trimflowscommand.cpp

   1 /*
   2  *  trimflowscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 12/22/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "trimflowscommand.h"
  11 #include "needlemanoverlap.hpp"
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> TrimFlowsCommand::setParameters(){
  16         try {
  17                 CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow-file",false,true,true); parameters.push_back(pflow);
  18                 CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(poligos);
  19                 CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
  20                 CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
  21                 CommandParameter pminflows("minflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pminflows);
  22                 CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
  23                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
  24         CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
  25                 CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
  26         CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
  27                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
  28                 CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
  29                 CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
  30                 CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);
  31                 CommandParameter porder("order", "String", "", "TACG", "", "", "","",false,false); parameters.push_back(porder);
  32                 CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfasta);
  33                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  34                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  35
  36                 vector<string> myArray;
  37                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  38                 return myArray;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "TrimFlowsCommand", "setParameters");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 string TrimFlowsCommand::getHelpString(){
  47         try {
  48                 string helpString = "";
  49                 helpString += "The trim.flows command reads a flowgram file and creates .....\n";
  50                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  51                 helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "TrimFlowsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 string TrimFlowsCommand::getOutputPattern(string type) {
  61     try {
  62         string pattern = "";
  63
  64         if (type == "flow") {  pattern = "[filename],[tag],flow"; }
  65         else if (type == "fasta") {  pattern = "[filename],flow.fasta"; }
  66         else if (type == "file") {  pattern = "[filename],flow.files"; }
  67         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  68
  69         return pattern;
  70     }
  71     catch(exception& e) {
  72         m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
  73         exit(1);
  74     }
  75 }
  76 //**********************************************************************************************************************
  77
  78 TrimFlowsCommand::TrimFlowsCommand(){
  79         try {
  80                 abort = true; calledHelp = true;
  81                 setParameters();
  82                 vector<string> tempOutNames;
  83                 outputTypes["flow"] = tempOutNames;
  84                 outputTypes["fasta"] = tempOutNames;
  85         outputTypes["file"] = tempOutNames;
  86         }
  87         catch(exception& e) {
  88                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
  89                 exit(1);
  90         }
  91 }
  92 //**********************************************************************************************************************
  93
  94 TrimFlowsCommand::TrimFlowsCommand(string option)  {
  95         try {
  96
  97                 abort = false; calledHelp = false;
  98                 comboStarts = 0;
  99
 100                 //allow user to run help
 101                 if(option == "help") { help(); abort = true; calledHelp = true; }
 102                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 103
 104                 else {
 105
 106                         vector<string> myArray = setParameters();
 107
 108                         OptionParser parser(option);
 109                         map<string,string> parameters = parser.getParameters();
 110
 111                         ValidParameters validParameter;
 112                         map<string,string>::iterator it;
 113
 114                         //check to make sure all parameters are valid for command
 115                         for (it = parameters.begin(); it != parameters.end(); it++) {
 116                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 117                         }
 118
 119                         //initialize outputTypes
 120                         vector<string> tempOutNames;
 121                         outputTypes["flow"] = tempOutNames;
 122                         outputTypes["fasta"] = tempOutNames;
 123             outputTypes["file"] = tempOutNames;
 124
 125                         //if the user changes the input directory command factory will send this info to us in the output parameter
 126                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 127                         if (inputDir == "not found"){   inputDir = "";          }
 128                         else {
 129                                 string path;
 130                                 it = parameters.find("flow");
 131                                 //user has given a template file
 132                                 if(it != parameters.end()){
 133                                         path = m->hasPath(it->second);
 134                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                         if (path == "") {       parameters["flow"] = inputDir + it->second;             }
 136                                 }
 137
 138                                 it = parameters.find("oligos");
 139                                 //user has given a template file
 140                                 if(it != parameters.end()){
 141                                         path = m->hasPath(it->second);
 142                                         //if the user has not given a path then, add inputdir. else leave path alone.
 143                                         if (path == "") {       parameters["oligos"] = inputDir + it->second;           }
 144                                 }
 145
 146                         }
 147
 148
 149                         //check for required parameters
 150                         flowFileName = validParameter.validFile(parameters, "flow", true);
 151                         if (flowFileName == "not found") {
 152                                 flowFileName = m->getFlowFile();
 153                                 if (flowFileName != "") {  m->mothurOut("Using " + flowFileName + " as input file for the flow parameter."); m->mothurOutEndLine(); }
 154                                 else {
 155                                         m->mothurOut("No valid current flow file. You must provide a flow file."); m->mothurOutEndLine();
 156                                         abort = true;
 157                                 }
 158                         }else if (flowFileName == "not open") { flowFileName = ""; abort = true; }
 159
 160                         //if the user changes the output directory command factory will send this info to us in the output parameter
 161                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 162                                 outputDir = "";
 163                                 outputDir += m->hasPath(flowFileName); //if user entered a file with a path then preserve it
 164                         }
 165
 166
 167                         //check for optional parameter and set defaults
 168                         // ...at some point should added some additional type checking...
 169
 170                         string temp;
 171                         temp = validParameter.validFile(parameters, "minflows", false); if (temp == "not found") { temp = "450"; }
 172                         m->mothurConvert(temp, minFlows);
 173
 174                         temp = validParameter.validFile(parameters, "maxflows", false); if (temp == "not found") { temp = "450"; }
 175                         m->mothurConvert(temp, maxFlows);
 176
 177
 178                         temp = validParameter.validFile(parameters, "oligos", true);
 179                         if (temp == "not found")        {       oligoFileName = "";             }
 180                         else if(temp == "not open")     {       abort = true;                   }
 181                         else                                            {       oligoFileName = temp;   m->setOligosFile(oligoFileName); }
 182
 183                         temp = validParameter.validFile(parameters, "fasta", false);            if (temp == "not found"){       fasta = 0;              }
 184                         else if(m->isTrue(temp))        {       fasta = 1;      }
 185
 186                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found"){       temp = "9";             }
 187                         m->mothurConvert(temp, maxHomoP);
 188
 189                         temp = validParameter.validFile(parameters, "signal", false);           if (temp == "not found"){       temp = "0.50";  }
 190                         m->mothurConvert(temp, signal);
 191
 192                         temp = validParameter.validFile(parameters, "noise", false);            if (temp == "not found"){       temp = "0.70";  }
 193                         m->mothurConvert(temp, noise);
 194
 195                         temp = validParameter.validFile(parameters, "bdiffs", false);           if (temp == "not found"){       temp = "0";             }
 196                         m->mothurConvert(temp, bdiffs);
 197
 198                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found"){       temp = "0";             }
 199                         m->mothurConvert(temp, pdiffs);
 200
 201             temp = validParameter.validFile(parameters, "ldiffs", false);               if (temp == "not found") { temp = "0"; }
 202                         m->mothurConvert(temp, ldiffs);
 203
 204             temp = validParameter.validFile(parameters, "sdiffs", false);               if (temp == "not found") { temp = "0"; }
 205                         m->mothurConvert(temp, sdiffs);
 206
 207                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs;  temp = toString(tempTotal); }
 208                         m->mothurConvert(temp, tdiffs);
 209
 210                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs + ldiffs + sdiffs;     }
 211
 212
 213                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 214                         m->setProcessors(temp);
 215                         m->mothurConvert(temp, processors);
 216
 217                         flowOrder = validParameter.validFile(parameters, "order", false);
 218                         if (flowOrder == "not found"){ flowOrder = "TACG";              }
 219                         else if(flowOrder.length() != 4){
 220                                 m->mothurOut("The value of the order option must be four bases long\n");
 221                         }
 222
 223                         if(oligoFileName == "") {       allFiles = 0;           }
 224                         else                                    {       allFiles = 1;           }
 225
 226                         numFPrimers = 0;
 227                         numRPrimers = 0;
 228             numLinkers = 0;
 229             numSpacers = 0;
 230                 }
 231
 232         }
 233         catch(exception& e) {
 234                 m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
 235                 exit(1);
 236         }
 237 }
 238
 239 //***************************************************************************************************************
 240
 241 int TrimFlowsCommand::execute(){
 242         try{
 243
 244                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 245
 246         map<string, string> variables;
 247                 variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 248         string fastaFileName = getOutputFileName("fasta",variables);
 249                 if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
 250
 251         variables["[tag]"] = "trim";
 252                 string trimFlowFileName = getOutputFileName("flow",variables);
 253                 outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
 254
 255         variables["[tag]"] = "scrap";
 256                 string scrapFlowFileName = getOutputFileName("flow",variables);
 257                 outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
 258
 259
 260
 261                 vector<unsigned long long> flowFilePos;
 262         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 263                 flowFilePos = getFlowFileBreaks();
 264                 for (int i = 0; i < (flowFilePos.size()-1); i++) {
 265                         lines.push_back(new linePair(flowFilePos[i], flowFilePos[(i+1)]));
 266                 }
 267         #else
 268                 ifstream in; m->openInputFile(flowFileName, in); in >> numFlows; in.close();
 269         ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
 270                 processors = 1;
 271         ///////////////////////////////////////// until I fix multiple processors for windows //////////////////
 272                 if (processors == 1) {
 273                         lines.push_back(new linePair(0, 1000));
 274                 }else {
 275                         int numFlowLines;
 276                         flowFilePos = m->setFilePosEachLine(flowFileName, numFlowLines);
 277                         flowFilePos.erase(flowFilePos.begin() + 1); numFlowLines--;
 278
 279                         //figure out how many sequences you have to process
 280                         int numSeqsPerProcessor = numFlowLines / processors;
 281                         cout << numSeqsPerProcessor << '\t' << numFlowLines << endl;
 282                         for (int i = 0; i < processors; i++) {
 283                                 int startIndex =  i * numSeqsPerProcessor;
 284                                 if(i == (processors - 1)){      numSeqsPerProcessor = numFlowLines - i * numSeqsPerProcessor;   }
 285                                 lines.push_back(new linePair(flowFilePos[startIndex], numSeqsPerProcessor));
 286                                 cout << flowFilePos[startIndex] << '\t' << numSeqsPerProcessor << endl;
 287                         }
 288                 }
 289         #endif
 290
 291                 vector<vector<string> > barcodePrimerComboFileNames;
 292                 if(oligoFileName != ""){
 293                         getOligos(barcodePrimerComboFileNames);
 294                 }
 295
 296                 if(processors == 1){
 297                         driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 298                 }else{
 299                         createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames);
 300                 }
 301
 302                 if (m->control_pressed) {  return 0; }
 303
 304                 string flowFilesFileName;
 305                 ofstream output;
 306
 307                 if(allFiles){
 308                         set<string> namesAlreadyProcessed;
 309                         flowFilesFileName = getOutputFileName("file",variables);
 310                         m->openOutputFile(flowFilesFileName, output);
 311
 312                         for(int i=0;i<barcodePrimerComboFileNames.size();i++){
 313                                 for(int j=0;j<barcodePrimerComboFileNames[0].size();j++){
 314                                         if (namesAlreadyProcessed.count(barcodePrimerComboFileNames[i][j]) == 0) {
 315                         if (barcodePrimerComboFileNames[i][j] != "") {
 316                             FILE * pFile;
 317                             unsigned long long size;
 318
 319                             //get num bytes in file
 320                             pFile = fopen (barcodePrimerComboFileNames[i][j].c_str(),"rb");
 321                             if (pFile==NULL) perror ("Error opening file");
 322                             else{
 323                                 fseek (pFile, 0, SEEK_END);
 324                                 size=ftell(pFile);
 325                                 fclose (pFile);
 326                             }
 327
 328                             if(size < 10){
 329                                 m->mothurRemove(barcodePrimerComboFileNames[i][j]);
 330                             }
 331                             else{
 332                                 output << m->getFullPathName(barcodePrimerComboFileNames[i][j]) << endl;
 333                                 outputNames.push_back(barcodePrimerComboFileNames[i][j]);
 334                                 outputTypes["flow"].push_back(barcodePrimerComboFileNames[i][j]);
 335                             }
 336                             namesAlreadyProcessed.insert(barcodePrimerComboFileNames[i][j]);
 337                         }
 338                                         }
 339                                 }
 340                         }
 341                         output.close();
 342                 }
 343                 else{
 344                         flowFilesFileName = getOutputFileName("file",variables);
 345                         m->openOutputFile(flowFilesFileName, output);
 346
 347                         output << m->getFullPathName(trimFlowFileName) << endl;
 348
 349                         output.close();
 350                 }
 351                 outputTypes["file"].push_back(flowFilesFileName);
 352                 outputNames.push_back(flowFilesFileName);
 353
 354                 m->mothurOutEndLine();
 355                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 356                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 357                 m->mothurOutEndLine();
 358
 359                 return 0;
 360         }
 361         catch(exception& e) {
 362                 m->errorOut(e, "TrimSeqsCommand", "execute");
 363                 exit(1);
 364         }
 365 }
 366
 367 //***************************************************************************************************************
 368
 369 int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > thisBarcodePrimerComboFileNames, linePair* line){
 370
 371         try {
 372                 ofstream trimFlowFile;
 373                 m->openOutputFile(trimFlowFileName, trimFlowFile);
 374                 trimFlowFile.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 375
 376                 ofstream scrapFlowFile;
 377                 m->openOutputFile(scrapFlowFileName, scrapFlowFile);
 378                 scrapFlowFile.setf(ios::fixed, ios::floatfield); scrapFlowFile.setf(ios::showpoint);
 379
 380                 ofstream fastaFile;
 381                 if(fasta){      m->openOutputFile(fastaFileName, fastaFile);    }
 382
 383                 ifstream flowFile;
 384                 m->openInputFile(flowFileName, flowFile);
 385
 386                 flowFile.seekg(line->start);
 387
 388                 if(line->start == 0){
 389                         flowFile >> numFlows; m->gobble(flowFile);
 390                         scrapFlowFile << maxFlows << endl;
 391                         trimFlowFile << maxFlows << endl;
 392                         if(allFiles){
 393                                 for(int i=0;i<thisBarcodePrimerComboFileNames.size();i++){
 394                                         for(int j=0;j<thisBarcodePrimerComboFileNames[0].size();j++){
 395                         if (thisBarcodePrimerComboFileNames[i][j] != "") {
 396                             ofstream temp;
 397                             m->openOutputFile(thisBarcodePrimerComboFileNames[i][j], temp);
 398                             temp << maxFlows << endl;
 399                             temp.close();
 400                         }
 401                                         }
 402                                 }
 403                         }
 404                 }
 405
 406                 FlowData flowData(numFlows, signal, noise, maxHomoP, flowOrder);
 407                 //cout << " driver flowdata address " <<  &flowData  << &flowFile << endl;
 408                 int count = 0;
 409                 bool moreSeqs = 1;
 410
 411                 TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
 412
 413                 while(moreSeqs) {
 414
 415                         if (m->control_pressed) { break; }
 416
 417                         int success = 1;
 418                         int currentSeqDiffs = 0;
 419                         string trashCode = "";
 420
 421                         flowData.getNext(flowFile);
 422                         flowData.capFlows(maxFlows);
 423
 424                         Sequence currSeq = flowData.getSequence();
 425                         if(!flowData.hasMinFlows(minFlows)){    //screen to see if sequence is of a minimum number of flows
 426                                 success = 0;
 427                                 trashCode += 'l';
 428                         }
 429
 430                         int primerIndex = 0;
 431                         int barcodeIndex = 0;
 432
 433             if(numLinkers != 0){
 434                 success = trimOligos.stripLinker(currSeq);
 435                 if(success > ldiffs)            {       trashCode += 'k';       }
 436                 else{ currentSeqDiffs += success;  }
 437
 438             }
 439
 440             if (m->debug) { m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
 441
 442                         if(barcodes.size() != 0){
 443                                 success = trimOligos.stripBarcode(currSeq, barcodeIndex);
 444                                 if(success > bdiffs)            {       trashCode += 'b';       }
 445                                 else{ currentSeqDiffs += success;  }
 446                         }
 447
 448             if(numSpacers != 0){
 449                 success = trimOligos.stripSpacer(currSeq);
 450                 if(success > sdiffs)            {       trashCode += 's';       }
 451                 else{ currentSeqDiffs += success;  }
 452
 453             }
 454
 455                         if(numFPrimers != 0){
 456                                 success = trimOligos.stripForward(currSeq, primerIndex);
 457                                 if(success > pdiffs)            {       trashCode += 'f';       }
 458                                 else{ currentSeqDiffs += success;  }
 459                         }
 460
 461                         if (currentSeqDiffs > tdiffs)   {       trashCode += 't';   }
 462
 463                         if(numRPrimers != 0){
 464                                 success = trimOligos.stripReverse(currSeq);
 465                                 if(!success)                            {       trashCode += 'r';       }
 466                         }
 467
 468                         if(trashCode.length() == 0){
 469                 string thisGroup = "";
 470                 if(barcodes.size() != 0){
 471                     thisGroup = barcodeNameVector[barcodeIndex];
 472                     if (primers.size() != 0) {
 473                         if (primerNameVector[primerIndex] != "") {
 474                             if(thisGroup != "") {
 475                                 thisGroup += "." + primerNameVector[primerIndex];
 476                             }else {
 477                                 thisGroup = primerNameVector[primerIndex];
 478                             }
 479                         }
 480                     }
 481                 }
 482
 483                 int pos = thisGroup.find("ignore");
 484                 if (pos == string::npos) {
 485                     flowData.printFlows(trimFlowFile);
 486
 487                     if(fasta)   {       currSeq.printSequence(fastaFile);       }
 488
 489                     if(allFiles){
 490                         ofstream output;
 491                         m->openOutputFileAppend(thisBarcodePrimerComboFileNames[barcodeIndex][primerIndex], output);
 492                         output.setf(ios::fixed, ios::floatfield); trimFlowFile.setf(ios::showpoint);
 493
 494                         flowData.printFlows(output);
 495                         output.close();
 496                     }
 497                 }
 498                         }
 499                         else{
 500                                 flowData.printFlows(scrapFlowFile, trashCode);
 501                         }
 502
 503                         count++;
 504                         //cout << "driver" << '\t' << currSeq.getName() << endl;
 505                         //report progress
 506                         if((count) % 10000 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 507
 508 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 509                         unsigned long long pos = flowFile.tellg();
 510
 511                         if ((pos == -1) || (pos >= line->end)) { break; }
 512 #else
 513                         if (flowFile.eof()) { break; }
 514 #endif
 515
 516                 }
 517                 //report progress
 518                 if((count) % 10000 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 519
 520                 trimFlowFile.close();
 521                 scrapFlowFile.close();
 522                 flowFile.close();
 523                 if(fasta){      fastaFile.close();      }
 524
 525                 return count;
 526         }
 527         catch(exception& e) {
 528                 m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
 529                 exit(1);
 530         }
 531 }
 532
 533 //***************************************************************************************************************
 534
 535 void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 536         try {
 537                 ifstream oligosFile;
 538                 m->openInputFile(oligoFileName, oligosFile);
 539
 540                 string type, oligo, group;
 541
 542                 int indexPrimer = 0;
 543                 int indexBarcode = 0;
 544
 545                 while(!oligosFile.eof()){
 546
 547                         oligosFile >> type; m->gobble(oligosFile);      //get the first column value of the row - is it a comment or a feature we are interested in?
 548
 549                         if(type[0] == '#'){     //igore the line because there's a comment
 550                                 while (!oligosFile.eof())       {       char c = oligosFile.get(); if (c == 10 || c == 13){     break;  }       } // get rest of line if there's any crap there
 551                         }
 552                         else{                           //there's a feature we're interested in
 553
 554                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }                                  //make type case insensitive
 555
 556                                 oligosFile >> oligo;    //get the DNA sequence for the feature
 557
 558                                 for(int i=0;i<oligo.length();i++){      //make type case insensitive and change any U's to T's
 559                                         oligo[i] = toupper(oligo[i]);
 560                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
 561                                 }
 562
 563                                 if(type == "FORWARD"){  //if the feature is a forward primer...
 564                                         group = "";
 565
 566                                         while (!oligosFile.eof())       {       // get rest of line in case there is a primer name = will have the name of the primer
 567                                                 char c = oligosFile.get();
 568                                                 if (c == 10 || c == 13){        break;  }
 569                                                 else if (c == 32 || c == 9){;} //space or tab
 570                                                 else {  group += c;  }
 571                                         }
 572
 573                                         //have we seen this primer already?
 574                                         map<string, int>::iterator itPrimer = primers.find(oligo);
 575                                         if (itPrimer != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 576
 577                                         primers[oligo]=indexPrimer; indexPrimer++;
 578                                         primerNameVector.push_back(group);
 579
 580                                 }
 581                                 else if(type == "REVERSE"){
 582                                         string oligoRC = reverseOligo(oligo);
 583                                         revPrimer.push_back(oligoRC);
 584                                 }
 585                                 else if(type == "BARCODE"){
 586                                         oligosFile >> group;
 587
 588                                         //check for repeat barcodes
 589                                         map<string, int>::iterator itBar = barcodes.find(oligo);
 590                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
 591
 592                                         barcodes[oligo]=indexBarcode; indexBarcode++;
 593                                         barcodeNameVector.push_back(group);
 594                                 }else if(type == "LINKER"){
 595                                         linker.push_back(oligo);
 596                                 }else if(type == "SPACER"){
 597                                         spacer.push_back(oligo);
 598                                 }
 599                                 else{
 600                                         m->mothurOut(type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine();
 601                                 }
 602                         }
 603
 604                         m->gobble(oligosFile);
 605                 }
 606                 oligosFile.close();
 607
 608                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ allFiles = 0;   }
 609
 610                 //add in potential combos
 611                 if(barcodeNameVector.size() == 0){
 612                         barcodes[""] = 0;
 613                         barcodeNameVector.push_back("");
 614                 }
 615
 616                 if(primerNameVector.size() == 0){
 617                         primers[""] = 0;
 618                         primerNameVector.push_back("");
 619                 }
 620
 621
 622                 outFlowFileNames.resize(barcodeNameVector.size());
 623                 for(int i=0;i<outFlowFileNames.size();i++){
 624                         outFlowFileNames[i].assign(primerNameVector.size(), "");
 625                 }
 626
 627                 if(allFiles){
 628
 629                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
 630                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
 631
 632                                         string primerName = primerNameVector[itPrimer->second];
 633                                         string barcodeName = barcodeNameVector[itBar->second];
 634
 635                                         if ((primerName == "ignore") || (barcodeName == "ignore")) { } //do nothing
 636                                         else {
 637                         string comboGroupName = "";
 638                         string fileName = "";
 639
 640                         map<string, string> variables;
 641                         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(flowFileName));
 642
 643                         if(primerName == ""){
 644                             comboGroupName = barcodeNameVector[itBar->second];
 645                             variables["[tag]"] = comboGroupName;
 646                             fileName = getOutputFileName("flow", variables);
 647                         }
 648                         else{
 649                             if(barcodeName == ""){
 650                                 comboGroupName = primerNameVector[itPrimer->second];
 651                             }
 652                             else{
 653                                 comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
 654                             }
 655                             variables["[tag]"] = comboGroupName;
 656                             fileName = getOutputFileName("flow", variables);
 657                         }
 658
 659                         outFlowFileNames[itBar->second][itPrimer->second] = fileName;
 660
 661                         ofstream temp;
 662                         m->openOutputFile(fileName, temp);
 663                         temp.close();
 664                     }
 665                                 }
 666                         }
 667                 }
 668
 669                 numFPrimers = primers.size();
 670                 numRPrimers = revPrimer.size();
 671         numLinkers = linker.size();
 672         numSpacers = spacer.size();
 673
 674         }
 675         catch(exception& e) {
 676                 m->errorOut(e, "TrimSeqsCommand", "getOligos");
 677                 exit(1);
 678         }
 679 }
 680 //********************************************************************/
 681 string TrimFlowsCommand::reverseOligo(string oligo){
 682         try {
 683         string reverse = "";
 684
 685         for(int i=oligo.length()-1;i>=0;i--){
 686
 687             if(oligo[i] == 'A')         {       reverse += 'T'; }
 688             else if(oligo[i] == 'T'){   reverse += 'A'; }
 689             else if(oligo[i] == 'U'){   reverse += 'A'; }
 690
 691             else if(oligo[i] == 'G'){   reverse += 'C'; }
 692             else if(oligo[i] == 'C'){   reverse += 'G'; }
 693
 694             else if(oligo[i] == 'R'){   reverse += 'Y'; }
 695             else if(oligo[i] == 'Y'){   reverse += 'R'; }
 696
 697             else if(oligo[i] == 'M'){   reverse += 'K'; }
 698             else if(oligo[i] == 'K'){   reverse += 'M'; }
 699
 700             else if(oligo[i] == 'W'){   reverse += 'W'; }
 701             else if(oligo[i] == 'S'){   reverse += 'S'; }
 702
 703             else if(oligo[i] == 'B'){   reverse += 'V'; }
 704             else if(oligo[i] == 'V'){   reverse += 'B'; }
 705
 706             else if(oligo[i] == 'D'){   reverse += 'H'; }
 707             else if(oligo[i] == 'H'){   reverse += 'D'; }
 708
 709             else                                                {       reverse += 'N'; }
 710         }
 711
 712
 713         return reverse;
 714     }
 715         catch(exception& e) {
 716                 m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
 717                 exit(1);
 718         }
 719 }
 720
 721 /**************************************************************************************************/
 722 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {
 723
 724         try{
 725
 726                 vector<unsigned long long> filePos;
 727                 filePos.push_back(0);
 728
 729                 FILE * pFile;
 730                 unsigned long long size;
 731
 732                 //get num bytes in file
 733                 pFile = fopen (flowFileName.c_str(),"rb");
 734                 if (pFile==NULL) perror ("Error opening file");
 735                 else{
 736                         fseek (pFile, 0, SEEK_END);
 737                         size=ftell (pFile);
 738                         fclose (pFile);
 739                 }
 740
 741                 //estimate file breaks
 742                 unsigned long long chunkSize = 0;
 743                 chunkSize = size / processors;
 744
 745                 //file too small to divide by processors
 746                 if (chunkSize == 0)  {  processors = 1; filePos.push_back(size); return filePos;        }
 747
 748                 //for each process seekg to closest file break and search for next '>' char. make that the filebreak
 749                 for (int i = 0; i < processors; i++) {
 750                         unsigned long long spot = (i+1) * chunkSize;
 751
 752                         ifstream in;
 753                         m->openInputFile(flowFileName, in);
 754                         in.seekg(spot);
 755
 756                         string dummy = m->getline(in);
 757
 758                         //there was not another sequence before the end of the file
 759                         unsigned long long sanityPos = in.tellg();
 760
 761 //                      if (sanityPos == -1) {  break;  }
 762 //                      else {  filePos.push_back(newSpot);  }
 763                         if (sanityPos == -1) {  break;  }
 764                         else {  filePos.push_back(sanityPos);  }
 765
 766                         in.close();
 767                 }
 768
 769                 //save end pos
 770                 filePos.push_back(size);
 771
 772                 //sanity check filePos
 773                 for (int i = 0; i < (filePos.size()-1); i++) {
 774                         if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
 775                 }
 776
 777                 ifstream in;
 778                 m->openInputFile(flowFileName, in);
 779                 in >> numFlows;
 780                 m->gobble(in);
 781                 //unsigned long long spot = in.tellg();
 782                 //filePos[0] = spot;
 783                 in.close();
 784
 785                 processors = (filePos.size() - 1);
 786
 787                 return filePos;
 788         }
 789         catch(exception& e) {
 790                 m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
 791                 exit(1);
 792         }
 793 }
 794
 795 /**************************************************************************************************/
 796
 797 int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName, vector<vector<string> > barcodePrimerComboFileNames){
 798
 799         try {
 800                 processIDS.clear();
 801                 int exitCommand = 1;
 802
 803 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 804                 int process = 1;
 805
 806                 //loop through and create all the processes you want
 807                 while (process != processors) {
 808                         int pid = fork();
 809
 810                         if (pid > 0) {
 811                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 812                                 process++;
 813                         }else if (pid == 0){
 814
 815                                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 816                                 if(allFiles){
 817                                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 818                                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 819                             if (tempBarcodePrimerComboFileNames[i][j] != "") {
 820                                 tempBarcodePrimerComboFileNames[i][j] += toString(getpid()) + ".temp";
 821                                 ofstream temp;
 822                                 m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 823                                 temp.close();
 824                             }
 825                                                 }
 826                                         }
 827                                 }
 828                                 driverCreateTrim(flowFileName,
 829                                                                  (trimFlowFileName + toString(getpid()) + ".temp"),
 830                                                                  (scrapFlowFileName + toString(getpid()) + ".temp"),
 831                                                                  (fastaFileName + toString(getpid()) + ".temp"),
 832                                                                  tempBarcodePrimerComboFileNames, lines[process]);
 833
 834                                 exit(0);
 835                         }else {
 836                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 837                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 838                                 exit(0);
 839                         }
 840                 }
 841
 842                 //parent do my part
 843                 ofstream temp;
 844                 m->openOutputFile(trimFlowFileName, temp);
 845                 temp.close();
 846
 847                 m->openOutputFile(scrapFlowFileName, temp);
 848                 temp.close();
 849
 850                 if(fasta){
 851                         m->openOutputFile(fastaFileName, temp);
 852                         temp.close();
 853                 }
 854
 855                 driverCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName, barcodePrimerComboFileNames, lines[0]);
 856
 857                 //force parent to wait until all the processes are done
 858                 for (int i=0;i<processIDS.size();i++) {
 859                         int temp = processIDS[i];
 860                         wait(&temp);
 861                 }
 862 #else
 863                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 864                 //Windows version shared memory, so be careful when passing variables through the trimFlowData struct.
 865                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 866                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 867
 868                 vector<trimFlowData*> pDataArray;
 869                 DWORD   dwThreadIdArray[processors-1];
 870                 HANDLE  hThreadArray[processors-1];
 871
 872                 //Create processor worker threads.
 873                 for( int i=0; i<processors-1; i++ ){
 874                         // Allocate memory for thread data.
 875                         string extension = "";
 876                         if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
 877
 878                         vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 879                         if(allFiles){
 880                                 for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 881                                         for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 882                         if (tempBarcodePrimerComboFileNames[i][j] != "") {
 883                             tempBarcodePrimerComboFileNames[i][j] += extension;
 884                             ofstream temp;
 885                             m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 886                             temp.close();
 887                                                 }
 888                                         }
 889                                 }
 890                         }
 891
 892                         trimFlowData* tempflow = new trimFlowData(flowFileName, (trimFlowFileName + extension), (scrapFlowFileName + extension), fastaFileName, flowOrder, tempBarcodePrimerComboFileNames, barcodes, primers, revPrimer, fasta, allFiles, lines[i]->start, lines[i]->end, m, signal, noise, numFlows, maxFlows, minFlows, maxHomoP, tdiffs, bdiffs, pdiffs, i);
 893                         pDataArray.push_back(tempflow);
 894
 895                         //MyTrimFlowThreadFunction is in header. It must be global or static to work with the threads.
 896                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 897                         hThreadArray[i] = CreateThread(NULL, 0, MyTrimFlowThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 898                 }
 899
 900                 //using the main process as a worker saves time and memory
 901                 ofstream temp;
 902                 m->openOutputFile(trimFlowFileName, temp);
 903                 temp.close();
 904
 905                 m->openOutputFile(scrapFlowFileName, temp);
 906                 temp.close();
 907
 908                 if(fasta){
 909                         m->openOutputFile(fastaFileName, temp);
 910                         temp.close();
 911                 }
 912
 913                 vector<vector<string> > tempBarcodePrimerComboFileNames = barcodePrimerComboFileNames;
 914                 if(allFiles){
 915                         for(int i=0;i<tempBarcodePrimerComboFileNames.size();i++){
 916                                 for(int j=0;j<tempBarcodePrimerComboFileNames[0].size();j++){
 917                     if (tempBarcodePrimerComboFileNames[i][j] != "") {
 918                         tempBarcodePrimerComboFileNames[i][j] += toString(processors-1) + ".temp";
 919                         ofstream temp;
 920                         m->openOutputFile(tempBarcodePrimerComboFileNames[i][j], temp);
 921                         temp.close();
 922                     }
 923
 924                                 }
 925                         }
 926                 }
 927
 928                 //do my part - do last piece because windows is looking for eof
 929                 int num = driverCreateTrim(flowFileName, (trimFlowFileName  + toString(processors-1) + ".temp"), (scrapFlowFileName  + toString(processors-1) + ".temp"), (fastaFileName + toString(processors-1) + ".temp"), tempBarcodePrimerComboFileNames, lines[processors-1]);
 930                 processIDS.push_back((processors-1));
 931
 932                 //Wait until all threads have terminated.
 933                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 934
 935                 //Close all thread handles and free memory allocations.
 936                 for(int i=0; i < pDataArray.size(); i++){
 937                         num += pDataArray[i]->count;
 938                         CloseHandle(hThreadArray[i]);
 939                         delete pDataArray[i];
 940                 }
 941
 942
 943 #endif
 944                 //append files
 945                 m->mothurOutEndLine();
 946                 for(int i=0;i<processIDS.size();i++){
 947
 948                         m->mothurOut("Appending files from process " + toString(processIDS[i])); m->mothurOutEndLine();
 949
 950                         m->appendFiles((trimFlowFileName + toString(processIDS[i]) + ".temp"), trimFlowFileName);
 951                         m->mothurRemove((trimFlowFileName + toString(processIDS[i]) + ".temp"));
 952 //                      m->mothurOut("\tDone with trim.flow file"); m->mothurOutEndLine();
 953
 954                         m->appendFiles((scrapFlowFileName + toString(processIDS[i]) + ".temp"), scrapFlowFileName);
 955                         m->mothurRemove((scrapFlowFileName + toString(processIDS[i]) + ".temp"));
 956 //                      m->mothurOut("\tDone with scrap.flow file"); m->mothurOutEndLine();
 957
 958                         if(fasta){
 959                                 m->appendFiles((fastaFileName + toString(processIDS[i]) + ".temp"), fastaFileName);
 960                                 m->mothurRemove((fastaFileName + toString(processIDS[i]) + ".temp"));
 961 //                              m->mothurOut("\tDone with flow.fasta file"); m->mothurOutEndLine();
 962                         }
 963                         if(allFiles){
 964                                 for (int j = 0; j < barcodePrimerComboFileNames.size(); j++) {
 965                                         for (int k = 0; k < barcodePrimerComboFileNames[0].size(); k++) {
 966                         if (barcodePrimerComboFileNames[j][k] != "") {
 967                             m->appendFiles((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"), barcodePrimerComboFileNames[j][k]);
 968                             m->mothurRemove((barcodePrimerComboFileNames[j][k] + toString(processIDS[i]) + ".temp"));
 969                         }
 970                                         }
 971                                 }
 972                         }
 973                 }
 974
 975                 return exitCommand;
 976
 977         }
 978         catch(exception& e) {
 979                 m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
 980                 exit(1);
 981         }
 982 }
 983
 984 //***************************************************************************************************************