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", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  18                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "TrimSeqsCommand", "getValidParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 TrimSeqsCommand::TrimSeqsCommand(){
  28         try {
  29                 abort = true;
  30                 //initialize outputTypes
  31                 vector<string> tempOutNames;
  32                 outputTypes["fasta"] = tempOutNames;
  33                 outputTypes["qual"] = tempOutNames;
  34                 outputTypes["group"] = tempOutNames;
  35         }
  36         catch(exception& e) {
  37                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
  38                 exit(1);
  39         }
  40 }
  41 //**********************************************************************************************************************
  42 vector<string> TrimSeqsCommand::getRequiredParameters(){
  43         try {
  44                 string Array[] =  {"fasta"};
  45                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  46                 return myArray;
  47         }
  48         catch(exception& e) {
  49                 m->errorOut(e, "TrimSeqsCommand", "getRequiredParameters");
  50                 exit(1);
  51         }
  52 }
  53 //**********************************************************************************************************************
  54 vector<string> TrimSeqsCommand::getRequiredFiles(){
  55         try {
  56                 vector<string> myArray;
  57                 return myArray;
  58         }
  59         catch(exception& e) {
  60                 m->errorOut(e, "TrimSeqsCommand", "getRequiredFiles");
  61                 exit(1);
  62         }
  63 }
  64 //***************************************************************************************************************
  65
  66 TrimSeqsCommand::TrimSeqsCommand(string option)  {
  67         try {
  68
  69                 abort = false;
  70                 comboStarts = 0;
  71
  72                 //allow user to run help
  73                 if(option == "help") { help(); abort = true; }
  74
  75                 else {
  76                         //valid paramters for this command
  77                         string AlignArray[] =  {"fasta", "flip", "group","oligos", "maxambig", "maxhomop", "minlength", "maxlength", "qfile",
  78                                                                         "qthreshold", "qwindowaverage", "qstepsize", "qwindowsize", "qaverage", "rollaverage", "allfiles", "qtrim","tdiffs", "pdiffs", "bdiffs", "processors", "outputdir","inputdir"};
  79
  80                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  81
  82                         OptionParser parser(option);
  83                         map<string,string> parameters = parser.getParameters();
  84
  85                         ValidParameters validParameter;
  86                         map<string,string>::iterator it;
  87
  88                         //check to make sure all parameters are valid for command
  89                         for (it = parameters.begin(); it != parameters.end(); it++) {
  90                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  91                         }
  92
  93                         //initialize outputTypes
  94                         vector<string> tempOutNames;
  95                         outputTypes["fasta"] = tempOutNames;
  96                         outputTypes["qual"] = tempOutNames;
  97                         outputTypes["group"] = tempOutNames;
  98
  99                         //if the user changes the input directory command factory will send this info to us in the output parameter
 100                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 101                         if (inputDir == "not found"){   inputDir = "";          }
 102                         else {
 103                                 string path;
 104                                 it = parameters.find("fasta");
 105                                 //user has given a template file
 106                                 if(it != parameters.end()){
 107                                         path = m->hasPath(it->second);
 108                                         //if the user has not given a path then, add inputdir. else leave path alone.
 109                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 110                                 }
 111
 112                                 it = parameters.find("oligos");
 113                                 //user has given a template file
 114                                 if(it != parameters.end()){
 115                                         path = m->hasPath(it->second);
 116                                         //if the user has not given a path then, add inputdir. else leave path alone.
 117                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 118                                 }
 119
 120                                 it = parameters.find("qfile");
 121                                 //user has given a template file
 122                                 if(it != parameters.end()){
 123                                         path = m->hasPath(it->second);
 124                                         //if the user has not given a path then, add inputdir. else leave path alone.
 125                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 126                                 }
 127
 128                                 it = parameters.find("group");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 134                                 }
 135                         }
 136
 137
 138                         //check for required parameters
 139                         fastaFile = validParameter.validFile(parameters, "fasta", true);
 140                         if (fastaFile == "not found") { m->mothurOut("fasta is a required parameter for the trim.seqs command."); m->mothurOutEndLine(); abort = true; }
 141                         else if (fastaFile == "not open") { abort = true; }
 142
 143                         //if the user changes the output directory command factory will send this info to us in the output parameter
 144                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 145                                 outputDir = "";
 146                                 outputDir += m->hasPath(fastaFile); //if user entered a file with a path then preserve it
 147                         }
 148
 149
 150                         //check for optional parameter and set defaults
 151                         // ...at some point should added some additional type checking...
 152                         string temp;
 153                         temp = validParameter.validFile(parameters, "flip", false);
 154                         if (temp == "not found"){       flip = 0;       }
 155                         else if(m->isTrue(temp))        {       flip = 1;       }
 156
 157                         temp = validParameter.validFile(parameters, "oligos", true);
 158                         if (temp == "not found"){       oligoFile = "";         }
 159                         else if(temp == "not open"){    abort = true;   }
 160                         else                                    {       oligoFile = temp;               }
 161
 162                         temp = validParameter.validFile(parameters, "group", true);
 163                         if (temp == "not found"){       groupfile = "";         }
 164                         else if(temp == "not open"){    abort = true;   }
 165                         else                                    {       groupfile = temp;               }
 166
 167                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 168                         convert(temp, maxAmbig);
 169
 170                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "0"; }
 171                         convert(temp, maxHomoP);
 172
 173                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "0"; }
 174                         convert(temp, minLength);
 175
 176                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "0"; }
 177                         convert(temp, maxLength);
 178
 179                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found") { temp = "0"; }
 180                         convert(temp, bdiffs);
 181
 182                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 183                         convert(temp, pdiffs);
 184
 185                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs;  temp = toString(tempTotal); }
 186                         convert(temp, tdiffs);
 187
 188                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs;       }
 189
 190                         temp = validParameter.validFile(parameters, "qfile", true);
 191                         if (temp == "not found")        {       qFileName = "";         }
 192                         else if(temp == "not open")     {       abort = true;           }
 193                         else                                            {       qFileName = temp;       }
 194
 195                         temp = validParameter.validFile(parameters, "qthreshold", false);       if (temp == "not found") { temp = "0"; }
 196                         convert(temp, qThreshold);
 197
 198                         temp = validParameter.validFile(parameters, "qtrim", false);            if (temp == "not found") { temp = "F"; }
 199                         qtrim = m->isTrue(temp);
 200
 201                         temp = validParameter.validFile(parameters, "rollaverage", false);      if (temp == "not found") { temp = "0"; }
 202                         convert(temp, qRollAverage);
 203
 204                         temp = validParameter.validFile(parameters, "qwindowaverage", false);if (temp == "not found") { temp = "0"; }
 205                         convert(temp, qWindowAverage);
 206
 207                         temp = validParameter.validFile(parameters, "qwindowsize", false);      if (temp == "not found") { temp = "100"; }
 208                         convert(temp, qWindowSize);
 209
 210                         temp = validParameter.validFile(parameters, "qstepsize", false);                if (temp == "not found") { temp = "10"; }
 211                         convert(temp, qWindowStep);
 212
 213                         temp = validParameter.validFile(parameters, "qaverage", false);         if (temp == "not found") { temp = "0"; }
 214                         convert(temp, qAverage);
 215
 216                         temp = validParameter.validFile(parameters, "allfiles", false);         if (temp == "not found") { temp = "F"; }
 217                         allFiles = m->isTrue(temp);
 218
 219                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found") { temp = "1"; }
 220                         convert(temp, processors);
 221
 222                         if ((oligoFile != "") && (groupfile != "")) {
 223                                 m->mothurOut("You given both a oligos file and a groupfile, only one is allowed."); m->mothurOutEndLine(); abort = true;
 224                         }
 225
 226
 227                         if(allFiles && (oligoFile == "") && (groupfile == "")){
 228                                 m->mothurOut("You selected allfiles, but didn't enter an oligos or group file.  Ignoring the allfiles request."); m->mothurOutEndLine();
 229                         }
 230                         if((qAverage != 0 && qThreshold != 0) && qFileName == ""){
 231                                 m->mothurOut("You didn't provide a quality file name, quality criteria will be ignored."); m->mothurOutEndLine();
 232                                 qAverage=0;
 233                                 qThreshold=0;
 234                         }
 235                         if(!flip && oligoFile=="" && !maxLength && !minLength && (maxAmbig==-1) && !maxHomoP && qFileName == ""){
 236                                 m->mothurOut("You didn't set any options... quiting command."); m->mothurOutEndLine();
 237                                 abort = true;
 238                         }
 239                 }
 240
 241         }
 242         catch(exception& e) {
 243                 m->errorOut(e, "TrimSeqsCommand", "TrimSeqsCommand");
 244                 exit(1);
 245         }
 246 }
 247 //**********************************************************************************************************************
 248
 249 void TrimSeqsCommand::help(){
 250         try {
 251                 m->mothurOut("The trim.seqs command reads a fastaFile and creates .....\n");
 252                 m->mothurOut("The trim.seqs command parameters are fasta, flip, oligos, group, maxambig, maxhomop, minlength, maxlength, qfile, qthreshold, qaverage, diffs, qtrim and allfiles.\n");
 253                 m->mothurOut("The fasta parameter is required.\n");
 254                 m->mothurOut("The group parameter allows you to enter a group file for your fasta file.\n");
 255                 m->mothurOut("The flip parameter will output the reverse compliment of your trimmed sequence. The default is false.\n");
 256                 m->mothurOut("The oligos parameter .... The default is "".\n");
 257                 m->mothurOut("The maxambig parameter .... The default is -1.\n");
 258                 m->mothurOut("The maxhomop parameter .... The default is 0.\n");
 259                 m->mothurOut("The minlength parameter .... The default is 0.\n");
 260                 m->mothurOut("The maxlength parameter .... The default is 0.\n");
 261                 m->mothurOut("The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs.\n");
 262                 m->mothurOut("The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n");
 263                 m->mothurOut("The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n");
 264                 m->mothurOut("The qfile parameter .....\n");
 265                 m->mothurOut("The qthreshold parameter .... The default is 0.\n");
 266                 m->mothurOut("The qaverage parameter .... The default is 0.\n");
 267                 m->mothurOut("The allfiles parameter .... The default is F.\n");
 268                 m->mothurOut("The qtrim parameter .... The default is F.\n");
 269                 m->mothurOut("The trim.seqs command should be in the following format: \n");
 270                 m->mothurOut("trim.seqs(fasta=yourFastaFile, flip=yourFlip, oligos=yourOligos, maxambig=yourMaxambig,  \n");
 271                 m->mothurOut("maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n");
 272                 m->mothurOut("Example trim.seqs(fasta=abrecovery.fasta, flip=..., oligos=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n");
 273                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n");
 274                 m->mothurOut("For more details please check out the wiki http://www.mothur.org/wiki/Trim.seqs .\n\n");
 275
 276         }
 277         catch(exception& e) {
 278                 m->errorOut(e, "TrimSeqsCommand", "help");
 279                 exit(1);
 280         }
 281 }
 282
 283
 284 //***************************************************************************************************************
 285
 286 TrimSeqsCommand::~TrimSeqsCommand(){    /*      do nothing      */      }
 287
 288 //***************************************************************************************************************
 289
 290 int TrimSeqsCommand::execute(){
 291         try{
 292
 293                 if (abort == true) { return 0; }
 294
 295                 numFPrimers = 0;  //this needs to be initialized
 296                 numRPrimers = 0;
 297                 vector<string> fastaFileNames;
 298                 vector<string> qualFileNames;
 299
 300                 string trimSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.fasta";
 301                 outputNames.push_back(trimSeqFile); outputTypes["fasta"].push_back(trimSeqFile);
 302                 string scrapSeqFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.fasta";
 303                 outputNames.push_back(scrapSeqFile); outputTypes["fasta"].push_back(scrapSeqFile);
 304                 string trimQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "trim.qual";
 305                 string scrapQualFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "scrap.qual";
 306                 if (qFileName != "") {  outputNames.push_back(trimQualFile); outputNames.push_back(scrapQualFile);  outputTypes["qual"].push_back(trimQualFile); outputTypes["qual"].push_back(scrapQualFile); }
 307                 string groupFile = "";
 308                 if (groupfile == "") { groupFile = outputDir + m->getRootName(m->getSimpleName(fastaFile)) + "groups"; }
 309                 else{
 310                         groupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "trim.groups";
 311                         outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
 312                         groupMap = new GroupMap(groupfile);
 313                         groupMap->readMap();
 314
 315                         if(allFiles){
 316                                 for (int i = 0; i < groupMap->namesOfGroups.size(); i++) {
 317                                         groupToIndex[groupMap->namesOfGroups[i]] = i;
 318                                         groupVector.push_back(groupMap->namesOfGroups[i]);
 319                                         fastaFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) +  groupMap->namesOfGroups[i] + ".fasta"));
 320
 321                                         //we append later, so we want to clear file
 322                                         ofstream outRemove;
 323                                         m->openOutputFile(fastaFileNames[i], outRemove);
 324                                         outRemove.close();
 325                                         if(qFileName != ""){
 326                                                 qualFileNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) +  groupMap->namesOfGroups[i] + ".qual"));
 327                                                 ofstream outRemove2;
 328                                                 m->openOutputFile(qualFileNames[i], outRemove2);
 329                                                 outRemove2.close();
 330                                         }
 331                                 }
 332                         }
 333                         comboStarts = fastaFileNames.size()-1;
 334                 }
 335
 336                 if(oligoFile != ""){
 337                         outputNames.push_back(groupFile); outputTypes["group"].push_back(groupFile);
 338                         getOligos(fastaFileNames, qualFileNames);
 339                 }
 340
 341                 vector<unsigned long int> fastaFilePos;
 342                 vector<unsigned long int> qFilePos;
 343
 344                 setLines(fastaFile, qFileName, fastaFilePos, qFilePos);
 345
 346                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 347                         lines.push_back(new linePair(fastaFilePos[i], fastaFilePos[(i+1)]));
 348                         if (qFileName != "") {  qLines.push_back(new linePair(qFilePos[i], qFilePos[(i+1)]));  }
 349                 }
 350                 if(qFileName == "")     {       qLines = lines; } //files with duds
 351
 352                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 353                                 if(processors == 1){
 354
 355                                         driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 356
 357                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 358                                                 rename((fastaFileNames[j] + toString(getpid()) + ".temp").c_str(), fastaFileNames[j].c_str());
 359                                         }
 360                                         if(qFileName != ""){
 361                                                 for (int j = 0; j < qualFileNames.size(); j++) {
 362                                                         rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
 363                                                 }
 364                                         }
 365
 366                                 }else{
 367                                         createProcessesCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames);
 368
 369                                         rename((trimSeqFile + toString(processIDS[0]) + ".temp").c_str(), trimSeqFile.c_str());
 370                                         rename((scrapSeqFile + toString(processIDS[0]) + ".temp").c_str(), scrapSeqFile.c_str());
 371                                         rename((groupFile + toString(processIDS[0]) + ".temp").c_str(), groupFile.c_str());
 372
 373                                         if(qFileName != ""){
 374                                                 rename((trimQualFile + toString(processIDS[0]) + ".temp").c_str(), trimQualFile.c_str());
 375                                                 rename((scrapQualFile + toString(processIDS[0]) + ".temp").c_str(), scrapQualFile.c_str());
 376                                         }
 377
 378
 379                                         for (int j = 0; j < fastaFileNames.size(); j++) {
 380                                                 rename((fastaFileNames[j] + toString(processIDS[0]) + ".temp").c_str(), fastaFileNames[j].c_str());
 381                                         }
 382                                         if(qFileName != ""){
 383                                                 for (int j = 0; j < qualFileNames.size(); j++) {
 384                                                         rename((qualFileNames[j] + toString(getpid()) + ".temp").c_str(), qualFileNames[j].c_str());
 385                                                 }
 386                                         }
 387
 388                                         //append files
 389                                         for(int i=1;i<processors;i++){
 390                                                 m->appendFiles((trimSeqFile + toString(processIDS[i]) + ".temp"), trimSeqFile);
 391                                                 remove((trimSeqFile + toString(processIDS[i]) + ".temp").c_str());
 392                                                 m->appendFiles((scrapSeqFile + toString(processIDS[i]) + ".temp"), scrapSeqFile);
 393                                                 remove((scrapSeqFile + toString(processIDS[i]) + ".temp").c_str());
 394
 395                                                 m->appendFiles((trimQualFile + toString(processIDS[i]) + ".temp"), trimQualFile);
 396                                                 remove((trimQualFile + toString(processIDS[i]) + ".temp").c_str());
 397                                                 m->appendFiles((scrapQualFile + toString(processIDS[i]) + ".temp"), scrapQualFile);
 398                                                 remove((scrapQualFile + toString(processIDS[i]) + ".temp").c_str());
 399
 400                                                 m->appendFiles((groupFile + toString(processIDS[i]) + ".temp"), groupFile);
 401                                                 remove((groupFile + toString(processIDS[i]) + ".temp").c_str());
 402                                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 403                                                         m->appendFiles((fastaFileNames[j] + toString(processIDS[i]) + ".temp"), fastaFileNames[j]);
 404                                                         remove((fastaFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 405                                                 }
 406
 407                                                 if(qFileName != ""){
 408                                                         for (int j = 0; j < qualFileNames.size(); j++) {
 409                                                                 m->appendFiles((qualFileNames[j] + toString(processIDS[i]) + ".temp"), qualFileNames[j]);
 410                                                                 remove((qualFileNames[j] + toString(processIDS[i]) + ".temp").c_str());
 411                                                         }
 412                                                 }
 413
 414
 415                                         }
 416                                 }
 417
 418                                 if (m->control_pressed) {  return 0; }
 419                 #else
 420                                 driverCreateTrim(fastaFile, qFileName, trimSeqFile, scrapSeqFile, trimQualFile, scrapQualFile, groupFile, fastaFileNames, qualFileNames, lines[0], qLines[0]);
 421
 422                                 for (int j = 0; j < fastaFileNames.size(); j++) {
 423                                         rename((fastaFileNames[j] + toString(j) + ".temp").c_str(), fastaFileNames[j].c_str());
 424                                 }
 425                                 if(qFileName != ""){
 426                                         for (int j = 0; j < qualFileNames.size(); j++) {
 427                                                 rename((qualFileNames[j] + toString(j) + ".temp").c_str(), qualFileNames[j].c_str());
 428                                         }
 429                                 }
 430
 431                                 if (m->control_pressed) {  return 0; }
 432                 #endif
 433
 434
 435                 for(int i=0;i<fastaFileNames.size();i++){
 436                         if (m->isBlank(fastaFileNames[i])) { remove(fastaFileNames[i].c_str()); }
 437                         else if (filesToRemove.count(fastaFileNames[i]) > 0) { remove(fastaFileNames[i].c_str()); }
 438                         else {
 439                                 ifstream inFASTA;
 440                                 string seqName;
 441                                 m->openInputFile(fastaFileNames[i], inFASTA);
 442                                 ofstream outGroups;
 443                                 string outGroupFilename = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + "groups";
 444                                 m->openOutputFile(outGroupFilename, outGroups);
 445                                 outputNames.push_back(outGroupFilename); outputTypes["group"].push_back(outGroupFilename);
 446
 447                                 string thisGroup = "";
 448                                 if (i > comboStarts) {
 449                                         map<string, int>::iterator itCombo;
 450                                         for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
 451                                                 if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
 452                                         }
 453                                 }else{ thisGroup = groupVector[i]; }
 454
 455                                 while(!inFASTA.eof()){
 456                                         if(inFASTA.get() == '>'){
 457                                                 inFASTA >> seqName;
 458                                                 outGroups << seqName << '\t' << thisGroup << endl;
 459                                         }
 460                                         while (!inFASTA.eof())  {       char c = inFASTA.get(); if (c == 10 || c == 13){        break;  }       }
 461                                 }
 462                                 outGroups.close();
 463                                 inFASTA.close();
 464                         }
 465                 }
 466
 467                 if(qFileName != ""){
 468                         for(int i=0;i<qualFileNames.size();i++){
 469                                 if (m->isBlank(qualFileNames[i])) { remove(qualFileNames[i].c_str());   }
 470                                 else if (filesToRemove.count(qualFileNames[i]) > 0) { remove(qualFileNames[i].c_str()); }
 471                                 else {
 472                                         ifstream inQual;
 473                                         string seqName;
 474                                         m->openInputFile(qualFileNames[i], inQual);
 475 //                                      ofstream outGroups;
 476 //
 477 //                                      string thisGroup = "";
 478 //                                      if (i > comboStarts) {
 479 //                                              map<string, int>::iterator itCombo;
 480 //                                              for(itCombo=combos.begin();itCombo!=combos.end(); itCombo++){
 481 //                                                      if(itCombo->second == i){       thisGroup = itCombo->first;     combos.erase(itCombo);  break;  }
 482 //                                              }
 483 //                                      }
 484 //                                      else{ thisGroup = groupVector[i]; }
 485
 486                                         inQual.close();
 487                                 }
 488                         }
 489                 }
 490
 491
 492                 if (m->control_pressed) {
 493                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 494                         return 0;
 495                 }
 496
 497                 m->mothurOutEndLine();
 498                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 499                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 500                 m->mothurOutEndLine();
 501
 502                 return 0;
 503
 504         }
 505         catch(exception& e) {
 506                 m->errorOut(e, "TrimSeqsCommand", "execute");
 507                 exit(1);
 508         }
 509 }
 510
 511 /**************************************************************************************/
 512
 513 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) {
 514
 515         try {
 516
 517                 ofstream outFASTA;
 518                 int able = m->openOutputFile(trimFile, outFASTA);
 519
 520                 ofstream scrapFASTA;
 521                 m->openOutputFile(scrapFile, scrapFASTA);
 522
 523                 ofstream outQual;
 524                 ofstream scrapQual;
 525                 if(qFileName != ""){
 526                         m->openOutputFile(trimQFile, outQual);
 527                         m->openOutputFile(scrapQFile, scrapQual);
 528                 }
 529
 530                 ofstream outGroups;
 531                 //vector<ofstream*> fastaFileNames;
 532                 //vector<ofstream*> qualFileNames;
 533
 534                 if (oligoFile != "") {
 535                         m->openOutputFile(groupFile, outGroups);
 536                         for (int i = 0; i < fastaNames.size(); i++) {
 537
 538                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 539                                 fastaNames[i] = (fastaNames[i] + toString(getpid()) + ".temp");
 540                                 //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 541                                 //clear old file if it exists
 542                                 ofstream temp;
 543                                 m->openOutputFile(fastaNames[i], temp);
 544                                 temp.close();
 545                                 if(qFileName != ""){
 546                                         qualNames[i] = (qualNames[i] + toString(getpid()) + ".temp");
 547                                         //qualFileNames.push_back(new ofstream((qualNames[i] + toString(getpid()) + ".temp").c_str(), ios::ate));
 548                                         //clear old file if it exists
 549                                         ofstream temp2;
 550                                         m->openOutputFile(qualNames[i], temp2);
 551                                         temp2.close();
 552                                 }
 553                         #else
 554                                 //fastaFileNames.push_back(new ofstream((fastaNames[i] + toString(i) + ".temp").c_str(), ios::ate));
 555                                 fastaNames[i] = (fastaNames[i] + toString(i) + ".temp");
 556                                 ofstream temp;
 557                                 m->openOutputFile(fastaNames[i], temp);
 558                                 temp.close();
 559                                 if(qFileName != ""){
 560                                         //qualFileNames.push_back(new ofstream((qualNames[i] + toString(i) + ".temp").c_str(), ios::ate));
 561                                         qualNames[i] = (qualNames[i] + toString(i) + ".temp");
 562                                         ofstream temp2;
 563                                         m->openOutputFile(qualNames[i], temp2);
 564                                         temp2.close();
 565                                 }
 566                         #endif
 567                         }
 568                 }
 569
 570                 ifstream inFASTA;
 571                 m->openInputFile(filename, inFASTA);
 572                 inFASTA.seekg(line->start);
 573
 574                 ifstream qFile;
 575                 if(qFileName != "")     {       m->openInputFile(qFileName, qFile);     qFile.seekg(qline->start);  }
 576
 577                 bool done = false;
 578                 int count = 0;
 579
 580                 while (!done) {
 581
 582                         if (m->control_pressed) {
 583                                 inFASTA.close(); outFASTA.close(); scrapFASTA.close();
 584                                 if (oligoFile != "") {   outGroups.close();   }
 585
 586                                 //for(int i=0;i<fastaFileNames.size();i++){  fastaFileNames[i]->close(); delete fastaFileNames[i];  }
 587
 588                                 if(qFileName != ""){
 589                                         qFile.close();
 590                                         //for(int i=0;i<qualFileNames.size();i++){  qualFileNames[i]->close(); delete qualFileNames[i];  }
 591                                 }
 592                                 for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str()); }
 593
 594                                 return 0;
 595                         }
 596
 597                         int success = 1;
 598
 599
 600                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
 601
 602                         QualityScores currQual;
 603                         if(qFileName != ""){
 604                                 currQual = QualityScores(qFile, currSeq.getNumBases());  m->gobble(qFile);
 605                         }
 606
 607                         string origSeq = currSeq.getUnaligned();
 608                         if (origSeq != "") {
 609                                 int groupBar, groupPrime;
 610                                 string trashCode = "";
 611                                 int currentSeqsDiffs = 0;
 612
 613                                 if(qFileName != ""){
 614                                         if(qThreshold != 0)                     {       success = currQual.stripQualThreshold(currSeq, qThreshold);                     }
 615                                         else if(qAverage != 0)          {       success = currQual.cullQualAverage(currSeq, qAverage);                          }
 616                                         else if(qRollAverage != 0)      {       success = currQual.stripQualRollingAverage(currSeq, qRollAverage);      }
 617                                         else if(qWindowAverage != 0){   success = currQual.stripQualWindowAverage(currSeq, qWindowStep, qWindowSize, qWindowAverage);   }
 618
 619                                         if (qtrim == 1 && (origSeq.length() != currSeq.getUnaligned().length())) {
 620                                                 success = 0; //if you don't want to trim and the sequence does not meet quality requirements, move to scrap
 621                                         }
 622
 623                                         if(!success)                            {       trashCode += 'q';       }
 624                                 }
 625
 626                                 if(barcodes.size() != 0){
 627                                         success = stripBarcode(currSeq, currQual, groupBar);
 628                                         if(success > bdiffs)            {       trashCode += 'b';       }
 629                                         else{ currentSeqsDiffs += success;  }
 630                                 }
 631
 632                                 if(numFPrimers != 0){
 633                                         success = stripForward(currSeq, currQual, groupPrime);
 634                                         if(success > pdiffs)            {       trashCode += 'f';       }
 635                                         else{ currentSeqsDiffs += success;  }
 636                                 }
 637
 638                                 if (currentSeqsDiffs > tdiffs)  {       trashCode += 't';   }
 639
 640                                 if(numRPrimers != 0){
 641                                         success = stripReverse(currSeq, currQual);
 642                                         if(!success)                            {       trashCode += 'r';       }
 643                                 }
 644
 645                                 if(minLength > 0 || maxLength > 0){
 646                                         success = cullLength(currSeq);
 647                                         if(!success)                            {       trashCode += 'l';       }
 648                                 }
 649                                 if(maxHomoP > 0){
 650                                         success = cullHomoP(currSeq);
 651                                         if(!success)                            {       trashCode += 'h';       }
 652                                 }
 653                                 if(maxAmbig != -1){
 654                                         success = cullAmbigs(currSeq);
 655                                         if(!success)                            {       trashCode += 'n';       }
 656                                 }
 657
 658                                 if(flip){       currSeq.reverseComplement();            currQual.flipQScores(); }               // should go last
 659
 660                                 if(trashCode.length() == 0){
 661                                         currSeq.setAligned(currSeq.getUnaligned());
 662                                         currSeq.printSequence(outFASTA);
 663                                         currQual.printQScores(outQual);
 664
 665                                         if(barcodes.size() != 0){
 666                                                 string thisGroup = groupVector[groupBar];
 667                                                 int indexToFastaFile = groupBar;
 668                                                 if (primers.size() != 0){
 669                                                         //does this primer have a group
 670                                                         if (groupVector[groupPrime] != "") {
 671                                                                 thisGroup += "." + groupVector[groupPrime];
 672                                                                 indexToFastaFile = combos[thisGroup];
 673                                                         }
 674                                                 }
 675                                                 outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 676                                                 if(allFiles){
 677                                                         ofstream outTemp;
 678                                                         m->openOutputFileAppend(fastaNames[indexToFastaFile], outTemp);
 679                                                         //currSeq.printSequence(*fastaFileNames[indexToFastaFile]);
 680                                                         currSeq.printSequence(outTemp);
 681                                                         outTemp.close();
 682
 683                                                         if(qFileName != ""){
 684                                                                 //currQual.printQScores(*qualFileNames[indexToFastaFile]);
 685                                                                 ofstream outTemp2;
 686                                                                 m->openOutputFileAppend(qualNames[indexToFastaFile], outTemp2);
 687                                                                 currQual.printQScores(outTemp2);
 688                                                                 outTemp2.close();
 689                                                         }
 690                                                 }
 691                                         }
 692
 693                                         if (groupfile != "") {
 694                                                 string thisGroup = groupMap->getGroup(currSeq.getName());
 695
 696                                                 if (thisGroup != "not found") {
 697                                                         outGroups << currSeq.getName() << '\t' << thisGroup << endl;
 698                                                         if (allFiles) {
 699                                                                 ofstream outTemp;
 700                                                                 m->openOutputFileAppend(fastaNames[groupToIndex[thisGroup]], outTemp);
 701                                                                 currSeq.printSequence(outTemp);
 702                                                                 outTemp.close();
 703                                                                 if(qFileName != ""){
 704                                                                         ofstream outTemp2;
 705                                                                         m->openOutputFileAppend(qualNames[groupToIndex[thisGroup]], outTemp2);
 706                                                                         currQual.printQScores(outTemp2);
 707                                                                         outTemp2.close();
 708                                                                 }
 709                                                         }
 710                                                 }else{
 711                                                         m->mothurOut(currSeq.getName() + " is not in your groupfile, adding to group XXX."); m->mothurOutEndLine();
 712                                                         outGroups << currSeq.getName() << '\t' << "XXX" << endl;
 713                                                         if (allFiles) {
 714                                                                 m->mothurOut("[ERROR]: " + currSeq.getName() + " will not be added to any .group.fasta or .group.qual file."); m->mothurOutEndLine();
 715                                                         }
 716                                                 }
 717                                         }
 718                                 }
 719                                 else{
 720                                         currSeq.setName(currSeq.getName() + '|' + trashCode);
 721                                         currSeq.setUnaligned(origSeq);
 722                                         currSeq.setAligned(origSeq);
 723                                         currSeq.printSequence(scrapFASTA);
 724                                         currQual.printQScores(scrapQual);
 725                                 }
 726                                 count++;
 727                         }
 728
 729                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 730                                 unsigned long int pos = inFASTA.tellg();
 731                                 if ((pos == -1) || (pos >= line->end)) { break; }
 732                         #else
 733                                 if (inFASTA.eof()) { break; }
 734                         #endif
 735
 736                         //report progress
 737                         if((count) % 1000 == 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 738
 739                 }
 740                 //report progress
 741                 if((count) % 1000 != 0){        m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 742
 743
 744                 inFASTA.close();
 745                 outFASTA.close();
 746                 scrapFASTA.close();
 747                 if (oligoFile != "") {   outGroups.close();   }
 748                 if(qFileName != "")     {       qFile.close();  scrapQual.close(); outQual.close();     }
 749
 750                 //for(int i=0;i<fastaFileNames.size();i++){
 751                 //      fastaFileNames[i]->close();
 752                 //      delete fastaFileNames[i];
 753                 //}
 754
 755                 //if(qFileName != ""){
 756                         //for(int i=0;i<qualFileNames.size();i++){
 757                                 //qualFileNames[i]->close();
 758                                 //delete qualFileNames[i];
 759                         //}
 760                 //}
 761
 762                 return count;
 763         }
 764         catch(exception& e) {
 765                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 766                 exit(1);
 767         }
 768 }
 769
 770 /**************************************************************************************************/
 771
 772 int TrimSeqsCommand::createProcessesCreateTrim(string filename, string qFileName, string trimFile, string scrapFile, string trimQFile, string scrapQFile, string groupFile, vector<string> fastaNames, vector<string> qualNames) {
 773         try {
 774 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 775                 int process = 0;
 776                 int exitCommand = 1;
 777                 processIDS.clear();
 778
 779                 //loop through and create all the processes you want
 780                 while (process != processors) {
 781                         int pid = fork();
 782
 783                         if (pid > 0) {
 784                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 785                                 process++;
 786                         }else if (pid == 0){
 787                                 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]);
 788                                 exit(0);
 789                         }else {
 790                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 791                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 792                                 exit(0);
 793                         }
 794                 }
 795
 796                 //force parent to wait until all the processes are done
 797                 for (int i=0;i<processors;i++) {
 798                         int temp = processIDS[i];
 799                         wait(&temp);
 800                 }
 801
 802                 return exitCommand;
 803 #endif
 804         }
 805         catch(exception& e) {
 806                 m->errorOut(e, "TrimSeqsCommand", "createProcessesCreateTrim");
 807                 exit(1);
 808         }
 809 }
 810
 811 /**************************************************************************************************/
 812
 813 int TrimSeqsCommand::setLines(string filename, string qfilename, vector<unsigned long int>& fastaFilePos, vector<unsigned long int>& qfileFilePos) {
 814         try {
 815
 816                 //set file positions for fasta file
 817                 fastaFilePos = m->divideFile(filename, processors);
 818
 819                 if (qfilename == "") { return processors; }
 820
 821                 //get name of first sequence in each chunk
 822                 map<string, int> firstSeqNames;
 823                 for (int i = 0; i < (fastaFilePos.size()-1); i++) {
 824                         ifstream in;
 825                         m->openInputFile(filename, in);
 826                         in.seekg(fastaFilePos[i]);
 827
 828                         Sequence temp(in);
 829                         firstSeqNames[temp.getName()] = i;
 830
 831                         in.close();
 832                 }
 833
 834                 //seach for filePos of each first name in the qfile and save in qfileFilePos
 835                 ifstream inQual;
 836                 m->openInputFile(qfilename, inQual);
 837
 838                 string input;
 839                 while(!inQual.eof()){
 840                         input = m->getline(inQual);
 841
 842                         if (input.length() != 0) {
 843                                 if(input[0] == '>'){ //this is a sequence name line
 844                                         istringstream nameStream(input);
 845
 846                                         string sname = "";  nameStream >> sname;
 847                                         sname = sname.substr(1);
 848
 849                                         map<string, int>::iterator it = firstSeqNames.find(sname);
 850
 851                                         if(it != firstSeqNames.end()) { //this is the start of a new chunk
 852                                                 unsigned long int pos = inQual.tellg();
 853                                                 qfileFilePos.push_back(pos - input.length() - 1);
 854                                                 firstSeqNames.erase(it);
 855                                         }
 856                                 }
 857                         }
 858
 859                         if (firstSeqNames.size() == 0) { break; }
 860                 }
 861                 inQual.close();
 862
 863
 864                 if (firstSeqNames.size() != 0) {
 865                         for (map<string, int>::iterator it = firstSeqNames.begin(); it != firstSeqNames.end(); it++) {
 866                                 m->mothurOut(it->first + " is in your fasta file and not in your quality file, not using quality file."); m->mothurOutEndLine();
 867                         }
 868                         qFileName = "";
 869                         return processors;
 870                 }
 871
 872                 //get last file position of qfile
 873                 FILE * pFile;
 874                 unsigned long int size;
 875
 876                 //get num bytes in file
 877                 pFile = fopen (qfilename.c_str(),"rb");
 878                 if (pFile==NULL) perror ("Error opening file");
 879                 else{
 880                         fseek (pFile, 0, SEEK_END);
 881                         size=ftell (pFile);
 882                         fclose (pFile);
 883                 }
 884
 885                 qfileFilePos.push_back(size);
 886
 887                 return processors;
 888         }
 889         catch(exception& e) {
 890                 m->errorOut(e, "TrimSeqsCommand", "setLines");
 891                 exit(1);
 892         }
 893 }
 894 //***************************************************************************************************************
 895
 896 void TrimSeqsCommand::getOligos(vector<string>& outFASTAVec, vector<string>& outQualVec){
 897         try {
 898                 ifstream inOligos;
 899                 m->openInputFile(oligoFile, inOligos);
 900
 901                 ofstream test;
 902
 903                 string type, oligo, group;
 904                 int index=0;
 905                 //int indexPrimer = 0;
 906
 907                 while(!inOligos.eof()){
 908                         inOligos >> type;
 909
 910                         if(type[0] == '#'){
 911                                 while (!inOligos.eof()) {       char c = inOligos.get(); if (c == 10 || c == 13){       break;  }       } // get rest of line if there's any crap there
 912                         }
 913                         else{
 914                                 //make type case insensitive
 915                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
 916
 917                                 inOligos >> oligo;
 918
 919                                 for(int i=0;i<oligo.length();i++){
 920                                         oligo[i] = toupper(oligo[i]);
 921                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 922                                 }
 923
 924                                 if(type == "FORWARD"){
 925                                         group = "";
 926
 927                                         // get rest of line in case there is a primer name
 928                                         while (!inOligos.eof()) {
 929                                                 char c = inOligos.get();
 930                                                 if (c == 10 || c == 13){        break;  }
 931                                                 else if (c == 32 || c == 9){;} //space or tab
 932                                                 else {  group += c;  }
 933                                         }
 934
 935                                         //check for repeat barcodes
 936                                         map<string, int>::iterator itPrime = primers.find(oligo);
 937                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 938
 939                                         primers[oligo]=index; index++;
 940                                         groupVector.push_back(group);
 941
 942                                         if(allFiles){
 943                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 944                                                 if(qFileName != ""){
 945                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 946                                                 }
 947                                                 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
 948                                                         filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 949                                                         if(qFileName != ""){
 950                                                                 filesToRemove.insert((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 951                                                         }
 952                                                 }else {
 953                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 954                                                         outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 955                                                         if(qFileName != ""){
 956                                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 957                                                                 outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 958                                                         }
 959                                                 }
 960                                         }
 961
 962                                 }
 963                                 else if(type == "REVERSE"){
 964                                         Sequence oligoRC("reverse", oligo);
 965                                         oligoRC.reverseComplement();
 966                                         revPrimer.push_back(oligoRC.getUnaligned());
 967                                 }
 968                                 else if(type == "BARCODE"){
 969                                         inOligos >> group;
 970
 971                                         //check for repeat barcodes
 972                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 973                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 974
 975                                         barcodes[oligo]=index; index++;
 976                                         groupVector.push_back(group);
 977
 978                                         if(allFiles){
 979                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 980                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 981                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + group + ".fasta"));
 982                                                 if(qFileName != ""){
 983                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 984                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 985                                                         outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + group + ".qual"));
 986                                                 }
 987                                         }
 988                                 }else{  m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();  }
 989                         }
 990                         m->gobble(inOligos);
 991                 }
 992
 993                 inOligos.close();
 994
 995                 //add in potential combos
 996                 if(allFiles){
 997                         comboStarts = outFASTAVec.size()-1;
 998                         for (map<string, int>::iterator itBar = barcodes.begin(); itBar != barcodes.end(); itBar++) {
 999                                 for (map<string, int>::iterator itPrime = primers.begin(); itPrime != primers.end(); itPrime++) {
1000                                         if (groupVector[itPrime->second] != "") { //there is a group for this primer
1001                                                 outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
1002                                                 outputTypes["fasta"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
1003                                                 outFASTAVec.push_back((outputDir + m->getRootName(m->getSimpleName(fastaFile)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".fasta"));
1004                                                 combos[(groupVector[itBar->second] + "." + groupVector[itPrime->second])] = outFASTAVec.size()-1;
1005
1006                                                 if(qFileName != ""){
1007                                                         outQualVec.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
1008                                                         outputNames.push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
1009                                                         outputTypes["qual"].push_back((outputDir + m->getRootName(m->getSimpleName(qFileName)) + groupVector[itBar->second] + "." + groupVector[itPrime->second] + ".qual"));
1010                                                 }
1011                                         }
1012                                 }
1013                         }
1014                 }
1015
1016                 numFPrimers = primers.size();
1017                 numRPrimers = revPrimer.size();
1018
1019         }
1020         catch(exception& e) {
1021                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
1022                 exit(1);
1023         }
1024 }
1025 //***************************************************************************************************************
1026
1027 int TrimSeqsCommand::stripBarcode(Sequence& seq, QualityScores& qual, int& group){
1028         try {
1029
1030                 string rawSequence = seq.getUnaligned();
1031                 int success = bdiffs + 1;       //guilty until proven innocent
1032
1033                 //can you find the barcode
1034                 for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
1035                         string oligo = it->first;
1036                         if(rawSequence.length() < oligo.length()){      //let's just assume that the barcodes are the same length
1037                                 success = bdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
1038                                 break;
1039                         }
1040
1041                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
1042                                 group = it->second;
1043                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
1044
1045                                 if(qual.getName() != ""){
1046                                         qual.trimQScores(oligo.length(), -1);
1047                                 }
1048
1049                                 success = 0;
1050                                 break;
1051                         }
1052                 }
1053
1054                 //if you found the barcode or if you don't want to allow for diffs
1055 //              cout << success;
1056                 if ((bdiffs == 0) || (success == 0)) { return success;  }
1057
1058                 else { //try aligning and see if you can find it
1059 //                      cout << endl;
1060
1061                         int maxLength = 0;
1062
1063                         Alignment* alignment;
1064                         if (barcodes.size() > 0) {
1065                                 map<string,int>::iterator it=barcodes.begin();
1066
1067                                 for(it;it!=barcodes.end();it++){
1068                                         if(it->first.length() > maxLength){
1069                                                 maxLength = it->first.length();
1070                                         }
1071                                 }
1072                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+bdiffs+1));
1073
1074                         }else{ alignment = NULL; }
1075
1076                         //can you find the barcode
1077                         int minDiff = 1e6;
1078                         int minCount = 1;
1079                         int minGroup = -1;
1080                         int minPos = 0;
1081
1082                         for(map<string,int>::iterator it=barcodes.begin();it!=barcodes.end();it++){
1083                                 string oligo = it->first;
1084 //                              int length = oligo.length();
1085
1086                                 if(rawSequence.length() < maxLength){   //let's just assume that the barcodes are the same length
1087                                         success = bdiffs + 10;
1088                                         break;
1089                                 }
1090
1091                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1092                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+bdiffs));
1093                                 oligo = alignment->getSeqAAln();
1094                                 string temp = alignment->getSeqBAln();
1095
1096                                 int alnLength = oligo.length();
1097
1098                                 for(int i=oligo.length()-1;i>=0;i--){
1099                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1100                                 }
1101                                 oligo = oligo.substr(0,alnLength);
1102                                 temp = temp.substr(0,alnLength);
1103
1104                                 int newStart=0;
1105                                 int numDiff = countDiffs(oligo, temp);
1106
1107 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1108
1109                                 if(numDiff < minDiff){
1110                                         minDiff = numDiff;
1111                                         minCount = 1;
1112                                         minGroup = it->second;
1113                                         minPos = 0;
1114                                         for(int i=0;i<alnLength;i++){
1115                                                 if(temp[i] != '-'){
1116                                                         minPos++;
1117                                                 }
1118                                         }
1119                                 }
1120                                 else if(numDiff == minDiff){
1121                                         minCount++;
1122                                 }
1123
1124                         }
1125
1126                         if(minDiff > bdiffs)    {       success = minDiff;              }       //no good matches
1127                         else if(minCount > 1)   {       success = bdiffs + 100; }       //can't tell the difference between multiple barcodes
1128                         else{                                                                                                   //use the best match
1129                                 group = minGroup;
1130                                 seq.setUnaligned(rawSequence.substr(minPos));
1131
1132                                 if(qual.getName() != ""){
1133                                         qual.trimQScores(minPos, -1);
1134                                 }
1135                                 success = minDiff;
1136                         }
1137
1138                         if (alignment != NULL) {  delete alignment;  }
1139
1140                 }
1141 //              cout << success << endl;
1142
1143                 return success;
1144
1145         }
1146         catch(exception& e) {
1147                 m->errorOut(e, "TrimSeqsCommand", "stripBarcode");
1148                 exit(1);
1149         }
1150
1151 }
1152
1153 //***************************************************************************************************************
1154
1155 int TrimSeqsCommand::stripForward(Sequence& seq, QualityScores& qual, int& group){
1156         try {
1157                 string rawSequence = seq.getUnaligned();
1158                 int success = pdiffs + 1;       //guilty until proven innocent
1159
1160                 //can you find the primer
1161                 for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1162                         string oligo = it->first;
1163                         if(rawSequence.length() < oligo.length()){      //let's just assume that the primers are the same length
1164                                 success = pdiffs + 10;                                  //if the sequence is shorter than the barcode then bail out
1165                                 break;
1166                         }
1167
1168                         if(compareDNASeq(oligo, rawSequence.substr(0,oligo.length()))){
1169                                 group = it->second;
1170                                 seq.setUnaligned(rawSequence.substr(oligo.length()));
1171                                 if(qual.getName() != ""){
1172                                         qual.trimQScores(oligo.length(), -1);
1173
1174                                 }
1175                                 success = 0;
1176                                 break;
1177                         }
1178                 }
1179
1180                 //if you found the barcode or if you don't want to allow for diffs
1181 //              cout << success;
1182                 if ((pdiffs == 0) || (success == 0)) { return success;  }
1183
1184                 else { //try aligning and see if you can find it
1185 //                      cout << endl;
1186
1187                         int maxLength = 0;
1188
1189                         Alignment* alignment;
1190                         if (primers.size() > 0) {
1191                                 map<string,int>::iterator it=primers.begin();
1192
1193                                 for(it;it!=primers.end();it++){
1194                                         if(it->first.length() > maxLength){
1195                                                 maxLength = it->first.length();
1196                                         }
1197                                 }
1198                                 alignment = new NeedlemanOverlap(-1.0, 1.0, -1.0, (maxLength+pdiffs+1));
1199
1200                         }else{ alignment = NULL; }
1201
1202                         //can you find the barcode
1203                         int minDiff = 1e6;
1204                         int minCount = 1;
1205                         int minGroup = -1;
1206                         int minPos = 0;
1207
1208                         for(map<string,int>::iterator it=primers.begin();it!=primers.end();it++){
1209                                 string oligo = it->first;
1210 //                              int length = oligo.length();
1211
1212                                 if(rawSequence.length() < maxLength){
1213                                         success = pdiffs + 100;
1214                                         break;
1215                                 }
1216
1217                                 //use needleman to align first barcode.length()+numdiffs of sequence to each barcode
1218                                 alignment->align(oligo, rawSequence.substr(0,oligo.length()+pdiffs));
1219                                 oligo = alignment->getSeqAAln();
1220                                 string temp = alignment->getSeqBAln();
1221
1222                                 int alnLength = oligo.length();
1223
1224                                 for(int i=oligo.length()-1;i>=0;i--){
1225                                         if(oligo[i] != '-'){    alnLength = i+1;        break;  }
1226                                 }
1227                                 oligo = oligo.substr(0,alnLength);
1228                                 temp = temp.substr(0,alnLength);
1229
1230                                 int newStart=0;
1231                                 int numDiff = countDiffs(oligo, temp);
1232
1233 //                              cout << oligo << '\t' << temp << '\t' << numDiff << endl;
1234
1235                                 if(numDiff < minDiff){
1236                                         minDiff = numDiff;
1237                                         minCount = 1;
1238                                         minGroup = it->second;
1239                                         minPos = 0;
1240                                         for(int i=0;i<alnLength;i++){
1241                                                 if(temp[i] != '-'){
1242                                                         minPos++;
1243                                                 }
1244                                         }
1245                                 }
1246                                 else if(numDiff == minDiff){
1247                                         minCount++;
1248                                 }
1249
1250                         }
1251
1252                         if(minDiff > pdiffs)    {       success = minDiff;              }       //no good matches
1253                         else if(minCount > 1)   {       success = pdiffs + 10;  }       //can't tell the difference between multiple primers
1254                         else{                                                                                                   //use the best match
1255                                 group = minGroup;
1256                                 seq.setUnaligned(rawSequence.substr(minPos));
1257                                 if(qual.getName() != ""){
1258                                         qual.trimQScores(minPos, -1);
1259                                 }
1260                                 success = minDiff;
1261                         }
1262
1263                         if (alignment != NULL) {  delete alignment;  }
1264
1265                 }
1266
1267                 return success;
1268
1269         }
1270         catch(exception& e) {
1271                 m->errorOut(e, "TrimSeqsCommand", "stripForward");
1272                 exit(1);
1273         }
1274 }
1275
1276 //***************************************************************************************************************
1277
1278 bool TrimSeqsCommand::stripReverse(Sequence& seq, QualityScores& qual){
1279         try {
1280                 string rawSequence = seq.getUnaligned();
1281                 bool success = 0;       //guilty until proven innocent
1282
1283                 for(int i=0;i<numRPrimers;i++){
1284                         string oligo = revPrimer[i];
1285
1286                         if(rawSequence.length() < oligo.length()){
1287                                 success = 0;
1288                                 break;
1289                         }
1290
1291                         if(compareDNASeq(oligo, rawSequence.substr(rawSequence.length()-oligo.length(),oligo.length()))){
1292                                 seq.setUnaligned(rawSequence.substr(0,rawSequence.length()-oligo.length()));
1293                                 if(qual.getName() != ""){
1294                                         qual.trimQScores(-1, rawSequence.length()-oligo.length());
1295                                 }
1296                                 success = 1;
1297                                 break;
1298                         }
1299                 }
1300                 return success;
1301
1302         }
1303         catch(exception& e) {
1304                 m->errorOut(e, "TrimSeqsCommand", "stripReverse");
1305                 exit(1);
1306         }
1307 }
1308
1309 //***************************************************************************************************************
1310
1311 bool TrimSeqsCommand::cullLength(Sequence& seq){
1312         try {
1313
1314                 int length = seq.getNumBases();
1315                 bool success = 0;       //guilty until proven innocent
1316
1317                 if(length >= minLength && maxLength == 0)                       {       success = 1;    }
1318                 else if(length >= minLength && length <= maxLength)     {       success = 1;    }
1319                 else                                                                                            {       success = 0;    }
1320
1321                 return success;
1322
1323         }
1324         catch(exception& e) {
1325                 m->errorOut(e, "TrimSeqsCommand", "cullLength");
1326                 exit(1);
1327         }
1328
1329 }
1330
1331 //***************************************************************************************************************
1332
1333 bool TrimSeqsCommand::cullHomoP(Sequence& seq){
1334         try {
1335                 int longHomoP = seq.getLongHomoPolymer();
1336                 bool success = 0;       //guilty until proven innocent
1337
1338                 if(longHomoP <= maxHomoP){      success = 1;    }
1339                 else                                    {       success = 0;    }
1340
1341                 return success;
1342         }
1343         catch(exception& e) {
1344                 m->errorOut(e, "TrimSeqsCommand", "cullHomoP");
1345                 exit(1);
1346         }
1347
1348 }
1349
1350 //***************************************************************************************************************
1351
1352 bool TrimSeqsCommand::cullAmbigs(Sequence& seq){
1353         try {
1354                 int numNs = seq.getAmbigBases();
1355                 bool success = 0;       //guilty until proven innocent
1356
1357                 if(numNs <= maxAmbig)   {       success = 1;    }
1358                 else                                    {       success = 0;    }
1359
1360                 return success;
1361         }
1362         catch(exception& e) {
1363                 m->errorOut(e, "TrimSeqsCommand", "cullAmbigs");
1364                 exit(1);
1365         }
1366
1367 }
1368
1369 //***************************************************************************************************************
1370
1371 bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
1372         try {
1373                 bool success = 1;
1374                 int length = oligo.length();
1375
1376                 for(int i=0;i<length;i++){
1377
1378                         if(oligo[i] != seq[i]){
1379                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C')    {       success = 0;    }
1380                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       success = 0;    }
1381                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       success = 0;    }
1382                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       success = 0;    }
1383                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       success = 0;    }
1384                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       success = 0;    }
1385                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       success = 0;    }
1386                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       success = 0;    }
1387                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1388                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       success = 0;    }
1389                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       success = 0;    }
1390                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       success = 0;    }
1391
1392                                 if(success == 0)        {       break;   }
1393                         }
1394                         else{
1395                                 success = 1;
1396                         }
1397                 }
1398
1399                 return success;
1400         }
1401         catch(exception& e) {
1402                 m->errorOut(e, "TrimSeqsCommand", "compareDNASeq");
1403                 exit(1);
1404         }
1405
1406 }
1407 //***************************************************************************************************************
1408
1409 int TrimSeqsCommand::countDiffs(string oligo, string seq){
1410         try {
1411
1412                 int length = oligo.length();
1413                 int countDiffs = 0;
1414
1415                 for(int i=0;i<length;i++){
1416
1417                         if(oligo[i] != seq[i]){
1418                                 if(oligo[i] == 'A' || oligo[i] == 'T' || oligo[i] == 'G' || oligo[i] == 'C' || oligo[i] == '-' || oligo[i] == '.')      {       countDiffs++;   }
1419                                 else if((oligo[i] == 'N' || oligo[i] == 'I') && (seq[i] == 'N'))                                {       countDiffs++;   }
1420                                 else if(oligo[i] == 'R' && (seq[i] != 'A' && seq[i] != 'G'))                                    {       countDiffs++;   }
1421                                 else if(oligo[i] == 'Y' && (seq[i] != 'C' && seq[i] != 'T'))                                    {       countDiffs++;   }
1422                                 else if(oligo[i] == 'M' && (seq[i] != 'C' && seq[i] != 'A'))                                    {       countDiffs++;   }
1423                                 else if(oligo[i] == 'K' && (seq[i] != 'T' && seq[i] != 'G'))                                    {       countDiffs++;   }
1424                                 else if(oligo[i] == 'W' && (seq[i] != 'T' && seq[i] != 'A'))                                    {       countDiffs++;   }
1425                                 else if(oligo[i] == 'S' && (seq[i] != 'C' && seq[i] != 'G'))                                    {       countDiffs++;   }
1426                                 else if(oligo[i] == 'B' && (seq[i] != 'C' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1427                                 else if(oligo[i] == 'D' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'G'))   {       countDiffs++;   }
1428                                 else if(oligo[i] == 'H' && (seq[i] != 'A' && seq[i] != 'T' && seq[i] != 'C'))   {       countDiffs++;   }
1429                                 else if(oligo[i] == 'V' && (seq[i] != 'A' && seq[i] != 'C' && seq[i] != 'G'))   {       countDiffs++;   }
1430                         }
1431
1432                 }
1433
1434                 return countDiffs;
1435         }
1436         catch(exception& e) {
1437                 m->errorOut(e, "TrimSeqsCommand", "countDiffs");
1438                 exit(1);
1439         }
1440
1441 }
1442 //***************************************************************************************************************
1443
1444 //bool TrimSeqsCommand::stripQualThreshold(Sequence& seq, ifstream& qFile){
1445 //      try {
1446 //
1447 //              string rawSequence = seq.getUnaligned();
1448 //              int seqLength = seq.getNumBases();
1449 //              bool success = 0;       //guilty until proven innocent
1450 //              string name;
1451 //
1452 //              qFile >> name;
1453 //              if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1454 //
1455 //              while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1456 //
1457 //              int score;
1458 //              int end = seqLength;
1459 //
1460 //              for(int i=0;i<seqLength;i++){
1461 //                      qFile >> score;
1462 //
1463 //                      if(score < qThreshold){
1464 //                              end = i;
1465 //                              break;
1466 //                      }
1467 //              }
1468 //              for(int i=end+1;i<seqLength;i++){
1469 //                      qFile >> score;
1470 //              }
1471 //
1472 //              seq.setUnaligned(rawSequence.substr(0,end));
1473 //
1474 //              return 1;
1475 //      }
1476 //      catch(exception& e) {
1477 //              m->errorOut(e, "TrimSeqsCommand", "stripQualThreshold");
1478 //              exit(1);
1479 //      }
1480 //}
1481
1482 //***************************************************************************************************************
1483
1484 //bool TrimSeqsCommand::cullQualAverage(Sequence& seq, ifstream& qFile){
1485 //      try {
1486 //              string rawSequence = seq.getUnaligned();
1487 //              int seqLength = seq.getNumBases();
1488 //              bool success = 0;       //guilty until proven innocent
1489 //              string name;
1490 //
1491 //              qFile >> name;
1492 //              if (name[0] == '>') {  if(name.substr(1) != seq.getName())      {       m->mothurOut("sequence name mismatch btwn fasta: " + seq.getName() + " and qual file: " + name); m->mothurOutEndLine(); }  }
1493 //
1494 //              while (!qFile.eof())    {       char c = qFile.get(); if (c == 10 || c == 13){  break;  }       }
1495 //
1496 //              float score;
1497 //              float average = 0;
1498 //
1499 //              for(int i=0;i<seqLength;i++){
1500 //                      qFile >> score;
1501 //                      average += score;
1502 //              }
1503 //              average /= seqLength;
1504 //
1505 //              if(average >= qAverage) {       success = 1;    }
1506 //              else                                    {       success = 0;    }
1507 //
1508 //              return success;
1509 //      }
1510 //      catch(exception& e) {
1511 //              m->errorOut(e, "TrimSeqsCommand", "cullQualAverage");
1512 //              exit(1);
1513 //      }
1514 //}
1515
1516 //***************************************************************************************************************