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