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         cout << "here" << endl;
 432                 if (oligoFile != "") {
 433                         m->openOutputFile(groupFile, outGroups);
 434                         for (int i = 0; i < fastaNames.size(); i++) {
 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 cout << "here " << filename << endl;
 449                 ifstream inFASTA;
 450                 m->openInputFile(filename, inFASTA);
 451                 inFASTA.seekg(line->start);
 452         cout << "here " << qFileName << endl;
 453                 ifstream qFile;
 454                 if(qFileName != "")     {       m->openInputFile(qFileName, qFile);     qFile.seekg(qline->start);  }
 455
 456                 bool done = false;
 457                 int count = 0;
 458         cout << "here" << endl;
 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                         unsigned long int pos = inFASTA.tellg();
 575                         if ((pos == -1) || (pos >= line->end)) { break; }
 576
 577                         //report progress
 578                         if((count) % 1000 == 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 579
 580                 }
 581                 //report progress
 582                 if((count) % 1000 != 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 583
 584
 585                 inFASTA.close();
 586                 outFASTA.close();
 587                 scrapFASTA.close();
 588                 if (oligoFile != "") {   outGroups.close();   }
 589                 if(qFileName != "")     {       qFile.close();  scrapQual.close(); outQual.close();     }
 590
 591                 for(int i=0;i<fastaFileNames.size();i++){
 592                         fastaFileNames[i]->close();
 593                         delete fastaFileNames[i];
 594                 }
 595
 596                 if(qFileName != ""){
 597                         for(int i=0;i<qualFileNames.size();i++){
 598                                 qualFileNames[i]->close();
 599                                 delete qualFileNames[i];
 600                         }
 601                 }
 602
 603                 return count;
 604         }
 605         catch(exception& e) {
 606                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 607                 exit(1);
 608         }
 609 }
 610
 611 /**************************************************************************************************/
 612
 613 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
 614         try {
 615 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 616                 int process = 0;
 617                 int exitCommand = 1;
 618                 processIDS.clear();
 619
 620                 //loop through and create all the processes you want
 621                 while (process != processors) {
 622                         int pid = fork();
 623
 624                         if (pid > 0) {
 625                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 626                                 process++;
 627                         }else if (pid == 0){
 628                                 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]);
 629                                 exit(0);
 630                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 631                 }
 632
 633                 //force parent to wait until all the processes are done
 634                 for (int i=0;i<processors;i++) {
 635                         int temp = processIDS[i];
 636                         wait(&temp);
 637                 }
 638
 639                 return exitCommand;
 640 #endif
 641         }
 642         catch(exception& e) {
 643                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 644                 exit(1);
 645         }
 646 }
 647
 648 /**************************************************************************************************/
 649
 650 int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
 651         try {
 652
 653                 //set file positions for fasta file
 654                 fastaFilePos = m->divideFile(filename, processors);
 655
 656                 if (qfilename == "") { return processors; }
 657
 658                 //get name of first sequence in each chunk
 659                 map<string, int> firstSeqNames;
 660                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 661                         ifstream in;
 662                         m->openInputFile(filename, in);
 663                         in.seekg(fastaFilePos[i]);
 664
 665                         Sequence temp(in);
 666                         firstSeqNames[temp.getName()] = i;
 667
 668                         in.close();
 669                 }
 670
 671                 //seach for filePos of each first name in the qfile and save in qfileFilePos
 672                 ifstream inQual;
 673                 m->openInputFile(qfilename, inQual);
 674
 675                 string input;
 676                 while(!inQual.eof()){
 677                         input = m->getline(inQual);
 678
 679                         if (input.length() != 0) {
 680                                 if(input[0] == '>'){ //this is a sequence name line
 681                                         istringstream nameStream(input);
 682
 683                                         string sname = "";  nameStream >> sname;
 684                                         sname = sname.substr(1);
 685
 686                                         map<string, int>::iterator it = firstSeqNames.find(sname);
 687
 688                                         if(it != firstSeqNames.end()) { //this is the start of a new chunk
 689                                                 unsigned long int pos = inQual.tellg();
 690                                                 qfileFilePos.push_back(pos - input.length() - 1);
 691                                                 firstSeqNames.erase(it);
 692                                         }
 693                                 }
 694                         }
 695
 696                         if (firstSeqNames.size() == 0) { break; }
 697                 }
 698                 inQual.close();
 699
 700                 if (firstSeqNames.size() != 0) {
 701                         for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
 702                                 m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
 703                         }
 704                         qFileName = "";
 705                         return processors;
 706                 }
 707
 708                 //get last file position of qfile
 709                 FILE * pFile;
 710                 unsigned long int size;
 711
 712                 //get num bytes in file
 713                 pFile = fopen (qfilename.c_str(),"rb");
 714                 if (pFile==NULL) perror ("Error opening file");
 715                 else{
 716                         fseek (pFile, 0, SEEK_END);
 717                         size=ftell (pFile);
 718                         fclose (pFile);
 719                 }
 720
 721                 qfileFilePos.push_back(size);
 722
 723                 return processors;
 724         }
 725         catch(exception& e) {
 726                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 727                 exit(1);
 728         }
 729 }
 730 //***************************************************************************************************************
 731
 732 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
 733         try {
 734                 ifstream inOligos;
 735                 m->openInputFile(oligoFile, inOligos);
 736
 737                 ofstream test;
 738
 739                 string type, oligo, group;
 740                 int index=0;
 741                 //int indexPrimer = 0;
 742
 743                 while(!inOligos.eof()){
 744                         inOligos >> type;
 745
 746                         if(type[0] == '#'){
 747                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 748                         }
 749                         else{
 750                                 //make type case insensitive
 751                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
 752
 753                                 inOligos >> oligo;
 754
 755                                 for(int i=0;i<oligo.length();i++){
 756                                         oligo[i] = toupper(oligo[i]);
 757                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 758                                 }
 759
 760                                 if(type == "FORWARD"){
 761                                         group = "";
 762
 763                                         // get rest of line in case there is a primer name
 764                                         while (!inOligos.eof()) {
 765                                                 char c = inOligos.get();
 766                                                 if (c == 10 || c == 13){        break;  }
 767                                                 else if (c == 32 || c == 9){;} //space or tab
 768                                                 else {  group += c;  }
 769                                         }
 770
 771                                         //check for repeat barcodes
 772                                         map<string, int>::iterator itPrime = primers.find(oligo);
 773                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 774
 775                                         primers[oligo]=index; index++;
 776                                         groupVector.push_back(group);
 777
 778                                         if(allFiles){
 779                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 780                                                 if(qFileName != ""){
 781                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 782                                                 }
 783                                                 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
 784                                                         filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 785                                                         if(qFileName != ""){
 786                                                                 filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 787                                                         }
 788                                                 }else {
 789                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 790                                                         if(qFileName != ""){
 791                                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 792                                                         }
 793                                                 }
 794                                         }
 795
 796                                 }
 797                                 else if(type == "REVERSE"){
 798                                         Sequence oligoRC("reverse", oligo);
 799                                         oligoRC.reverseComplement();
 800                                         revPrimer.push_back(oligoRC.getUnaligned());
 801                                 }
 802                                 else if(type == "BARCODE"){
 803                                         inOligos >> group;
 804
 805                                         //check for repeat barcodes
 806                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 807                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 808
 809                                         barcodes[oligo]=index; index++;
 810                                         groupVector.push_back(group);
 811
 812                                         if(allFiles){
 813                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 814                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 815                                                 if(qFileName != ""){
 816                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 817                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 818                                                 }
 819                                         }
 820                                 }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
 821                         }
 822                         m->gobble(inOligos);
 823                 }
 824
 825                 inOligos.close();
 826
 827                 //add in potential combos
 828                 if(allFiles){
 829                         comboStarts = outFASTAVec.size()-1;
 830                         for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
 831                                 for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
 832                                         if (groupVector[itPrime->second] != "") { //there is a group for this primer
 833                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 834                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 835                                                 combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
 836
 837                                                 if(qFileName != ""){
 838                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 839                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 840                                                 }
 841                                         }
 842                                 }
 843                         }
 844                 }
 845
 846                 numFPrimers = primers.size();
 847                 numRPrimers = revPrimer.size();
 848
 849         }
 850         catch(exception& e) {
 851                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 852                 exit(1);
 853         }
 854 }
 855 //***************************************************************************************************************
 856
 857 int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
 858         try {
 859
 860                 string rawSequence = seq.getUnaligned();
 861                 int success = bdiffs + 1;       //guilty until proven innocent
 862
 863                 //can you find the barcode
 864                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 865                         string oligo = it->first;
 866                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 867                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 868                                 break;
 869                         }
 870
 871                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 872                                 group = it->second;
 873                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 874
 875                                 if(qual.getName() != ""){
 876                                         qual.trimQScores(oligo.length(), -1);
 877                                 }
 878
 879                                 success = 0;
 880                                 break;
 881                         }
 882                 }
 883
 884                 //if you found the barcode or if you don't want to allow for diffs
 885 //              cout << success;
 886                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 887
 888                 else { //try aligning and see if you can find it
 889 //                      cout << endl;
 890
 891                         int maxLength = 0;
 892
 893                         Alignment* alignment;
 894                         if (barcodes.size() > 0) {
 895                                 map<string,int>::iterator it=barcodes.begin();
 896
 897                                 for(it;it!=barcodes.end();it++){
 898                                         if(it->first.length() > maxLength){
 899                                                 maxLength = it->first.length();
 900                                         }
 901                                 }
 902                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
 903
 904                         }else{ alignment = NULL; }
 905
 906                         //can you find the barcode
 907                         int minDiff = 1e6;
 908                         int minCount = 1;
 909                         int minGroup = -1;
 910                         int minPos = 0;
 911
 912                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 913                                 string oligo = it->first;
 914 //                              int length = oligo.length();
 915
 916                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 917                                         success = bdiffs + 10;
 918                                         break;
 919                                 }
 920
 921                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 922                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 923                                 oligo = alignment->getSeqAAln();
 924                                 string temp = alignment->getSeqBAln();
 925
 926                                 int alnLength = oligo.length();
 927
 928                                 for(int i=oligo.length()-1;i>=0;i--){
 929                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 930                                 }
 931                                 oligo = oligo.substr(0,alnLength);
 932                                 temp = temp.substr(0,alnLength);
 933
 934                                 int newStart=0;
 935                                 int numDiff = countDiffs(oligo, temp);
 936
 937 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
 938
 939                                 if(numDiff < minDiff){
 940                                         minDiff = numDiff;
 941                                         minCount = 1;
 942                                         minGroup = it->second;
 943                                         minPos = 0;
 944                                         for(int i=0;i<alnLength;i++){
 945                                                 if(temp[i] != '-'){
 946                                                         minPos++;
 947                                                 }
 948                                         }
 949                                 }
 950                                 else if(numDiff == minDiff){
 951                                         minCount++;
 952                                 }
 953
 954                         }
 955
 956                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 957                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 958                         else{                                                                                                   //use the best match
 959                                 group = minGroup;
 960                                 seq.setUnaligned(rawSequence.substr(minPos));
 961
 962                                 if(qual.getName() != ""){
 963                                         qual.trimQScores(minPos, -1);
 964                                 }
 965                                 success = minDiff;
 966                         }
 967
 968                         if (alignment != NULL) {  delete alignment;  }
 969
 970                 }
 971 //              cout << success << endl;
 972
 973                 return success;
 974
 975         }
 976         catch(exception& e) {
 977                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
 978                 exit(1);
 979         }
 980
 981 }
 982
 983 //***************************************************************************************************************
 984
 985 int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
 986         try {
 987                 string rawSequence = seq.getUnaligned();
 988                 int success = pdiffs + 1;       //guilty until proven innocent
 989
 990                 //can you find the primer
 991                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 992                         string oligo = it->first;
 993                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
 994                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 995                                 break;
 996                         }
 997
 998                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 999                                 group = it->second;
1000                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
1001                                 if(qual.getName() != ""){
1002                                         qual.trimQScores(oligo.length(), -1);
1003
1004                                 }
1005                                 success = 0;
1006                                 break;
1007                         }
1008                 }
1009
1010                 //if you found the barcode or if you don't want to allow for diffs
1011 //              cout << success;
1012                 if ((pdiffs == 0) || (success == 0)) { return success;  }
1013
1014                 else { //try aligning and see if you can find it
1015 //                      cout << endl;
1016
1017                         int maxLength = 0;
1018
1019                         Alignment* alignment;
1020                         if (primers.size() > 0) {
1021                                 map<string,int>::iterator it=primers.begin();
1022
1023                                 for(it;it!=primers.end();it++){
1024                                         if(it->first.length() > maxLength){
1025                                                 maxLength = it->first.length();
1026                                         }
1027                                 }
1028                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
1029
1030                         }else{ alignment = NULL; }
1031
1032                         //can you find the barcode
1033                         int minDiff = 1e6;
1034                         int minCount = 1;
1035                         int minGroup = -1;
1036                         int minPos = 0;
1037
1038                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1039                                 string oligo = it->first;
1040 //                              int length = oligo.length();
1041
1042                                 if(rawSequence.length() < maxLength){
1043                                         success = pdiffs + 100;
1044                                         break;
1045                                 }
1046
1047                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1048                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
1049                                 oligo = alignment->getSeqAAln();
1050                                 string temp = alignment->getSeqBAln();
1051
1052                                 int alnLength = oligo.length();
1053
1054                                 for(int i=oligo.length()-1;i>=0;i--){
1055                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1056                                 }
1057                                 oligo = oligo.substr(0,alnLength);
1058                                 temp = temp.substr(0,alnLength);
1059
1060                                 int newStart=0;
1061                                 int numDiff = countDiffs(oligo, temp);
1062
1063 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1064
1065                                 if(numDiff < minDiff){
1066                                         minDiff = numDiff;
1067                                         minCount = 1;
1068                                         minGroup = it->second;
1069                                         minPos = 0;
1070                                         for(int i=0;i<alnLength;i++){
1071                                                 if(temp[i] != '-'){
1072                                                         minPos++;
1073                                                 }
1074                                         }
1075                                 }
1076                                 else if(numDiff == minDiff){
1077                                         minCount++;
1078                                 }
1079
1080                         }
1081
1082                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
1083                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
1084                         else{                                                                                                   //use the best match
1085                                 group = minGroup;
1086                                 seq.setUnaligned(rawSequence.substr(minPos));
1087                                 if(qual.getName() != ""){
1088                                         qual.trimQScores(minPos, -1);
1089                                 }
1090                                 success = minDiff;
1091                         }
1092
1093                         if (alignment != NULL) {  delete alignment;  }
1094
1095                 }
1096
1097                 return success;
1098
1099         }
1100         catch(exception& e) {
1101                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
1102                 exit(1);
1103         }
1104 }
1105
1106 //***************************************************************************************************************
1107
1108 bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
1109         try {
1110                 string rawSequence = seq.getUnaligned();
1111                 bool success = 0;       //guilty until proven innocent
1112
1113                 for(int i=0;i<numRPrimers;i++){
1114                         string oligo = revPrimer[i];
1115
1116                         if(rawSequence.length() < oligo.length()){
1117                                 success = 0;
1118                                 break;
1119                         }
1120
1121                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
1122                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
1123                                 if(qual.getName() != ""){
1124                                         qual.trimQScores(-1, rawSequence.length()-oligo.length());
1125                                 }
1126                                 success = 1;
1127                                 break;
1128                         }
1129                 }
1130                 return success;
1131
1132         }
1133         catch(exception& e) {
1134                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
1135                 exit(1);
1136         }
1137 }
1138
1139 //***************************************************************************************************************
1140
1141 bool TrimSeqsCommand::cullLength(Sequence& seq){
1142         try {
1143
1144                 int length = seq.getNumBases();
1145                 bool success = 0;       //guilty until proven innocent
1146
1147                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
1148                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
1149                 else                                                                                            {       success = 0;    }
1150
1151                 return success;
1152
1153         }
1154         catch(exception& e) {
1155                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1156                 exit(1);
1157         }
1158
1159 }
1160
1161 //***************************************************************************************************************
1162
1163 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1164         try {
1165                 int longHomoP = seq.getLongHomoPolymer();
1166                 bool success = 0;       //guilty until proven innocent
1167
1168                 if(longHomoP <= maxHomoP){      success = 1;    }
1169                 else                                    {       success = 0;    }
1170
1171                 return success;
1172         }
1173         catch(exception& e) {
1174                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1175                 exit(1);
1176         }
1177
1178 }
1179
1180 //***************************************************************************************************************
1181
1182 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1183         try {
1184                 int numNs = seq.getAmbigBases();
1185                 bool success = 0;       //guilty until proven innocent
1186
1187                 if(numNs <= maxAmbig)   {       success = 1;    }
1188                 else                                    {       success = 0;    }
1189
1190                 return success;
1191         }
1192         catch(exception& e) {
1193                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1194                 exit(1);
1195         }
1196
1197 }
1198
1199 //***************************************************************************************************************
1200
1201 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
1202         try {
1203                 bool success = 1;
1204                 int length = oligo.length();
1205
1206                 for(int i=0;i<length;i++){
1207
1208                         if(oligo[i] != seq[i]){
1209                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
1210                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
1211                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
1212                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
1213                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
1214                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
1215                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
1216                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
1217                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1218                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1219                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
1220                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
1221
1222                                 if(success == 0)        {       break;   }
1223                         }
1224                         else{
1225                                 success = 1;
1226                         }
1227                 }
1228
1229                 return success;
1230         }
1231         catch(exception& e) {
1232                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
1233                 exit(1);
1234         }
1235
1236 }
1237 //***************************************************************************************************************
1238
1239 int TrimSeqsCommand::countDiffs(string oligo, string seq){
1240         try {
1241
1242                 int length = oligo.length();
1243                 int countDiffs = 0;
1244
1245                 for(int i=0;i<length;i++){
1246
1247                         if(oligo[i] != seq[i]){
1248                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
1249                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
1250                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
1251                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
1252                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
1253                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
1254                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
1255                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
1256                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1257                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1258                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
1259                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
1260                         }
1261
1262                 }
1263
1264                 return countDiffs;
1265         }
1266         catch(exception& e) {
1267                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
1268                 exit(1);
1269         }
1270
1271 }
1272 //***************************************************************************************************************
1273
1274 //bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
1275 //      try {
1276 //
1277 //              string rawSequence = seq.getUnaligned();
1278 //              int seqLength = seq.getNumBases();
1279 //              bool success = 0;       //guilty until proven innocent
1280 //              string name;
1281 //
1282 //              qFile >> name;
1283 //              if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1284 //
1285 //              while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1286 //
1287 //              int score;
1288 //              int end = seqLength;
1289 //
1290 //              for(int i=0;i<seqLength;i++){
1291 //                      qFile >> score;
1292 //
1293 //                      if(score < qThreshold){
1294 //                              end = i;
1295 //                              break;
1296 //                      }
1297 //              }
1298 //              for(int i=end+1;i<seqLength;i++){
1299 //                      qFile >> score;
1300 //              }
1301 //
1302 //              seq.setUnaligned(rawSequence.substr(0,end));
1303 //
1304 //              return 1;
1305 //      }
1306 //      catch(exception& e) {
1307 //              m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1308 //              exit(1);
1309 //      }
1310 //}
1311
1312 //***************************************************************************************************************
1313
1314 //bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1315 //      try {
1316 //              string rawSequence = seq.getUnaligned();
1317 //              int seqLength = seq.getNumBases();
1318 //              bool success = 0;       //guilty until proven innocent
1319 //              string name;
1320 //
1321 //              qFile >> name;
1322 //              if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1323 //
1324 //              while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1325 //
1326 //              float score;
1327 //              float average = 0;
1328 //
1329 //              for(int i=0;i<seqLength;i++){
1330 //                      qFile >> score;
1331 //                      average += score;
1332 //              }
1333 //              average /= seqLength;
1334 //
1335 //              if(average >= qAverage) {       success = 1;    }
1336 //              else                                    {       success = 0;    }
1337 //
1338 //              return success;
1339 //      }
1340 //      catch(exception& e) {
1341 //              m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1342 //              exit(1);
1343 //      }
1344 //}
1345
1346 //***************************************************************************************************************