                 string path;
 103                                 it = parameters.find("fasta");
 104                                 //user has given a template file
 105                                 if(it != parameters.end()){
 106                                         path = m->hasPath(it->second);
 107                                         //if the user has not given a path then, add inputdir. else leave path alone.
 108                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 109                                 }
 110
 111                                 it = parameters.find("oligos");
 112                                 //user has given a template file
 113                                 if(it != parameters.end()){
 114                                         path = m->hasPath(it->second);
 115                                         //if the user has not given a path then, add inputdir. else leave path alone.
 116                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 117                                 }
 118
 119                                 it = parameters.find("qfile");
 120                                 //user has given a template file
 121                                 if(it != parameters.end()){
 122                                         path = m->hasPath(it->second);
 123                                         //if the user has not given a path then, add inputdir. else leave path alone.
 124                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 125                                 }
 126                         }
 127
 128
 129                         //check for required parameters
 130                         fastaFile = validParameter.validFile(parameters, "fasta", true);
 131                         if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the trim.seqs command."); m->mothurOutEndLine(); abort = true; }
 132                         else if (fastaFile == "not open") { abort = true; }
 133
 134                         //if the user changes the output directory command factory will send this info to us in the output parameter
 135                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 136                                 outputDir = "";
 137                                 outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
 138                         }
 139
 140
 141                         //check for optional parameter and set defaults
 142                         // ...at some point should added some additional type checking...
 143                         string temp;
 144                         temp = validParameter.validFile(parameters, "flip", false);
 145                         if (temp == "not found"){       flip = 0;       }
 146                         else if(m->isTrue(temp))        {       flip = 1;       }
 147
 148                         temp = validParameter.validFile(parameters, "oligos", true);
 149                         if (temp == "not found"){       oligoFile = "";         }
 150                         else if(temp == "not open"){    abort = true;   }
 151                         else                                    {       oligoFile = temp;               }
 152
 153                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 154                         convert(temp, maxAmbig);
 155
 156                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
 157                         convert(temp, maxHomoP);
 158
 159                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
 160                         convert(temp, minLength);
 161
 162                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
 163                         convert(temp, maxLength);
 164
 165                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
 166                         convert(temp, bdiffs);
 167
 168                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 169                         convert(temp, pdiffs);
 170
 171                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 172                         convert(temp, tdiffs);
 173
 174                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 175
 176                         temp = validParameter.validFile(parameters, "qfile", true);
 177                         if (temp == "not found")        {       qFileName = "";         }
 178                         else if(temp == "not open")     {       abort = true;           }
 179                         else                                            {       qFileName = temp;       }
 180
 181                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 182                         convert(temp, qThreshold);
 183
 184                         temp = validParameter.validFile(parameters, "qtrim", false);            if (temp == "not found") { temp = "F"; }
 185                         qtrim = m->isTrue(temp);
 186
 187                         temp = validParameter.validFile(parameters, "rollaverage", false);      if (temp == "not found") { temp = "0"; }
 188                         convert(temp, qRollAverage);
 189
 190                         temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
 191                         convert(temp, qWindowAverage);
 192
 193                         temp = validParameter.validFile(parameters, "qwindowsize", false);      if (temp == "not found") { temp = "100"; }
 194                         convert(temp, qWindowSize);
 195
 196                         temp = validParameter.validFile(parameters, "qstepsize", false);                if (temp == "not found") { temp = "10"; }
 197                         convert(temp, qWindowStep);
 198
 199                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 200                         convert(temp, qAverage);
 201
 202                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 203                         allFiles = m->isTrue(temp);
 204
 205                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found") { temp = "1"; }
 206                         convert(temp, processors);
 207
 208                         if(allFiles && oligoFile == ""){
 209                                 m->mothurOut("You selected allfiles, but didn't enter an oligos file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 210                         }
 211                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 212                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 213                                 qAverage=0;
 214                                 qThreshold=0;
 215                         }
 216                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 217                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 218                                 abort = true;
 219                         }
 220                 }
 221
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 225                 exit(1);
 226         }
 227 }
 228 //**********************************************************************************************************************
 229
 230 void TrimSeqsCommand::help(){
 231         try {
 232                 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 233                 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 234                 m->mothurOut("The fasta parameter is required.\n");
 235                 m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
 236                 m->mothurOut("The oligos parameter .... The default is "".\n");
 237                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 238                 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 239                 m->mothurOut("The minlength parameter .... The default is 0.\n");
 240                 m->mothurOut("The maxlength parameter .... The default is 0.\n");
 241                 m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
 242                 m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
 243                 m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 244                 m->mothurOut("The qfile parameter .....\n");
 245                 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 246                 m->mothurOut("The qaverage parameter .... The default is 0.\n");
 247                 m->mothurOut("The allfiles parameter .... The default is F.\n");
 248                 m->mothurOut("The qtrim parameter .... The default is F.\n");
 249                 m->mothurOut("The trim.seqs command should be in the following format: \n");
 250                 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 251                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 252                 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 253                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 254                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 255
 256         }
 257         catch(exception& e) {
 258                 m->errorOut(e, "TrimSeqsCommand", "help");
 259                 exit(1);
 260         }
 261 }
 262
 263
 264 //***************************************************************************************************************
 265
 266 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 267
 268 //***************************************************************************************************************
 269
 270 int TrimSeqsCommand::execute(){
 271         try{
 272
 273                 if (abort == true) { return 0; }
 274
 275                 numFPrimers = 0;  //this needs to be initialized
 276                 numRPrimers = 0;
 277
 278                 string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
 279                 outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
 280                 string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
 281                 outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
 282                 string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
 283                 string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
 284                 if (qFileName != "") {  outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile);  outputTypes["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
 285                 string groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups";
 286
 287                 vector<string> fastaFileNames;
 288                 vector<string> qualFileNames;
 289                 if(oligoFile != ""){
 290                         outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
 291                         getOligos(fastaFileNames, qualFileNames);
 292                 }
 293
 294                 vector<unsigned long int> fastaFilePos;
 295                 vector<unsigned long int> qFilePos;
 296
 297                 setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
 298
 299                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 300                         lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
 301                         if (qFileName != "") {  qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)]));  }
 302                 }
 303                 if(qFileName == "")     {       qLines = lines; } //files with duds
 304
 305                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 306                                 if(processors == 1){
 307
 308                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 309
 310                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 311                                                 rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
 312                                         }
 313                                         if(qFileName != ""){
 314                                                 for (int j = 0; j < qualFileNames.size(); j++) {
 315                                                         rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
 316                                                 }
 317                                         }
 318
 319                                 }else{
 320                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
 321
 322                                         rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 323                                         rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 324                                         rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
 325
 326                                         if(qFileName != ""){
 327                                                 rename((trimQualFile + toString(processIDS[0]) + ".temp").c_str(), trimQualFile.c_str());
 328                                                 rename((scrapQualFile + toString(processIDS[0]) + ".temp").c_str(), scrapQualFile.c_str());
 329                                         }
 330
 331
 332                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 333                                                 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 334                                         }
 335                                         if(qFileName != ""){
 336                                                 for (int j = 0; j < qualFileNames.size(); j++) {
 337                                                         rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
 338                                                 }
 339                                         }
 340
 341                                         //append files
 342                                         for(int i=1;i<processors;i++){
 343                                                 m->appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 344                                                 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
 345                                                 m->appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 346                                                 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
 347
 348                                                 m->appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
 349                                                 remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
 350                                                 m->appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
 351                                                 remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
 352
 353                                                 m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 354                                                 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 355                                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 356                                                         m->appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 357                                                         remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 358                                                 }
 359
 360                                                 if(qFileName != ""){
 361                                                         for (int j = 0; j < qualFileNames.size(); j++) {
 362                                                                 m->appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
 363                                                                 remove((qualFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 364                                                         }
 365                                                 }
 366
 367
 368                                         }
 369                                 }
 370
 371                                 if (m->control_pressed) {  return 0; }
 372                 #else
 373                                 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 374
 375                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 376                                         rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
 377                                 }
 378                                 if(qFileName != ""){
 379                                         for (int j = 0; j < qualFileNames.size(); j++) {
 380                                                 rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
 381                                         }
 382                                 }
 383
 384                                 if (m->control_pressed) {  return 0; }
 385                 #endif
 386
 387
 388                 for(int i=0;i<fastaFileNames.size();i++){
 389                         if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
 390                         else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
 391                         else {
 392                                 ifstream inFASTA;
 393                                 string seqName;
 394                                 m->openInputFile(fastaFileNames[i], inFASTA);
 395                                 ofstream outGroups;
 396                                 string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
 397                                 m->openOutputFile(outGroupFilename, outGroups);
 398                                 outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
 399
 400                                 string thisGroup = "";
 401                                 if (i > comboStarts) {
 402                                         map<string, int>::iterator itCombo;
 403                                         for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
 404                                                 if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
 405                                         }
 406                                 }else{ thisGroup = groupVector[i]; }
 407
 408                                 while(!inFASTA.eof()){
 409                                         if(inFASTA.get() == '>'){
 410                                                 inFASTA >> seqName;
 411                                                 outGroups << seqName << '\t' << thisGroup << endl;
 412                                         }
 413                                         while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 414                                 }
 415                                 outGroups.close();
 416                                 inFASTA.close();
 417                         }
 418                 }
 419
 420                 if(qFileName != ""){
 421                         for(int i=0;i<qualFileNames.size();i++){
 422                                 if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str());   }
 423                                 else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
 424                                 else {
 425                                         ifstream inQual;
 426                                         string seqName;
 427                                         m->openInputFile(qualFileNames[i], inQual);
 428 //                                      ofstream outGroups;
 429 //
 430 //                                      string thisGroup = "";
 431 //                                      if (i > comboStarts) {
 432 //                                              map<string, int>::iterator itCombo;
 433 //                                              for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
 434 //                                                      if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
 435 //                                              }
 436 //                                      }
 437 //                                      else{ thisGroup = groupVector[i]; }
 438
 439                                         inQual.close();
 440                                 }
 441                         }
 442                 }
 443
 444
 445                 if (m->control_pressed) {
 446                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 447                         return 0;
 448                 }
 449
 450                 m->mothurOutEndLine();
 451                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 452                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 453                 m->mothurOutEndLine();
 454
 455                 return 0;
 456
 457         }
 458         catch(exception& e) {
 459                 m->errorOut(e, "TrimSeqsCommand", "execute");
 460                 exit(1);
 461         }
 462 }
 463
 464 /**************************************************************************************/
 465
 466 int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames, linePair* line, linePair* qline) {
 467
 468         try {
 469
 470                 ofstream outFASTA;
 471                 int able = m->openOutputFile(trimFile, outFASTA);
 472
 473                 ofstream scrapFASTA;
 474                 m->openOutputFile(scrapFile, scrapFASTA);
 475
 476                 ofstream outQual;
 477                 ofstream scrapQual;
 478                 if(qFileName != ""){
 479                         m->openOutputFile(trimQFile, outQual);
 480                         m->openOutputFile(scrapQFile, scrapQual);
 481                 }
 482
 483                 ofstream outGroups;
 484                 //vector<ofstream*> fastaFileNames;
 485                 //vector<ofstream*> qualFileNames;
 486
 487                 if (oligoFile != "") {
 488                         m->openOutputFile(groupFile, outGroups);
 489                         for (int i = 0; i < fastaNames.size(); i++) {
 490
 491                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 492                                 fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
 493                                 //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 494                                 //clear old file if it exists
 495                                 ofstream temp;
 496                                 m->openOutputFile(fastaNames[i], temp);
 497                                 temp.close();
 498                                 if(qFileName != ""){
 499                                         qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
 500                                         //qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 501                                         //clear old file if it exists
 502                                         ofstream temp2;
 503                                         m->openOutputFile(qualNames[i], temp2);
 504                                         temp2.close();
 505                                 }
 506                         #else
 507                                 //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
 508                                 fastaNames[i] = (fastaNames[i] + toString(i) + ".temp");
 509                                 ofstream temp;
 510                                 m->openOutputFile(fastaNames[i], temp);
 511                                 temp.close();
 512                                 if(qFileName != ""){
 513                                         //qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));
 514                                         qualNames[i] = (qualNames[i] + toString(i) + ".temp");
 515                                         ofstream temp2;
 516                                         m->openOutputFile(qualNames[i], temp2);
 517                                         temp2.close();
 518                                 }
 519                         #endif
 520                         }
 521                 }
 522
 523                 ifstream inFASTA;
 524                 m->openInputFile(filename, inFASTA);
 525                 inFASTA.seekg(line->start);
 526
 527                 ifstream qFile;
 528                 if(qFileName != "")     {       m->openInputFile(qFileName, qFile);     qFile.seekg(qline->start);  }
 529
 530                 bool done = false;
 531                 int count = 0;
 532
 533                 while (!done) {
 534
 535                         if (m->control_pressed) {
 536                                 inFASTA.close(); outFASTA.close(); scrapFASTA.close();
 537                                 if (oligoFile != "") {   outGroups.close();   }
 538
 539                                 //for(int i=0;i<fastaFileNames.size();i++){  fastaFileNames[i]->close(); delete fastaFileNames[i];  }
 540
 541                                 if(qFileName != ""){
 542                                         qFile.close();
 543                                         //for(int i=0;i<qualFileNames.size();i++){  qualFileNames[i]->close(); delete qualFileNames[i];  }
 544                                 }
 545                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 546
 547                                 return 0;
 548                         }
 549
 550                         int success = 1;
 551
 552
 553                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 554
 555                         QualityScores currQual;
 556                         if(qFileName != ""){
 557                                 currQual = QualityScores(qFile, currSeq.getNumBases());  m->gobble(qFile);
 558                         }
 559
 560                         string origSeq = currSeq.getUnaligned();
 561                         if (origSeq != "") {
 562                                 int groupBar, groupPrime;
 563                                 string trashCode = "";
 564                                 int currentSeqsDiffs = 0;
 565
 566                                 if(qFileName != ""){
 567                                         if(qThreshold != 0)                     {       success = currQual.stripQualThreshold(currSeq, qThreshold);                     }
 568                                         else if(qAverage != 0)          {       success = currQual.cullQualAverage(currSeq, qAverage);                          }
 569                                         else if(qRollAverage != 0)      {       success = currQual.stripQualRollingAverage(currSeq, qRollAverage);      }
 570                                         else if(qWindowAverage != 0){   success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);   }
 571
 572                                         if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
 573                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 574                                         }
 575
 576                                         if(!success)                            {       trashCode += 'q';       }
 577                                 }
 578
 579                                 if(barcodes.size() != 0){
 580                                         success = stripBarcode(currSeq, currQual, groupBar);
 581                                         if(success > bdiffs)            {       trashCode += 'b';       }
 582                                         else{ currentSeqsDiffs += success;  }
 583                                 }
 584
 585                                 if(numFPrimers != 0){
 586                                         success = stripForward(currSeq, currQual, groupPrime);
 587                                         if(success > pdiffs)            {       trashCode += 'f';       }
 588                                         else{ currentSeqsDiffs += success;  }
 589                                 }
 590
 591                                 if (currentSeqsDiffs > tdiffs)  {       trashCode += 't';   }
 592
 593                                 if(numRPrimers != 0){
 594                                         success = stripReverse(currSeq, currQual);
 595                                         if(!success)                            {       trashCode += 'r';       }
 596                                 }
 597
 598                                 if(minLength > 0 || maxLength > 0){
 599                                         success = cullLength(currSeq);
 600                                         if(!success)                            {       trashCode += 'l';       }
 601                                 }
 602                                 if(maxHomoP > 0){
 603                                         success = cullHomoP(currSeq);
 604                                         if(!success)                            {       trashCode += 'h';       }
 605                                 }
 606                                 if(maxAmbig != -1){
 607                                         success = cullAmbigs(currSeq);
 608                                         if(!success)                            {       trashCode += 'n';       }
 609                                 }
 610
 611                                 if(flip){       currSeq.reverseComplement();            currQual.flipQScores(); }               // should go last
 612
 613                                 if(trashCode.length() == 0){
 614                                         currSeq.setAligned(currSeq.getUnaligned());
 615                                         currSeq.printSequence(outFASTA);
 616                                         currQual.printQScores(outQual);
 617
 618                                         if(barcodes.size() != 0){
 619                                                 string thisGroup = groupVector[groupBar];
 620                                                 int indexToFastaFile = groupBar;
 621                                                 if (primers.size() != 0){
 622                                                         //does this primer have a group
 623                                                         if (groupVector[groupPrime] != "") {
 624                                                                 thisGroup += "." + groupVector[groupPrime];
 625                                                                 indexToFastaFile = combos[thisGroup];
 626                                                         }
 627                                                 }
 628                                                 outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 629                                                 if(allFiles){
 630                                                         ofstream outTemp;
 631                                                         m->openOutputFileAppend(fastaNames[indexToFastaFile], outTemp);
 632                                                         //currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
 633                                                         currSeq.printSequence(outTemp);
 634                                                         outTemp.close();
 635
 636                                                         if(qFileName != ""){
 637                                                                 //currQual.printQScores(*qualFileNames[indexToFastaFile]);
 638                                                                 ofstream outTemp2;
 639                                                                 m->openOutputFileAppend(qualNames[indexToFastaFile], outTemp2);
 640                                                                 currQual.printQScores(outTemp2);
 641                                                                 outTemp2.close();
 642                                                         }
 643                                                 }
 644                                         }
 645                                 }
 646                                 else{
 647                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 648                                         currSeq.setUnaligned(origSeq);
 649                                         currSeq.setAligned(origSeq);
 650                                         currSeq.printSequence(scrapFASTA);
 651                                         currQual.printQScores(scrapQual);
 652                                 }
 653                                 count++;
 654                         }
 655
 656                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 657                                 unsigned long int pos = inFASTA.tellg();
 658                                 if ((pos == -1) || (pos >= line->end)) { break; }
 659                         #else
 660                                 if (inFASTA.eof()) { break; }
 661                         #endif
 662
 663                         //report progress
 664                         if((count) % 1000 == 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 665
 666                 }
 667                 //report progress
 668                 if((count) % 1000 != 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 669
 670
 671                 inFASTA.close();
 672                 outFASTA.close();
 673                 scrapFASTA.close();
 674                 if (oligoFile != "") {   outGroups.close();   }
 675                 if(qFileName != "")     {       qFile.close();  scrapQual.close(); outQual.close();     }
 676
 677                 //for(int i=0;i<fastaFileNames.size();i++){
 678                 //      fastaFileNames[i]->close();
 679                 //      delete fastaFileNames[i];
 680                 //}
 681
 682                 //if(qFileName != ""){
 683                         //for(int i=0;i<qualFileNames.size();i++){
 684                                 //qualFileNames[i]->close();
 685                                 //delete qualFileNames[i];
 686                         //}
 687                 //}
 688
 689                 return count;
 690         }
 691         catch(exception& e) {
 692                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 693                 exit(1);
 694         }
 695 }
 696
 697 /**************************************************************************************************/
 698
 699 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
 700         try {
 701 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 702                 int process = 0;
 703                 int exitCommand = 1;
 704                 processIDS.clear();
 705
 706                 //loop through and create all the processes you want
 707                 while (process != processors) {
 708                         int pid = fork();
 709
 710                         if (pid > 0) {
 711                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 712                                 process++;
 713                         }else if (pid == 0){
 714                                 driverCreateTrim(filename, qFileName, (trimFile + toString(getpid()) + ".temp"), (scrapFile + toString(getpid()) + ".temp"), (trimQFile + toString(getpid()) + ".temp"), (scrapQFile + toString(getpid()) + ".temp"), (groupFile + toString(getpid()) + ".temp"), fastaNames, qualNames, lines[process], qLines[process]);
 715                                 exit(0);
 716                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 717                 }
 718
 719                 //force parent to wait until all the processes are done
 720                 for (int i=0;i<processors;i++) {
 721                         int temp = processIDS[i];
 722                         wait(&temp);
 723                 }
 724
 725                 return exitCommand;
 726 #endif
 727         }
 728         catch(exception& e) {
 729                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 730                 exit(1);
 731         }
 732 }
 733
 734 /**************************************************************************************************/
 735
 736 int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
 737         try {
 738
 739                 //set file positions for fasta file
 740                 fastaFilePos = m->divideFile(filename, processors);
 741
 742                 if (qfilename == "") { return processors; }
 743
 744                 //get name of first sequence in each chunk
 745                 map<string, int> firstSeqNames;
 746                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 747                         ifstream in;
 748                         m->openInputFile(filename, in);
 749                         in.seekg(fastaFilePos[i]);
 750
 751                         Sequence temp(in);
 752                         firstSeqNames[temp.getName()] = i;
 753
 754                         in.close();
 755                 }
 756
 757                 //seach for filePos of each first name in the qfile and save in qfileFilePos
 758                 ifstream inQual;
 759                 m->openInputFile(qfilename, inQual);
 760
 761                 string input;
 762                 while(!inQual.eof()){
 763                         input = m->getline(inQual);
 764
 765                         if (input.length() != 0) {
 766                                 if(input[0] == '>'){ //this is a sequence name line
 767                                         istringstream nameStream(input);
 768
 769                                         string sname = "";  nameStream >> sname;
 770                                         sname = sname.substr(1);
 771
 772                                         map<string, int>::iterator it = firstSeqNames.find(sname);
 773
 774                                         if(it != firstSeqNames.end()) { //this is the start of a new chunk
 775                                                 unsigned long int pos = inQual.tellg();
 776                                                 qfileFilePos.push_back(pos - input.length() - 1);
 777                                                 firstSeqNames.erase(it);
 778                                         }
 779                                 }
 780                         }
 781
 782                         if (firstSeqNames.size() == 0) { break; }
 783                 }
 784                 inQual.close();
 785
 786                 if (firstSeqNames.size() != 0) {
 787                         for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
 788                                 m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
 789                         }
 790                         qFileName = "";
 791                         return processors;
 792                 }
 793
 794                 //get last file position of qfile
 795                 FILE * pFile;
 796                 unsigned long int size;
 797
 798                 //get num bytes in file
 799                 pFile = fopen (qfilename.c_str(),"rb");
 800                 if (pFile==NULL) perror ("Error opening file");
 801                 else{
 802                         fseek (pFile, 0, SEEK_END);
 803                         size=ftell (pFile);
 804                         fclose (pFile);
 805                 }
 806
 807                 qfileFilePos.push_back(size);
 808
 809                 return processors;
 810         }
 811         catch(exception& e) {
 812                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 813                 exit(1);
 814         }
 815 }
 816 //***************************************************************************************************************
 817
 818 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
 819         try {
 820                 ifstream inOligos;
 821                 m->openInputFile(oligoFile, inOligos);
 822
 823                 ofstream test;
 824
 825                 string type, oligo, group;
 826                 int index=0;
 827                 //int indexPrimer = 0;
 828
 829                 while(!inOligos.eof()){
 830                         inOligos >> type;
 831
 832                         if(type[0] == '#'){
 833                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 834                         }
 835                         else{
 836                                 //make type case insensitive
 837                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
 838
 839                                 inOligos >> oligo;
 840
 841                                 for(int i=0;i<oligo.length();i++){
 842                                         oligo[i] = toupper(oligo[i]);
 843                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 844                                 }
 845
 846                                 if(type == "FORWARD"){
 847                                         group = "";
 848
 849                                         // get rest of line in case there is a primer name
 850                                         while (!inOligos.eof()) {
 851                                                 char c = inOligos.get();
 852                                                 if (c == 10 || c == 13){        break;  }
 853                                                 else if (c == 32 || c == 9){;} //space or tab
 854                                                 else {  group += c;  }
 855                                         }
 856
 857                                         //check for repeat barcodes
 858                                         map<string, int>::iterator itPrime = primers.find(oligo);
 859                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 860
 861                                         primers[oligo]=index; index++;
 862                                         groupVector.push_back(group);
 863
 864                                         if(allFiles){
 865                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 866                                                 if(qFileName != ""){
 867                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 868                                                 }
 869                                                 if (group == "") { //if there is not a group for this primer, then this file will not get written to, but we add it to keep the indexes correct
 870                                                         filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 871                                                         if(qFileName != ""){
 872                                                                 filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 873                                                         }
 874                                                 }else {
 875                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 876                                                         outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 877                                                         if(qFileName != ""){
 878                                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 879                                                                 outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 880                                                         }
 881                                                 }
 882                                         }
 883
 884                                 }
 885                                 else if(type == "REVERSE"){
 886                                         Sequence oligoRC("reverse", oligo);
 887                                         oligoRC.reverseComplement();
 888                                         revPrimer.push_back(oligoRC.getUnaligned());
 889                                 }
 890                                 else if(type == "BARCODE"){
 891                                         inOligos >> group;
 892
 893                                         //check for repeat barcodes
 894                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 895                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 896
 897                                         barcodes[oligo]=index; index++;
 898                                         groupVector.push_back(group);
 899
 900                                         if(allFiles){
 901                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 902                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 903                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 904                                                 if(qFileName != ""){
 905                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 906                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 907                                                         outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 908                                                 }
 909                                         }
 910                                 }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
 911                         }
 912                         m->gobble(inOligos);
 913                 }
 914
 915                 inOligos.close();
 916
 917                 //add in potential combos
 918                 if(allFiles){
 919                         comboStarts = outFASTAVec.size()-1;
 920                         for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
 921                                 for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
 922                                         if (groupVector[itPrime->second] != "") { //there is a group for this primer
 923                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 924                                                 outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 925                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 926                                                 combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
 927
 928                                                 if(qFileName != ""){
 929                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 930                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 931                                                         outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 932                                                 }
 933                                         }
 934                                 }
 935                         }
 936                 }
 937
 938                 numFPrimers = primers.size();
 939                 numRPrimers = revPrimer.size();
 940
 941         }
 942         catch(exception& e) {
 943                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 944                 exit(1);
 945         }
 946 }
 947 //***************************************************************************************************************
 948
 949 int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
 950         try {
 951
 952                 string rawSequence = seq.getUnaligned();
 953                 int success = bdiffs + 1;       //guilty until proven innocent
 954
 955                 //can you find the barcode
 956                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 957                         string oligo = it->first;
 958                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 959                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 960                                 break;
 961                         }
 962
 963                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 964                                 group = it->second;
 965                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 966
 967                                 if(qual.getName() != ""){
 968                                         qual.trimQScores(oligo.length(), -1);
 969                                 }
 970
 971                                 success = 0;
 972                                 break;
 973                         }
 974                 }
 975
 976                 //if you found the barcode or if you don't want to allow for diffs
 977 //              cout << success;
 978                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 979
 980                 else { //try aligning and see if you can find it
 981 //                      cout << endl;
 982
 983                         int maxLength = 0;
 984
 985                         Alignment* alignment;
 986                         if (barcodes.size() > 0) {
 987                                 map<string,int>::iterator it=barcodes.begin();
 988
 989                                 for(it;it!=barcodes.end();it++){
 990                                         if(it->first.length() > maxLength){
 991                                                 maxLength = it->first.length();
 992                                         }
 993                                 }
 994                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
 995
 996                         }else{ alignment = NULL; }
 997
 998                         //can you find the barcode
 999                         int minDiff = 1e6;
1000                         int minCount = 1;
1001                         int minGroup = -1;
1002                         int minPos = 0;
1003
1004                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
1005                                 string oligo = it->first;
1006 //                              int length = oligo.length();
1007
1008                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
1009                                         success = bdiffs + 10;
1010                                         break;
1011                                 }
1012
1013                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1014                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
1015                                 oligo = alignment->getSeqAAln();
1016                                 string temp = alignment->getSeqBAln();
1017
1018                                 int alnLength = oligo.length();
1019
1020                                 for(int i=oligo.length()-1;i>=0;i--){
1021                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1022                                 }
1023                                 oligo = oligo.substr(0,alnLength);
1024                                 temp = temp.substr(0,alnLength);
1025
1026                                 int newStart=0;
1027                                 int numDiff = countDiffs(oligo, temp);
1028
1029 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1030
1031                                 if(numDiff < minDiff){
1032                                         minDiff = numDiff;
1033                                         minCount = 1;
1034                                         minGroup = it->second;
1035                                         minPos = 0;
1036                                         for(int i=0;i<alnLength;i++){
1037                                                 if(temp[i] != '-'){
1038                                                         minPos++;
1039                                                 }
1040                                         }
1041                                 }
1042                                 else if(numDiff == minDiff){
1043                                         minCount++;
1044                                 }
1045
1046                         }
1047
1048                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
1049                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
1050                         else{                                                                                                   //use the best match
1051                                 group = minGroup;
1052                                 seq.setUnaligned(rawSequence.substr(minPos));
1053
1054                                 if(qual.getName() != ""){
1055                                         qual.trimQScores(minPos, -1);
1056                                 }
1057                                 success = minDiff;
1058                         }
1059
1060                         if (alignment != NULL) {  delete alignment;  }
1061
1062                 }
1063 //              cout << success << endl;
1064
1065                 return success;
1066
1067         }
1068         catch(exception& e) {
1069                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
1070                 exit(1);
1071         }
1072
1073 }
1074
1075 //***************************************************************************************************************
1076
1077 int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
1078         try {
1079                 string rawSequence = seq.getUnaligned();
1080                 int success = pdiffs + 1;       //guilty until proven innocent
1081
1082                 //can you find the primer
1083                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1084                         string oligo = it->first;
1085                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
1086                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
1087                                 break;
1088                         }
1089
1090                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
1091                                 group = it->second;
1092                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
1093                                 if(qual.getName() != ""){
1094                                         qual.trimQScores(oligo.length(), -1);
1095
1096                                 }
1097                                 success = 0;
1098                                 break;
1099                         }
1100                 }
1101
1102                 //if you found the barcode or if you don't want to allow for diffs
1103 //              cout << success;
1104                 if ((pdiffs == 0) || (success == 0)) { return success;  }
1105
1106                 else { //try aligning and see if you can find it
1107 //                      cout << endl;
1108
1109                         int maxLength = 0;
1110
1111                         Alignment* alignment;
1112                         if (primers.size() > 0) {
1113                                 map<string,int>::iterator it=primers.begin();
1114
1115                                 for(it;it!=primers.end();it++){
1116                                         if(it->first.length() > maxLength){
1117                                                 maxLength = it->first.length();
1118                                         }
1119                                 }
1120                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
1121
1122                         }else{ alignment = NULL; }
1123
1124                         //can you find the barcode
1125                         int minDiff = 1e6;
1126                         int minCount = 1;
1127                         int minGroup = -1;
1128                         int minPos = 0;
1129
1130                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1131                                 string oligo = it->first;
1132 //                              int length = oligo.length();
1133
1134                                 if(rawSequence.length() < maxLength){
1135                                         success = pdiffs + 100;
1136                                         break;
1137                                 }
1138
1139                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1140                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
1141                                 oligo = alignment->getSeqAAln();
1142                                 string temp = alignment->getSeqBAln();
1143
1144                                 int alnLength = oligo.length();
1145
1146                                 for(int i=oligo.length()-1;i>=0;i--){
1147                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1148                                 }
1149                                 oligo = oligo.substr(0,alnLength);
1150                                 temp = temp.substr(0,alnLength);
1151
1152                                 int newStart=0;
1153                                 int numDiff = countDiffs(oligo, temp);
1154
1155 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1156
1157                                 if(numDiff < minDiff){
1158                                         minDiff = numDiff;
1159                                         minCount = 1;
1160                                         minGroup = it->second;
1161                                         minPos = 0;
1162                                         for(int i=0;i<alnLength;i++){
1163                                                 if(temp[i] != '-'){
1164                                                         minPos++;
1165                                                 }
1166                                         }
1167                                 }
1168                                 else if(numDiff == minDiff){
1169                                         minCount++;
1170                                 }
1171
1172                         }
1173
1174                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
1175                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
1176                         else{                                                                                                   //use the best match
1177                                 group = minGroup;
1178                                 seq.setUnaligned(rawSequence.substr(minPos));
1179                                 if(qual.getName() != ""){
1180                                         qual.trimQScores(minPos, -1);
1181                                 }
1182                                 success = minDiff;
1183                         }
1184
1185                         if (alignment != NULL) {  delete alignment;  }
1186
1187                 }
1188
1189                 return success;
1190
1191         }
1192         catch(exception& e) {
1193                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
1194                 exit(1);
1195         }
1196 }
1197
1198 //***************************************************************************************************************
1199
1200 bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
1201         try {
1202                 string rawSequence = seq.getUnaligned();
1203                 bool success = 0;       //guilty until proven innocent
1204
1205                 for(int i=0;i<numRPrimers;i++){
1206                         string oligo = revPrimer[i];
1207
1208                         if(rawSequence.length() < oligo.length()){
1209                                 success = 0;
1210                                 break;
1211                         }
1212
1213                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
1214                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
1215                                 if(qual.getName() != ""){
1216                                         qual.trimQScores(-1, rawSequence.length()-oligo.length());
1217                                 }
1218                                 success = 1;
1219                                 break;
1220                         }
1221                 }
1222                 return success;
1223
1224         }
1225         catch(exception& e) {
1226                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
1227                 exit(1);
1228         }
1229 }
1230
1231 //***************************************************************************************************************
1232
1233 bool TrimSeqsCommand::cullLength(Sequence& seq){
1234         try {
1235
1236                 int length = seq.getNumBases();
1237                 bool success = 0;       //guilty until proven innocent
1238
1239                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
1240                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
1241                 else                                                                                            {       success = 0;    }
1242
1243                 return success;
1244
1245         }
1246         catch(exception& e) {
1247                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1248                 exit(1);
1249         }
1250
1251 }
1252
1253 //***************************************************************************************************************
1254
1255 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1256         try {
1257                 int longHomoP = seq.getLongHomoPolymer();
1258                 bool success = 0;       //guilty until proven innocent
1259
1260                 if(longHomoP <= maxHomoP){      success = 1;    }
1261                 else                                    {       success = 0;    }
1262
1263                 return success;
1264         }
1265         catch(exception& e) {
1266                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1267                 exit(1);
1268         }
1269
1270 }
1271
1272 //***************************************************************************************************************
1273
1274 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1275         try {
1276                 int numNs = seq.getAmbigBases();
1277                 bool success = 0;       //guilty until proven innocent
1278
1279                 if(numNs <= maxAmbig)   {       success = 1;    }
1280                 else                                    {       success = 0;    }
1281
1282                 return success;
1283         }
1284         catch(exception& e) {
1285                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1286                 exit(1);
1287         }
1288
1289 }
1290
1291 //***************************************************************************************************************
1292
1293 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
1294         try {
1295                 bool success = 1;
1296                 int length = oligo.length();
1297
1298                 for(int i=0;i<length;i++){
1299
1300                         if(oligo[i] != seq[i]){
1301                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
1302                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
1303                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
1304                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
1305                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
1306                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
1307                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
1308                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
1309                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1310                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1311                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
1312                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
1313
1314                                 if(success == 0)        {       break;   }
1315                         }
1316                         else{
1317                                 success = 1;
1318                         }
1319                 }
1320
1321                 return success;
1322         }
1323         catch(exception& e) {
1324                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
1325                 exit(1);
1326         }
1327
1328 }
1329 //***************************************************************************************************************
1330
1331 int TrimSeqsCommand::countDiffs(string oligo, string seq){
1332         try {
1333
1334                 int length = oligo.length();
1335                 int countDiffs = 0;
1336
1337                 for(int i=0;i<length;i++){
1338
1339                         if(oligo[i] != seq[i]){
1340                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
1341                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
1342                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
1343                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
1344                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
1345                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
1346                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
1347                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
1348                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1349                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1350                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
1351                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
1352                         }
1353
1354                 }
1355
1356                 return countDiffs;
1357         }
1358         catch(exception& e) {
1359                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
1360                 exit(1);
1361         }
1362
1363 }
1364 //***************************************************************************************************************
1365
1366 //bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
1367 //      try {
1368 //
1369 //              string rawSequence = seq.getUnaligned();
1370 //              int seqLength = seq.getNumBases();
1371 //              bool success = 0;       //guilty until proven innocent
1372 //              string name;
1373 //
1374 //              qFile >> name;
1375 //              if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1376 //
1377 //              while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1378 //
1379 //              int score;
1380 //              int end = seqLength;
1381 //
1382 //              for(int i=0;i<seqLength;i++){
1383 //                      qFile >> score;
1384 //
1385 //                      if(score < qThreshold){
1386 //                              end = i;
1387 //                              break;
1388 //                      }
1389 //              }
1390 //              for(int i=end+1;i<seqLength;i++){
1391 //                      qFile >> score;
1392 //              }
1393 //
1394 //              seq.setUnaligned(rawSequence.substr(0,end));
1395 //
1396 //              return 1;
1397 //      }
1398 //      catch(exception& e) {
1399 //              m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1400 //              exit(1);
1401 //      }
1402 //}
1403
1404 //***************************************************************************************************************
1405
1406 //bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1407 //      try {
1408 //              string rawSequence = seq.getUnaligned();
1409 //              int seqLength = seq.getNumBases();
1410 //              bool success = 0;       //guilty until proven innocent
1411 //              string name;
1412 //
1413 //              qFile >> name;
1414 //              if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1415 //
1416 //              while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1417 //
1418 //              float score;
1419 //              float average = 0;
1420 //
1421 //              for(int i=0;i<seqLength;i++){
1422 //                      qFile >> score;
1423 //                      average += score;
1424 //              }
1425 //              average /= seqLength;
1426 //
1427 //              if(average >= qAverage) {       success = 1;    }
1428 //              else                                    {       success = 0;    }
1429 //
1430 //              return success;
1431 //      }
1432 //      catch(exception& e) {
1433 //              m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1434 //              exit(1);
1435 //      }
1436 //}
1437
1438 //***************************************************************************************************************