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 = 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 = 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 = 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 += 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(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 = 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 = 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 + getRootName(getSimpleName(fastaFile)) + "trim.fasta";
 223                 outputNames.push_back(trimSeqFile);
 224                 string scrapSeqFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.fasta";
 225                 outputNames.push_back(scrapSeqFile);
 226                 string trimQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "trim.qual";
 227                 outputNames.push_back(trimQualFile);
 228                 string scrapQualFile = outputDir + getRootName(getSimpleName(fastaFile)) + "scrap.qual";
 229                 outputNames.push_back(scrapQualFile);
 230                 string groupFile = outputDir + getRootName(getSimpleName(fastaFile)) + "groups";
 231
 232                 vector<string> fastaFileNames;
 233                 vector<string> qualFileNames;
 234                 if(oligoFile != ""){
 235                         outputNames.push_back(groupFile);
 236                         getOligos(fastaFileNames, qualFileNames);
 237                 }
 238
 239                 if(qFileName != "")     {       setLines(qFileName, qLines);    }
 240
 241
 242                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 243                                 if(processors == 1){
 244                                         ifstream inFASTA;
 245                                         int numSeqs;
 246                                         openInputFile(fastaFile, inFASTA);
 247                                         getNumSeqs(inFASTA, numSeqs);
 248                                         inFASTA.close();
 249
 250                                         lines.push_back(new linePair(0, numSeqs));
 251
 252                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[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                                         setLines(fastaFile, lines);
 265                                         if(qFileName == "")     {       qLines = lines; }
 266
 267                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
 268
 269                                         rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 270                                         rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 271                                         rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
 272
 273                                         if(qFileName != ""){
 274                                                 rename((trimQualFile + toString(processIDS[0]) + ".temp").c_str(), trimQualFile.c_str());
 275                                                 rename((scrapQualFile + toString(processIDS[0]) + ".temp").c_str(), scrapQualFile.c_str());
 276                                         }
 277
 278
 279                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 280                                                 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 281                                         }
 282                                         if(qFileName != ""){
 283                                                 for (int j = 0; j < qualFileNames.size(); j++) {
 284                                                         rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
 285                                                 }
 286                                         }
 287
 288                                         //append files
 289                                         for(int i=1;i<processors;i++){
 290                                                 appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 291                                                 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
 292                                                 appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 293                                                 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
 294
 295                                                 appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
 296                                                 remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
 297                                                 appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
 298                                                 remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
 299
 300                                                 appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 301                                                 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 302                                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 303                                                         appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 304                                                         remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 305                                                 }
 306
 307                                                 if(qFileName != ""){
 308                                                         for (int j = 0; j < qualFileNames.size(); j++) {
 309                                                                 appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
 310                                                                 remove((qualFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 311                                                         }
 312                                                 }
 313
 314
 315                                         }
 316                                 }
 317
 318                                 if (m->control_pressed) {  return 0; }
 319                 #else
 320                                 ifstream inFASTA;
 321                                 int numSeqs;
 322                                 openInputFile(fastaFile, inFASTA);
 323                                 getNumSeqs(inFASTA, numSeqs);
 324                                 inFASTA.close();
 325
 326                                 lines.push_back(new linePair(0, numSeqs));
 327
 328                                 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], lines[0]);
 329
 330                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 331                                         rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
 332                                 }
 333                                 if(qFileName != ""){
 334                                         for (int j = 0; j < qualFileNames.size(); j++) {
 335                                                 rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
 336                                         }
 337                                 }
 338
 339                                 if (m->control_pressed) {  return 0; }
 340                 #endif
 341
 342
 343                 for(int i=0;i<fastaFileNames.size();i++){
 344                         if (isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str());    }
 345                         else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
 346                         else {
 347                                 ifstream inFASTA;
 348                                 string seqName;
 349                                 openInputFile(fastaFileNames[i], inFASTA);
 350                                 ofstream outGroups;
 351                                 string outGroupFilename = outputDir + getRootName(getSimpleName(fastaFileNames[i])) + "groups";
 352                                 openOutputFile(outGroupFilename, outGroups);
 353                                 outputNames.push_back(outGroupFilename);
 354
 355                                 string thisGroup = "";
 356                                 if (i > comboStarts) {
 357                                         map<string, int>::iterator itCombo;
 358                                         for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
 359                                                 if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
 360                                         }
 361                                 }else{ thisGroup = groupVector[i]; }
 362
 363                                 while(!inFASTA.eof()){
 364                                         if(inFASTA.get() == '>'){
 365                                                 inFASTA >> seqName;
 366                                                 outGroups << seqName << '\t' << thisGroup << endl;
 367                                         }
 368                                         while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 369                                 }
 370                                 outGroups.close();
 371                                 inFASTA.close();
 372                         }
 373                 }
 374
 375                 if(qFileName != ""){
 376                         for(int i=0;i<qualFileNames.size();i++){
 377                                 if (isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str());      }
 378                                 else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
 379                                 else {
 380                                         ifstream inQual;
 381                                         string seqName;
 382                                         openInputFile(qualFileNames[i], inQual);
 383 //                                      ofstream outGroups;
 384 //
 385 //                                      string thisGroup = "";
 386 //                                      if (i > comboStarts) {
 387 //                                              map<string, int>::iterator itCombo;
 388 //                                              for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
 389 //                                                      if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
 390 //                                              }
 391 //                                      }
 392 //                                      else{ thisGroup = groupVector[i]; }
 393
 394                                         inQual.close();
 395                                 }
 396                         }
 397                 }
 398
 399
 400                 if (m->control_pressed) {
 401                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 402                         return 0;
 403                 }
 404
 405                 m->mothurOutEndLine();
 406                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 407                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 408                 m->mothurOutEndLine();
 409
 410                 return 0;
 411
 412         }
 413         catch(exception& e) {
 414                 m->errorOut(e, "TrimSeqsCommand", "execute");
 415                 exit(1);
 416         }
 417 }
 418
 419 /**************************************************************************************/
 420
 421 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) {
 422
 423         try {
 424
 425                 ofstream outFASTA;
 426                 int able = openOutputFile(trimFile, outFASTA);
 427
 428                 ofstream scrapFASTA;
 429                 openOutputFile(scrapFile, scrapFASTA);
 430
 431                 ofstream outQual;
 432                 ofstream scrapQual;
 433                 if(qFileName != ""){
 434                         openOutputFile(trimQFile, outQual);
 435                         openOutputFile(scrapQFile, scrapQual);
 436                 }
 437
 438                 ofstream outGroups;
 439                 vector<ofstream*> fastaFileNames;
 440                 vector<ofstream*> qualFileNames;
 441
 442
 443                 if (oligoFile != "") {
 444                         openOutputFile(groupFile, outGroups);
 445                         for (int i = 0; i < fastaNames.size(); i++) {
 446                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 447                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 448                                 if(qFileName != ""){
 449                                         qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 450                                 }
 451                         #else
 452                                 fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
 453                                 if(qFileName != ""){
 454                                         qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));
 455                                 }
 456                         #endif
 457                         }
 458                 }
 459
 460                 ifstream inFASTA;
 461                 openInputFile(filename, inFASTA);
 462
 463                 ifstream qFile;
 464                 if(qFileName != "")     {       openInputFile(qFileName, qFile);        }
 465
 466                 qFile.seekg(qline->start);
 467                 inFASTA.seekg(line->start);
 468
 469                 for(int i=0;i<line->num;i++){
 470
 471                         if (m->control_pressed) {
 472                                 inFASTA.close(); outFASTA.close(); scrapFASTA.close();
 473                                 if (oligoFile != "") {   outGroups.close();   }
 474
 475                                 for(int i=0;i<fastaFileNames.size();i++){  fastaFileNames[i]->close(); delete fastaFileNames[i];  }
 476
 477                                 if(qFileName != ""){
 478                                         qFile.close();
 479                                         for(int i=0;i<qualFileNames.size();i++){  qualFileNames[i]->close(); delete qualFileNames[i];  }
 480                                 }
 481                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 482
 483                                 return 0;
 484                         }
 485
 486                         int success = 1;
 487
 488                         Sequence currSeq(inFASTA);
 489                         QualityScores currQual;
 490                         if(qFileName != ""){
 491                                 currQual = QualityScores(qFile, currSeq.getNumBases());
 492                         }
 493
 494                         string origSeq = currSeq.getUnaligned();
 495                         if (origSeq != "") {
 496                                 int groupBar, groupPrime;
 497                                 string trashCode = "";
 498                                 int currentSeqsDiffs = 0;
 499
 500                                 if(qFileName != ""){
 501                                         if(qThreshold != 0)                     {       success = currQual.stripQualThreshold(currSeq, qThreshold);                     }
 502                                         else if(qAverage != 0)          {       success = currQual.cullQualAverage(currSeq, qAverage);                          }
 503                                         else if(qRollAverage != 0)      {       success = currQual.stripQualRollingAverage(currSeq, qRollAverage);      }
 504                                         else if(qWindowAverage != 0){   success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);   }
 505
 506                                         if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
 507                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 508                                         }
 509
 510                                         if(!success)                            {       trashCode += 'q';       }
 511                                 }
 512
 513                                 if(barcodes.size() != 0){
 514                                         success = stripBarcode(currSeq, currQual, groupBar);
 515                                         if(success > bdiffs)            {       trashCode += 'b';       }
 516                                         else{ currentSeqsDiffs += success;  }
 517                                 }
 518
 519                                 if(numFPrimers != 0){
 520                                         success = stripForward(currSeq, currQual, groupPrime);
 521                                         if(success > pdiffs)            {       trashCode += 'f';       }
 522                                         else{ currentSeqsDiffs += success;  }
 523                                 }
 524
 525                                 if (currentSeqsDiffs > tdiffs)  {       trashCode += 't';   }
 526
 527                                 if(numRPrimers != 0){
 528                                         success = stripReverse(currSeq, currQual);
 529                                         if(!success)                            {       trashCode += 'r';       }
 530                                 }
 531
 532                                 if(minLength > 0 || maxLength > 0){
 533                                         success = cullLength(currSeq);
 534                                         if(!success)                            {       trashCode += 'l';       }
 535                                 }
 536                                 if(maxHomoP > 0){
 537                                         success = cullHomoP(currSeq);
 538                                         if(!success)                            {       trashCode += 'h';       }
 539                                 }
 540                                 if(maxAmbig != -1){
 541                                         success = cullAmbigs(currSeq);
 542                                         if(!success)                            {       trashCode += 'n';       }
 543                                 }
 544
 545                                 if(flip){       currSeq.reverseComplement();            currQual.flipQScores(); }               // should go last
 546
 547                                 if(trashCode.length() == 0){
 548                                         currSeq.setAligned(currSeq.getUnaligned());
 549                                         currSeq.printSequence(outFASTA);
 550                                         currQual.printQScores(outQual);
 551
 552                                         if(barcodes.size() != 0){
 553                                                 string thisGroup = groupVector[groupBar];
 554                                                 int indexToFastaFile = groupBar;
 555                                                 if (primers.size() != 0){
 556                                                         //does this primer have a group
 557                                                         if (groupVector[groupPrime] != "") {
 558                                                                 thisGroup += "." + groupVector[groupPrime];
 559                                                                 indexToFastaFile = combos[thisGroup];
 560                                                         }
 561                                                 }
 562                                                 outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 563                                                 if(allFiles){
 564                                                         currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
 565
 566                                                         if(qFileName != ""){
 567                                                                 currQual.printQScores(*qualFileNames[indexToFastaFile]);
 568                                                         }
 569                                                 }
 570                                         }
 571                                 }
 572                                 else{
 573                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 574                                         currSeq.setUnaligned(origSeq);
 575                                         currSeq.setAligned(origSeq);
 576                                         currSeq.printSequence(scrapFASTA);
 577                                         currQual.printQScores(scrapQual);
 578                                 }
 579                         }
 580                         gobble(inFASTA);
 581                         gobble(qFile);
 582                 }
 583
 584                 inFASTA.close();
 585                 outFASTA.close();
 586                 scrapFASTA.close();
 587                 if (oligoFile != "") {   outGroups.close();   }
 588                 if(qFileName != "")     {       qFile.close();  scrapQual.close(); outQual.close();     }
 589
 590                 for(int i=0;i<fastaFileNames.size();i++){
 591                         fastaFileNames[i]->close();
 592                         delete fastaFileNames[i];
 593                 }
 594
 595                 if(qFileName != ""){
 596                         for(int i=0;i<qualFileNames.size();i++){
 597                                 qualFileNames[i]->close();
 598                                 delete qualFileNames[i];
 599                         }
 600                 }
 601
 602                 return 0;
 603         }
 604         catch(exception& e) {
 605                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 606                 exit(1);
 607         }
 608 }
 609
 610 /**************************************************************************************************/
 611
 612 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
 613         try {
 614 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 615                 int process = 0;
 616                 int exitCommand = 1;
 617                 processIDS.clear();
 618
 619                 //loop through and create all the processes you want
 620                 while (process != processors) {
 621                         int pid = fork();
 622
 623                         if (pid > 0) {
 624                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 625                                 process++;
 626                         }else if (pid == 0){
 627                                 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]);
 628                                 exit(0);
 629                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 630                 }
 631
 632                 //force parent to wait until all the processes are done
 633                 for (int i=0;i<processors;i++) {
 634                         int temp = processIDS[i];
 635                         wait(&temp);
 636                 }
 637
 638                 return exitCommand;
 639 #endif
 640         }
 641         catch(exception& e) {
 642                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 643                 exit(1);
 644         }
 645 }
 646
 647 /**************************************************************************************************/
 648
 649 int TrimSeqsCommand::setLines(string filename, vector<linePair*>& lines) {
 650         try {
 651
 652                 lines.clear();
 653
 654                 vector<unsigned long int> positions;
 655
 656                 ifstream inFASTA;
 657                 openInputFile(filename, inFASTA);
 658
 659                 string input;
 660                 while(!inFASTA.eof()){
 661                         input = getline(inFASTA);
 662
 663                         if (input.length() != 0) {
 664                                 if(input[0] == '>'){ unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);    }
 665                         }
 666                 }
 667                 inFASTA.close();
 668
 669                 int numFastaSeqs = positions.size();
 670
 671                 FILE * pFile;
 672                 unsigned long int size;
 673
 674                 //get num bytes in file
 675                 pFile = fopen (filename.c_str(),"rb");
 676                 if (pFile==NULL) perror ("Error opening file");
 677                 else{
 678                         fseek (pFile, 0, SEEK_END);
 679                         size=ftell (pFile);
 680                         fclose (pFile);
 681                 }
 682
 683                 int numSeqsPerProcessor = numFastaSeqs / processors;
 684
 685                 for (int i = 0; i < processors; i++) {
 686
 687                         unsigned long int startPos = positions[ i * numSeqsPerProcessor ];
 688                         if(i == processors - 1){
 689                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 690                         }else{
 691                                 unsigned long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 692                         }
 693                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 694                 }
 695
 696                 return numFastaSeqs;
 697         }
 698         catch(exception& e) {
 699                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 700                 exit(1);
 701         }
 702 }
 703 //***************************************************************************************************************
 704
 705 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
 706         try {
 707                 ifstream inOligos;
 708                 openInputFile(oligoFile, inOligos);
 709
 710                 ofstream test;
 711
 712                 string type, oligo, group;
 713                 int index=0;
 714                 //int indexPrimer = 0;
 715
 716                 while(!inOligos.eof()){
 717                         inOligos >> type;
 718
 719                         if(type[0] == '#'){
 720                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 721                         }
 722                         else{
 723                                 //make type case insensitive
 724                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
 725
 726                                 inOligos >> oligo;
 727
 728                                 for(int i=0;i<oligo.length();i++){
 729                                         oligo[i] = toupper(oligo[i]);
 730                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 731                                 }
 732
 733                                 if(type == "FORWARD"){
 734                                         group = "";
 735
 736                                         // get rest of line in case there is a primer name
 737                                         while (!inOligos.eof()) {
 738                                                 char c = inOligos.get();
 739                                                 if (c == 10 || c == 13){        break;  }
 740                                                 else if (c == 32 || c == 9){;} //space or tab
 741                                                 else {  group += c;  }
 742                                         }
 743
 744                                         //check for repeat barcodes
 745                                         map<string, int>::iterator itPrime = primers.find(oligo);
 746                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 747
 748                                         primers[oligo]=index; index++;
 749                                         groupVector.push_back(group);
 750
 751                                         if(allFiles){
 752                                                 outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 753                                                 if(qFileName != ""){
 754                                                         outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
 755                                                 }
 756                                                 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
 757                                                         filesToRemove.insert((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 758                                                         if(qFileName != ""){
 759                                                                 filesToRemove.insert((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
 760                                                         }
 761                                                 }else {
 762                                                         outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 763                                                         if(qFileName != ""){
 764                                                                 outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
 765                                                         }
 766                                                 }
 767                                         }
 768
 769                                 }
 770                                 else if(type == "REVERSE"){
 771                                         Sequence oligoRC("reverse", oligo);
 772                                         oligoRC.reverseComplement();
 773                                         revPrimer.push_back(oligoRC.getUnaligned());
 774                                 }
 775                                 else if(type == "BARCODE"){
 776                                         inOligos >> group;
 777
 778                                         //check for repeat barcodes
 779                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 780                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 781
 782                                         barcodes[oligo]=index; index++;
 783                                         groupVector.push_back(group);
 784
 785                                         if(allFiles){
 786                                                 outputNames.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 787                                                 outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + group + ".fasta"));
 788                                                 if(qFileName != ""){
 789                                                         outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
 790                                                         outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + group + ".qual"));
 791                                                 }
 792                                         }
 793                                 }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
 794                         }
 795                         gobble(inOligos);
 796                 }
 797
 798                 inOligos.close();
 799
 800                 //add in potential combos
 801                 if(allFiles){
 802                         comboStarts = outFASTAVec.size()-1;
 803                         for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
 804                                 for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
 805                                         if (groupVector[itPrime->second] != "") { //there is a group for this primer
 806                                                 outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 807                                                 outFASTAVec.push_back((outputDir + getRootName(getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 808                                                 combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
 809
 810                                                 if(qFileName != ""){
 811                                                         outQualVec.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 812                                                         outputNames.push_back((outputDir + getRootName(getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 813                                                 }
 814                                         }
 815                                 }
 816                         }
 817                 }
 818
 819                 numFPrimers = primers.size();
 820                 numRPrimers = revPrimer.size();
 821
 822         }
 823         catch(exception& e) {
 824                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 825                 exit(1);
 826         }
 827 }
 828 //***************************************************************************************************************
 829
 830 int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
 831         try {
 832
 833                 string rawSequence = seq.getUnaligned();
 834                 int success = bdiffs + 1;       //guilty until proven innocent
 835
 836                 //can you find the barcode
 837                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 838                         string oligo = it->first;
 839                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
 840                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 841                                 break;
 842                         }
 843
 844                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 845                                 group = it->second;
 846                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 847
 848                                 if(qual.getName() != ""){
 849                                         qual.trimQScores(oligo.length(), -1);
 850                                 }
 851
 852                                 success = 0;
 853                                 break;
 854                         }
 855                 }
 856
 857                 //if you found the barcode or if you don't want to allow for diffs
 858 //              cout << success;
 859                 if ((bdiffs == 0) || (success == 0)) { return success;  }
 860
 861                 else { //try aligning and see if you can find it
 862 //                      cout << endl;
 863
 864                         int maxLength = 0;
 865
 866                         Alignment* alignment;
 867                         if (barcodes.size() > 0) {
 868                                 map<string,int>::iterator it=barcodes.begin();
 869
 870                                 for(it;it!=barcodes.end();it++){
 871                                         if(it->first.length() > maxLength){
 872                                                 maxLength = it->first.length();
 873                                         }
 874                                 }
 875                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
 876
 877                         }else{ alignment = NULL; }
 878
 879                         //can you find the barcode
 880                         int minDiff = 1e6;
 881                         int minCount = 1;
 882                         int minGroup = -1;
 883                         int minPos = 0;
 884
 885                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
 886                                 string oligo = it->first;
 887 //                              int length = oligo.length();
 888
 889                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
 890                                         success = bdiffs + 10;
 891                                         break;
 892                                 }
 893
 894                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
 895                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
 896                                 oligo = alignment->getSeqAAln();
 897                                 string temp = alignment->getSeqBAln();
 898
 899                                 int alnLength = oligo.length();
 900
 901                                 for(int i=oligo.length()-1;i>=0;i--){
 902                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
 903                                 }
 904                                 oligo = oligo.substr(0,alnLength);
 905                                 temp = temp.substr(0,alnLength);
 906
 907                                 int newStart=0;
 908                                 int numDiff = countDiffs(oligo, temp);
 909
 910 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
 911
 912                                 if(numDiff < minDiff){
 913                                         minDiff = numDiff;
 914                                         minCount = 1;
 915                                         minGroup = it->second;
 916                                         minPos = 0;
 917                                         for(int i=0;i<alnLength;i++){
 918                                                 if(temp[i] != '-'){
 919                                                         minPos++;
 920                                                 }
 921                                         }
 922                                 }
 923                                 else if(numDiff == minDiff){
 924                                         minCount++;
 925                                 }
 926
 927                         }
 928
 929                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
 930                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
 931                         else{                                                                                                   //use the best match
 932                                 group = minGroup;
 933                                 seq.setUnaligned(rawSequence.substr(minPos));
 934
 935                                 if(qual.getName() != ""){
 936                                         qual.trimQScores(minPos, -1);
 937                                 }
 938                                 success = minDiff;
 939                         }
 940
 941                         if (alignment != NULL) {  delete alignment;  }
 942
 943                 }
 944 //              cout << success << endl;
 945
 946                 return success;
 947
 948         }
 949         catch(exception& e) {
 950                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
 951                 exit(1);
 952         }
 953
 954 }
 955
 956 //***************************************************************************************************************
 957
 958 int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
 959         try {
 960                 string rawSequence = seq.getUnaligned();
 961                 int success = pdiffs + 1;       //guilty until proven innocent
 962
 963                 //can you find the primer
 964                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
 965                         string oligo = it->first;
 966                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
 967                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
 968                                 break;
 969                         }
 970
 971                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
 972                                 group = it->second;
 973                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
 974                                 if(qual.getName() != ""){
 975                                         qual.trimQScores(oligo.length(), -1);
 976
 977                                 }
 978                                 success = 0;
 979                                 break;
 980                         }
 981                 }
 982
 983                 //if you found the barcode or if you don't want to allow for diffs
 984 //              cout << success;
 985                 if ((pdiffs == 0) || (success == 0)) { return success;  }
 986
 987                 else { //try aligning and see if you can find it
 988 //                      cout << endl;
 989
 990                         int maxLength = 0;
 991
 992                         Alignment* alignment;
 993                         if (primers.size() > 0) {
 994                                 map<string,int>::iterator it=primers.begin();
 995
 996                                 for(it;it!=primers.end();it++){
 997                                         if(it->first.length() > maxLength){
 998                                                 maxLength = it->first.length();
 999                                         }
1000                                 }
1001                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
1002
1003                         }else{ alignment = NULL; }
1004
1005                         //can you find the barcode
1006                         int minDiff = 1e6;
1007                         int minCount = 1;
1008                         int minGroup = -1;
1009                         int minPos = 0;
1010
1011                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1012                                 string oligo = it->first;
1013 //                              int length = oligo.length();
1014
1015                                 if(rawSequence.length() < maxLength){
1016                                         success = pdiffs + 100;
1017                                         break;
1018                                 }
1019
1020                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1021                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
1022                                 oligo = alignment->getSeqAAln();
1023                                 string temp = alignment->getSeqBAln();
1024
1025                                 int alnLength = oligo.length();
1026
1027                                 for(int i=oligo.length()-1;i>=0;i--){
1028                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1029                                 }
1030                                 oligo = oligo.substr(0,alnLength);
1031                                 temp = temp.substr(0,alnLength);
1032
1033                                 int newStart=0;
1034                                 int numDiff = countDiffs(oligo, temp);
1035
1036 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1037
1038                                 if(numDiff < minDiff){
1039                                         minDiff = numDiff;
1040                                         minCount = 1;
1041                                         minGroup = it->second;
1042                                         minPos = 0;
1043                                         for(int i=0;i<alnLength;i++){
1044                                                 if(temp[i] != '-'){
1045                                                         minPos++;
1046                                                 }
1047                                         }
1048                                 }
1049                                 else if(numDiff == minDiff){
1050                                         minCount++;
1051                                 }
1052
1053                         }
1054
1055                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
1056                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
1057                         else{                                                                                                   //use the best match
1058                                 group = minGroup;
1059                                 seq.setUnaligned(rawSequence.substr(minPos));
1060                                 if(qual.getName() != ""){
1061                                         qual.trimQScores(minPos, -1);
1062                                 }
1063                                 success = minDiff;
1064                         }
1065
1066                         if (alignment != NULL) {  delete alignment;  }
1067
1068                 }
1069
1070                 return success;
1071
1072         }
1073         catch(exception& e) {
1074                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
1075                 exit(1);
1076         }
1077 }
1078
1079 //***************************************************************************************************************
1080
1081 bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
1082         try {
1083                 string rawSequence = seq.getUnaligned();
1084                 bool success = 0;       //guilty until proven innocent
1085
1086                 for(int i=0;i<numRPrimers;i++){
1087                         string oligo = revPrimer[i];
1088
1089                         if(rawSequence.length() < oligo.length()){
1090                                 success = 0;
1091                                 break;
1092                         }
1093
1094                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
1095                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
1096                                 if(qual.getName() != ""){
1097                                         qual.trimQScores(-1, rawSequence.length()-oligo.length());
1098                                 }
1099                                 success = 1;
1100                                 break;
1101                         }
1102                 }
1103                 return success;
1104
1105         }
1106         catch(exception& e) {
1107                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
1108                 exit(1);
1109         }
1110 }
1111
1112 //***************************************************************************************************************
1113
1114 bool TrimSeqsCommand::cullLength(Sequence& seq){
1115         try {
1116
1117                 int length = seq.getNumBases();
1118                 bool success = 0;       //guilty until proven innocent
1119
1120                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
1121                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
1122                 else                                                                                            {       success = 0;    }
1123
1124                 return success;
1125
1126         }
1127         catch(exception& e) {
1128                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1129                 exit(1);
1130         }
1131
1132 }
1133
1134 //***************************************************************************************************************
1135
1136 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1137         try {
1138                 int longHomoP = seq.getLongHomoPolymer();
1139                 bool success = 0;       //guilty until proven innocent
1140
1141                 if(longHomoP <= maxHomoP){      success = 1;    }
1142                 else                                    {       success = 0;    }
1143
1144                 return success;
1145         }
1146         catch(exception& e) {
1147                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1148                 exit(1);
1149         }
1150
1151 }
1152
1153 //***************************************************************************************************************
1154
1155 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1156         try {
1157                 int numNs = seq.getAmbigBases();
1158                 bool success = 0;       //guilty until proven innocent
1159
1160                 if(numNs <= maxAmbig)   {       success = 1;    }
1161                 else                                    {       success = 0;    }
1162
1163                 return success;
1164         }
1165         catch(exception& e) {
1166                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1167                 exit(1);
1168         }
1169
1170 }
1171
1172 //***************************************************************************************************************
1173
1174 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
1175         try {
1176                 bool success = 1;
1177                 int length = oligo.length();
1178
1179                 for(int i=0;i<length;i++){
1180
1181                         if(oligo[i] != seq[i]){
1182                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
1183                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
1184                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
1185                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
1186                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
1187                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
1188                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
1189                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
1190                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1191                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1192                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
1193                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
1194
1195                                 if(success == 0)        {       break;   }
1196                         }
1197                         else{
1198                                 success = 1;
1199                         }
1200                 }
1201
1202                 return success;
1203         }
1204         catch(exception& e) {
1205                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
1206                 exit(1);
1207         }
1208
1209 }
1210 //***************************************************************************************************************
1211
1212 int TrimSeqsCommand::countDiffs(string oligo, string seq){
1213         try {
1214
1215                 int length = oligo.length();
1216                 int countDiffs = 0;
1217
1218                 for(int i=0;i<length;i++){
1219
1220                         if(oligo[i] != seq[i]){
1221                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
1222                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
1223                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
1224                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
1225                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
1226                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
1227                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
1228                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
1229                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1230                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1231                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
1232                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
1233
1234                         }
1235                 }
1236
1237                 return countDiffs;
1238         }
1239         catch(exception& e) {
1240                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
1241                 exit(1);
1242         }
1243
1244 }
1245 //***************************************************************************************************************
1246
1247 //bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
1248 //      try {
1249 //
1250 //              string rawSequence = seq.getUnaligned();
1251 //              int seqLength = seq.getNumBases();
1252 //              bool success = 0;       //guilty until proven innocent
1253 //              string name;
1254 //
1255 //              qFile >> name;
1256 //              if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1257 //
1258 //              while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1259 //
1260 //              int score;
1261 //              int end = seqLength;
1262 //
1263 //              for(int i=0;i<seqLength;i++){
1264 //                      qFile >> score;
1265 //
1266 //                      if(score < qThreshold){
1267 //                              end = i;
1268 //                              break;
1269 //                      }
1270 //              }
1271 //              for(int i=end+1;i<seqLength;i++){
1272 //                      qFile >> score;
1273 //              }
1274 //
1275 //              seq.setUnaligned(rawSequence.substr(0,end));
1276 //
1277 //              return 1;
1278 //      }
1279 //      catch(exception& e) {
1280 //              m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1281 //              exit(1);
1282 //      }
1283 //}
1284
1285 //***************************************************************************************************************
1286
1287 //bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1288 //      try {
1289 //              string rawSequence = seq.getUnaligned();
1290 //              int seqLength = seq.getNumBases();
1291 //              bool success = 0;       //guilty until proven innocent
1292 //              string name;
1293 //
1294 //              qFile >> name;
1295 //              if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1296 //
1297 //              while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1298 //
1299 //              float score;
1300 //              float average = 0;
1301 //
1302 //              for(int i=0;i<seqLength;i++){
1303 //                      qFile >> score;
1304 //                      average += score;
1305 //              }
1306 //              average /= seqLength;
1307 //
1308 //              if(average >= qAverage) {       success = 1;    }
1309 //              else                                    {       success = 0;    }
1310 //
1311 //              return success;
1312 //      }
1313 //      catch(exception& e) {
1314 //              m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1315 //              exit(1);
1316 //      }
1317 //}
1318
1319 //***************************************************************************************************************