trimseqscommand.cpp

   1 /*
   2  *  trimseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/6/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "trimseqscommand.h"
  11 #include "needlemanoverlap.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> TrimSeqsCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
  17                                                                         "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
  18                                                                         "keepfirst", "removelast",
  19                                                                         "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  20                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  21                 return myArray;
  22         }
  23         catch(exception& e) {
  24                 m->errorOut(e, "TrimSeqsCommand", "getValidParameters");
  25                 exit(1);
  26         }
  27 }
  28 //**********************************************************************************************************************
  29 TrimSeqsCommand::TrimSeqsCommand(){
  30         try {
  31                 abort = true;
  32                 //initialize outputTypes
  33                 vector<string> tempOutNames;
  34                 outputTypes["fasta"] = tempOutNames;
  35                 outputTypes["qual"] = tempOutNames;
  36                 outputTypes["group"] = tempOutNames;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 vector<string> TrimSeqsCommand::getRequiredParameters(){
  45         try {
  46                 string Array[] =  {"fasta"};
  47                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  48                 return myArray;
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "TrimSeqsCommand", "getRequiredParameters");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 vector<string> TrimSeqsCommand::getRequiredFiles(){
  57         try {
  58                 vector<string> myArray;
  59                 return myArray;
  60         }
  61         catch(exception& e) {
  62                 m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
  63                 exit(1);
  64         }
  65 }
  66 //***************************************************************************************************************
  67
  68 TrimSeqsCommand::TrimSeqsCommand(string option)  {
  69         try {
  70
  71                 abort = false;
  72                 comboStarts = 0;
  73
  74                 //allow user to run help
  75                 if(option == "help") { help(); abort = true; }
  76
  77                 else {
  78                         //valid paramters for this command
  79                         string AlignArray[] =  {        "fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile",
  80                                                                 "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage",
  81                                                                 "keepfirst", "removelast",
  82                                                                 "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  83
  84                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  85
  86                         OptionParser parser(option);
  87                         map<string,string> parameters = parser.getParameters();
  88
  89                         ValidParameters validParameter;
  90                         map<string,string>::iterator it;
  91
  92                         //check to make sure all parameters are valid for command
  93                         for (it = parameters.begin(); it != parameters.end(); it++) {
  94                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  95                         }
  96
  97                         //initialize outputTypes
  98                         vector<string> tempOutNames;
  99                         outputTypes["fasta"] = tempOutNames;
 100                         outputTypes["qual"] = tempOutNames;
 101                         outputTypes["group"] = tempOutNames;
 102
 103                         //if the user changes the input directory command factory will send this info to us in the output parameter
 104                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 105                         if (inputDir == "not found"){   inputDir = "";          }
 106                         else {
 107                                 string path;
 108                                 it = parameters.find("fasta");
 109                                 //user has given a template file
 110                                 if(it != parameters.end()){
 111                                         path = m->hasPath(it->second);
 112                                         //if the user has not given a path then, add inputdir. else leave path alone.
 113                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 114                                 }
 115
 116                                 it = parameters.find("oligos");
 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["oligos"] = inputDir + it->second;           }
 122                                 }
 123
 124                                 it = parameters.find("qfile");
 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["qfile"] = inputDir + it->second;            }
 130                                 }
 131
 132                                 it = parameters.find("group");
 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["group"] = inputDir + it->second;            }
 138                                 }
 139                         }
 140
 141
 142                         //check for required parameters
 143                         fastaFile = validParameter.validFile(parameters, "fasta", true);
 144                         if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the trim.seqs command."); m->mothurOutEndLine(); abort = true; }
 145                         else if (fastaFile == "not open") { abort = true; }
 146
 147                         //if the user changes the output directory command factory will send this info to us in the output parameter
 148                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 149                                 outputDir = "";
 150                                 outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
 151                         }
 152
 153
 154                         //check for optional parameter and set defaults
 155                         // ...at some point should added some additional type checking...
 156                         string temp;
 157                         temp = validParameter.validFile(parameters, "flip", false);
 158                         if (temp == "not found"){       flip = 0;       }
 159                         else if(m->isTrue(temp))        {       flip = 1;       }
 160
 161                         temp = validParameter.validFile(parameters, "oligos", true);
 162                         if (temp == "not found"){       oligoFile = "";         }
 163                         else if(temp == "not open"){    abort = true;   }
 164                         else                                    {       oligoFile = temp;               }
 165
 166                         temp = validParameter.validFile(parameters, "group", true);
 167                         if (temp == "not found"){       groupfile = "";         }
 168                         else if(temp == "not open"){    abort = true;   }
 169                         else                                    {       groupfile = temp;               }
 170
 171                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 172                         convert(temp, maxAmbig);
 173
 174                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
 175                         convert(temp, maxHomoP);
 176
 177                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
 178                         convert(temp, minLength);
 179
 180                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
 181                         convert(temp, maxLength);
 182
 183                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
 184                         convert(temp, bdiffs);
 185
 186                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 187                         convert(temp, pdiffs);
 188
 189                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 190                         convert(temp, tdiffs);
 191
 192                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 193
 194                         temp = validParameter.validFile(parameters, "qfile", true);
 195                         if (temp == "not found")        {       qFileName = "";         }
 196                         else if(temp == "not open")     {       abort = true;           }
 197                         else                                            {       qFileName = temp;       }
 198
 199                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 200                         convert(temp, qThreshold);
 201
 202                         temp = validParameter.validFile(parameters, "qtrim", false);            if (temp == "not found") { temp = "F"; }
 203                         qtrim = m->isTrue(temp);
 204
 205                         temp = validParameter.validFile(parameters, "rollaverage", false);      if (temp == "not found") { temp = "0"; }
 206                         convert(temp, qRollAverage);
 207
 208                         temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
 209                         convert(temp, qWindowAverage);
 210
 211                         temp = validParameter.validFile(parameters, "qwindowsize", false);      if (temp == "not found") { temp = "50"; }
 212                         convert(temp, qWindowSize);
 213
 214                         temp = validParameter.validFile(parameters, "qstepsize", false);        if (temp == "not found") { temp = "1"; }
 215                         convert(temp, qWindowStep);
 216
 217                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 218                         convert(temp, qAverage);
 219
 220                         temp = validParameter.validFile(parameters, "keepfirst", false);        if (temp == "not found") { temp = "0"; }
 221                         convert(temp, keepFirst);
 222
 223                         temp = validParameter.validFile(parameters, "removelast", false);       if (temp == "not found") { temp = "0"; }
 224                         convert(temp, removeLast);
 225
 226                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 227                         allFiles = m->isTrue(temp);
 228
 229                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found") { temp = "1"; }
 230                         convert(temp, processors);
 231
 232                         if ((oligoFile != "") && (groupfile != "")) {
 233                                 m->mothurOut("You given both a oligos file and a groupfile, only one is allowed."); m->mothurOutEndLine(); abort = true;
 234                         }
 235
 236
 237                         if(allFiles && (oligoFile == "") && (groupfile == "")){
 238                                 m->mothurOut("You selected allfiles, but didn't enter an oligos or group file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 239                         }
 240                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 241                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 242                                 qAverage=0;
 243                                 qThreshold=0;
 244                         }
 245                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 246                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 247                                 abort = true;
 248                         }
 249                 }
 250
 251         }
 252         catch(exception& e) {
 253                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 254                 exit(1);
 255         }
 256 }
 257 //**********************************************************************************************************************
 258
 259 void TrimSeqsCommand::help(){
 260         try {
 261                 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 262                 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, group, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 263                 m->mothurOut("The fasta parameter is required.\n");
 264                 m->mothurOut("The group parameter allows you to enter a group file for your fasta file.\n");
 265                 m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
 266                 m->mothurOut("The oligos parameter .... The default is "".\n");
 267                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 268                 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 269                 m->mothurOut("The minlength parameter .... The default is 0.\n");
 270                 m->mothurOut("The maxlength parameter .... The default is 0.\n");
 271                 m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
 272                 m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
 273                 m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 274                 m->mothurOut("The qfile parameter .....\n");
 275                 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 276                 m->mothurOut("The qaverage parameter .... The default is 0.\n");
 277                 m->mothurOut("The allfiles parameter .... The default is F.\n");
 278                 m->mothurOut("The qtrim parameter .... The default is F.\n");
 279                 m->mothurOut("The trim.seqs command should be in the following format: \n");
 280                 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 281                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 282                 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 283                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 284                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 285
 286         }
 287         catch(exception& e) {
 288                 m->errorOut(e, "TrimSeqsCommand", "help");
 289                 exit(1);
 290         }
 291 }
 292
 293
 294 //***************************************************************************************************************
 295
 296 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 297
 298 //***************************************************************************************************************
 299
 300 int TrimSeqsCommand::execute(){
 301         try{
 302
 303                 if (abort == true) { return 0; }
 304
 305                 numFPrimers = 0;  //this needs to be initialized
 306                 numRPrimers = 0;
 307                 vector<string> fastaFileNames;
 308                 vector<string> qualFileNames;
 309
 310                 string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
 311                 outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
 312                 string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
 313                 outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
 314                 string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
 315                 string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
 316                 if (qFileName != "") {  outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile);  outputTypes["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
 317                 string groupFile = "";
 318                 if (groupfile == "") { groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups"; }
 319                 else{
 320                         groupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "trim.groups";
 321                         outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
 322                         groupMap = new GroupMap(groupfile);
 323                         groupMap->readMap();
 324
 325                         if(allFiles){
 326                                 for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {
 327                                         groupToIndex[groupMap->namesOfGroups[i]] = i;
 328                                         groupVector.push_back(groupMap->namesOfGroups[i]);
 329                                         fastaFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) +  groupMap->namesOfGroups[i] + ".fasta"));
 330
 331                                         //we append later, so we want to clear file
 332                                         ofstream outRemove;
 333                                         m->openOutputFile(fastaFileNames[i], outRemove);
 334                                         outRemove.close();
 335                                         if(qFileName != ""){
 336                                                 qualFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) +  groupMap->namesOfGroups[i] + ".qual"));
 337                                                 ofstream outRemove2;
 338                                                 m->openOutputFile(qualFileNames[i], outRemove2);
 339                                                 outRemove2.close();
 340                                         }
 341                                 }
 342                         }
 343                         comboStarts = fastaFileNames.size()-1;
 344                 }
 345
 346                 if(oligoFile != ""){
 347                         outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
 348                         getOligos(fastaFileNames, qualFileNames);
 349                 }
 350
 351                 vector<unsigned long int> fastaFilePos;
 352                 vector<unsigned long int> qFilePos;
 353
 354                 setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
 355
 356                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 357                         lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
 358                         if (qFileName != "") {  qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)]));  }
 359                 }
 360                 if(qFileName == "")     {       qLines = lines; } //files with duds
 361
 362                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 363                                 if(processors == 1){
 364                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 365                                 }else{
 366                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
 367                                 }
 368                 #else
 369                                 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 370                 #endif
 371
 372                 if (m->control_pressed) {  return 0; }
 373
 374                 set<string> blanks;
 375                 for(int i=0;i<fastaFileNames.size();i++){
 376                         if (m->isBlank(fastaFileNames[i])) {   blanks.insert(fastaFileNames[i]);        }
 377                         else if (filesToRemove.count(fastaFileNames[i]) > 0) {  remove(fastaFileNames[i].c_str()); }
 378                         else {
 379                                 ifstream inFASTA;
 380                                 string seqName;
 381                                 m->openInputFile(fastaFileNames[i], inFASTA);
 382                                 ofstream outGroups;
 383                                 string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
 384
 385                                 //if the fastafile is on the blanks list then the groups file should be as well
 386                                 if (blanks.count(fastaFileNames[i]) != 0) { blanks.insert(outGroupFilename); }
 387
 388                                 m->openOutputFile(outGroupFilename, outGroups);
 389                                 outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
 390
 391                                 string thisGroup = "";
 392                                 if (i > comboStarts) {
 393                                         map<string, int>::iterator itCombo;
 394                                         for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
 395                                                 if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
 396                                         }
 397                                 }else{ thisGroup = groupVector[i]; }
 398
 399                                 while(!inFASTA.eof()){
 400                                         if(inFASTA.get() == '>'){
 401                                                 inFASTA >> seqName;
 402                                                 outGroups << seqName << '\t' << thisGroup << endl;
 403                                         }
 404                                         while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 405                                 }
 406                                 outGroups.close();
 407                                 inFASTA.close();
 408                         }
 409                 }
 410
 411                 for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) {  remove((*(itBlanks)).c_str()); }
 412
 413                 blanks.clear();
 414                 if(qFileName != ""){
 415                         for(int i=0;i<qualFileNames.size();i++){
 416                                 if (m->isBlank(qualFileNames[i])) {  blanks.insert(qualFileNames[i]);   }
 417                                 else if (filesToRemove.count(qualFileNames[i]) > 0) {  remove(qualFileNames[i].c_str()); }
 418                         }
 419                 }
 420
 421                 for (set<string>::iterator itBlanks = blanks.begin(); itBlanks != blanks.end(); itBlanks++) {  remove((*(itBlanks)).c_str()); }
 422
 423                 if (m->control_pressed) {
 424                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 425                         return 0;
 426                 }
 427
 428                 m->mothurOutEndLine();
 429                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 430                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 431                 m->mothurOutEndLine();
 432
 433                 return 0;
 434
 435         }
 436         catch(exception& e) {
 437                 m->errorOut(e, "TrimSeqsCommand", "execute");
 438                 exit(1);
 439         }
 440 }
 441
 442 /**************************************************************************************/
 443
 444 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) {
 445
 446         try {
 447
 448                 ofstream outFASTA;
 449                 int able = m->openOutputFile(trimFile, outFASTA);
 450
 451                 ofstream scrapFASTA;
 452                 m->openOutputFile(scrapFile, scrapFASTA);
 453
 454                 ofstream outQual;
 455                 ofstream scrapQual;
 456                 if(qFileName != ""){
 457                         m->openOutputFile(trimQFile, outQual);
 458                         m->openOutputFile(scrapQFile, scrapQual);
 459                 }
 460
 461                 ofstream outGroups;
 462
 463                 if (oligoFile != "") {
 464                         m->openOutputFile(groupFile, outGroups);
 465                 }
 466
 467                 ifstream inFASTA;
 468                 m->openInputFile(filename, inFASTA);
 469                 inFASTA.seekg(line->start);
 470
 471                 ifstream qFile;
 472                 if(qFileName != "")     {       m->openInputFile(qFileName, qFile);     qFile.seekg(qline->start);  }
 473
 474
 475                 for (int i = 0; i < fastaNames.size(); i++) { //clears old file
 476                         ofstream temp;
 477                         m->openOutputFile(fastaNames[i], temp);
 478                         temp.close();
 479                 }
 480                 for (int i = 0; i < qualNames.size(); i++) { //clears old file
 481                         ofstream temp;
 482                         m->openOutputFile(qualNames[i], temp);
 483                         temp.close();
 484                 }
 485
 486
 487                 bool done = false;
 488                 int count = 0;
 489
 490                 while (!done) {
 491
 492                         if (m->control_pressed) {
 493                                 inFASTA.close(); outFASTA.close(); scrapFASTA.close();
 494                                 if (oligoFile != "") {   outGroups.close();   }
 495
 496                                 if(qFileName != ""){
 497                                         qFile.close();
 498                                 }
 499                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 500
 501                                 return 0;
 502                         }
 503
 504                         int success = 1;
 505
 506
 507                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 508
 509                         QualityScores currQual;
 510                         if(qFileName != ""){
 511                                 currQual = QualityScores(qFile, currSeq.getNumBases());  m->gobble(qFile);
 512                         }
 513
 514                         string origSeq = currSeq.getUnaligned();
 515                         if (origSeq != "") {
 516                                 int groupBar, groupPrime;
 517                                 string trashCode = "";
 518                                 int currentSeqsDiffs = 0;
 519
 520                                 if(barcodes.size() != 0){
 521                                         success = stripBarcode(currSeq, currQual, groupBar);
 522                                         if(success > bdiffs)            {       trashCode += 'b';       }
 523                                         else{ currentSeqsDiffs += success;  }
 524                                 }
 525
 526                                 if(numFPrimers != 0){
 527                                         success = stripForward(currSeq, currQual, groupPrime);
 528                                         if(success > pdiffs)            {       trashCode += 'f';       }
 529                                         else{ currentSeqsDiffs += success;  }
 530                                 }
 531
 532                                 if (currentSeqsDiffs > tdiffs)  {       trashCode += 't';   }
 533
 534                                 if(numRPrimers != 0){
 535                                         success = stripReverse(currSeq, currQual);
 536                                         if(!success)                            {       trashCode += 'r';       }
 537                                 }
 538
 539                                 if(keepFirst != 0){
 540                                         success = keepFirstTrim(currSeq, currQual);
 541                                 }
 542
 543                                 if(removeLast != 0){
 544                                         success = removeLastTrim(currSeq, currQual);
 545                                         if(!success)                            {       trashCode += 'l';       }
 546                                 }
 547
 548
 549                                 if(qFileName != ""){
 550
 551                                         if(qThreshold != 0)                     {       success = currQual.stripQualThreshold(currSeq, qThreshold);                     }
 552                                         else if(qAverage != 0)          {       success = currQual.cullQualAverage(currSeq, qAverage);                          }
 553                                         else if(qRollAverage != 0)      {       success = currQual.stripQualRollingAverage(currSeq, qRollAverage);      }
 554                                         else if(qWindowAverage != 0){   success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);   }
 555                                         else                                            {       success = 1;                            }
 556
 557 //                                      if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
 558 //                                              success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 559 //                                      }
 560
 561                                         if(!success)                            {       trashCode += 'q';       }
 562                                 }
 563
 564                                 if(minLength > 0 || maxLength > 0){
 565                                         success = cullLength(currSeq);
 566                                         if(!success)                            {       trashCode += 'l';       }
 567                                 }
 568                                 if(maxHomoP > 0){
 569                                         success = cullHomoP(currSeq);
 570                                         if(!success)                            {       trashCode += 'h';       }
 571                                 }
 572                                 if(maxAmbig != -1){
 573                                         success = cullAmbigs(currSeq);
 574                                         if(!success)                            {       trashCode += 'n';       }
 575                                 }
 576
 577                                 if(flip){               // should go last
 578                                         currSeq.reverseComplement();
 579                                         currQual.flipQScores();
 580                                 }
 581
 582                                 if(trashCode.length() == 0){
 583                                         currSeq.setAligned(currSeq.getUnaligned());
 584                                         currSeq.printSequence(outFASTA);
 585                                         currQual.printQScores(outQual);
 586
 587                                         if(barcodes.size() != 0){
 588                                                 string thisGroup = groupVector[groupBar];
 589                                                 int indexToFastaFile = groupBar;
 590                                                 if (primers.size() != 0){
 591                                                         //does this primer have a group
 592                                                         if (groupVector[groupPrime] != "") {
 593                                                                 thisGroup += "." + groupVector[groupPrime];
 594                                                                 indexToFastaFile = combos[thisGroup];
 595                                                         }
 596                                                 }
 597                                                 outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 598                                                 if(allFiles){
 599                                                         ofstream outTemp;
 600                                                         m->openOutputFileAppend(fastaNames[indexToFastaFile], outTemp);
 601                                                         //currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
 602                                                         currSeq.printSequence(outTemp);
 603                                                         outTemp.close();
 604
 605                                                         if(qFileName != ""){
 606                                                                 //currQual.printQScores(*qualFileNames[indexToFastaFile]);
 607                                                                 ofstream outTemp2;
 608                                                                 m->openOutputFileAppend(qualNames[indexToFastaFile], outTemp2);
 609                                                                 currQual.printQScores(outTemp2);
 610                                                                 outTemp2.close();
 611                                                         }
 612                                                 }
 613                                         }
 614
 615                                         if (groupfile != "") {
 616                                                 string thisGroup = groupMap->getGroup(currSeq.getName());
 617
 618                                                 if (thisGroup != "not found") {
 619                                                         outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 620                                                         if (allFiles) {
 621                                                                 ofstream outTemp;
 622                                                                 m->openOutputFileAppend(fastaNames[groupToIndex[thisGroup]], outTemp);
 623                                                                 currSeq.printSequence(outTemp);
 624                                                                 outTemp.close();
 625                                                                 if(qFileName != ""){
 626                                                                         ofstream outTemp2;
 627                                                                         m->openOutputFileAppend(qualNames[groupToIndex[thisGroup]], outTemp2);
 628                                                                         currQual.printQScores(outTemp2);
 629                                                                         outTemp2.close();
 630                                                                 }
 631                                                         }
 632                                                 }else{
 633                                                         m->mothurOut(currSeq.getName() + " is not in your groupfile, adding to group XXX."); m->mothurOutEndLine();
 634                                                         outGroups << currSeq.getName() << '\t' << "XXX" << endl;
 635                                                         if (allFiles) {
 636                                                                 m->mothurOut("[ERROR]: " + currSeq.getName() + " will not be added to any .group.fasta or .group.qual file."); m->mothurOutEndLine();
 637                                                         }
 638                                                 }
 639                                         }
 640                                 }
 641                                 else{
 642                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 643                                         currSeq.setUnaligned(origSeq);
 644                                         currSeq.setAligned(origSeq);
 645                                         currSeq.printSequence(scrapFASTA);
 646                                         currQual.printQScores(scrapQual);
 647                                 }
 648                                 count++;
 649                         }
 650
 651                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 652                                 unsigned long int pos = inFASTA.tellg();
 653                                 if ((pos == -1) || (pos >= line->end)) { break; }
 654                         #else
 655                                 if (inFASTA.eof()) { break; }
 656                         #endif
 657
 658                         //report progress
 659                         if((count) % 1000 == 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 660
 661                 }
 662                 //report progress
 663                 if((count) % 1000 != 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 664
 665
 666                 inFASTA.close();
 667                 outFASTA.close();
 668                 scrapFASTA.close();
 669                 if (oligoFile != "") {   outGroups.close();   }
 670                 if(qFileName != "")     {       qFile.close();  scrapQual.close(); outQual.close();     }
 671
 672                 return count;
 673         }
 674         catch(exception& e) {
 675                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 676                 exit(1);
 677         }
 678 }
 679
 680 /**************************************************************************************************/
 681
 682 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
 683         try {
 684 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 685                 int process = 1;
 686                 int exitCommand = 1;
 687                 processIDS.clear();
 688
 689                 //loop through and create all the processes you want
 690                 while (process != processors) {
 691                         int pid = fork();
 692
 693                         if (pid > 0) {
 694                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 695                                 process++;
 696                         }else if (pid == 0){
 697                                 for (int i = 0; i < fastaNames.size(); i++) {
 698                                         fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
 699                                         //clear old file if it exists
 700                                         ofstream temp;
 701                                         m->openOutputFile(fastaNames[i], temp);
 702                                         temp.close();
 703                                         if(qFileName != ""){
 704                                                 qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
 705                                                 //clear old file if it exists
 706                                                 ofstream temp2;
 707                                                 m->openOutputFile(qualNames[i], temp2);
 708                                                 temp2.close();
 709                                         }
 710                                 }
 711
 712                                 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]);
 713                                 exit(0);
 714                         }else {
 715                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 716                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 717                                 exit(0);
 718                         }
 719                 }
 720
 721                 //parent do my part
 722                 for (int i = 0; i < fastaNames.size(); i++) {
 723                         //clear old file if it exists
 724                         ofstream temp;
 725                         m->openOutputFile(fastaNames[i], temp);
 726                         temp.close();
 727                         if(qFileName != ""){
 728                                 //clear old file if it exists
 729                                 ofstream temp2;
 730                                 m->openOutputFile(qualNames[i], temp2);
 731                                 temp2.close();
 732                         }
 733                 }
 734
 735                 driverCreateTrim(filename, qFileName, trimFile, scrapFile, trimQFile, scrapQFile, groupFile, fastaNames, qualNames, lines[0], qLines[0]);
 736
 737
 738                 //force parent to wait until all the processes are done
 739                 for (int i=0;i<processIDS.size();i++) {
 740                         int temp = processIDS[i];
 741                         wait(&temp);
 742                 }
 743
 744                 //append files
 745                 for(int i=0;i<processIDS.size();i++){
 746
 747                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 748
 749                         m->appendFiles((trimFile + toString(processIDS[i]) + ".temp"), trimFile);
 750                         remove((trimFile + toString(processIDS[i]) + ".temp").c_str());
 751                         m->appendFiles((scrapFile + toString(processIDS[i]) + ".temp"), scrapFile);
 752                         remove((scrapFile + toString(processIDS[i]) + ".temp").c_str());
 753
 754                         m->mothurOut("Done with fasta files"); m->mothurOutEndLine();
 755
 756                         if(qFileName != ""){
 757                                 m->appendFiles((trimQFile + toString(processIDS[i]) + ".temp"), trimQFile);
 758                                 remove((trimQFile + toString(processIDS[i]) + ".temp").c_str());
 759                                 m->appendFiles((scrapQFile + toString(processIDS[i]) + ".temp"), scrapQFile);
 760                                 remove((scrapQFile + toString(processIDS[i]) + ".temp").c_str());
 761
 762                                 m->mothurOut("Done with quality files"); m->mothurOutEndLine();
 763                         }
 764
 765                         m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 766                         remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 767
 768                         m->mothurOut("Done with group file"); m->mothurOutEndLine();
 769
 770                         for (int j = 0; j < fastaNames.size(); j++) {
 771                                 m->appendFiles((fastaNames[j] + toString(processIDS[i]) + ".temp"), fastaNames[j]);
 772                                 remove((fastaNames[j] + toString(processIDS[i]) + ".temp").c_str());
 773                         }
 774
 775                         if(qFileName != ""){
 776                                 for (int j = 0; j < qualNames.size(); j++) {
 777                                         m->appendFiles((qualNames[j] + toString(processIDS[i]) + ".temp"), qualNames[j]);
 778                                         remove((qualNames[j] + toString(processIDS[i]) + ".temp").c_str());
 779                                 }
 780                         }
 781
 782                         if (allFiles) { m->mothurOut("Done with allfiles"); m->mothurOutEndLine(); }
 783                 }
 784
 785                 return exitCommand;
 786 #endif
 787         }
 788         catch(exception& e) {
 789                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 790                 exit(1);
 791         }
 792 }
 793
 794 /**************************************************************************************************/
 795
 796 int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
 797         try {
 798
 799                 //set file positions for fasta file
 800                 fastaFilePos = m->divideFile(filename, processors);
 801
 802                 if (qfilename == "") { return processors; }
 803
 804                 //get name of first sequence in each chunk
 805                 map<string, int> firstSeqNames;
 806                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 807                         ifstream in;
 808                         m->openInputFile(filename, in);
 809                         in.seekg(fastaFilePos[i]);
 810
 811                         Sequence temp(in);
 812                         firstSeqNames[temp.getName()] = i;
 813
 814                         in.close();
 815                 }
 816
 817                 //seach for filePos of each first name in the qfile and save in qfileFilePos
 818                 ifstream inQual;
 819                 m->openInputFile(qfilename, inQual);
 820
 821                 string input;
 822                 while(!inQual.eof()){
 823                         input = m->getline(inQual);
 824
 825                         if (input.length() != 0) {
 826                                 if(input[0] == '>'){ //this is a sequence name line
 827                                         istringstream nameStream(input);
 828
 829                                         string sname = "";  nameStream >> sname;
 830                                         sname = sname.substr(1);
 831
 832                                         map<string, int>::iterator it = firstSeqNames.find(sname);
 833
 834                                         if(it != firstSeqNames.end()) { //this is the start of a new chunk
 835                                                 unsigned long int pos = inQual.tellg();
 836                                                 qfileFilePos.push_back(pos - input.length() - 1);
 837                                                 firstSeqNames.erase(it);
 838                                         }
 839                                 }
 840                         }
 841
 842                         if (firstSeqNames.size() == 0) { break; }
 843                 }
 844                 inQual.close();
 845
 846
 847                 if (firstSeqNames.size() != 0) {
 848                         for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
 849                                 m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
 850                         }
 851                         qFileName = "";
 852                         return processors;
 853                 }
 854
 855                 //get last file position of qfile
 856                 FILE * pFile;
 857                 unsigned long int size;
 858
 859                 //get num bytes in file
 860                 pFile = fopen (qfilename.c_str(),"rb");
 861                 if (pFile==NULL) perror ("Error opening file");
 862                 else{
 863                         fseek (pFile, 0, SEEK_END);
 864                         size=ftell (pFile);
 865                         fclose (pFile);
 866                 }
 867
 868                 qfileFilePos.push_back(size);
 869
 870                 return processors;
 871         }
 872         catch(exception& e) {
 873                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 874                 exit(1);
 875         }
 876 }
 877 //***************************************************************************************************************
 878
 879 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
 880         try {
 881                 ifstream inOligos;
 882                 m->openInputFile(oligoFile, inOligos);
 883
 884                 ofstream test;
 885
 886                 string type, oligo, group;
 887                 int index=0;
 888                 //int indexPrimer = 0;
 889
 890                 while(!inOligos.eof()){
 891                         inOligos >> type; m->gobble(inOligos);
 892
 893                         if(type[0] == '#'){
 894                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 895                         }
 896                         else{
 897                                 //make type case insensitive
 898                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
 899
 900                                 inOligos >> oligo;
 901
 902                                 for(int i=0;i<oligo.length();i++){
 903                                         oligo[i] = toupper(oligo[i]);
 904                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 905                                 }
 906
 907                                 if(type == "FORWARD"){
 908                                         group = "";
 909
 910                                         // get rest of line in case there is a primer name
 911                                         while (!inOligos.eof()) {
 912                                                 char c = inOligos.get();
 913                                                 if (c == 10 || c == 13){        break;  }
 914                                                 else if (c == 32 || c == 9){;} //space or tab
 915                                                 else {  group += c;  }
 916                                         }
 917
 918                                         //check for repeat barcodes
 919                                         map<string, int>::iterator itPrime = primers.find(oligo);
 920                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 921
 922                                                 primers[oligo]=index; index++;
 923                                                 groupVector.push_back(group);
 924
 925                                                 if(allFiles){
 926                                                         outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 927                                                         if(qFileName != ""){
 928                                                                 outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 929                                                         }
 930                                                         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
 931                                                                 filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 932                                                                 if(qFileName != ""){
 933                                                                         filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 934                                                                 }
 935                                                         }else {
 936                                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 937                                                                 outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 938                                                                 if(qFileName != ""){
 939                                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 940                                                                         outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 941                                                                 }
 942                                                         }
 943                                                 }
 944
 945                                 }
 946                                 else if(type == "REVERSE"){
 947                                         Sequence oligoRC("reverse", oligo);
 948                                         oligoRC.reverseComplement();
 949                                         revPrimer.push_back(oligoRC.getUnaligned());
 950                                 }
 951                                 else if(type == "BARCODE"){
 952                                         inOligos >> group;
 953
 954                                         //check for repeat barcodes
 955                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 956                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 957
 958                                                 barcodes[oligo]=index; index++;
 959                                                 groupVector.push_back(group);
 960
 961                                                 if(allFiles){
 962                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 963                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 964                                                         outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 965                                                         if(qFileName != ""){
 966                                                                 outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 967                                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 968                                                                 outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 969                                                         }
 970                                                 }
 971
 972                                 }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
 973                         }
 974                         m->gobble(inOligos);
 975                 }
 976
 977                 inOligos.close();
 978
 979                 //add in potential combos
 980                 if(allFiles){
 981                         comboStarts = outFASTAVec.size()-1;
 982                         for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
 983                                 for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
 984                                         if (groupVector[itPrime->second] != "") { //there is a group for this primer
 985                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 986                                                 outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 987                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
 988                                                 combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
 989
 990                                                 if(qFileName != ""){
 991                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 992                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 993                                                         outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
 994                                                 }
 995                                         }
 996                                 }
 997                         }
 998                 }
 999
1000                 numFPrimers = primers.size();
1001                 numRPrimers = revPrimer.size();
1002
1003         }
1004         catch(exception& e) {
1005                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
1006                 exit(1);
1007         }
1008 }
1009 //***************************************************************************************************************
1010
1011 int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
1012         try {
1013
1014                 string rawSequence = seq.getUnaligned();
1015                 int success = bdiffs + 1;       //guilty until proven innocent
1016
1017                 //can you find the barcode
1018                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
1019                         string oligo = it->first;
1020                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
1021                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
1022                                 break;
1023                         }
1024
1025                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
1026                                 group = it->second;
1027                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
1028
1029                                 if(qual.getName() != ""){
1030                                         qual.trimQScores(oligo.length(), -1);
1031                                 }
1032
1033                                 success = 0;
1034                                 break;
1035                         }
1036                 }
1037
1038                 //if you found the barcode or if you don't want to allow for diffs
1039 //              cout << success;
1040                 if ((bdiffs == 0) || (success == 0)) { return success;  }
1041
1042                 else { //try aligning and see if you can find it
1043 //                      cout << endl;
1044
1045                         int maxLength = 0;
1046
1047                         Alignment* alignment;
1048                         if (barcodes.size() > 0) {
1049                                 map<string,int>::iterator it=barcodes.begin();
1050
1051                                 for(it;it!=barcodes.end();it++){
1052                                         if(it->first.length() > maxLength){
1053                                                 maxLength = it->first.length();
1054                                         }
1055                                 }
1056                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
1057
1058                         }else{ alignment = NULL; }
1059
1060                         //can you find the barcode
1061                         int minDiff = 1e6;
1062                         int minCount = 1;
1063                         int minGroup = -1;
1064                         int minPos = 0;
1065
1066                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
1067                                 string oligo = it->first;
1068 //                              int length = oligo.length();
1069
1070                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
1071                                         success = bdiffs + 10;
1072                                         break;
1073                                 }
1074
1075                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1076                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
1077                                 oligo = alignment->getSeqAAln();
1078                                 string temp = alignment->getSeqBAln();
1079
1080                                 int alnLength = oligo.length();
1081
1082                                 for(int i=oligo.length()-1;i>=0;i--){
1083                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1084                                 }
1085                                 oligo = oligo.substr(0,alnLength);
1086                                 temp = temp.substr(0,alnLength);
1087
1088                                 int newStart=0;
1089                                 int numDiff = countDiffs(oligo, temp);
1090
1091 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1092
1093                                 if(numDiff < minDiff){
1094                                         minDiff = numDiff;
1095                                         minCount = 1;
1096                                         minGroup = it->second;
1097                                         minPos = 0;
1098                                         for(int i=0;i<alnLength;i++){
1099                                                 if(temp[i] != '-'){
1100                                                         minPos++;
1101                                                 }
1102                                         }
1103                                 }
1104                                 else if(numDiff == minDiff){
1105                                         minCount++;
1106                                 }
1107
1108                         }
1109
1110                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
1111                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
1112                         else{                                                                                                   //use the best match
1113                                 group = minGroup;
1114                                 seq.setUnaligned(rawSequence.substr(minPos));
1115
1116                                 if(qual.getName() != ""){
1117                                         qual.trimQScores(minPos, -1);
1118                                 }
1119                                 success = minDiff;
1120                         }
1121
1122                         if (alignment != NULL) {  delete alignment;  }
1123
1124                 }
1125 //              cout << success << endl;
1126
1127                 return success;
1128
1129         }
1130         catch(exception& e) {
1131                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
1132                 exit(1);
1133         }
1134
1135 }
1136
1137 //***************************************************************************************************************
1138
1139 int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
1140         try {
1141                 string rawSequence = seq.getUnaligned();
1142                 int success = pdiffs + 1;       //guilty until proven innocent
1143
1144                 //can you find the primer
1145                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1146                         string oligo = it->first;
1147                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
1148                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
1149                                 break;
1150                         }
1151
1152                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
1153                                 group = it->second;
1154                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
1155                                 if(qual.getName() != ""){
1156                                         qual.trimQScores(oligo.length(), -1);
1157                                 }
1158                                 success = 0;
1159                                 break;
1160                         }
1161                 }
1162
1163                 //if you found the barcode or if you don't want to allow for diffs
1164 //              cout << success;
1165                 if ((pdiffs == 0) || (success == 0)) { return success;  }
1166
1167                 else { //try aligning and see if you can find it
1168 //                      cout << endl;
1169
1170                         int maxLength = 0;
1171
1172                         Alignment* alignment;
1173                         if (primers.size() > 0) {
1174                                 map<string,int>::iterator it=primers.begin();
1175
1176                                 for(it;it!=primers.end();it++){
1177                                         if(it->first.length() > maxLength){
1178                                                 maxLength = it->first.length();
1179                                         }
1180                                 }
1181                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
1182
1183                         }else{ alignment = NULL; }
1184
1185                         //can you find the barcode
1186                         int minDiff = 1e6;
1187                         int minCount = 1;
1188                         int minGroup = -1;
1189                         int minPos = 0;
1190
1191                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1192                                 string oligo = it->first;
1193 //                              int length = oligo.length();
1194
1195                                 if(rawSequence.length() < maxLength){
1196                                         success = pdiffs + 100;
1197                                         break;
1198                                 }
1199
1200                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1201                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
1202                                 oligo = alignment->getSeqAAln();
1203                                 string temp = alignment->getSeqBAln();
1204
1205                                 int alnLength = oligo.length();
1206
1207                                 for(int i=oligo.length()-1;i>=0;i--){
1208                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1209                                 }
1210                                 oligo = oligo.substr(0,alnLength);
1211                                 temp = temp.substr(0,alnLength);
1212
1213                                 int newStart=0;
1214                                 int numDiff = countDiffs(oligo, temp);
1215
1216 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1217
1218                                 if(numDiff < minDiff){
1219                                         minDiff = numDiff;
1220                                         minCount = 1;
1221                                         minGroup = it->second;
1222                                         minPos = 0;
1223                                         for(int i=0;i<alnLength;i++){
1224                                                 if(temp[i] != '-'){
1225                                                         minPos++;
1226                                                 }
1227                                         }
1228                                 }
1229                                 else if(numDiff == minDiff){
1230                                         minCount++;
1231                                 }
1232
1233                         }
1234
1235                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
1236                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
1237                         else{                                                                                                   //use the best match
1238                                 group = minGroup;
1239                                 seq.setUnaligned(rawSequence.substr(minPos));
1240                                 if(qual.getName() != ""){
1241                                         qual.trimQScores(minPos, -1);
1242                                 }
1243                                 success = minDiff;
1244                         }
1245
1246                         if (alignment != NULL) {  delete alignment;  }
1247
1248                 }
1249
1250                 return success;
1251
1252         }
1253         catch(exception& e) {
1254                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
1255                 exit(1);
1256         }
1257 }
1258
1259 //***************************************************************************************************************
1260
1261 bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
1262         try {
1263                 string rawSequence = seq.getUnaligned();
1264                 bool success = 0;       //guilty until proven innocent
1265
1266                 for(int i=0;i<numRPrimers;i++){
1267                         string oligo = revPrimer[i];
1268
1269                         if(rawSequence.length() < oligo.length()){
1270                                 success = 0;
1271                                 break;
1272                         }
1273
1274                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
1275                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
1276                                 if(qual.getName() != ""){
1277                                         qual.trimQScores(-1, rawSequence.length()-oligo.length());
1278                                 }
1279                                 success = 1;
1280                                 break;
1281                         }
1282                 }
1283                 return success;
1284
1285         }
1286         catch(exception& e) {
1287                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
1288                 exit(1);
1289         }
1290 }
1291
1292 //***************************************************************************************************************
1293
1294 bool TrimSeqsCommand::keepFirstTrim(Sequence& sequence, QualityScores& qscores){
1295         try {
1296                 bool success = 1;
1297                 if(qscores.getName() != ""){
1298                         qscores.trimQScores(-1, keepFirst);
1299                 }
1300                 sequence.trim(keepFirst);
1301                 return success;
1302         }
1303         catch(exception& e) {
1304                 m->errorOut(e, "keepFirstTrim", "countDiffs");
1305                 exit(1);
1306         }
1307
1308 }
1309
1310 //***************************************************************************************************************
1311
1312 bool TrimSeqsCommand::removeLastTrim(Sequence& sequence, QualityScores& qscores){
1313         try {
1314                 bool success = 0;
1315
1316                 int length = sequence.getNumBases() - removeLast;
1317
1318                 if(length > 0){
1319                         if(qscores.getName() != ""){
1320                                 qscores.trimQScores(-1, length);
1321                         }
1322                         sequence.trim(length);
1323                         success = 1;
1324                 }
1325                 else{
1326                         success = 0;
1327                 }
1328
1329                 return success;
1330         }
1331         catch(exception& e) {
1332                 m->errorOut(e, "removeLastTrim", "countDiffs");
1333                 exit(1);
1334         }
1335
1336 }
1337
1338 //***************************************************************************************************************
1339
1340 bool TrimSeqsCommand::cullLength(Sequence& seq){
1341         try {
1342
1343                 int length = seq.getNumBases();
1344                 bool success = 0;       //guilty until proven innocent
1345
1346                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
1347                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
1348                 else                                                                                            {       success = 0;    }
1349
1350                 return success;
1351
1352         }
1353         catch(exception& e) {
1354                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1355                 exit(1);
1356         }
1357
1358 }
1359
1360 //***************************************************************************************************************
1361
1362 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1363         try {
1364                 int longHomoP = seq.getLongHomoPolymer();
1365                 bool success = 0;       //guilty until proven innocent
1366
1367                 if(longHomoP <= maxHomoP){      success = 1;    }
1368                 else                                    {       success = 0;    }
1369
1370                 return success;
1371         }
1372         catch(exception& e) {
1373                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1374                 exit(1);
1375         }
1376
1377 }
1378
1379 //***************************************************************************************************************
1380
1381 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1382         try {
1383                 int numNs = seq.getAmbigBases();
1384                 bool success = 0;       //guilty until proven innocent
1385
1386                 if(numNs <= maxAmbig)   {       success = 1;    }
1387                 else                                    {       success = 0;    }
1388
1389                 return success;
1390         }
1391         catch(exception& e) {
1392                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1393                 exit(1);
1394         }
1395
1396 }
1397
1398 //***************************************************************************************************************
1399
1400 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
1401         try {
1402                 bool success = 1;
1403                 int length = oligo.length();
1404
1405                 for(int i=0;i<length;i++){
1406
1407                         if(oligo[i] != seq[i]){
1408                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
1409                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
1410                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
1411                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
1412                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
1413                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
1414                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
1415                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
1416                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1417                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1418                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
1419                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
1420
1421                                 if(success == 0)        {       break;   }
1422                         }
1423                         else{
1424                                 success = 1;
1425                         }
1426                 }
1427
1428                 return success;
1429         }
1430         catch(exception& e) {
1431                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
1432                 exit(1);
1433         }
1434
1435 }
1436 //***************************************************************************************************************
1437
1438 int TrimSeqsCommand::countDiffs(string oligo, string seq){
1439         try {
1440
1441                 int length = oligo.length();
1442                 int countDiffs = 0;
1443
1444                 for(int i=0;i<length;i++){
1445
1446                         if(oligo[i] != seq[i]){
1447                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
1448                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
1449                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
1450                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
1451                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
1452                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
1453                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
1454                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
1455                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1456                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1457                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
1458                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
1459                         }
1460
1461                 }
1462
1463                 return countDiffs;
1464         }
1465         catch(exception& e) {
1466                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
1467                 exit(1);
1468         }
1469
1470 }
1471
1472 //***************************************************************************************************************