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;
  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<long> 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                                                 //send file positions to all processes
 149                                                 MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD);  //send numSeqs
 150                                                 MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //send file pos
 151
 152                                                 //figure out how many sequences you have to do
 153                                                 numSeqsPerProcessor = numSeqs / processors;
 154                                                 int startIndex =  pid * numSeqsPerProcessor;
 155                                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 156
 157                                                 //do your part
 158                                                 MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 159
 160                                                 if (m->control_pressed) {  MPI_File_close(&inMPI); MPI_File_close(&outMPI);  return 0;  }
 161
 162                                                 //get the info from the child processes
 163                                                 for(int i = 1; i < processors; i++) {
 164
 165                                                         int size;
 166                                                         MPI_Recv(&size, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 167
 168                                                         vector<int> temp; temp.resize(size+1);
 169
 170                                                         for(int j = 0; j < 5; j++) {
 171
 172                                                                 MPI_Recv(&temp[0], (size+1), MPI_INT, i, 2001, MPI_COMM_WORLD, &status);
 173                                                                 int receiveTag = temp[temp.size()-1];  //child process added a int to the end to indicate what count this is for
 174
 175                                                                 if (receiveTag == startTag) {
 176                                                                         for (int k = 0; k < size; k++) {                startPosition.push_back(temp[k]);       }
 177                                                                 }else if (receiveTag == endTag) {
 178                                                                         for (int k = 0; k < size; k++) {                endPosition.push_back(temp[k]); }
 179                                                                 }else if (receiveTag == lengthTag) {
 180                                                                         for (int k = 0; k < size; k++) {                seqLength.push_back(temp[k]);   }
 181                                                                 }else if (receiveTag == baseTag) {
 182                                                                         for (int k = 0; k < size; k++) {                ambigBases.push_back(temp[k]);  }
 183                                                                 }else if (receiveTag == lhomoTag) {
 184                                                                         for (int k = 0; k < size; k++) {                longHomoPolymer.push_back(temp[k]);     }
 185                                                                 }
 186                                                         }
 187
 188                                                 }
 189
 190
 191                                 }else { //i am the child process
 192
 193                                         MPI_Bcast(&numSeqs, 1, MPI_INT, 0, MPI_COMM_WORLD); //get numSeqs
 194                                         MPIPos.resize(numSeqs+1);
 195                                         MPI_Bcast(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, MPI_COMM_WORLD); //get file positions
 196
 197                                         //figure out how many sequences you have to align
 198                                         numSeqsPerProcessor = numSeqs / processors;
 199                                         int startIndex =  pid * numSeqsPerProcessor;
 200                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 201
 202                                         //do your part
 203                                         MPICreateSummary(startIndex, numSeqsPerProcessor, startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, inMPI, outMPI, MPIPos);
 204
 205                                         if (m->control_pressed) {  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); return 0;  }
 206
 207                                         //send my counts
 208                                         int size = startPosition.size();
 209                                         MPI_Send(&size, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 210
 211                                         startPosition.push_back(startTag);
 212                                         int ierr = MPI_Send(&(startPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 213                                         endPosition.push_back(endTag);
 214                                         ierr = MPI_Send (&(endPosition[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 215                                         seqLength.push_back(lengthTag);
 216                                         ierr = MPI_Send(&(seqLength[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 217                                         ambigBases.push_back(baseTag);
 218                                         ierr = MPI_Send(&(ambigBases[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 219                                         longHomoPolymer.push_back(lhomoTag);
 220                                         ierr = MPI_Send(&(longHomoPolymer[0]), (size+1), MPI_INT, 0, 2001, MPI_COMM_WORLD);
 221
 222                                 }
 223
 224                                 MPI_File_close(&inMPI);
 225                                 MPI_File_close(&outMPI);
 226
 227 #else
 228                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 229                                 if(processors == 1){
 230                                         ifstream inFASTA;
 231                                         openInputFile(fastafile, inFASTA);
 232                                         numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 233                                         inFASTA.close();
 234
 235                                         lines.push_back(new linePair(0, numSeqs));
 236
 237                                         driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 238                                 }else{
 239                                         numSeqs = setLines(fastafile);
 240                                         createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile);
 241
 242                                         rename((summaryFile + toString(processIDS[0]) + ".temp").c_str(), summaryFile.c_str());
 243                                         //append files
 244                                         for(int i=1;i<processors;i++){
 245                                                 appendFiles((summaryFile + toString(processIDS[i]) + ".temp"), summaryFile);
 246                                                 remove((summaryFile + toString(processIDS[i]) + ".temp").c_str());
 247                                         }
 248                                 }
 249
 250                                 if (m->control_pressed) {  return 0; }
 251                 #else
 252                                 ifstream inFASTA;
 253                                 openInputFile(fastafileNames[s], inFASTA);
 254                                 numSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 255                                 inFASTA.close();
 256
 257                                 lines.push_back(new linePair(0, numSeqs));
 258
 259                                 driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, summaryFile, lines[0]);
 260                                 if (m->control_pressed) {  return 0; }
 261                 #endif
 262 #endif
 263
 264                 #ifdef USE_MPI
 265                         if (pid == 0) {
 266                 #endif
 267
 268                 sort(startPosition.begin(), startPosition.end());
 269                 sort(endPosition.begin(), endPosition.end());
 270                 sort(seqLength.begin(), seqLength.end());
 271                 sort(ambigBases.begin(), ambigBases.end());
 272                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 273
 274                 int ptile0_25   = int(numSeqs * 0.025);
 275                 int ptile25             = int(numSeqs * 0.250);
 276                 int ptile50             = int(numSeqs * 0.500);
 277                 int ptile75             = int(numSeqs * 0.750);
 278                 int ptile97_5   = int(numSeqs * 0.975);
 279                 int ptile100    = numSeqs - 1;
 280
 281                 //to compensate for blank sequences that would result in startPosition and endPostion equalling -1
 282                 if (startPosition[0] == -1) {  startPosition[0] = 0;    }
 283                 if (endPosition[0] == -1)       {  endPosition[0] = 0;          }
 284
 285                 if (m->control_pressed) {  remove(summaryFile.c_str()); return 0; }
 286
 287                 m->mothurOutEndLine();
 288                 m->mothurOut("\t\tStart\tEnd\tNBases\tAmbigs\tPolymer"); m->mothurOutEndLine();
 289                 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();
 290                 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();
 291                 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();
 292                 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();
 293                 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();
 294                 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();
 295                 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();
 296                 m->mothurOut("# of Seqs:\t" + toString(numSeqs)); m->mothurOutEndLine();
 297
 298                 if (m->control_pressed) {  remove(summaryFile.c_str()); return 0; }
 299
 300                 m->mothurOutEndLine();
 301                 m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 302                 m->mothurOut(summaryFile); m->mothurOutEndLine();
 303                 m->mothurOutEndLine();
 304
 305                 #ifdef USE_MPI
 306                         }
 307                 #endif
 308
 309                 return 0;
 310         }
 311         catch(exception& e) {
 312                 m->errorOut(e, "SeqSummaryCommand", "execute");
 313                 exit(1);
 314         }
 315 }
 316 /**************************************************************************************/
 317 int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile, linePair* line) {
 318         try {
 319
 320                 ofstream outSummary;
 321                 openOutputFile(sumFile, outSummary);
 322
 323                 //print header if you are process 0
 324                 if (line->start == 0) {
 325                         outSummary << "seqname\tstart\tend\tnbases\tambigs\tpolymer" << endl;
 326                 }
 327
 328                 ifstream in;
 329                 openInputFile(filename, in);
 330
 331                 in.seekg(line->start);
 332
 333                 for(int i=0;i<line->num;i++){
 334
 335                         if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
 336
 337                         Sequence current(in);
 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<long>& MPIPos) {
 364         try {
 365
 366                 MPI_Status status;
 367
 368                 for(int i=0;i<num;i++){
 369
 370                         if (m->control_pressed) { return 0; }
 371
 372                         //read next sequence
 373                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 374
 375                         char* buf4 = new char[length];
 376                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 377
 378                         string tempBuf = buf4;
 379                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 380                         istringstream iss (tempBuf,istringstream::in);
 381                         delete buf4;
 382
 383                         Sequence current(iss);
 384
 385                         if (current.getName() != "") {
 386                                 startPosition.push_back(current.getStartPos());
 387                                 endPosition.push_back(current.getEndPos());
 388                                 seqLength.push_back(current.getNumBases());
 389                                 ambigBases.push_back(current.getAmbigBases());
 390                                 longHomoPolymer.push_back(current.getLongHomoPolymer());
 391
 392                                 string outputString = current.getName() + "\t" + toString(current.getStartPos()) + "\t" + toString(current.getEndPos()) + "\t";
 393                                 outputString += toString(current.getNumBases()) + "\t" + toString(current.getAmbigBases()) + "\t" + toString(current.getLongHomoPolymer()) + "\n";
 394
 395                                 //output to file
 396                                 length = outputString.length();
 397                                 char* buf3 = new char[length];
 398                                 memcpy(buf3, outputString.c_str(), length);
 399
 400                                 MPI_File_write_shared(outMPI, buf3, length, MPI_CHAR, &status);
 401                                 delete buf3;
 402                         }
 403                 }
 404
 405                 return 0;
 406         }
 407         catch(exception& e) {
 408                 m->errorOut(e, "SeqSummaryCommand", "MPICreateSummary");
 409                 exit(1);
 410         }
 411 }
 412 #endif
 413 /**************************************************************************************************/
 414 int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, string sumFile) {
 415         try {
 416 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 417                 int process = 0;
 418                 int exitCommand = 1;
 419                 processIDS.clear();
 420
 421                 //loop through and create all the processes you want
 422                 while (process != processors) {
 423                         int pid = vfork();
 424
 425                         if (pid > 0) {
 426                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 427                                 process++;
 428                         }else if (pid == 0){
 429                                 driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, sumFile + toString(getpid()) + ".temp", lines[process]);
 430                                 exit(0);
 431                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 432                 }
 433
 434                 //force parent to wait until all the processes are done
 435                 for (int i=0;i<processors;i++) {
 436                         int temp = processIDS[i];
 437                         wait(&temp);
 438                 }
 439
 440                 return exitCommand;
 441 #endif
 442         }
 443         catch(exception& e) {
 444                 m->errorOut(e, "SeqSummaryCommand", "createProcessesCreateSummary");
 445                 exit(1);
 446         }
 447 }
 448 /**************************************************************************************************/
 449
 450 int SeqSummaryCommand::setLines(string filename) {
 451         try {
 452
 453                 vector<long int> positions;
 454
 455                 ifstream inFASTA;
 456                 openInputFile(filename, inFASTA);
 457
 458                 string input;
 459                 while(!inFASTA.eof()){
 460                         input = getline(inFASTA);
 461
 462                         if (input.length() != 0) {
 463                                 if(input[0] == '>'){ long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);     }
 464                         }
 465                 }
 466                 inFASTA.close();
 467
 468                 int numFastaSeqs = positions.size();
 469
 470                 FILE * pFile;
 471                 long size;
 472
 473                 //get num bytes in file
 474                 pFile = fopen (filename.c_str(),"rb");
 475                 if (pFile==NULL) perror ("Error opening file");
 476                 else{
 477                         fseek (pFile, 0, SEEK_END);
 478                         size=ftell (pFile);
 479                         fclose (pFile);
 480                 }
 481
 482                 int numSeqsPerProcessor = numFastaSeqs / processors;
 483
 484                 for (int i = 0; i < processors; i++) {
 485
 486                         long int startPos = positions[ i * numSeqsPerProcessor ];
 487                         if(i == processors - 1){
 488                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 489                         }else{
 490                                 long int myEnd = positions[ (i+1) * numSeqsPerProcessor ];
 491                         }
 492                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 493                 }
 494
 495                 return numFastaSeqs;
 496         }
 497         catch(exception& e) {
 498                 m->errorOut(e, "SeqSummaryCommand", "setLines");
 499                 exit(1);
 500         }
 501 }
 502 //***************************************************************************************************************
 503
 504