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