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