filterseqscommand.cpp

   1 /*
   2  *  filterseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Thomas Ryabin on 5/4/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "filterseqscommand.h"
  11 #include "sequence.hpp"
  12
  13
  14 //**********************************************************************************************************************
  15 vector<string> FilterSeqsCommand::setParameters(){
  16         try {
  17                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  18                 CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
  19                 CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
  20                 CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
  21                 CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
  22                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "FilterSeqsCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string FilterSeqsCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The filter.seqs command reads a file containing sequences and creates a .filter and .filter.fasta file.\n";
  40                 helpString += "The filter.seqs command parameters are fasta, trump, soft, hard, processors and vertical. \n";
  41                 helpString += "The fasta parameter is required, unless you have a valid current fasta file. You may enter several fasta files to build the filter from and filter, by separating their names with -'s.\n";
  42                 helpString += "For example: fasta=abrecovery.fasta-amazon.fasta \n";
  43                 helpString += "The trump option will remove a column if the trump character is found at that position in any sequence of the alignment. Default=*, meaning no trump. \n";
  44                 helpString += "A soft mask removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences. Default=0.\n";
  45                 helpString += "The hard parameter allows you to enter a file containing the filter you want to use.\n";
  46                 helpString += "The vertical parameter removes columns where all sequences contain a gap character. The default is T.\n";
  47                 helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
  48                 helpString += "The filter.seqs command should be in the following format: \n";
  49                 helpString += "filter.seqs(fasta=yourFastaFile, trump=yourTrump) \n";
  50                 helpString += "Example filter.seqs(fasta=abrecovery.fasta, trump=.).\n";
  51                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  52                 return helpString;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "FilterSeqsCommand", "getHelpString");
  56                 exit(1);
  57         }
  58 }
  59 //**********************************************************************************************************************
  60 string FilterSeqsCommand::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 == "fasta") {  outputFileName =  "filter.fasta"; }
  70             else if (type == "filter") {  outputFileName =  "filter"; }
  71             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  72         }
  73         return outputFileName;
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "FilterSeqsCommand", "getOutputFileNameTag");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81 FilterSeqsCommand::FilterSeqsCommand(){
  82         try {
  83                 abort = true; calledHelp = true;
  84                 setParameters();
  85                 vector<string> tempOutNames;
  86                 outputTypes["fasta"] = tempOutNames;
  87                 outputTypes["filter"] = tempOutNames;
  88         }
  89         catch(exception& e) {
  90                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
  91                 exit(1);
  92         }
  93 }
  94 /**************************************************************************************/
  95 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  96         try {
  97                 abort = false; calledHelp = false;
  98                 filterFileName = "";
  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                         vector<string> myArray = setParameters();
 106
 107                         OptionParser parser(option);
 108                         map<string,string> parameters = parser.getParameters();
 109
 110                         ValidParameters validParameter("filter.seqs");
 111                         map<string,string>::iterator it;
 112
 113                         //check to make sure all parameters are valid for command
 114                         for (it = parameters.begin(); it != parameters.end(); it++) {
 115                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 116                         }
 117
 118                         //initialize outputTypes
 119                         vector<string> tempOutNames;
 120                         outputTypes["fasta"] = tempOutNames;
 121                         outputTypes["filter"] = tempOutNames;
 122
 123                         //if the user changes the input directory command factory will send this info to us in the output parameter
 124                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 125                         if (inputDir == "not found"){   inputDir = "";          }
 126                         else {
 127                                 string path;
 128                                 it = parameters.find("fasta");
 129                                 //user has given a template file
 130                                 if(it != parameters.end()){
 131                                         path = m->hasPath(it->second);
 132                                         //if the user has not given a path then, add inputdir. else leave path alone.
 133                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 134                                 }
 135
 136                                 it = parameters.find("hard");
 137                                 //user has given a template file
 138                                 if(it != parameters.end()){
 139                                         path = m->hasPath(it->second);
 140                                         //if the user has not given a path then, add inputdir. else leave path alone.
 141                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
 142                                 }
 143                         }
 144
 145                         //check for required parameters
 146                         fasta = validParameter.validFile(parameters, "fasta", false);
 147                         if (fasta == "not found") {
 148                                 fasta = m->getFastaFile();
 149                                 if (fasta != "") {
 150                     fastafileNames.push_back(fasta);
 151                     m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
 152                     string simpleName = m->getSimpleName(fasta);
 153                     filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 154                 }
 155                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 156                         }
 157                         else {
 158                                 m->splitAtDash(fasta, fastafileNames);
 159
 160                                 //go through files and make sure they are good, if not, then disregard them
 161                                 for (int i = 0; i < fastafileNames.size(); i++) {
 162
 163                                         bool ignore = false;
 164                                         if (fastafileNames[i] == "current") {
 165                                                 fastafileNames[i] = m->getFastaFile();
 166                                                 if (fastafileNames[i] != "") {  m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 167                                                 else {
 168                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 169                                                         //erase from file list
 170                                                         fastafileNames.erase(fastafileNames.begin()+i);
 171                                                         i--;
 172                                                 }
 173                                         }
 174
 175                                         if (!ignore) {
 176                                                 if (inputDir != "") {
 177                                                         string path = m->hasPath(fastafileNames[i]);
 178                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 179                                                         if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
 180                                                 }
 181
 182                                                 ifstream in;
 183                                                 int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
 184
 185                                                 //if you can't open it, try default location
 186                                                 if (ableToOpen == 1) {
 187                                                         if (m->getDefaultPath() != "") { //default path is set
 188                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
 189                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 190                                                                 ifstream in2;
 191                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 192                                                                 in2.close();
 193                                                                 fastafileNames[i] = tryPath;
 194                                                         }
 195                                                 }
 196
 197                                                 //if you can't open it, try default location
 198                                                 if (ableToOpen == 1) {
 199                                                         if (m->getOutputDir() != "") { //default path is set
 200                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 201                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 202                                                                 ifstream in2;
 203                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 204                                                                 in2.close();
 205                                                                 fastafileNames[i] = tryPath;
 206                                                         }
 207                                                 }
 208
 209                                                 in.close();
 210
 211                                                 if (ableToOpen == 1) {
 212                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 213                                                         //erase from file list
 214                                                         fastafileNames.erase(fastafileNames.begin()+i);
 215                                                         i--;
 216                                                 }else{
 217                                                         string simpleName = m->getSimpleName(fastafileNames[i]);
 218                                                         filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 219                                                         m->setFastaFile(fastafileNames[i]);
 220                                                 }
 221                                                 in.close();
 222                                         }
 223                                 }
 224
 225                                 //make sure there is at least one valid file left
 226                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 227                         }
 228
 229                         if (!abort) {
 230                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 231                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 232                                         outputDir = "";
 233                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 234                                 }
 235                         }
 236                         //check for optional parameter and set defaults
 237                         // ...at some point should added some additional type checking...
 238
 239                         string temp;
 240                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 241                         else if (hard == "not open") { hard = ""; abort = true; }
 242
 243                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 244                         trump = temp[0];
 245
 246                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 247                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 248
 249                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 250                         m->setProcessors(temp);
 251                         m->mothurConvert(temp, processors);
 252
 253                         vertical = validParameter.validFile(parameters, "vertical", false);
 254                         if (vertical == "not found") {
 255                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 256                                 else { vertical = "F";  }
 257                         }
 258
 259                         numSeqs = 0;
 260                 }
 261
 262         }
 263         catch(exception& e) {
 264                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 265                 exit(1);
 266         }
 267 }
 268 /**************************************************************************************/
 269
 270 int FilterSeqsCommand::execute() {
 271         try {
 272
 273                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 274
 275                 ifstream inFASTA;
 276                 m->openInputFile(fastafileNames[0], inFASTA);
 277
 278                 Sequence testSeq(inFASTA);
 279                 alignmentLength = testSeq.getAlignLength();
 280                 inFASTA.close();
 281
 282                 ////////////create filter/////////////////
 283                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 284
 285                 filter = createFilter();
 286
 287                 m->mothurOutEndLine();  m->mothurOutEndLine();
 288
 289                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 290
 291                 #ifdef USE_MPI
 292                         int pid;
 293                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 294
 295                         if (pid == 0) { //only one process should output the filter
 296                 #endif
 297
 298                 ofstream outFilter;
 299
 300                 //prevent giantic file name
 301                 string filterFile;
 302                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge." + getOutputFileNameTag("filter"); }
 303                 else {  filterFile = outputDir + filterFileName + "." + getOutputFileNameTag("filter");  }
 304
 305                 m->openOutputFile(filterFile, outFilter);
 306                 outFilter << filter << endl;
 307                 outFilter.close();
 308                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 309
 310                 #ifdef USE_MPI
 311                         }
 312                 #endif
 313
 314                 ////////////run filter/////////////////
 315
 316                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 317
 318                 filterSequences();
 319
 320                 m->mothurOutEndLine();  m->mothurOutEndLine();
 321
 322                 int filteredLength = 0;
 323                 for(int i=0;i<alignmentLength;i++){
 324                         if(filter[i] == '1'){   filteredLength++;       }
 325                 }
 326
 327                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 328
 329
 330                 m->mothurOutEndLine();
 331                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 332                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 333                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 334                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 335
 336                 //set fasta file as new current fastafile
 337                 string current = "";
 338                 itTypes = outputTypes.find("fasta");
 339                 if (itTypes != outputTypes.end()) {
 340                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 341                 }
 342
 343                 m->mothurOutEndLine();
 344                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 345                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 346                 m->mothurOutEndLine();
 347
 348                 return 0;
 349
 350         }
 351         catch(exception& e) {
 352                 m->errorOut(e, "FilterSeqsCommand", "execute");
 353                 exit(1);
 354         }
 355 }
 356 /**************************************************************************************/
 357 int FilterSeqsCommand::filterSequences() {
 358         try {
 359
 360                 numSeqs = 0;
 361
 362                 for (int s = 0; s < fastafileNames.size(); s++) {
 363
 364                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 365
 366                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + getOutputFileNameTag("fasta");
 367 #ifdef USE_MPI
 368                                 int pid, numSeqsPerProcessor, num;
 369                                 int tag = 2001;
 370                                 vector<unsigned long long>MPIPos;
 371
 372                                 MPI_Status status;
 373                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 374                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 375
 376                                 MPI_File outMPI;
 377                                 MPI_File inMPI;
 378                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 379                                 int inMode=MPI_MODE_RDONLY;
 380
 381                                 char outFilename[1024];
 382                                 strcpy(outFilename, filteredFasta.c_str());
 383
 384                                 char inFileName[1024];
 385                                 strcpy(inFileName, fastafileNames[s].c_str());
 386
 387                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 388                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 389
 390                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 391
 392                                 if (pid == 0) { //you are the root process
 393
 394                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 395                                         numSeqs += num;
 396
 397                                         //send file positions to all processes
 398                                         for(int i = 1; i < processors; i++) {
 399                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 400                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 401                                         }
 402
 403                                         //figure out how many sequences you have to do
 404                                         numSeqsPerProcessor = num / processors;
 405                                         int startIndex =  pid * numSeqsPerProcessor;
 406                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 407
 408
 409                                         //do your part
 410                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 411
 412                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 413
 414                                         //wait on chidren
 415                                         for(int i = 1; i < processors; i++) {
 416                                                 char buf[5];
 417                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 418                                         }
 419
 420                                 }else { //you are a child process
 421                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 422                                         MPIPos.resize(num+1);
 423                                         numSeqs += num;
 424                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 425
 426                                         //figure out how many sequences you have to align
 427                                         numSeqsPerProcessor = num / processors;
 428                                         int startIndex =  pid * numSeqsPerProcessor;
 429                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 430
 431
 432                                         //align your part
 433                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 434
 435                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 436
 437                                         char buf[5];
 438                                         strcpy(buf, "done");
 439
 440                                         //tell parent you are done.
 441                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 442                                 }
 443
 444                                 MPI_File_close(&outMPI);
 445                                 MPI_File_close(&inMPI);
 446                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 447
 448 #else
 449
 450             vector<unsigned long long> positions;
 451             if (savedPositions.size() != 0) { positions = savedPositions[s]; }
 452             else {
 453 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 454                                 positions = m->divideFile(fastafileNames[s], processors);
 455 #else
 456                 if(processors != 1){
 457                     int numFastaSeqs = 0;
 458                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 459                     if (positions.size() < processors) { processors = positions.size(); }
 460                 }
 461 #endif
 462             }
 463                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 464                         //vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
 465
 466                         for (int i = 0; i < (positions.size()-1); i++) {
 467                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 468                         }
 469
 470                                 if(processors == 1){
 471                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 472                                         numSeqs += numFastaSeqs;
 473                                 }else{
 474                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
 475                                         numSeqs += numFastaSeqs;
 476                                 }
 477
 478                                 if (m->control_pressed) {  return 1; }
 479                 #else
 480             if(processors == 1){
 481                 lines.push_back(new linePair(0, 1000));
 482                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 483                                 numSeqs += numFastaSeqs;
 484             }else {
 485                 int numFastaSeqs = positions.size()-1;
 486                 //positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 487
 488                 //figure out how many sequences you have to process
 489                 int numSeqsPerProcessor = numFastaSeqs / processors;
 490                 for (int i = 0; i < processors; i++) {
 491                     int startIndex =  i * numSeqsPerProcessor;
 492                     if(i == (processors - 1)){  numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 493                     lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 494                 }
 495
 496                 numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
 497                 numSeqs += numFastaSeqs;
 498             }
 499
 500                                 if (m->control_pressed) {  return 1; }
 501                 #endif
 502 #endif
 503                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 504                 }
 505
 506                 return 0;
 507         }
 508         catch(exception& e) {
 509                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 510                 exit(1);
 511         }
 512 }
 513 #ifdef USE_MPI
 514 /**************************************************************************************/
 515 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
 516         try {
 517                 string outputString = "";
 518                 int count = 0;
 519                 MPI_Status status;
 520
 521                 for(int i=0;i<num;i++){
 522
 523                         if (m->control_pressed) { return 0; }
 524
 525                         //read next sequence
 526                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 527                         char* buf4 = new char[length];
 528                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 529
 530                         string tempBuf = buf4;
 531                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 532                         istringstream iss (tempBuf,istringstream::in);
 533                         delete buf4;
 534
 535                         Sequence seq(iss);  m->gobble(iss);
 536
 537                         if (seq.getName() != "") {
 538                                 string align = seq.getAligned();
 539                                 string filterSeq = "";
 540
 541                                 for(int j=0;j<alignmentLength;j++){
 542                                         if(filter[j] == '1'){
 543                                                 filterSeq += align[j];
 544                                         }
 545                                 }
 546
 547                                 count++;
 548                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 549
 550                                 if(count % 10 == 0){ //output to file
 551                                         //send results to parent
 552                                         int length = outputString.length();
 553                                         char* buf = new char[length];
 554                                         memcpy(buf, outputString.c_str(), length);
 555
 556                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 557                                         outputString = "";
 558                                         delete buf;
 559                                 }
 560
 561                         }
 562
 563                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 564                 }
 565
 566                 if(outputString != ""){ //output to file
 567                         //send results to parent
 568                         int length = outputString.length();
 569                         char* buf = new char[length];
 570                         memcpy(buf, outputString.c_str(), length);
 571
 572                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 573                         outputString = "";
 574                         delete buf;
 575                 }
 576
 577                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 578
 579                 return 0;
 580         }
 581         catch(exception& e) {
 582                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 583                 exit(1);
 584         }
 585 }
 586 #endif
 587 /**************************************************************************************/
 588 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 589         try {
 590                 ofstream out;
 591                 m->openOutputFile(outputFilename, out);
 592
 593                 ifstream in;
 594                 m->openInputFile(inputFilename, in);
 595
 596                 in.seekg(filePos->start);
 597
 598                 bool done = false;
 599                 int count = 0;
 600
 601                 while (!done) {
 602
 603                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 604
 605                                 Sequence seq(in); m->gobble(in);
 606                                 if (seq.getName() != "") {
 607                                         string align = seq.getAligned();
 608                                         string filterSeq = "";
 609
 610                                         for(int j=0;j<alignmentLength;j++){
 611                                                 if(filter[j] == '1'){
 612                                                         filterSeq += align[j];
 613                                                 }
 614                                         }
 615
 616                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 617                                 count++;
 618                         }
 619
 620                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 621                                 unsigned long long pos = in.tellg();
 622                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 623                         #else
 624                                 if (in.eof()) { break; }
 625                         #endif
 626
 627                         //report progress
 628                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 629                 }
 630                 //report progress
 631                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 632
 633
 634                 out.close();
 635                 in.close();
 636
 637                 return count;
 638         }
 639         catch(exception& e) {
 640                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 641                 exit(1);
 642         }
 643 }
 644 /**************************************************************************************************/
 645
 646 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, string filteredFastaName) {
 647         try {
 648
 649         int process = 1;
 650                 int num = 0;
 651                 processIDS.clear();
 652
 653 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 654
 655
 656                 //loop through and create all the processes you want
 657                 while (process != processors) {
 658                         int pid = fork();
 659
 660                         if (pid > 0) {
 661                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 662                                 process++;
 663                         }else if (pid == 0){
 664                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 665                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 666
 667                                 //pass numSeqs to parent
 668                                 ofstream out;
 669                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 670                                 m->openOutputFile(tempFile, out);
 671                                 out << num << endl;
 672                                 out.close();
 673
 674                                 exit(0);
 675                         }else {
 676                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 677                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 678                                 exit(0);
 679                         }
 680                 }
 681
 682         num = driverRunFilter(F, filteredFastaName, filename, lines[0]);
 683
 684                 //force parent to wait until all the processes are done
 685                 for (int i=0;i<processIDS.size();i++) {
 686                         int temp = processIDS[i];
 687                         wait(&temp);
 688                 }
 689
 690                 for (int i = 0; i < processIDS.size(); i++) {
 691                         ifstream in;
 692                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 693                         m->openInputFile(tempFile, in);
 694                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 695                         in.close(); m->mothurRemove(tempFile);
 696
 697             m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filteredFastaName);
 698             m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 699                 }
 700
 701 #else
 702
 703         //////////////////////////////////////////////////////////////////////////////////////////////////////
 704                 //Windows version shared memory, so be careful when passing variables through the filterData struct.
 705                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 706                 //Taking advantage of shared memory to allow both threads to add info to F.
 707                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 708
 709                 vector<filterRunData*> pDataArray;
 710                 DWORD   dwThreadIdArray[processors-1];
 711                 HANDLE  hThreadArray[processors-1];
 712
 713                 //Create processor worker threads.
 714                 for( int i=0; i<processors-1; i++){
 715
 716             string extension = "";
 717                         if (i != 0) { extension = toString(i) + ".temp"; }
 718
 719                         filterRunData* tempFilter = new filterRunData(filter, filename, (filteredFastaName + extension), m, lines[i]->start, lines[i]->end, alignmentLength, i);
 720                         pDataArray.push_back(tempFilter);
 721                         processIDS.push_back(i);
 722
 723                         hThreadArray[i] = CreateThread(NULL, 0, MyRunFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 724                 }
 725
 726         num = driverRunFilter(F, (filteredFastaName + toString(processors-1) + ".temp"), filename, lines[processors-1]);
 727
 728                 //Wait until all threads have terminated.
 729                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 730
 731                 //Close all thread handles and free memory allocations.
 732                 for(int i=0; i < pDataArray.size(); i++){
 733                         num += pDataArray[i]->count;
 734             CloseHandle(hThreadArray[i]);
 735                         delete pDataArray[i];
 736                 }
 737
 738         for (int i = 1; i < processors; i++) {
 739             m->appendFiles((filteredFastaName + toString(i) + ".temp"), filteredFastaName);
 740             m->mothurRemove((filteredFastaName + toString(i) + ".temp"));
 741                 }
 742 #endif
 743
 744         return num;
 745
 746         }
 747         catch(exception& e) {
 748                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 749                 exit(1);
 750         }
 751 }
 752 /**************************************************************************************/
 753 string FilterSeqsCommand::createFilter() {
 754         try {
 755                 string filterString = "";
 756                 Filters F;
 757
 758                 if (soft != 0)                  {  F.setSoft(soft);             }
 759                 if (trump != '*')               {  F.setTrump(trump);   }
 760
 761                 F.setLength(alignmentLength);
 762
 763                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 764                         F.initialize();
 765                 }
 766
 767                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 768                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 769
 770                 numSeqs = 0;
 771                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 772                         for (int s = 0; s < fastafileNames.size(); s++) {
 773
 774                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 775
 776 #ifdef USE_MPI
 777                                 int pid, numSeqsPerProcessor, num;
 778                                 int tag = 2001;
 779                                 vector<unsigned long long> MPIPos;
 780
 781                                 MPI_Status status;
 782                                 MPI_File inMPI;
 783                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 784                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 785
 786                                 //char* tempFileName = new char(fastafileNames[s].length());
 787                                 //tempFileName = &(fastafileNames[s][0]);
 788
 789                                 char tempFileName[1024];
 790                                 strcpy(tempFileName, fastafileNames[s].c_str());
 791
 792                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 793
 794                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 795
 796                                 if (pid == 0) { //you are the root process
 797                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 798                                                 numSeqs += num;
 799
 800                                                 //send file positions to all processes
 801                                                 for(int i = 1; i < processors; i++) {
 802                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 803                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 804                                                 }
 805
 806                                                 //figure out how many sequences you have to do
 807                                                 numSeqsPerProcessor = num / processors;
 808                                                 int startIndex =  pid * numSeqsPerProcessor;
 809                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 810
 811
 812                                                 //do your part
 813                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 814
 815                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 816
 817                                 }else { //i am the child process
 818                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 819                                         MPIPos.resize(num+1);
 820                                         numSeqs += num;
 821                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 822
 823                                         //figure out how many sequences you have to align
 824                                         numSeqsPerProcessor = num / processors;
 825                                         int startIndex =  pid * numSeqsPerProcessor;
 826                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 827
 828
 829                                         //do your part
 830                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 831
 832                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 833                                 }
 834
 835                                 MPI_File_close(&inMPI);
 836                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 837
 838 #else
 839
 840                 vector<unsigned long long> positions;
 841                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 842                                 positions = m->divideFile(fastafileNames[s], processors);
 843                                 for (int i = 0; i < (positions.size()-1); i++) {
 844                                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 845                                 }
 846
 847                                 if(processors == 1){
 848                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 849                                         numSeqs += numFastaSeqs;
 850                                 }else{
 851                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 852                                         numSeqs += numFastaSeqs;
 853                                 }
 854                 #else
 855                 if(processors == 1){
 856                     lines.push_back(new linePair(0, 1000));
 857                     int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 858                     numSeqs += numFastaSeqs;
 859                                 }else {
 860                     int numFastaSeqs = 0;
 861                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 862                     if (positions.size() < processors) { processors = positions.size(); }
 863
 864                     //figure out how many sequences you have to process
 865                     int numSeqsPerProcessor = numFastaSeqs / processors;
 866                     for (int i = 0; i < processors; i++) {
 867                         int startIndex =  i * numSeqsPerProcessor;
 868                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 869                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 870                     }
 871
 872                     numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 873                                         numSeqs += numFastaSeqs;
 874                 }
 875                 #endif
 876                 //save the file positions so we can reuse them in the runFilter function
 877                 savedPositions[s] = positions;
 878
 879                                 if (m->control_pressed) {  return filterString; }
 880 #endif
 881
 882                         }
 883                 }
 884
 885
 886 #ifdef USE_MPI
 887                 int pid;
 888                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 889                 MPI_Status status;
 890
 891                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 892
 893                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 894
 895                         if (pid == 0) { //only one process should output the filter
 896
 897                                 vector<int> temp; temp.resize(alignmentLength+1);
 898
 899                                 //get the frequencies from the child processes
 900                                 for(int i = 1; i < processors; i++) {
 901
 902                                         for (int j = 0; j < 5; j++) {
 903
 904                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 905                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 906
 907                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 908                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 909                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 910                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 911                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 912                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 913                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 914                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 915                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 916                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 917                                                 }
 918                                         }
 919                                 }
 920                         }else{
 921
 922                                 //send my fequency counts
 923                                 F.a.push_back(Atag);
 924                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 925                                 F.t.push_back(Ttag);
 926                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 927                                 F.c.push_back(Ctag);
 928                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 929                                 F.g.push_back(Gtag);
 930                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 931                                 F.gap.push_back(Gaptag);
 932                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 933                         }
 934
 935                 }
 936
 937                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 938
 939                 if (pid == 0) { //only one process should output the filter
 940 #endif
 941
 942                 F.setNumSeqs(numSeqs);
 943                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 944                 if(soft != 0)                           {       F.doSoft();             }
 945                 filterString = F.getFilter();
 946
 947 #ifdef USE_MPI
 948                 //send filter string to kids
 949                 //for(int i = 1; i < processors; i++) {
 950                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 951                 //}
 952                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 953         }else{
 954                 //recieve filterString
 955                 char* tempBuf = new char[alignmentLength];
 956                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 957                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 958
 959                 filterString = tempBuf;
 960                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 961                 delete tempBuf;
 962         }
 963
 964         MPI_Barrier(MPI_COMM_WORLD);
 965 #endif
 966
 967                 return filterString;
 968         }
 969         catch(exception& e) {
 970                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 971                 exit(1);
 972         }
 973 }
 974 /**************************************************************************************/
 975 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 976         try {
 977
 978                 ifstream in;
 979                 m->openInputFile(filename, in);
 980
 981                 in.seekg(filePos->start);
 982
 983                 bool done = false;
 984                 int count = 0;
 985
 986                 while (!done) {
 987
 988                         if (m->control_pressed) { in.close(); return 1; }
 989
 990                         Sequence seq(in); m->gobble(in);
 991                         if (seq.getName() != "") {
 992                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 993
 994                                         if(trump != '*')                        {       F.doTrump(seq);         }
 995                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 996                                         cout.flush();
 997                                         count++;
 998                         }
 999
1000                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1001                                 unsigned long long pos = in.tellg();
1002                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
1003                         #else
1004                                 if (in.eof()) { break; }
1005                         #endif
1006
1007                         //report progress
1008                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1009                 }
1010                 //report progress
1011                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
1012                 in.close();
1013
1014                 return count;
1015         }
1016         catch(exception& e) {
1017                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
1018                 exit(1);
1019         }
1020 }
1021 #ifdef USE_MPI
1022 /**************************************************************************************/
1023 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long long>& MPIPos) {
1024         try {
1025
1026                 MPI_Status status;
1027                 int pid;
1028                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1029
1030                 for(int i=0;i<num;i++){
1031
1032                         if (m->control_pressed) { return 0; }
1033
1034                         //read next sequence
1035                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1036
1037                         char* buf4 = new char[length];
1038                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1039
1040                         string tempBuf = buf4;
1041                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1042                         istringstream iss (tempBuf,istringstream::in);
1043                         delete buf4;
1044
1045                         Sequence seq(iss);
1046
1047                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
1048
1049                         if(trump != '*'){       F.doTrump(seq); }
1050                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
1051                         cout.flush();
1052
1053                         //report progress
1054                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
1055                 }
1056
1057                 //report progress
1058                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
1059
1060                 return 0;
1061         }
1062         catch(exception& e) {
1063                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
1064                 exit(1);
1065         }
1066 }
1067 #endif
1068 /**************************************************************************************************/
1069
1070 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
1071         try {
1072         int process = 1;
1073                 int num = 0;
1074                 processIDS.clear();
1075
1076 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1077
1078                 //loop through and create all the processes you want
1079                 while (process != processors) {
1080                         int pid = fork();
1081
1082                         if (pid > 0) {
1083                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1084                                 process++;
1085                         }else if (pid == 0){
1086                                 //reset child's filter counts to 0;
1087                                 F.a.clear(); F.a.resize(alignmentLength, 0);
1088                                 F.t.clear(); F.t.resize(alignmentLength, 0);
1089                                 F.g.clear(); F.g.resize(alignmentLength, 0);
1090                                 F.c.clear(); F.c.resize(alignmentLength, 0);
1091                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
1092
1093                                 num = driverCreateFilter(F, filename, lines[process]);
1094
1095                                 //write out filter counts to file
1096                                 filename += toString(getpid()) + "filterValues.temp";
1097                                 ofstream out;
1098                                 m->openOutputFile(filename, out);
1099
1100                                 out << num << endl;
1101                                 out << F.getFilter() << endl;
1102                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
1103                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
1104                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
1105                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
1106                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
1107
1108                                 //cout << F.getFilter() << endl;
1109                                 out.close();
1110
1111                                 exit(0);
1112                         }else {
1113                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1114                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1115                                 exit(0);
1116                         }
1117                 }
1118
1119                 //parent do your part
1120                 num = driverCreateFilter(F, filename, lines[0]);
1121
1122                 //force parent to wait until all the processes are done
1123                 for (int i=0;i<(processors-1);i++) {
1124                         int temp = processIDS[i];
1125                         wait(&temp);
1126                 }
1127
1128                 //parent reads in and combines Filter info
1129                 for (int i = 0; i < processIDS.size(); i++) {
1130                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
1131                         ifstream in;
1132                         m->openInputFile(tempFilename, in);
1133
1134                         int temp, tempNum;
1135                         string tempFilterString;
1136
1137                         in >> tempNum; m->gobble(in); num += tempNum;
1138
1139                         in >> tempFilterString;
1140                         F.mergeFilter(tempFilterString);
1141
1142                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
1143                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1144                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1145                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1146                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1147
1148                         in.close();
1149                         m->mothurRemove(tempFilename);
1150                 }
1151
1152
1153 #else
1154
1155         //////////////////////////////////////////////////////////////////////////////////////////////////////
1156                 //Windows version shared memory, so be careful when passing variables through the filterData struct.
1157                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1158                 //Taking advantage of shared memory to allow both threads to add info to F.
1159                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1160
1161                 vector<filterData*> pDataArray;
1162                 DWORD   dwThreadIdArray[processors];
1163                 HANDLE  hThreadArray[processors];
1164
1165                 //Create processor worker threads.
1166                 for( int i=0; i<processors; i++ ){
1167
1168                         filterData* tempFilter = new filterData(filename, m, lines[i]->start, lines[i]->end, alignmentLength, trump, vertical, soft, hard, i);
1169                         pDataArray.push_back(tempFilter);
1170                         processIDS.push_back(i);
1171
1172                         hThreadArray[i] = CreateThread(NULL, 0, MyCreateFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1173                 }
1174
1175                 //Wait until all threads have terminated.
1176                 WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
1177
1178                 //Close all thread handles and free memory allocations.
1179                 for(int i=0; i < pDataArray.size(); i++){
1180                         num += pDataArray[i]->count;
1181             F.mergeFilter(pDataArray[i]->F.getFilter());
1182
1183                         for (int k = 0; k < alignmentLength; k++) {      F.a[k] += pDataArray[i]->F.a[k];       }
1184                         for (int k = 0; k < alignmentLength; k++) {      F.t[k] += pDataArray[i]->F.t[k];       }
1185                         for (int k = 0; k < alignmentLength; k++) {      F.g[k] += pDataArray[i]->F.g[k];       }
1186                         for (int k = 0; k < alignmentLength; k++) {      F.c[k] += pDataArray[i]->F.c[k];       }
1187                         for (int k = 0; k < alignmentLength; k++) {      F.gap[k] += pDataArray[i]->F.gap[k];   }
1188
1189                         CloseHandle(hThreadArray[i]);
1190                         delete pDataArray[i];
1191                 }
1192
1193 #endif
1194         return num;
1195
1196         }
1197         catch(exception& e) {
1198                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1199                 exit(1);
1200         }
1201 }
1202 /**************************************************************************************/