seqsummarycommand.cpp

   1 /*
   2  *  seqcoordcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 5/30/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "seqsummarycommand.h"
  11 #include "sequence.hpp"
  12
  13 //**********************************************************************************************************************
  14 vector<string> SeqSummaryCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"fasta","processors","outputdir","inputdir"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "SeqSummaryCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 SeqSummaryCommand::SeqSummaryCommand(){
  27         try {
  28                 abort = true;
  29                 //initialize outputTypes
  30                 vector<string> tempOutNames;
  31                 outputTypes["summary"] = tempOutNames;
  32         }
  33         catch(exception& e) {
  34                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
  35                 exit(1);
  36         }
  37 }
  38 //**********************************************************************************************************************
  39 vector<string> SeqSummaryCommand::getRequiredParameters(){
  40         try {
  41                 string Array[] =  {"fasta"};
  42                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  43                 return myArray;
  44         }
  45         catch(exception& e) {
  46                 m->errorOut(e, "SeqSummaryCommand", "getRequiredParameters");
  47                 exit(1);
  48         }
  49 }
  50 //**********************************************************************************************************************
  51 vector<string> SeqSummaryCommand::getRequiredFiles(){
  52         try {
  53                 vector<string> myArray;
  54                 return myArray;
  55         }
  56         catch(exception& e) {
  57                 m->errorOut(e, "SeqSummaryCommand", "getRequiredFiles");
  58                 exit(1);
  59         }
  60 }
  61 //***************************************************************************************************************
  62
  63 SeqSummaryCommand::SeqSummaryCommand(string option)  {
  64         try {
  65                 abort = false;
  66
  67                 //allow user to run help
  68                 if(option == "help") { help(); abort = true; }
  69
  70                 else {
  71                         //valid paramters for this command
  72                         string Array[] =  {"fasta","processors","outputdir","inputdir"};
  73                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  74
  75                         OptionParser parser(option);
  76                         map<string,string> parameters = parser.getParameters();
  77
  78                         ValidParameters validParameter("summary.seqs");
  79                         map<string,string>::iterator it;
  80
  81                         //check to make sure all parameters are valid for command
  82                         for (it = parameters.begin(); it != parameters.end(); it++) {
  83                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  84                         }
  85
  86                         //if the user changes the input directory command factory will send this info to us in the output parameter
  87                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  88                         if (inputDir == "not found"){   inputDir = "";          }
  89                         else {
  90                                 string path;
  91                                 it = parameters.find("fasta");
  92                                 //user has given a template file
  93                                 if(it != parameters.end()){
  94                                         path = m->hasPath(it->second);
  95                                         //if the user has not given a path then, add inputdir. else leave path alone.
  96                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
  97                                 }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["summary"] = tempOutNames;
 103
 104                         //check for required parameters
 105                         fastafile = validParameter.validFile(parameters, "fasta", true);
 106                         if (fastafile == "not open") { abort = true; }
 107                         else if (fastafile == "not found") { fastafile = ""; m->mothurOut("fasta is a required parameter for the summary.seqs command."); m->mothurOutEndLine(); abort = true;  }
 108
 109                         //if the user changes the output directory command factory will send this info to us in the output parameter
 110                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 111                                 outputDir = "";
 112                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 113                         }
 114
 115                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = "1";                             }
 116                         convert(temp, processors);
 117
 118
 119                 }
 120         }
 121         catch(exception& e) {
 122                 m->errorOut(e, "SeqSummaryCommand", "SeqSummaryCommand");
 123                 exit(1);
 124         }
 125 }
 126 //**********************************************************************************************************************
 127
 128 void SeqSummaryCommand::help(){
 129         try {
 130                 m->mothurOut("The summary.seqs command reads a fastafile and summarizes the sequences.\n");
 131                 m->mothurOut("The summary.seqs command parameters are fasta and processors, fasta is required.\n");
 132                 m->mothurOut("The summary.seqs command should be in the following format: \n");
 133                 m->mothurOut("summary.seqs(fasta=yourFastaFile, processors=2) \n");
 134                 m->mothurOut("Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n\n");
 135         }
 136         catch(exception& e) {
 137                 m->errorOut(e, "SeqSummaryCommand", "help");
 138                 exit(1);
 139         }
 140 }
 141
 142 //***************************************************************************************************************
 143
 144 SeqSummaryCommand::~SeqSummaryCommand(){        /*      do nothing      */      }
 145
 146 //***************************************************************************************************************
 147
 148 int SeqSummaryCommand::execute(){
 149         try{
 150
 151                 if (abort == true) { return 0; }
 152
 153                 string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
 154
 155                 int numSeqs = 0;
 156
 157                 vector<int> startPosition;
 158                 vector<int> endPosition;
 159                 vector<int> seqLength;
 160                 vector<int> ambigBases;
 161                 vector<int> longHomoPolymer;
 162
 163 #ifdef USE_MPI
 164                                 int pid, numSeqsPerProcessor;
 165                                 int tag = 2001;
 166                                 int startTag = 1; int endTag = 2; int lengthTag = 3; int baseTag = 4; int lhomoTag = 5;
 167                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 168                                 vector<unsigned long int> MPIPos;
 169
 170                                 MPI_Status status;
 171                                 MPI_Status statusOut;
 172                                 MPI_File inMPI;
 173                                 MPI_File outMPI;
 174                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 175                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 176
 177                                 char tempFileName[1024];
 178                                 strcpy(tempFileName, fastafile.c_str());
 179
 180                                 char sumFileName[1024];
 181                                 strcpy(sumFileName, summaryFile.c_str());
 182
 183                                 MPI_File_open(MPI_COMM_WORLD, tempFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 184                                 MPI_File_open(MPI_COMM_WORLD, sumFileName, outMode, MPI_INFO_NULL, &outMPI);
 185
 186                                 if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
 187
 188                                 if (pid == 0) { //you are the root process
 189                                                 //print header
 190                                                 string outputString = "seqname\tstart\tend\tnbases\tambigs\tpolymer\n";
 191                                                 int length = outputString.length();
 192                                                 char* buf2 = new char[length];
 193                                                 memcpy(buf2, outputString.c_str(), length);
 194
 195                                                 MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &statusOut);
 196                                                 delete buf2;
 197
 198                                                 MPIPos = m->setFilePosFasta(fastafile, numSeqs); //fills MPIPos, returns numSeqs
 199
 200                                                 for(int i = 1; i < processors; i++) {
 201                                                         MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 202                                                         MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 203                                                 }
 204
 205                                                 //figure out how many sequences you have to do
 206                                                 numSeqsPerProcessor = numSeqs / processors;
 207                                                 int startIndex =  pid * numSeqsPerProcessor;
 208                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 209
 210                                                 //do your part
 211                                                 MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 212
 213                                 }else { //i am the child process
 214
 215                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 216                                         MPIPos.resize(numSeqs+1);
 217                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 218
 219                                         //figure out how many sequences you have to align
 220                                         numSeqsPerProcessor = numSeqs / processors;
 221                                         int startIndex =  pid * numSeqsPerProcessor;
 222                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 223
 224                                         //do your part
 225                                         MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 226                                 }
 227
 228                                 MPI_File_close(&inMPI);
 229                                 MPI_File_close(&outMPI);
 230                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 231
 232                                 if (pid == 0) {
 233                                         //get the info from the child processes
 234                                         for(int i = 1; i < processors; i++) {
 235                                                 int size;
 236                                                 MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 237
 238                                                 vector<int> temp; temp.resize(size+1);
 239
 240                                                 for(int j = 0; j < 5; j++) {
 241
 242                                                         MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 243                                                         int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
 244
 245                                                         if (receiveTag == startTag) {
 246                                                                 for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
 247                                                         }else if (receiveTag == endTag) {
 248                                                                 for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
 249                                                         }else if (receiveTag == lengthTag) {
 250                                                                 for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
 251                                                         }else if (receiveTag == baseTag) {
 252                                                                 for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
 253                                                         }else if (receiveTag == lhomoTag) {
 254                                                                 for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
 255                                                         }
 256                                                 }
 257                                         }
 258
 259                                 }else{
 260
 261                                         //send my counts
 262                                         int size = startPosition.size();
 263                                         MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 264
 265                                         startPosition.push_back(startTag);
 266                                         int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 267                                         endPosition.push_back(endTag);
 268                                         ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 269                                         seqLength.push_back(lengthTag);
 270                                         ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 271                                         ambigBases.push_back(baseTag);
 272                                         ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 273                                         longHomoPolymer.push_back(lhomoTag);
 274                                         ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 275                                 }
 276
 277                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 278 #else
 279                         vector<unsigned long int> positions = m->divideFile(fastafile, processors);
 280
 281                         for (int i = 0; i < (positions.size()-1); i++) {
 282                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 283                         }
 284
 285                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 286                                 if(processors == 1){
 287                                         numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 288                                 }else{
 289                                         numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
 290
 291                                         rename((summaryFile + toString(processIDS[0]) + ".temp").c_str(), summaryFile.c_str());
 292                                         //append files
 293                                         for(int i=1;i<processors;i++){
 294                                                 m->appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
 295                                                 remove((summaryFile + toString(processIDS[i]) + ".temp").c_str());
 296                                         }
 297                                 }
 298
 299                                 if (m->control_pressed) {  return 0; }
 300                 #else
 301                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 302                                 if (m->control_pressed) {  return 0; }
 303                 #endif
 304 #endif
 305
 306                 #ifdef USE_MPI
 307                         if (pid == 0) {
 308                 #endif
 309
 310                 sort(startPosition.begin(), startPosition.end());
 311                 sort(endPosition.begin(), endPosition.end());
 312                 sort(seqLength.begin(), seqLength.end());
 313                 sort(ambigBases.begin(), ambigBases.end());
 314                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 315
 316                 int ptile0_25   = int(numSeqs * 0.025);
 317                 int ptile25             = int(numSeqs * 0.250);
 318                 int ptile50             = int(numSeqs * 0.500);
 319                 int ptile75             = int(numSeqs * 0.750);
 320                 int ptile97_5   = int(numSeqs * 0.975);
 321                 int ptile100    = numSeqs - 1;
 322
 323                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 324                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 325                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 326
 327                 if (m->control_pressed) {  remove(summaryFile.c_str()); return 0; }
 328
 329                 m->mothurOutEndLine();
 330                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); m->mothurOutEndLine();
 331                 m->mothurOut("Minimum:\t" + toString(startPosition[0]) + "\t" + toString(endPosition[0]) + "\t" + toString(seqLength[0]) + "\t" + toString(ambigBases[0]) + "\t" + toString(longHomoPolymer[0])); m->mothurOutEndLine();
 332                 m->mothurOut("2.5%-tile:\t" + toString(startPosition[ptile0_25]) + "\t" + toString(endPosition[ptile0_25]) + "\t" + toString(seqLength[ptile0_25]) + "\t" + toString(ambigBases[ptile0_25]) + "\t"+ toString(longHomoPolymer[ptile0_25])); m->mothurOutEndLine();
 333                 m->mothurOut("25%-tile:\t" + toString(startPosition[ptile25]) + "\t" + toString(endPosition[ptile25]) + "\t" + toString(seqLength[ptile25]) + "\t" + toString(ambigBases[ptile25]) + "\t" + toString(longHomoPolymer[ptile25])); m->mothurOutEndLine();
 334                 m->mothurOut("Median: \t" + toString(startPosition[ptile50]) + "\t" + toString(endPosition[ptile50]) + "\t" + toString(seqLength[ptile50]) + "\t" + toString(ambigBases[ptile50]) + "\t" + toString(longHomoPolymer[ptile50])); m->mothurOutEndLine();
 335                 m->mothurOut("75%-tile:\t" + toString(startPosition[ptile75]) + "\t" + toString(endPosition[ptile75]) + "\t" + toString(seqLength[ptile75]) + "\t" + toString(ambigBases[ptile75]) + "\t" + toString(longHomoPolymer[ptile75])); m->mothurOutEndLine();
 336                 m->mothurOut("97.5%-tile:\t" + toString(startPosition[ptile97_5]) + "\t" + toString(endPosition[ptile97_5]) + "\t" + toString(seqLength[ptile97_5]) + "\t" + toString(ambigBases[ptile97_5]) + "\t" + toString(longHomoPolymer[ptile97_5])); m->mothurOutEndLine();
 337                 m->mothurOut("Maximum:\t" + toString(startPosition[ptile100]) + "\t" + toString(endPosition[ptile100]) + "\t" + toString(seqLength[ptile100]) + "\t" + toString(ambigBases[ptile100]) + "\t" + toString(longHomoPolymer[ptile100])); m->mothurOutEndLine();
 338                 m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
 339
 340                 if (m->control_pressed) {  remove(summaryFile.c_str()); return 0; }
 341
 342                 m->mothurOutEndLine();
 343                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 344                 m->mothurOut(summaryFile); m->mothurOutEndLine();       outputNames.push_back(summaryFile); outputTypes["summary"].push_back(summaryFile);
 345                 m->mothurOutEndLine();
 346
 347                 #ifdef USE_MPI
 348                         }
 349                 #endif
 350
 351                 return 0;
 352         }
 353         catch(exception& e) {
 354                 m->errorOut(e, "SeqSummaryCommand", "execute");
 355                 exit(1);
 356         }
 357 }
 358 /**************************************************************************************/
 359 int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* filePos) {
 360         try {
 361
 362                 ofstream outSummary;
 363                 m->openOutputFile(sumFile, outSummary);
 364
 365                 //print header if you are process 0
 366                 if (filePos->start == 0) {
 367                         outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;
 368                 }
 369
 370                 ifstream in;
 371                 m->openInputFile(filename, in);
 372
 373                 in.seekg(filePos->start);
 374
 375                 bool done = false;
 376                 int count = 0;
 377
 378                 while (!done) {
 379
 380                         if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 381
 382                         Sequence current(in); m->gobble(in);
 383
 384                         if (current.getName() != "") {
 385                                 startPosition.push_back(current.getStartPos());
 386                                 endPosition.push_back(current.getEndPos());
 387                                 seqLength.push_back(current.getNumBases());
 388                                 ambigBases.push_back(current.getAmbigBases());
 389                                 longHomoPolymer.push_back(current.getLongHomoPolymer());
 390
 391                                 outSummary << current.getName() << '\t';
 392                                 outSummary << current.getStartPos() << '\t' << current.getEndPos() << '\t';
 393                                 outSummary << current.getNumBases() << '\t' << current.getAmbigBases() << '\t';
 394                                 outSummary << current.getLongHomoPolymer() << endl;
 395                                 count++;
 396                         }
 397
 398                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 399                                 unsigned long int pos = in.tellg();
 400                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 401                         #else
 402                                 if (in.eof()) { break; }
 403                         #endif
 404
 405                         //report progress
 406                         //if((count) % 100 == 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 407                 }
 408                 //report progress
 409                 //if((count) % 100 != 0){       m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 410
 411                 in.close();
 412
 413                 return count;
 414         }
 415         catch(exception& e) {
 416                 m->errorOut(e, "SeqSummaryCommand", "driverCreateSummary");
 417                 exit(1);
 418         }
 419 }
 420 #ifdef USE_MPI
 421 /**************************************************************************************/
 422 int SeqSummaryCommand::MPICreateSummary(int start, int num, vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, MPI_File& inMPI, MPI_File& outMPI, vector<unsigned long int>& MPIPos) {
 423         try {
 424
 425                 int pid;
 426                 MPI_Status status;
 427                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 428
 429
 430                 for(int i=0;i<num;i++){
 431
 432                         if (m->control_pressed) { return 0; }
 433
 434                         //read next sequence
 435                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 436
 437                         char* buf4 = new char[length];
 438                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 439
 440                         string tempBuf = buf4;
 441                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 442                         istringstream iss (tempBuf,istringstream::in);
 443                         delete buf4;
 444
 445                         Sequence current(iss);
 446
 447                         if (current.getName() != "") {
 448                                 startPosition.push_back(current.getStartPos());
 449                                 endPosition.push_back(current.getEndPos());
 450                                 seqLength.push_back(current.getNumBases());
 451                                 ambigBases.push_back(current.getAmbigBases());
 452                                 longHomoPolymer.push_back(current.getLongHomoPolymer());
 453
 454                                 string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
 455                                 outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\n";
 456
 457                                 //output to file
 458                                 length = outputString.length();
 459                                 char* buf3 = new char[length];
 460                                 memcpy(buf3, outputString.c_str(), length);
 461
 462                                 MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
 463                                 delete buf3;
 464                         }
 465                 }
 466
 467                 return 0;
 468         }
 469         catch(exception& e) {
 470                 m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
 471                 exit(1);
 472         }
 473 }
 474 #endif
 475 /**************************************************************************************************/
 476 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 477         try {
 478 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 479                 int process = 0;
 480                 int num = 0;
 481                 processIDS.clear();
 482
 483                 //loop through and create all the processes you want
 484                 while (process != processors) {
 485                         int pid = fork();
 486
 487                         if (pid > 0) {
 488                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 489                                 process++;
 490                         }else if (pid == 0){
 491                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
 492
 493                                 //pass numSeqs to parent
 494                                 ofstream out;
 495                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 496                                 m->openOutputFile(tempFile, out);
 497
 498                                 out << num << endl;
 499                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 500                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 501                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 502                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 503                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 504
 505                                 out.close();
 506
 507                                 exit(0);
 508                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 509                 }
 510
 511                 //force parent to wait until all the processes are done
 512                 for (int i=0;i<processors;i++) {
 513                         int temp = processIDS[i];
 514                         wait(&temp);
 515                 }
 516
 517                 //parent reads in and combine Filter info
 518                 for (int i = 0; i < processIDS.size(); i++) {
 519                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 520                         ifstream in;
 521                         m->openInputFile(tempFilename, in);
 522
 523                         int temp, tempNum;
 524                         in >> tempNum; m->gobble(in); num += tempNum;
 525                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 526                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 527                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 528                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 529                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 530
 531                         in.close();
 532                         remove(tempFilename.c_str());
 533                 }
 534
 535                 return num;
 536 #endif
 537         }
 538         catch(exception& e) {
 539                 m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
 540                 exit(1);
 541         }
 542 }
 543 //***************************************************************************************************************
 544
 545