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 vector<string> TrimSeqsCommand::getValidParameters(){
  16         try {
  17                 string Array[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
  18                                                                         "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
  19                                                                         "keepfirst", "removelast",
  20                                                                         "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  21                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  22                 return myArray;
  23         }
  24         catch(exception& e) {
  25                 m->errorOut(e, "TrimSeqsCommand", "getValidParameters");
  26                 exit(1);
  27         }
  28 }
  29
  30 //**********************************************************************************************************************
  31
  32 TrimSeqsCommand::TrimSeqsCommand(){
  33         try {
  34                 abort = true;
  35                 //initialize outputTypes
  36                 vector<string> tempOutNames;
  37                 outputTypes["fasta"] = tempOutNames;
  38                 outputTypes["qual"] = tempOutNames;
  39                 outputTypes["group"] = tempOutNames;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
  43                 exit(1);
  44         }
  45 }
  46
  47 //**********************************************************************************************************************
  48
  49 vector<string> TrimSeqsCommand::getRequiredParameters(){
  50         try {
  51                 string Array[] =  {"fasta"};
  52                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  53                 return myArray;
  54         }
  55         catch(exception& e) {
  56                 m->errorOut(e, "TrimSeqsCommand", "getRequiredParameters");
  57                 exit(1);
  58         }
  59 }
  60
  61 //**********************************************************************************************************************
  62
  63 vector<string> TrimSeqsCommand::getRequiredFiles(){
  64         try {
  65                 vector<string> myArray;
  66                 return myArray;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
  70                 exit(1);
  71         }
  72 }
  73
  74 //***************************************************************************************************************
  75
  76 TrimSeqsCommand::TrimSeqsCommand(string option)  {
  77         try {
  78
  79                 abort = false;
  80                 comboStarts = 0;
  81
  82                 //allow user to run help
  83                 if(option == "help") { help(); abort = true; }
  84
  85                 else {
  86                         //valid paramters for this command
  87                         string AlignArray[] =  {        "fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
  88                                                                 "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
  89                                                                 "keepfirst", "removelast",
  90                                                                 "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  91
  92                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  93
  94                         OptionParser parser(option);
  95                         map<string,string> parameters = parser.getParameters();
  96
  97                         ValidParameters validParameter;
  98                         map<string,string>::iterator it;
  99
 100                         //check to make sure all parameters are valid for command
 101                         for (it = parameters.begin(); it != parameters.end(); it++) {
 102                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 103                         }
 104
 105                         //initialize outputTypes
 106                         vector<string> tempOutNames;
 107                         outputTypes["fasta"] = tempOutNames;
 108                         outputTypes["qual"] = tempOutNames;
 109                         outputTypes["group"] = tempOutNames;
 110
 111                         //if the user changes the input directory command factory will send this info to us in the output parameter
 112                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 113                         if (inputDir == "not found"){   inputDir = "";          }
 114                         else {
 115                                 string path;
 116                                 it = parameters.find("fasta");
 117                                 //user has given a template file
 118                                 if(it != parameters.end()){
 119                                         path = m->hasPath(it->second);
 120                                         //if the user has not given a path then, add inputdir. else leave path alone.
 121                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 122                                 }
 123
 124                                 it = parameters.find("oligos");
 125                                 //user has given a template file
 126                                 if(it != parameters.end()){
 127                                         path = m->hasPath(it->second);
 128                                         //if the user has not given a path then, add inputdir. else leave path alone.
 129                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 130                                 }
 131
 132                                 it = parameters.find("qfile");
 133                                 //user has given a template file
 134                                 if(it != parameters.end()){
 135                                         path = m->hasPath(it->second);
 136                                         //if the user has not given a path then, add inputdir. else leave path alone.
 137                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 138                                 }
 139
 140                                 it = parameters.find("group");
 141                                 //user has given a template file
 142                                 if(it != parameters.end()){
 143                                         path = m->hasPath(it->second);
 144                                         //if the user has not given a path then, add inputdir. else leave path alone.
 145                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 146                                 }
 147                         }
 148
 149
 150                         //check for required parameters
 151                         fastaFile = validParameter.validFile(parameters, "fasta", true);
 152                         if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the trim.seqs command."); m->mothurOutEndLine(); abort = true; }
 153                         else if (fastaFile == "not open") { abort = true; }
 154
 155                         //if the user changes the output directory command factory will send this info to us in the output parameter
 156                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 157                                 outputDir = "";
 158                                 outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
 159                         }
 160
 161
 162                         //check for optional parameter and set defaults
 163                         // ...at some point should added some additional type checking...
 164                         string temp;
 165                         temp = validParameter.validFile(parameters, "flip", false);
 166                         if (temp == "not found"){       flip = 0;       }
 167                         else if(m->isTrue(temp))        {       flip = 1;       }
 168
 169                         temp = validParameter.validFile(parameters, "oligos", true);
 170                         if (temp == "not found"){       oligoFile = "";         }
 171                         else if(temp == "not open"){    abort = true;   }
 172                         else                                    {       oligoFile = temp;               }
 173
 174                         temp = validParameter.validFile(parameters, "group", true);
 175                         if (temp == "not found"){       groupfile = "";         }
 176                         else if(temp == "not open"){    abort = true;   }
 177                         else                                    {       groupfile = temp;               }
 178
 179                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 180                         convert(temp, maxAmbig);
 181
 182                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
 183                         convert(temp, maxHomoP);
 184
 185                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
 186                         convert(temp, minLength);
 187
 188                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
 189                         convert(temp, maxLength);
 190
 191                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
 192                         convert(temp, bdiffs);
 193
 194                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 195                         convert(temp, pdiffs);
 196
 197                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 198                         convert(temp, tdiffs);
 199
 200                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 201
 202                         temp = validParameter.validFile(parameters, "qfile", true);
 203                         if (temp == "not found")        {       qFileName = "";         }
 204                         else if(temp == "not open")     {       abort = true;           }
 205                         else                                            {       qFileName = temp;       }
 206
 207                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 208                         convert(temp, qThreshold);
 209
 210                         temp = validParameter.validFile(parameters, "qtrim", false);            if (temp == "not found") { temp = "F"; }
 211                         qtrim = m->isTrue(temp);
 212
 213                         temp = validParameter.validFile(parameters, "rollaverage", false);      if (temp == "not found") { temp = "0"; }
 214                         convert(temp, qRollAverage);
 215
 216                         temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
 217                         convert(temp, qWindowAverage);
 218
 219                         temp = validParameter.validFile(parameters, "qwindowsize", false);      if (temp == "not found") { temp = "50"; }
 220                         convert(temp, qWindowSize);
 221
 222                         temp = validParameter.validFile(parameters, "qstepsize", false);        if (temp == "not found") { temp = "1"; }
 223                         convert(temp, qWindowStep);
 224
 225                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 226                         convert(temp, qAverage);
 227
 228                         temp = validParameter.validFile(parameters, "keepfirst", false);        if (temp == "not found") { temp = "0"; }
 229                         convert(temp, keepFirst);
 230
 231                         temp = validParameter.validFile(parameters, "removelast", false);       if (temp == "not found") { temp = "0"; }
 232                         convert(temp, removeLast);
 233
 234                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 235                         allFiles = m->isTrue(temp);
 236
 237                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found") { temp = "1"; }
 238                         convert(temp, processors);
 239
 240                         if ((oligoFile != "") && (groupfile != "")) {
 241                                 m->mothurOut("You given both a oligos file and a groupfile, only one is allowed."); m->mothurOutEndLine(); abort = true;
 242                         }
 243
 244
 245                         if(allFiles && (oligoFile == "") && (groupfile == "")){
 246                                 m->mothurOut("You selected allfiles, but didn't enter an oligos or group file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 247                         }
 248                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 249                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 250                                 qAverage=0;
 251                                 qThreshold=0;
 252                         }
 253                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 254                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 255                                 abort = true;
 256                         }
 257                 }
 258
 259         }
 260         catch(exception& e) {
 261                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 262                 exit(1);
 263         }
 264 }
 265
 266 //**********************************************************************************************************************
 267
 268 void TrimSeqsCommand::help(){
 269         try {
 270                 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 271                 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, group, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 272                 m->mothurOut("The fasta parameter is required.\n");
 273                 m->mothurOut("The group parameter allows you to enter a group file for your fasta file.\n");
 274                 m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
 275                 m->mothurOut("The oligos parameter .... The default is "".\n");
 276                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 277                 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 278                 m->mothurOut("The minlength parameter .... The default is 0.\n");
 279                 m->mothurOut("The maxlength parameter .... The default is 0.\n");
 280                 m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
 281                 m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
 282                 m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 283                 m->mothurOut("The qfile parameter .....\n");
 284                 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 285                 m->mothurOut("The qaverage parameter .... The default is 0.\n");
 286                 m->mothurOut("The allfiles parameter .... The default is F.\n");
 287                 m->mothurOut("The qtrim parameter .... The default is F.\n");
 288                 m->mothurOut("The trim.seqs command should be in the following format: \n");
 289                 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 290                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 291                 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 292                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 293                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 294
 295         }
 296         catch(exception& e) {
 297                 m->errorOut(e, "TrimSeqsCommand", "help");
 298                 exit(1);
 299         }
 300 }
 301
 302
 303 //***************************************************************************************************************
 304
 305 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 306
 307 //***************************************************************************************************************
 308
 309 int TrimSeqsCommand::execute(){
 310         try{
 311
 312                 if (abort == true) { return 0; }
 313
 314                 numFPrimers = 0;  //this needs to be initialized
 315                 numRPrimers = 0;
 316                 vector<string> fastaFileNames;
 317                 vector<string> qualFileNames;
 318
 319                 string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
 320                 outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
 321                 string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
 322                 outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
 323                 string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
 324                 string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
 325                 if (qFileName != "") {  outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile);  outputTypes["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
 326                 string groupFile = "";
 327                 if (groupfile == "") { groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups"; }
 328                 else{
 329                         groupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "trim.groups";
 330                         outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
 331                         groupMap = new GroupMap(groupfile);
 332                         groupMap->readMap();
 333
 334                         if(allFiles){
 335                                 for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {
 336                                         groupToIndex[groupMap->namesOfGroups[i]] = i;
 337                                         groupVector.push_back(groupMap->namesOfGroups[i]);
 338                                         fastaFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) +  groupMap->namesOfGroups[i] + ".fasta"));
 339
 340                                         //we append later, so we want to clear file
 341                                         ofstream outRemove;
 342                                         m->openOutputFile(fastaFileNames[i], outRemove);
 343                                         outRemove.close();
 344                                         if(qFileName != ""){
 345                                                 qualFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) +  groupMap->namesOfGroups[i] + ".qual"));
 346                                                 ofstream outRemove2;
 347                                                 m->openOutputFile(qualFileNames[i], outRemove2);
 348                                                 outRemove2.close();
 349                                         }
 350                                 }
 351                         }
 352                         comboStarts = fastaFileNames.size()-1;
 353                 }
 354
 355                 if(oligoFile != ""){
 356                         outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
 357                         getOligos(fastaFileNames, qualFileNames);
 358                 }
 359
 360                 vector<unsigned long int> fastaFilePos;
 361                 vector<unsigned long int> qFilePos;
 362
 363                 setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
 364
 365                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 366                         lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
 367                         if (qFileName != "") {  qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)]));  }
 368                 }
 369                 if(qFileName == "")     {       qLines = lines; } //files with duds
 370
 371                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 372                                 if(processors == 1){
 373                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 374                                 }else{
 375                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
 376                                 }
 377                 #else
 378                                 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 379                 #endif
 380
 381                 if (m->control_pressed) {  return 0; }
 382
 383                 set<string> blanks;
 384                 for(int i=0;i<fastaFileNames.size();i++){
 385                         if (m->isBlank(fastaFileNames[i])) {   blanks.insert(fastaFileNames[i]);        }
 386                         else if (filesToRemove.count(fastaFileNames[i]) > 0) {  remove(fastaFileNames[i].c_str()); }
 387                         else {
 388                                 ifstream inFASTA;
 389                                 string seqName;
 390                                 m->openInputFile(fastaFileNames[i], inFASTA);
 391                                 ofstream outGroups;
 392                                 string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
 393
 394                                 //if the fastafile is on the blanks list then the groups file should be as well
 395                                 if (blanks.count(fastaFileNames[i]) != 0) { blanks.insert(outGroupFilename); }
 396
 397                                 m->openOutputFile(outGroupFilename, outGroups);
 398                                 outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
 399
 400                                 string thisGroup = "";
 401                                 if (i > comboStarts) {
 402                                         map<string, int>::iterator itCombo;
 403                                         for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
 404                                                 if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
 405                                         }
 406                                 }else{ thisGroup = groupVector[i]; }
 407
 408                                 while(!inFASTA.eof()){
 409                                         if(inFASTA.get() == '>'){
 410                                                 inFASTA >> seqName;
 411                                                 outGroups << seqName << '\t' << thisGroup << endl;
 412                                         }
 413                                         while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 414                                 }
 415                                 outGroups.close();
 416                                 inFASTA.close();
 417                         }
 418                 }
 419
 420                 for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) {  remove((*(itBlanks)).c_str()); }
 421
 422                 blanks.clear();
 423                 if(qFileName != ""){
 424                         for(int i=0;i<qualFileNames.size();i++){
 425                                 if (m->isBlank(qualFileNames[i])) {  blanks.insert(qualFileNames[i]);   }
 426                                 else if (filesToRemove.count(qualFileNames[i]) > 0) {  remove(qualFileNames[i].c_str()); }
 427                         }
 428                 }
 429
 430                 for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) {  remove((*(itBlanks)).c_str()); }
 431
 432                 if (m->control_pressed) {
 433                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 434                         return 0;
 435                 }
 436
 437                 m->mothurOutEndLine();
 438                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 439                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 440                 m->mothurOutEndLine();
 441
 442                 return 0;
 443
 444         }
 445         catch(exception& e) {
 446                 m->errorOut(e, "TrimSeqsCommand", "execute");
 447                 exit(1);
 448         }
 449 }
 450
 451 /**************************************************************************************/
 452
 453 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) {
 454
 455         try {
 456
 457                 ofstream outFASTA;
 458                 m->openOutputFile(trimFile, outFASTA);
 459
 460                 ofstream scrapFASTA;
 461                 m->openOutputFile(scrapFile, scrapFASTA);
 462
 463                 ofstream outQual;
 464                 ofstream scrapQual;
 465                 if(qFileName != ""){
 466                         m->openOutputFile(trimQFile, outQual);
 467                         m->openOutputFile(scrapQFile, scrapQual);
 468                 }
 469
 470                 ofstream outGroups;
 471
 472                 if (oligoFile != "") {
 473                         m->openOutputFile(groupFile, outGroups);
 474                 }
 475
 476                 ifstream inFASTA;
 477                 m->openInputFile(filename, inFASTA);
 478                 inFASTA.seekg(line->start);
 479
 480                 ifstream qFile;
 481                 if(qFileName != "")     {       m->openInputFile(qFileName, qFile);     qFile.seekg(qline->start);  }
 482
 483
 484                 for (int i = 0; i < fastaNames.size(); i++) { //clears old file
 485                         ofstream temp;
 486                         m->openOutputFile(fastaNames[i], temp);
 487                         temp.close();
 488                 }
 489                 for (int i = 0; i < qualNames.size(); i++) { //clears old file
 490                         ofstream temp;
 491                         m->openOutputFile(qualNames[i], temp);
 492                         temp.close();
 493                 }
 494
 495
 496                 bool done = false;
 497                 int count = 0;
 498
 499                 while (!done) {
 500
 501                         if (m->control_pressed) {
 502                                 inFASTA.close(); outFASTA.close(); scrapFASTA.close();
 503                                 if (oligoFile != "") {   outGroups.close();   }
 504
 505                                 if(qFileName != ""){
 506                                         qFile.close();
 507                                 }
 508                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 509
 510                                 return 0;
 511                         }
 512
 513                         int success = 1;
 514
 515
 516                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 517
 518                         QualityScores currQual;
 519                         if(qFileName != ""){
 520                                 currQual = QualityScores(qFile, currSeq.getNumBases());  m->gobble(qFile);
 521                         }
 522
 523                         string origSeq = currSeq.getUnaligned();
 524                         if (origSeq != "") {
 525                                 int groupBar, groupPrime;
 526                                 string trashCode = "";
 527                                 int currentSeqsDiffs = 0;
 528
 529                                 if(barcodes.size() != 0){
 530                                         success = stripBarcode(currSeq, currQual, groupBar);
 531                                         if(success > bdiffs)            {       trashCode += 'b';       }
 532                                         else{ currentSeqsDiffs += success;  }
 533                                 }
 534
 535                                 if(numFPrimers != 0){
 536                                         success = stripForward(currSeq, currQual, groupPrime);
 537                                         if(success > pdiffs)            {       trashCode += 'f';       }
 538                                         else{ currentSeqsDiffs += success;  }
 539                                 }
 540
 541                                 if (currentSeqsDiffs > tdiffs)  {       trashCode += 't';   }
 542
 543                                 if(numRPrimers != 0){
 544                                         success = stripReverse(currSeq, currQual);
 545                                         if(!success)                            {       trashCode += 'r';       }
 546                                 }
 547
 548                                 if(keepFirst != 0){
 549                                         success = keepFirstTrim(currSeq, currQual);
 550                                 }
 551
 552                                 if(removeLast != 0){
 553                                         success = removeLastTrim(currSeq, currQual);
 554                                         if(!success)                            {       trashCode += 'l';       }
 555                                 }
 556
 557
 558                                 if(qFileName != ""){
 559
 560                                         if(qThreshold != 0)                     {       success = currQual.stripQualThreshold(currSeq, qThreshold);                     }
 561                                         else if(qAverage != 0)          {       success = currQual.cullQualAverage(currSeq, qAverage);                          }
 562                                         else if(qRollAverage != 0)      {       success = currQual.stripQualRollingAverage(currSeq, qRollAverage);      }
 563                                         else if(qWindowAverage != 0){   success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);   }
 564                                         else                                            {       success = 1;                            }
 565
 566 //                                      if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
 567 //                                              success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 568 //                                      }
 569
 570                                         if(!success)                            {       trashCode += 'q';       }
 571                                 }
 572
 573                                 if(minLength > 0 || maxLength > 0){
 574                                         success = cullLength(currSeq);
 575                                         if(!success)                            {       trashCode += 'l';       }
 576                                 }
 577                                 if(maxHomoP > 0){
 578                                         success = cullHomoP(currSeq);
 579                                         if(!success)                            {       trashCode += 'h';       }
 580                                 }
 581                                 if(maxAmbig != -1){
 582                                         success = cullAmbigs(currSeq);
 583                                         if(!success)                            {       trashCode += 'n';       }
 584                                 }
 585
 586                                 if(flip){               // should go last
 587                                         currSeq.reverseComplement();
 588                                         currQual.flipQScores();
 589                                 }
 590
 591                                 if(trashCode.length() == 0){
 592                                         currSeq.setAligned(currSeq.getUnaligned());
 593                                         currSeq.printSequence(outFASTA);
 594                                         currQual.printQScores(outQual);
 595
 596                                         if(barcodes.size() != 0){
 597                                                 string thisGroup = groupVector[groupBar];
 598                                                 int indexToFastaFile = groupBar;
 599                                                 if (primers.size() != 0){
 600                                                         //does this primer have a group
 601                                                         if (groupVector[groupPrime] != "") {
 602                                                                 thisGroup += "." + groupVector[groupPrime];
 603                                                                 indexToFastaFile = combos[thisGroup];
 604                                                         }
 605                                                 }
 606                                                 outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 607                                                 if(allFiles){
 608                                                         ofstream outTemp;
 609                                                         m->openOutputFileAppend(fastaNames[indexToFastaFile], outTemp);
 610                                                         //currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
 611                                                         currSeq.printSequence(outTemp);
 612                                                         outTemp.close();
 613
 614                                                         if(qFileName != ""){
 615                                                                 //currQual.printQScores(*qualFileNames[indexToFastaFile]);
 616                                                                 ofstream outTemp2;
 617                                                                 m->openOutputFileAppend(qualNames[indexToFastaFile], outTemp2);
 618                                                                 currQual.printQScores(outTemp2);
 619                                                                 outTemp2.close();
 620                                                         }
 621                                                 }
 622                                         }
 623
 624                                         if (groupfile != "") {
 625                                                 string thisGroup = groupMap->getGroup(currSeq.getName());
 626
 627                                                 if (thisGroup != "not found") {
 628                                                         outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 629                                                         if (allFiles) {
 630                                                                 ofstream outTemp;
 631                                                                 m->openOutputFileAppend(fastaNames[groupToIndex[thisGroup]], outTemp);
 632                                                                 currSeq.printSequence(outTemp);
 633                                                                 outTemp.close();
 634                                                                 if(qFileName != ""){
 635                                                                         ofstream outTemp2;
 636                                                                         m->openOutputFileAppend(qualNames[groupToIndex[thisGroup]], outTemp2);
 637                                                                         currQual.printQScores(outTemp2);
 638                                                                         outTemp2.close();
 639                                                                 }
 640                                                         }
 641                                                 }else{
 642                                                         m->mothurOut(currSeq.getName() + " is not in your groupfile, adding to group XXX."); m->mothurOutEndLine();
 643                                                         outGroups << currSeq.getName() << '\t' << "XXX" << endl;
 644                                                         if (allFiles) {
 645                                                                 m->mothurOut("[ERROR]: " + currSeq.getName() + " will not be added to any .group.fasta or .group.qual file."); m->mothurOutEndLine();
 646                                                         }
 647                                                 }
 648                                         }
 649                                 }
 650                                 else{
 651                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 652                                         currSeq.setUnaligned(origSeq);
 653                                         currSeq.setAligned(origSeq);
 654                                         currSeq.printSequence(scrapFASTA);
 655                                         currQual.printQScores(scrapQual);
 656                                 }
 657                                 count++;
 658                         }
 659
 660                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 661                                 unsigned long int pos = inFASTA.tellg();
 662                                 if ((pos == -1) || (pos >= line->end)) { break; }
 663                         #else
 664                                 if (inFASTA.eof()) { break; }
 665                         #endif
 666
 667                         //report progress
 668                         if((count) % 1000 == 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 669
 670                 }
 671                 //report progress
 672                 if((count) % 1000 != 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 673
 674
 675                 inFASTA.close();
 676                 outFASTA.close();
 677                 scrapFASTA.close();
 678                 if (oligoFile != "") {   outGroups.close();   }
 679                 if(qFileName != "")     {       qFile.close();  scrapQual.close(); outQual.close();     }
 680
 681                 return count;
 682         }
 683         catch(exception& e) {
 684                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 685                 exit(1);
 686         }
 687 }
 688
 689 /**************************************************************************************************/
 690
 691 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
 692         try {
 693 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 694                 int process = 1;
 695                 int exitCommand = 1;
 696                 processIDS.clear();
 697
 698                 //loop through and create all the processes you want
 699                 while (process != processors) {
 700                         int pid = fork();
 701
 702                         if (pid > 0) {
 703                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 704                                 process++;
 705                         }else if (pid == 0){
 706                                 for (int i = 0; i < fastaNames.size(); i++) {
 707                                         fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
 708                                         //clear old file if it exists
 709                                         ofstream temp;
 710                                         m->openOutputFile(fastaNames[i], temp);
 711                                         temp.close();
 712                                         if(qFileName != ""){
 713                                                 qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
 714                                                 //clear old file if it exists
 715                                                 ofstream temp2;
 716                                                 m->openOutputFile(qualNames[i], temp2);
 717                                                 temp2.close();
 718                                         }
 719                                 }
 720
 721                                 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]);
 722                                 exit(0);
 723                         }else {
 724                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 725                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 726                                 exit(0);
 727                         }
 728                 }
 729
 730                 //parent do my part
 731                 for (int i = 0; i < fastaNames.size(); i++) {
 732                         //clear old file if it exists
 733                         ofstream temp;
 734                         m->openOutputFile(fastaNames[i], temp);
 735                         temp.close();
 736                         if(qFileName != ""){
 737                                 //clear old file if it exists
 738                                 ofstream temp2;
 739                                 m->openOutputFile(qualNames[i], temp2);
 740                                 temp2.close();
 741                         }
 742                 }
 743
 744                 driverCreateTrim(filename, qFileName, trimFile, scrapFile, trimQFile, scrapQFile, groupFile, fastaNames, qualNames, lines[0], qLines[0]);
 745
 746
 747                 //force parent to wait until all the processes are done
 748                 for (int i=0;i<processIDS.size();i++) {
 749                         int temp = processIDS[i];
 750                         wait(&temp);
 751                 }
 752
 753                 //append files
 754                 for(int i=0;i<processIDS.size();i++){
 755
 756                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 757
 758                         m->appendFiles((trimFile + toString(processIDS[i]) + ".temp"), trimFile);
 759                         remove((trimFile + toString(processIDS[i]) + ".temp").c_str());
 760                         m->appendFiles((scrapFile + toString(processIDS[i]) + ".temp"), scrapFile);
 761                         remove((scrapFile + toString(processIDS[i]) + ".temp").c_str());
 762
 763                         m->mothurOut("Done with fasta files"); m->mothurOutEndLine();
 764
 765                         if(qFileName != ""){
 766                                 m->appendFiles((trimQFile + toString(processIDS[i]) + ".temp"), trimQFile);
 767                                 remove((trimQFile + toString(processIDS[i]) + ".temp").c_str());
 768                                 m->appendFiles((scrapQFile + toString(processIDS[i]) + ".temp"), scrapQFile);
 769                                 remove((scrapQFile + toString(processIDS[i]) + ".temp").c_str());
 770
 771                                 m->mothurOut("Done with quality files"); m->mothurOutEndLine();
 772                         }
 773
 774                         m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 775                         remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 776
 777                         m->mothurOut("Done with group file"); m->mothurOutEndLine();
 778
 779                         for (int j = 0; j < fastaNames.size(); j++) {
 780                                 m->appendFiles((fastaNames[j] + toString(processIDS[i]) + ".temp"), fastaNames[j]);
 781                                 remove((fastaNames[j] + toString(processIDS[i]) + ".temp").c_str());
 782                         }
 783
 784                         if(qFileName != ""){
 785                                 for (int j = 0; j < qualNames.size(); j++) {
 786                                         m->appendFiles((qualNames[j] + toString(processIDS[i]) + ".temp"), qualNames[j]);
 787                                         remove((qualNames[j] + toString(processIDS[i]) + ".temp").c_str());
 788                                 }
 789                         }
 790
 791                         if (allFiles) { m->mothurOut("Done with allfiles"); m->mothurOutEndLine(); }
 792                 }
 793
 794                 return exitCommand;
 795 #endif
 796         }
 797         catch(exception& e) {
 798                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 799                 exit(1);
 800         }
 801 }
 802
 803 /**************************************************************************************************/
 804
 805 int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
 806         try {
 807
 808                 //set file positions for fasta file
 809                 fastaFilePos = m->divideFile(filename, processors);
 810
 811                 if (qfilename == "") { return processors; }
 812
 813                 //get name of first sequence in each chunk
 814                 map<string, int> firstSeqNames;
 815                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 816                         ifstream in;
 817                         m->openInputFile(filename, in);
 818                         in.seekg(fastaFilePos[i]);
 819
 820                         Sequence temp(in);
 821                         firstSeqNames[temp.getName()] = i;
 822
 823                         in.close();
 824                 }
 825
 826                 //seach for filePos of each first name in the qfile and save in qfileFilePos
 827                 ifstream inQual;
 828                 m->openInputFile(qfilename, inQual);
 829
 830                 string input;
 831                 while(!inQual.eof()){
 832                         input = m->getline(inQual);
 833
 834                         if (input.length() != 0) {
 835                                 if(input[0] == '>'){ //this is a sequence name line
 836                                         istringstream nameStream(input);
 837
 838                                         string sname = "";  nameStream >> sname;
 839                                         sname = sname.substr(1);
 840
 841                                         map<string, int>::iterator it = firstSeqNames.find(sname);
 842
 843                                         if(it != firstSeqNames.end()) { //this is the start of a new chunk
 844                                                 unsigned long int pos = inQual.tellg();
 845                                                 qfileFilePos.push_back(pos - input.length() - 1);
 846                                                 firstSeqNames.erase(it);
 847                                         }
 848                                 }
 849                         }
 850
 851                         if (firstSeqNames.size() == 0) { break; }
 852                 }
 853                 inQual.close();
 854
 855
 856                 if (firstSeqNames.size() != 0) {
 857                         for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
 858                                 m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
 859                         }
 860                         qFileName = "";
 861                         return processors;
 862                 }
 863
 864                 //get last file position of qfile
 865                 FILE * pFile;
 866                 unsigned long int size;
 867
 868                 //get num bytes in file
 869                 pFile = fopen (qfilename.c_str(),"rb");
 870                 if (pFile==NULL) perror ("Error opening file");
 871                 else{
 872                         fseek (pFile, 0, SEEK_END);
 873                         size=ftell (pFile);
 874                         fclose (pFile);
 875                 }
 876
 877                 qfileFilePos.push_back(size);
 878
 879                 return processors;
 880         }
 881         catch(exception& e) {
 882                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 883                 exit(1);
 884         }
 885 }
 886
 887 //***************************************************************************************************************
 888
 889 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
 890         try {
 891                 ifstream inOligos;
 892                 m->openInputFile(oligoFile, inOligos);
 893
 894                 ofstream test;
 895
 896                 string type, oligo, group;
 897                 int index=0;
 898                 //int indexPrimer = 0;
 899
 900                 while(!inOligos.eof()){
 901                         inOligos >> type; m->gobble(inOligos);
 902
 903                         if(type[0] == '#'){
 904                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 905                         }
 906                         else{
 907                                 //make type case insensitive
 908                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
 909
 910                                 inOligos >> oligo;
 911
 912                                 for(int i=0;i<oligo.length();i++){
 913                                         oligo[i] = toupper(oligo[i]);
 914                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 915                                 }
 916
 917                                 if(type == "FORWARD"){
 918                                         group = "";
 919
 920                                         // get rest of line in case there is a primer name
 921                                         while (!inOligos.eof()) {
 922                                                 char c = inOligos.get();
 923                                                 if (c == 10 || c == 13){        break;  }
 924                                                 else if (c == 32 || c == 9){;} //space or tab
 925                                                 else {  group += c;  }
 926                                         }
 927
 928                                         //check for repeat barcodes
 929                                         map<string, int>::iterator itPrime = primers.find(oligo);
 930                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 931
 932                                                 primers[oligo]=index; index++;
 933                                                 groupVector.push_back(group);
 934
 935                                                 if(allFiles){
 936                                                         outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 937                                                         if(qFileName != ""){
 938                                                                 outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 939                                                         }
 940                                                         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
 941                                                                 filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 942                                                                 if(qFileName != ""){
 943                                                                         filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 944                                                                 }
 945                                                         }else {
 946                                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 947                                                                 outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 948                                                                 if(qFileName != ""){
 949                                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 950                                                                         outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 951                                                                 }
 952                                                         }
 953                                                 }
 954
 955                                 }
 956                                 else if(type == "REVERSE"){
 957                                         Sequence oligoRC("reverse", oligo);
 958                                         oligoRC.reverseComplement();
 959                                         revPrimer.push_back(oligoRC.getUnaligned());
 960                                 }
 961                                 else if(type == "BARCODE"){
 962                                         inOligos >> group;
 963
 964                                         //check for repeat barcodes
 965                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 966                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 967
 968                                                 barcodes[oligo]=index; index++;
 969                                                 groupVector.push_back(group);
 970
 971                                                 if(allFiles){
 972                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 973                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 974                                                         outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 975                                                         if(qFileName != ""){
 976                                                                 outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 977                                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 978                                                                 outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 979                                                         }
 980                                                 }
 981
 982                                 }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
 983                         }
 984                         m->gobble(inOligos);
 985                 }
 986
 987                 inOligos.close();
 988
 989                 //add in potential combos
 990                 if(allFiles){
 991                         comboStarts = outFASTAVec.size()-1;
 992                         for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
 993                                 for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
 994                                         if (groupVector[itPrime->second] != "") { //there is a group for this primer
 995                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 996                                                 outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 997                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 998                                                 combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
 999
1000                                                 if(qFileName != ""){
1001                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
1002                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
1003                                                         outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
1004                                                 }
1005                                         }
1006                                 }
1007                         }
1008                 }
1009
1010                 numFPrimers = primers.size();
1011                 numRPrimers = revPrimer.size();
1012
1013         }
1014         catch(exception& e) {
1015                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
1016                 exit(1);
1017         }
1018 }
1019 //***************************************************************************************************************
1020
1021 int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
1022         try {
1023
1024                 string rawSequence = seq.getUnaligned();
1025                 int success = bdiffs + 1;       //guilty until proven innocent
1026
1027                 //can you find the barcode
1028                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
1029                         string oligo = it->first;
1030                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
1031                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
1032                                 break;
1033                         }
1034
1035                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
1036                                 group = it->second;
1037                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
1038
1039                                 if(qual.getName() != ""){
1040                                         qual.trimQScores(oligo.length(), -1);
1041                                 }
1042
1043                                 success = 0;
1044                                 break;
1045                         }
1046                 }
1047
1048                 //if you found the barcode or if you don't want to allow for diffs
1049 //              cout << success;
1050                 if ((bdiffs == 0) || (success == 0)) { return success;  }
1051
1052                 else { //try aligning and see if you can find it
1053 //                      cout << endl;
1054
1055                         int maxLength = 0;
1056
1057                         Alignment* alignment;
1058                         if (barcodes.size() > 0) {
1059                                 map<string,int>::iterator it=barcodes.begin();
1060
1061                                 for(it;it!=barcodes.end();it++){
1062                                         if(it->first.length() > maxLength){
1063                                                 maxLength = it->first.length();
1064                                         }
1065                                 }
1066                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
1067
1068                         }else{ alignment = NULL; }
1069
1070                         //can you find the barcode
1071                         int minDiff = 1e6;
1072                         int minCount = 1;
1073                         int minGroup = -1;
1074                         int minPos = 0;
1075
1076                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
1077                                 string oligo = it->first;
1078 //                              int length = oligo.length();
1079
1080                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
1081                                         success = bdiffs + 10;
1082                                         break;
1083                                 }
1084
1085                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1086                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
1087                                 oligo = alignment->getSeqAAln();
1088                                 string temp = alignment->getSeqBAln();
1089
1090                                 int alnLength = oligo.length();
1091
1092                                 for(int i=oligo.length()-1;i>=0;i--){
1093                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1094                                 }
1095                                 oligo = oligo.substr(0,alnLength);
1096                                 temp = temp.substr(0,alnLength);
1097
1098                                 int numDiff = countDiffs(oligo, temp);
1099
1100 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1101
1102                                 if(numDiff < minDiff){
1103                                         minDiff = numDiff;
1104                                         minCount = 1;
1105                                         minGroup = it->second;
1106                                         minPos = 0;
1107                                         for(int i=0;i<alnLength;i++){
1108                                                 if(temp[i] != '-'){
1109                                                         minPos++;
1110                                                 }
1111                                         }
1112                                 }
1113                                 else if(numDiff == minDiff){
1114                                         minCount++;
1115                                 }
1116
1117                         }
1118
1119                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
1120                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
1121                         else{                                                                                                   //use the best match
1122                                 group = minGroup;
1123                                 seq.setUnaligned(rawSequence.substr(minPos));
1124
1125                                 if(qual.getName() != ""){
1126                                         qual.trimQScores(minPos, -1);
1127                                 }
1128                                 success = minDiff;
1129                         }
1130
1131                         if (alignment != NULL) {  delete alignment;  }
1132
1133                 }
1134 //              cout << success << endl;
1135
1136                 return success;
1137
1138         }
1139         catch(exception& e) {
1140                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
1141                 exit(1);
1142         }
1143
1144 }
1145
1146 //***************************************************************************************************************
1147
1148 int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
1149         try {
1150                 string rawSequence = seq.getUnaligned();
1151                 int success = pdiffs + 1;       //guilty until proven innocent
1152
1153                 //can you find the primer
1154                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1155                         string oligo = it->first;
1156                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
1157                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
1158                                 break;
1159                         }
1160
1161                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
1162                                 group = it->second;
1163                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
1164                                 if(qual.getName() != ""){
1165                                         qual.trimQScores(oligo.length(), -1);
1166                                 }
1167                                 success = 0;
1168                                 break;
1169                         }
1170                 }
1171
1172                 //if you found the barcode or if you don't want to allow for diffs
1173 //              cout << success;
1174                 if ((pdiffs == 0) || (success == 0)) { return success;  }
1175
1176                 else { //try aligning and see if you can find it
1177 //                      cout << endl;
1178
1179                         int maxLength = 0;
1180
1181                         Alignment* alignment;
1182                         if (primers.size() > 0) {
1183                                 map<string,int>::iterator it=primers.begin();
1184
1185                                 for(it;it!=primers.end();it++){
1186                                         if(it->first.length() > maxLength){
1187                                                 maxLength = it->first.length();
1188                                         }
1189                                 }
1190                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
1191
1192                         }else{ alignment = NULL; }
1193
1194                         //can you find the barcode
1195                         int minDiff = 1e6;
1196                         int minCount = 1;
1197                         int minGroup = -1;
1198                         int minPos = 0;
1199
1200                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1201                                 string oligo = it->first;
1202 //                              int length = oligo.length();
1203
1204                                 if(rawSequence.length() < maxLength){
1205                                         success = pdiffs + 100;
1206                                         break;
1207                                 }
1208
1209                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1210                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
1211                                 oligo = alignment->getSeqAAln();
1212                                 string temp = alignment->getSeqBAln();
1213
1214                                 int alnLength = oligo.length();
1215
1216                                 for(int i=oligo.length()-1;i>=0;i--){
1217                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1218                                 }
1219                                 oligo = oligo.substr(0,alnLength);
1220                                 temp = temp.substr(0,alnLength);
1221
1222                                 int numDiff = countDiffs(oligo, temp);
1223
1224 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1225
1226                                 if(numDiff < minDiff){
1227                                         minDiff = numDiff;
1228                                         minCount = 1;
1229                                         minGroup = it->second;
1230                                         minPos = 0;
1231                                         for(int i=0;i<alnLength;i++){
1232                                                 if(temp[i] != '-'){
1233                                                         minPos++;
1234                                                 }
1235                                         }
1236                                 }
1237                                 else if(numDiff == minDiff){
1238                                         minCount++;
1239                                 }
1240
1241                         }
1242
1243                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
1244                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
1245                         else{                                                                                                   //use the best match
1246                                 group = minGroup;
1247                                 seq.setUnaligned(rawSequence.substr(minPos));
1248                                 if(qual.getName() != ""){
1249                                         qual.trimQScores(minPos, -1);
1250                                 }
1251                                 success = minDiff;
1252                         }
1253
1254                         if (alignment != NULL) {  delete alignment;  }
1255
1256                 }
1257
1258                 return success;
1259
1260         }
1261         catch(exception& e) {
1262                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
1263                 exit(1);
1264         }
1265 }
1266
1267 //***************************************************************************************************************
1268
1269 bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
1270         try {
1271                 string rawSequence = seq.getUnaligned();
1272                 bool success = 0;       //guilty until proven innocent
1273
1274                 for(int i=0;i<numRPrimers;i++){
1275                         string oligo = revPrimer[i];
1276
1277                         if(rawSequence.length() < oligo.length()){
1278                                 success = 0;
1279                                 break;
1280                         }
1281
1282                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
1283                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
1284                                 if(qual.getName() != ""){
1285                                         qual.trimQScores(-1, rawSequence.length()-oligo.length());
1286                                 }
1287                                 success = 1;
1288                                 break;
1289                         }
1290                 }
1291                 return success;
1292
1293         }
1294         catch(exception& e) {
1295                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
1296                 exit(1);
1297         }
1298 }
1299
1300 //***************************************************************************************************************
1301
1302 bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
1303         try {
1304                 bool success = 1;
1305                 if(qscores.getName() != ""){
1306                         qscores.trimQScores(-1, keepFirst);
1307                 }
1308                 sequence.trim(keepFirst);
1309                 return success;
1310         }
1311         catch(exception& e) {
1312                 m->errorOut(e, "keepFirstTrim", "countDiffs");
1313                 exit(1);
1314         }
1315
1316 }
1317
1318 //***************************************************************************************************************
1319
1320 bool TrimSeqsCommand::removeLastTrim(Sequence& sequence, QualityScores& qscores){
1321         try {
1322                 bool success = 0;
1323
1324                 int length = sequence.getNumBases() - removeLast;
1325
1326                 if(length > 0){
1327                         if(qscores.getName() != ""){
1328                                 qscores.trimQScores(-1, length);
1329                         }
1330                         sequence.trim(length);
1331                         success = 1;
1332                 }
1333                 else{
1334                         success = 0;
1335                 }
1336
1337                 return success;
1338         }
1339         catch(exception& e) {
1340                 m->errorOut(e, "removeLastTrim", "countDiffs");
1341                 exit(1);
1342         }
1343
1344 }
1345
1346 //***************************************************************************************************************
1347
1348 bool TrimSeqsCommand::cullLength(Sequence& seq){
1349         try {
1350
1351                 int length = seq.getNumBases();
1352                 bool success = 0;       //guilty until proven innocent
1353
1354                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
1355                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
1356                 else                                                                                            {       success = 0;    }
1357
1358                 return success;
1359
1360         }
1361         catch(exception& e) {
1362                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1363                 exit(1);
1364         }
1365
1366 }
1367
1368 //***************************************************************************************************************
1369
1370 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1371         try {
1372                 int longHomoP = seq.getLongHomoPolymer();
1373                 bool success = 0;       //guilty until proven innocent
1374
1375                 if(longHomoP <= maxHomoP){      success = 1;    }
1376                 else                                    {       success = 0;    }
1377
1378                 return success;
1379         }
1380         catch(exception& e) {
1381                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1382                 exit(1);
1383         }
1384
1385 }
1386
1387 //***************************************************************************************************************
1388
1389 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1390         try {
1391                 int numNs = seq.getAmbigBases();
1392                 bool success = 0;       //guilty until proven innocent
1393
1394                 if(numNs <= maxAmbig)   {       success = 1;    }
1395                 else                                    {       success = 0;    }
1396
1397                 return success;
1398         }
1399         catch(exception& e) {
1400                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1401                 exit(1);
1402         }
1403
1404 }
1405
1406 //***************************************************************************************************************
1407
1408 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
1409         try {
1410                 bool success = 1;
1411                 int length = oligo.length();
1412
1413                 for(int i=0;i<length;i++){
1414
1415                         if(oligo[i] != seq[i]){
1416                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
1417                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
1418                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
1419                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
1420                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
1421                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
1422                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
1423                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
1424                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1425                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1426                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
1427                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
1428
1429                                 if(success == 0)        {       break;   }
1430                         }
1431                         else{
1432                                 success = 1;
1433                         }
1434                 }
1435
1436                 return success;
1437         }
1438         catch(exception& e) {
1439                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
1440                 exit(1);
1441         }
1442
1443 }
1444
1445 //***************************************************************************************************************
1446
1447 int TrimSeqsCommand::countDiffs(string oligo, string seq){
1448         try {
1449
1450                 int length = oligo.length();
1451                 int countDiffs = 0;
1452
1453                 for(int i=0;i<length;i++){
1454
1455                         if(oligo[i] != seq[i]){
1456                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
1457                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
1458                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
1459                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
1460                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
1461                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
1462                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
1463                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
1464                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1465                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1466                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
1467                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
1468                         }
1469
1470                 }
1471
1472                 return countDiffs;
1473         }
1474         catch(exception& e) {
1475                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
1476                 exit(1);
1477         }
1478
1479 }
1480
1481 //***************************************************************************************************************