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 FilterSeqsCommand::FilterSeqsCommand(){
  61         try {
  62                 abort = true; calledHelp = true;
  63                 setParameters();
  64                 vector<string> tempOutNames;
  65                 outputTypes["fasta"] = tempOutNames;
  66                 outputTypes["filter"] = tempOutNames;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
  70                 exit(1);
  71         }
  72 }
  73 /**************************************************************************************/
  74 FilterSeqsCommand::FilterSeqsCommand(string option)  {
  75         try {
  76                 abort = false; calledHelp = false;
  77                 filterFileName = "";
  78
  79                 //allow user to run help
  80                 if(option == "help") { help(); abort = true; calledHelp = true; }
  81                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  82
  83                 else {
  84                         vector<string> myArray = setParameters();
  85
  86                         OptionParser parser(option);
  87                         map<string,string> parameters = parser.getParameters();
  88
  89                         ValidParameters validParameter("filter.seqs");
  90                         map<string,string>::iterator it;
  91
  92                         //check to make sure all parameters are valid for command
  93                         for (it = parameters.begin(); it != parameters.end(); it++) {
  94                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  95                         }
  96
  97                         //initialize outputTypes
  98                         vector<string> tempOutNames;
  99                         outputTypes["fasta"] = tempOutNames;
 100                         outputTypes["filter"] = tempOutNames;
 101
 102                         //if the user changes the input directory command factory will send this info to us in the output parameter
 103                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 104                         if (inputDir == "not found"){   inputDir = "";          }
 105                         else {
 106                                 string path;
 107                                 it = parameters.find("fasta");
 108                                 //user has given a template file
 109                                 if(it != parameters.end()){
 110                                         path = m->hasPath(it->second);
 111                                         //if the user has not given a path then, add inputdir. else leave path alone.
 112                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 113                                 }
 114
 115                                 it = parameters.find("hard");
 116                                 //user has given a template file
 117                                 if(it != parameters.end()){
 118                                         path = m->hasPath(it->second);
 119                                         //if the user has not given a path then, add inputdir. else leave path alone.
 120                                         if (path == "") {       parameters["hard"] = inputDir + it->second;             }
 121                                 }
 122                         }
 123
 124                         //check for required parameters
 125                         fasta = validParameter.validFile(parameters, "fasta", false);
 126                         if (fasta == "not found") {
 127                                 fasta = m->getFastaFile();
 128                                 if (fasta != "") {
 129                     fastafileNames.push_back(fasta);
 130                     m->mothurOut("Using " + fasta + " as input file for the fasta parameter."); m->mothurOutEndLine();
 131                     string simpleName = m->getSimpleName(fasta);
 132                     filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 133                 }
 134                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 135                         }
 136                         else {
 137                                 m->splitAtDash(fasta, fastafileNames);
 138
 139                                 //go through files and make sure they are good, if not, then disregard them
 140                                 for (int i = 0; i < fastafileNames.size(); i++) {
 141
 142                                         bool ignore = false;
 143                                         if (fastafileNames[i] == "current") {
 144                                                 fastafileNames[i] = m->getFastaFile();
 145                                                 if (fastafileNames[i] != "") {  m->mothurOut("Using " + fastafileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 146                                                 else {
 147                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 148                                                         //erase from file list
 149                                                         fastafileNames.erase(fastafileNames.begin()+i);
 150                                                         i--;
 151                                                 }
 152                                         }
 153
 154                                         if (!ignore) {
 155                                                 if (inputDir != "") {
 156                                                         string path = m->hasPath(fastafileNames[i]);
 157                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 158                                                         if (path == "") {       fastafileNames[i] = inputDir + fastafileNames[i];               }
 159                                                 }
 160
 161                                                 ifstream in;
 162                                                 int ableToOpen = m->openInputFile(fastafileNames[i], in, "noerror");
 163
 164                                                 //if you can't open it, try default location
 165                                                 if (ableToOpen == 1) {
 166                                                         if (m->getDefaultPath() != "") { //default path is set
 167                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(fastafileNames[i]);
 168                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 169                                                                 ifstream in2;
 170                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 171                                                                 in2.close();
 172                                                                 fastafileNames[i] = tryPath;
 173                                                         }
 174                                                 }
 175
 176                                                 //if you can't open it, try default location
 177                                                 if (ableToOpen == 1) {
 178                                                         if (m->getOutputDir() != "") { //default path is set
 179                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(fastafileNames[i]);
 180                                                                 m->mothurOut("Unable to open " + fastafileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 181                                                                 ifstream in2;
 182                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 183                                                                 in2.close();
 184                                                                 fastafileNames[i] = tryPath;
 185                                                         }
 186                                                 }
 187
 188                                                 in.close();
 189
 190                                                 if (ableToOpen == 1) {
 191                                                         m->mothurOut("Unable to open " + fastafileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 192                                                         //erase from file list
 193                                                         fastafileNames.erase(fastafileNames.begin()+i);
 194                                                         i--;
 195                                                 }else{
 196                                                         string simpleName = m->getSimpleName(fastafileNames[i]);
 197                                                         filterFileName += simpleName.substr(0, simpleName.find_first_of('.'));
 198                                                         m->setFastaFile(fastafileNames[i]);
 199                                                 }
 200                                                 in.close();
 201                                         }
 202                                 }
 203
 204                                 //make sure there is at least one valid file left
 205                                 if (fastafileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 206                         }
 207
 208                         if (!abort) {
 209                                 //if the user changes the output directory command factory will send this info to us in the output parameter
 210                                 outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 211                                         outputDir = "";
 212                                         outputDir += m->hasPath(fastafileNames[0]); //if user entered a file with a path then preserve it
 213                                 }
 214                         }
 215                         //check for optional parameter and set defaults
 216                         // ...at some point should added some additional type checking...
 217
 218                         string temp;
 219                         hard = validParameter.validFile(parameters, "hard", true);                              if (hard == "not found") { hard = ""; }
 220                         else if (hard == "not open") { hard = ""; abort = true; }
 221
 222                         temp = validParameter.validFile(parameters, "trump", false);                    if (temp == "not found") { temp = "*"; }
 223                         trump = temp[0];
 224
 225                         temp = validParameter.validFile(parameters, "soft", false);                             if (temp == "not found") { soft = 0; }
 226                         else {  soft = (float)atoi(temp.c_str()) / 100.0;  }
 227
 228                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 229                         m->setProcessors(temp);
 230                         m->mothurConvert(temp, processors);
 231
 232                         vertical = validParameter.validFile(parameters, "vertical", false);
 233                         if (vertical == "not found") {
 234                                 if ((hard == "") && (trump == '*') && (soft == 0)) { vertical = "T"; } //you have not given a hard file or set the trump char.
 235                                 else { vertical = "F";  }
 236                         }
 237
 238                         numSeqs = 0;
 239                 }
 240
 241         }
 242         catch(exception& e) {
 243                 m->errorOut(e, "FilterSeqsCommand", "FilterSeqsCommand");
 244                 exit(1);
 245         }
 246 }
 247 /**************************************************************************************/
 248
 249 int FilterSeqsCommand::execute() {
 250         try {
 251
 252                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 253
 254                 ifstream inFASTA;
 255                 m->openInputFile(fastafileNames[0], inFASTA);
 256
 257                 Sequence testSeq(inFASTA);
 258                 alignmentLength = testSeq.getAlignLength();
 259                 inFASTA.close();
 260
 261                 ////////////create filter/////////////////
 262                 m->mothurOut("Creating Filter... "); m->mothurOutEndLine();
 263
 264                 filter = createFilter();
 265
 266                 m->mothurOutEndLine();  m->mothurOutEndLine();
 267
 268                 if (m->control_pressed) { outputTypes.clear(); return 0; }
 269
 270                 #ifdef USE_MPI
 271                         int pid;
 272                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 273
 274                         if (pid == 0) { //only one process should output the filter
 275                 #endif
 276
 277                 ofstream outFilter;
 278
 279                 //prevent giantic file name
 280                 string filterFile;
 281                 if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
 282                 else {  filterFile = outputDir + filterFileName + ".filter";  }
 283
 284                 m->openOutputFile(filterFile, outFilter);
 285                 outFilter << filter << endl;
 286                 outFilter.close();
 287                 outputNames.push_back(filterFile); outputTypes["filter"].push_back(filterFile);
 288
 289                 #ifdef USE_MPI
 290                         }
 291                 #endif
 292
 293                 ////////////run filter/////////////////
 294
 295                 m->mothurOut("Running Filter... "); m->mothurOutEndLine();
 296
 297                 filterSequences();
 298
 299                 m->mothurOutEndLine();  m->mothurOutEndLine();
 300
 301                 int filteredLength = 0;
 302                 for(int i=0;i<alignmentLength;i++){
 303                         if(filter[i] == '1'){   filteredLength++;       }
 304                 }
 305
 306                 if (m->control_pressed) {  outputTypes.clear(); for(int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }  return 0; }
 307
 308
 309                 m->mothurOutEndLine();
 310                 m->mothurOut("Length of filtered alignment: " + toString(filteredLength)); m->mothurOutEndLine();
 311                 m->mothurOut("Number of columns removed: " + toString((alignmentLength-filteredLength))); m->mothurOutEndLine();
 312                 m->mothurOut("Length of the original alignment: " + toString(alignmentLength)); m->mothurOutEndLine();
 313                 m->mothurOut("Number of sequences used to construct filter: " + toString(numSeqs)); m->mothurOutEndLine();
 314
 315                 //set fasta file as new current fastafile
 316                 string current = "";
 317                 itTypes = outputTypes.find("fasta");
 318                 if (itTypes != outputTypes.end()) {
 319                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 320                 }
 321
 322                 m->mothurOutEndLine();
 323                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 324                 for(int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();      }
 325                 m->mothurOutEndLine();
 326
 327                 return 0;
 328
 329         }
 330         catch(exception& e) {
 331                 m->errorOut(e, "FilterSeqsCommand", "execute");
 332                 exit(1);
 333         }
 334 }
 335 /**************************************************************************************/
 336 int FilterSeqsCommand::filterSequences() {
 337         try {
 338
 339                 numSeqs = 0;
 340
 341                 for (int s = 0; s < fastafileNames.size(); s++) {
 342
 343                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 344
 345                                 string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
 346 #ifdef USE_MPI
 347                                 int pid, numSeqsPerProcessor, num;
 348                                 int tag = 2001;
 349                                 vector<unsigned long long>MPIPos;
 350
 351                                 MPI_Status status;
 352                                 MPI_Comm_size(MPI_COMM_WORLD, &processors); //set processors to the number of mpi processes running
 353                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 354
 355                                 MPI_File outMPI;
 356                                 MPI_File inMPI;
 357                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 358                                 int inMode=MPI_MODE_RDONLY;
 359
 360                                 char outFilename[1024];
 361                                 strcpy(outFilename, filteredFasta.c_str());
 362
 363                                 char inFileName[1024];
 364                                 strcpy(inFileName, fastafileNames[s].c_str());
 365
 366                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 367                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 368
 369                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 370
 371                                 if (pid == 0) { //you are the root process
 372
 373                                         MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 374                                         numSeqs += num;
 375
 376                                         //send file positions to all processes
 377                                         for(int i = 1; i < processors; i++) {
 378                                                 MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 379                                                 MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 380                                         }
 381
 382                                         //figure out how many sequences you have to do
 383                                         numSeqsPerProcessor = num / processors;
 384                                         int startIndex =  pid * numSeqsPerProcessor;
 385                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 386
 387
 388                                         //do your part
 389                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 390
 391                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 392
 393                                         //wait on chidren
 394                                         for(int i = 1; i < processors; i++) {
 395                                                 char buf[5];
 396                                                 MPI_Recv(buf, 5, MPI_CHAR, i, tag, MPI_COMM_WORLD, &status);
 397                                         }
 398
 399                                 }else { //you are a child process
 400                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 401                                         MPIPos.resize(num+1);
 402                                         numSeqs += num;
 403                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 404
 405                                         //figure out how many sequences you have to align
 406                                         numSeqsPerProcessor = num / processors;
 407                                         int startIndex =  pid * numSeqsPerProcessor;
 408                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 409
 410
 411                                         //align your part
 412                                         driverMPIRun(startIndex, numSeqsPerProcessor, inMPI, outMPI, MPIPos);
 413
 414                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI);  return 0;  }
 415
 416                                         char buf[5];
 417                                         strcpy(buf, "done");
 418
 419                                         //tell parent you are done.
 420                                         MPI_Send(buf, 5, MPI_CHAR, 0, tag, MPI_COMM_WORLD);
 421                                 }
 422
 423                                 MPI_File_close(&outMPI);
 424                                 MPI_File_close(&inMPI);
 425                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 426
 427 #else
 428
 429             vector<unsigned long long> positions;
 430             if (savedPositions.size() != 0) { positions = savedPositions[s]; }
 431             else {
 432 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 433                                 positions = m->divideFile(fastafileNames[s], processors);
 434 #else
 435                 if(processors != 1){
 436                     int numFastaSeqs = 0;
 437                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 438                     if (positions.size() < processors) { processors = positions.size(); }
 439                 }
 440 #endif
 441             }
 442                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 443                         //vector<unsigned long long> positions = m->divideFile(fastafileNames[s], processors);
 444
 445                         for (int i = 0; i < (positions.size()-1); i++) {
 446                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 447                         }
 448
 449                                 if(processors == 1){
 450                                         int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 451                                         numSeqs += numFastaSeqs;
 452                                 }else{
 453                                         int numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
 454                                         numSeqs += numFastaSeqs;
 455                                 }
 456
 457                                 if (m->control_pressed) {  return 1; }
 458                 #else
 459             if(processors == 1){
 460                 lines.push_back(new linePair(0, 1000));
 461                                 int numFastaSeqs = driverRunFilter(filter, filteredFasta, fastafileNames[s], lines[0]);
 462                                 numSeqs += numFastaSeqs;
 463             }else {
 464                 int numFastaSeqs = positions.size()-1;
 465                 //positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 466
 467                 //figure out how many sequences you have to process
 468                 int numSeqsPerProcessor = numFastaSeqs / processors;
 469                 for (int i = 0; i < processors; i++) {
 470                     int startIndex =  i * numSeqsPerProcessor;
 471                     if(i == (processors - 1)){  numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 472                     lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 473                 }
 474
 475                 numFastaSeqs = createProcessesRunFilter(filter, fastafileNames[s], filteredFasta);
 476                 numSeqs += numFastaSeqs;
 477             }
 478
 479                                 if (m->control_pressed) {  return 1; }
 480                 #endif
 481 #endif
 482                         outputNames.push_back(filteredFasta); outputTypes["fasta"].push_back(filteredFasta);
 483                 }
 484
 485                 return 0;
 486         }
 487         catch(exception& e) {
 488                 m->errorOut(e, "FilterSeqsCommand", "filterSequences");
 489                 exit(1);
 490         }
 491 }
 492 #ifdef USE_MPI
 493 /**************************************************************************************/
 494 int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long long>& MPIPos) {
 495         try {
 496                 string outputString = "";
 497                 int count = 0;
 498                 MPI_Status status;
 499
 500                 for(int i=0;i<num;i++){
 501
 502                         if (m->control_pressed) { return 0; }
 503
 504                         //read next sequence
 505                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 506                         char* buf4 = new char[length];
 507                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 508
 509                         string tempBuf = buf4;
 510                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 511                         istringstream iss (tempBuf,istringstream::in);
 512                         delete buf4;
 513
 514                         Sequence seq(iss);  m->gobble(iss);
 515
 516                         if (seq.getName() != "") {
 517                                 string align = seq.getAligned();
 518                                 string filterSeq = "";
 519
 520                                 for(int j=0;j<alignmentLength;j++){
 521                                         if(filter[j] == '1'){
 522                                                 filterSeq += align[j];
 523                                         }
 524                                 }
 525
 526                                 count++;
 527                                 outputString += ">" + seq.getName() + "\n" + filterSeq + "\n";
 528
 529                                 if(count % 10 == 0){ //output to file
 530                                         //send results to parent
 531                                         int length = outputString.length();
 532                                         char* buf = new char[length];
 533                                         memcpy(buf, outputString.c_str(), length);
 534
 535                                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 536                                         outputString = "";
 537                                         delete buf;
 538                                 }
 539
 540                         }
 541
 542                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
 543                 }
 544
 545                 if(outputString != ""){ //output to file
 546                         //send results to parent
 547                         int length = outputString.length();
 548                         char* buf = new char[length];
 549                         memcpy(buf, outputString.c_str(), length);
 550
 551                         MPI_File_write_shared(outMPI, buf, length, MPI_CHAR, &status);
 552                         outputString = "";
 553                         delete buf;
 554                 }
 555
 556                 if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
 557
 558                 return 0;
 559         }
 560         catch(exception& e) {
 561                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 562                 exit(1);
 563         }
 564 }
 565 #endif
 566 /**************************************************************************************/
 567 int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string inputFilename, linePair* filePos) {
 568         try {
 569                 ofstream out;
 570                 m->openOutputFile(outputFilename, out);
 571
 572                 ifstream in;
 573                 m->openInputFile(inputFilename, in);
 574
 575                 in.seekg(filePos->start);
 576
 577                 bool done = false;
 578                 int count = 0;
 579
 580                 while (!done) {
 581
 582                                 if (m->control_pressed) { in.close(); out.close(); return 0; }
 583
 584                                 Sequence seq(in); m->gobble(in);
 585                                 if (seq.getName() != "") {
 586                                         string align = seq.getAligned();
 587                                         string filterSeq = "";
 588
 589                                         for(int j=0;j<alignmentLength;j++){
 590                                                 if(filter[j] == '1'){
 591                                                         filterSeq += align[j];
 592                                                 }
 593                                         }
 594
 595                                         out << '>' << seq.getName() << endl << filterSeq << endl;
 596                                 count++;
 597                         }
 598
 599                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 600                                 unsigned long long pos = in.tellg();
 601                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 602                         #else
 603                                 if (in.eof()) { break; }
 604                         #endif
 605
 606                         //report progress
 607                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 608                 }
 609                 //report progress
 610                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 611
 612
 613                 out.close();
 614                 in.close();
 615
 616                 return count;
 617         }
 618         catch(exception& e) {
 619                 m->errorOut(e, "FilterSeqsCommand", "driverRunFilter");
 620                 exit(1);
 621         }
 622 }
 623 /**************************************************************************************************/
 624
 625 int FilterSeqsCommand::createProcessesRunFilter(string F, string filename, string filteredFastaName) {
 626         try {
 627
 628         int process = 1;
 629                 int num = 0;
 630                 processIDS.clear();
 631
 632 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 633
 634
 635                 //loop through and create all the processes you want
 636                 while (process != processors) {
 637                         int pid = fork();
 638
 639                         if (pid > 0) {
 640                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 641                                 process++;
 642                         }else if (pid == 0){
 643                                 string filteredFasta = filename + toString(getpid()) + ".temp";
 644                                 num = driverRunFilter(F, filteredFasta, filename, lines[process]);
 645
 646                                 //pass numSeqs to parent
 647                                 ofstream out;
 648                                 string tempFile = filename +  toString(getpid()) + ".num.temp";
 649                                 m->openOutputFile(tempFile, out);
 650                                 out << num << endl;
 651                                 out.close();
 652
 653                                 exit(0);
 654                         }else {
 655                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 656                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 657                                 exit(0);
 658                         }
 659                 }
 660
 661         num = driverRunFilter(F, filteredFastaName, filename, lines[0]);
 662
 663                 //force parent to wait until all the processes are done
 664                 for (int i=0;i<processIDS.size();i++) {
 665                         int temp = processIDS[i];
 666                         wait(&temp);
 667                 }
 668
 669                 for (int i = 0; i < processIDS.size(); i++) {
 670                         ifstream in;
 671                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
 672                         m->openInputFile(tempFile, in);
 673                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 674                         in.close(); m->mothurRemove(tempFile);
 675
 676             m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filteredFastaName);
 677             m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
 678                 }
 679
 680 #else
 681
 682         //////////////////////////////////////////////////////////////////////////////////////////////////////
 683                 //Windows version shared memory, so be careful when passing variables through the filterData struct.
 684                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 685                 //Taking advantage of shared memory to allow both threads to add info to F.
 686                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 687
 688                 vector<filterRunData*> pDataArray;
 689                 DWORD   dwThreadIdArray[processors-1];
 690                 HANDLE  hThreadArray[processors-1];
 691
 692                 //Create processor worker threads.
 693                 for( int i=0; i<processors-1; i++){
 694
 695             string extension = "";
 696                         if (i != 0) { extension = toString(i) + ".temp"; }
 697
 698                         filterRunData* tempFilter = new filterRunData(filter, filename, (filteredFastaName + extension), m, lines[i]->start, lines[i]->end, alignmentLength, i);
 699                         pDataArray.push_back(tempFilter);
 700                         processIDS.push_back(i);
 701
 702                         hThreadArray[i] = CreateThread(NULL, 0, MyRunFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 703                 }
 704
 705         num = driverRunFilter(F, (filteredFastaName + toString(processors-1) + ".temp"), filename, lines[processors-1]);
 706
 707                 //Wait until all threads have terminated.
 708                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 709
 710                 //Close all thread handles and free memory allocations.
 711                 for(int i=0; i < pDataArray.size(); i++){
 712                         num += pDataArray[i]->count;
 713             CloseHandle(hThreadArray[i]);
 714                         delete pDataArray[i];
 715                 }
 716
 717         for (int i = 1; i < processors; i++) {
 718             m->appendFiles((filteredFastaName + toString(i) + ".temp"), filteredFastaName);
 719             m->mothurRemove((filteredFastaName + toString(i) + ".temp"));
 720                 }
 721 #endif
 722
 723         return num;
 724
 725         }
 726         catch(exception& e) {
 727                 m->errorOut(e, "FilterSeqsCommand", "createProcessesRunFilter");
 728                 exit(1);
 729         }
 730 }
 731 /**************************************************************************************/
 732 string FilterSeqsCommand::createFilter() {
 733         try {
 734                 string filterString = "";
 735                 Filters F;
 736
 737                 if (soft != 0)                  {  F.setSoft(soft);             }
 738                 if (trump != '*')               {  F.setTrump(trump);   }
 739
 740                 F.setLength(alignmentLength);
 741
 742                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 743                         F.initialize();
 744                 }
 745
 746                 if(hard.compare("") != 0)       {       F.doHard(hard);         }
 747                 else                                            {       F.setFilter(string(alignmentLength, '1'));      }
 748
 749                 numSeqs = 0;
 750                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 751                         for (int s = 0; s < fastafileNames.size(); s++) {
 752
 753                                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 754
 755 #ifdef USE_MPI
 756                                 int pid, numSeqsPerProcessor, num;
 757                                 int tag = 2001;
 758                                 vector<unsigned long long> MPIPos;
 759
 760                                 MPI_Status status;
 761                                 MPI_File inMPI;
 762                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 763                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 764
 765                                 //char* tempFileName = new char(fastafileNames[s].length());
 766                                 //tempFileName = &(fastafileNames[s][0]);
 767
 768                                 char tempFileName[1024];
 769                                 strcpy(tempFileName, fastafileNames[s].c_str());
 770
 771                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 772
 773                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 774
 775                                 if (pid == 0) { //you are the root process
 776                                                 MPIPos = m->setFilePosFasta(fastafileNames[s], num); //fills MPIPos, returns numSeqs
 777                                                 numSeqs += num;
 778
 779                                                 //send file positions to all processes
 780                                                 for(int i = 1; i < processors; i++) {
 781                                                         MPI_Send(&num, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 782                                                         MPI_Send(&MPIPos[0], (num+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 783                                                 }
 784
 785                                                 //figure out how many sequences you have to do
 786                                                 numSeqsPerProcessor = num / processors;
 787                                                 int startIndex =  pid * numSeqsPerProcessor;
 788                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 789
 790
 791                                                 //do your part
 792                                                 MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI, MPIPos);
 793
 794                                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 795
 796                                 }else { //i am the child process
 797                                         MPI_Recv(&num, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 798                                         MPIPos.resize(num+1);
 799                                         numSeqs += num;
 800                                         MPI_Recv(&MPIPos[0], (num+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 801
 802                                         //figure out how many sequences you have to align
 803                                         numSeqsPerProcessor = num / processors;
 804                                         int startIndex =  pid * numSeqsPerProcessor;
 805                                         if(pid == (processors - 1)){    numSeqsPerProcessor = num - pid * numSeqsPerProcessor;  }
 806
 807
 808                                         //do your part
 809                                         MPICreateFilter(startIndex, numSeqsPerProcessor, F, inMPI,  MPIPos);
 810
 811                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  return 0;  }
 812                                 }
 813
 814                                 MPI_File_close(&inMPI);
 815                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 816
 817 #else
 818
 819                 vector<unsigned long long> positions;
 820                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 821                                 positions = m->divideFile(fastafileNames[s], processors);
 822                                 for (int i = 0; i < (positions.size()-1); i++) {
 823                                         lines.push_back(new linePair(positions[i], positions[(i+1)]));
 824                                 }
 825
 826                                 if(processors == 1){
 827                                         int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 828                                         numSeqs += numFastaSeqs;
 829                                 }else{
 830                                         int numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 831                                         numSeqs += numFastaSeqs;
 832                                 }
 833                 #else
 834                 if(processors == 1){
 835                     lines.push_back(new linePair(0, 1000));
 836                     int numFastaSeqs = driverCreateFilter(F, fastafileNames[s], lines[0]);
 837                     numSeqs += numFastaSeqs;
 838                                 }else {
 839                     int numFastaSeqs = 0;
 840                     positions = m->setFilePosFasta(fastafileNames[s], numFastaSeqs);
 841                     if (positions.size() < processors) { processors = positions.size(); }
 842
 843                     //figure out how many sequences you have to process
 844                     int numSeqsPerProcessor = numFastaSeqs / processors;
 845                     for (int i = 0; i < processors; i++) {
 846                         int startIndex =  i * numSeqsPerProcessor;
 847                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 848                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 849                     }
 850
 851                     numFastaSeqs = createProcessesCreateFilter(F, fastafileNames[s]);
 852                                         numSeqs += numFastaSeqs;
 853                 }
 854                 #endif
 855                 //save the file positions so we can reuse them in the runFilter function
 856                 savedPositions[s] = positions;
 857
 858                                 if (m->control_pressed) {  return filterString; }
 859 #endif
 860
 861                         }
 862                 }
 863
 864
 865 #ifdef USE_MPI
 866                 int pid;
 867                 int Atag = 1; int Ttag = 2; int Ctag = 3; int Gtag = 4; int Gaptag = 5;
 868                 MPI_Status status;
 869
 870                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 871
 872                 if(trump != '*' || m->isTrue(vertical) || soft != 0){
 873
 874                         if (pid == 0) { //only one process should output the filter
 875
 876                                 vector<int> temp; temp.resize(alignmentLength+1);
 877
 878                                 //get the frequencies from the child processes
 879                                 for(int i = 1; i < processors; i++) {
 880
 881                                         for (int j = 0; j < 5; j++) {
 882
 883                                                 MPI_Recv(&temp[0], (alignmentLength+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 884                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what letter count this is for
 885
 886                                                 if (receiveTag == Atag) { //you are recieveing the A frequencies
 887                                                         for (int k = 0; k < alignmentLength; k++) {             F.a[k] += temp[k];      }
 888                                                 }else if (receiveTag == Ttag) { //you are recieveing the T frequencies
 889                                                         for (int k = 0; k < alignmentLength; k++) {             F.t[k] += temp[k];      }
 890                                                 }else if (receiveTag == Ctag) { //you are recieveing the C frequencies
 891                                                         for (int k = 0; k < alignmentLength; k++) {             F.c[k] += temp[k];      }
 892                                                 }else if (receiveTag == Gtag) { //you are recieveing the G frequencies
 893                                                         for (int k = 0; k < alignmentLength; k++) {             F.g[k] += temp[k];      }
 894                                                 }else if (receiveTag == Gaptag) { //you are recieveing the gap frequencies
 895                                                         for (int k = 0; k < alignmentLength; k++) {             F.gap[k] += temp[k];    }
 896                                                 }
 897                                         }
 898                                 }
 899                         }else{
 900
 901                                 //send my fequency counts
 902                                 F.a.push_back(Atag);
 903                                 int ierr = MPI_Send(&(F.a[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 904                                 F.t.push_back(Ttag);
 905                                 ierr = MPI_Send (&(F.t[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 906                                 F.c.push_back(Ctag);
 907                                 ierr = MPI_Send(&(F.c[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 908                                 F.g.push_back(Gtag);
 909                                 ierr = MPI_Send(&(F.g[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 910                                 F.gap.push_back(Gaptag);
 911                                 ierr = MPI_Send(&(F.gap[0]), (alignmentLength+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 912                         }
 913
 914                 }
 915
 916                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 917
 918                 if (pid == 0) { //only one process should output the filter
 919 #endif
 920
 921                 F.setNumSeqs(numSeqs);
 922                 if(m->isTrue(vertical) == 1)    {       F.doVertical(); }
 923                 if(soft != 0)                           {       F.doSoft();             }
 924                 filterString = F.getFilter();
 925
 926 #ifdef USE_MPI
 927                 //send filter string to kids
 928                 //for(int i = 1; i < processors; i++) {
 929                 //      MPI_Send(&filterString[0], alignmentLength, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 930                 //}
 931                 MPI_Bcast(&filterString[0], alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 932         }else{
 933                 //recieve filterString
 934                 char* tempBuf = new char[alignmentLength];
 935                 //MPI_Recv(&tempBuf[0], alignmentLength, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 936                 MPI_Bcast(tempBuf, alignmentLength, MPI_CHAR, 0, MPI_COMM_WORLD);
 937
 938                 filterString = tempBuf;
 939                 if (filterString.length() > alignmentLength) { filterString = filterString.substr(0, alignmentLength);  }
 940                 delete tempBuf;
 941         }
 942
 943         MPI_Barrier(MPI_COMM_WORLD);
 944 #endif
 945
 946                 return filterString;
 947         }
 948         catch(exception& e) {
 949                 m->errorOut(e, "FilterSeqsCommand", "createFilter");
 950                 exit(1);
 951         }
 952 }
 953 /**************************************************************************************/
 954 int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair* filePos) {
 955         try {
 956
 957                 ifstream in;
 958                 m->openInputFile(filename, in);
 959
 960                 in.seekg(filePos->start);
 961
 962                 bool done = false;
 963                 int count = 0;
 964
 965                 while (!done) {
 966
 967                         if (m->control_pressed) { in.close(); return 1; }
 968
 969                         Sequence seq(in); m->gobble(in);
 970                         if (seq.getName() != "") {
 971                                         if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
 972
 973                                         if(trump != '*')                        {       F.doTrump(seq);         }
 974                                         if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
 975                                         cout.flush();
 976                                         count++;
 977                         }
 978
 979                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 980                                 unsigned long long pos = in.tellg();
 981                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 982                         #else
 983                                 if (in.eof()) { break; }
 984                         #endif
 985
 986                         //report progress
 987                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 988                 }
 989                 //report progress
 990                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 991                 in.close();
 992
 993                 return count;
 994         }
 995         catch(exception& e) {
 996                 m->errorOut(e, "FilterSeqsCommand", "driverCreateFilter");
 997                 exit(1);
 998         }
 999 }
1000 #ifdef USE_MPI
1001 /**************************************************************************************/
1002 int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File& inMPI, vector<unsigned long long>& MPIPos) {
1003         try {
1004
1005                 MPI_Status status;
1006                 int pid;
1007                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1008
1009                 for(int i=0;i<num;i++){
1010
1011                         if (m->control_pressed) { return 0; }
1012
1013                         //read next sequence
1014                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1015
1016                         char* buf4 = new char[length];
1017                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1018
1019                         string tempBuf = buf4;
1020                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1021                         istringstream iss (tempBuf,istringstream::in);
1022                         delete buf4;
1023
1024                         Sequence seq(iss);
1025
1026                         if (seq.getAligned().length() != alignmentLength) {  cout << "Alignment length is " << alignmentLength << " and sequence " << seq.getName() << " has length " << seq.getAligned().length() << ", please correct." << endl; exit(1);  }
1027
1028                         if(trump != '*'){       F.doTrump(seq); }
1029                         if(m->isTrue(vertical) || soft != 0){   F.getFreqs(seq);        }
1030                         cout.flush();
1031
1032                         //report progress
1033                         if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
1034                 }
1035
1036                 //report progress
1037                 if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
1038
1039                 return 0;
1040         }
1041         catch(exception& e) {
1042                 m->errorOut(e, "FilterSeqsCommand", "MPICreateFilter");
1043                 exit(1);
1044         }
1045 }
1046 #endif
1047 /**************************************************************************************************/
1048
1049 int FilterSeqsCommand::createProcessesCreateFilter(Filters& F, string filename) {
1050         try {
1051         int process = 1;
1052                 int num = 0;
1053                 processIDS.clear();
1054
1055 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
1056
1057                 //loop through and create all the processes you want
1058                 while (process != processors) {
1059                         int pid = fork();
1060
1061                         if (pid > 0) {
1062                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1063                                 process++;
1064                         }else if (pid == 0){
1065                                 //reset child's filter counts to 0;
1066                                 F.a.clear(); F.a.resize(alignmentLength, 0);
1067                                 F.t.clear(); F.t.resize(alignmentLength, 0);
1068                                 F.g.clear(); F.g.resize(alignmentLength, 0);
1069                                 F.c.clear(); F.c.resize(alignmentLength, 0);
1070                                 F.gap.clear(); F.gap.resize(alignmentLength, 0);
1071
1072                                 num = driverCreateFilter(F, filename, lines[process]);
1073
1074                                 //write out filter counts to file
1075                                 filename += toString(getpid()) + "filterValues.temp";
1076                                 ofstream out;
1077                                 m->openOutputFile(filename, out);
1078
1079                                 out << num << endl;
1080                                 out << F.getFilter() << endl;
1081                                 for (int k = 0; k < alignmentLength; k++) {             out << F.a[k] << '\t'; }  out << endl;
1082                                 for (int k = 0; k < alignmentLength; k++) {             out << F.t[k] << '\t'; }  out << endl;
1083                                 for (int k = 0; k < alignmentLength; k++) {             out << F.g[k] << '\t'; }  out << endl;
1084                                 for (int k = 0; k < alignmentLength; k++) {             out << F.c[k] << '\t'; }  out << endl;
1085                                 for (int k = 0; k < alignmentLength; k++) {             out << F.gap[k] << '\t'; }  out << endl;
1086
1087                                 //cout << F.getFilter() << endl;
1088                                 out.close();
1089
1090                                 exit(0);
1091                         }else {
1092                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1093                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1094                                 exit(0);
1095                         }
1096                 }
1097
1098                 //parent do your part
1099                 num = driverCreateFilter(F, filename, lines[0]);
1100
1101                 //force parent to wait until all the processes are done
1102                 for (int i=0;i<(processors-1);i++) {
1103                         int temp = processIDS[i];
1104                         wait(&temp);
1105                 }
1106
1107                 //parent reads in and combines Filter info
1108                 for (int i = 0; i < processIDS.size(); i++) {
1109                         string tempFilename = filename + toString(processIDS[i]) + "filterValues.temp";
1110                         ifstream in;
1111                         m->openInputFile(tempFilename, in);
1112
1113                         int temp, tempNum;
1114                         string tempFilterString;
1115
1116                         in >> tempNum; m->gobble(in); num += tempNum;
1117
1118                         in >> tempFilterString;
1119                         F.mergeFilter(tempFilterString);
1120
1121                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.a[k] += temp; }           m->gobble(in);
1122                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.t[k] += temp; }           m->gobble(in);
1123                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.g[k] += temp; }           m->gobble(in);
1124                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.c[k] += temp; }           m->gobble(in);
1125                         for (int k = 0; k < alignmentLength; k++) {             in >> temp; F.gap[k] += temp; } m->gobble(in);
1126
1127                         in.close();
1128                         m->mothurRemove(tempFilename);
1129                 }
1130
1131
1132 #else
1133
1134         //////////////////////////////////////////////////////////////////////////////////////////////////////
1135                 //Windows version shared memory, so be careful when passing variables through the filterData struct.
1136                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1137                 //Taking advantage of shared memory to allow both threads to add info to F.
1138                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1139
1140                 vector<filterData*> pDataArray;
1141                 DWORD   dwThreadIdArray[processors];
1142                 HANDLE  hThreadArray[processors];
1143
1144                 //Create processor worker threads.
1145                 for( int i=0; i<processors; i++ ){
1146
1147                         filterData* tempFilter = new filterData(filename, m, lines[i]->start, lines[i]->end, alignmentLength, trump, vertical, soft, hard, i);
1148                         pDataArray.push_back(tempFilter);
1149                         processIDS.push_back(i);
1150
1151                         hThreadArray[i] = CreateThread(NULL, 0, MyCreateFilterThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1152                 }
1153
1154                 //Wait until all threads have terminated.
1155                 WaitForMultipleObjects(processors, hThreadArray, TRUE, INFINITE);
1156
1157                 //Close all thread handles and free memory allocations.
1158                 for(int i=0; i < pDataArray.size(); i++){
1159                         num += pDataArray[i]->count;
1160             F.mergeFilter(pDataArray[i]->F.getFilter());
1161
1162                         for (int k = 0; k < alignmentLength; k++) {      F.a[k] += pDataArray[i]->F.a[k];       }
1163                         for (int k = 0; k < alignmentLength; k++) {      F.t[k] += pDataArray[i]->F.t[k];       }
1164                         for (int k = 0; k < alignmentLength; k++) {      F.g[k] += pDataArray[i]->F.g[k];       }
1165                         for (int k = 0; k < alignmentLength; k++) {      F.c[k] += pDataArray[i]->F.c[k];       }
1166                         for (int k = 0; k < alignmentLength; k++) {      F.gap[k] += pDataArray[i]->F.gap[k];   }
1167
1168                         CloseHandle(hThreadArray[i]);
1169                         delete pDataArray[i];
1170                 }
1171
1172 #endif
1173         return num;
1174
1175         }
1176         catch(exception& e) {
1177                 m->errorOut(e, "FilterSeqsCommand", "createProcessesCreateFilter");
1178                 exit(1);
1179         }
1180 }
1181 /**************************************************************************************/