pintail.cpp

   1 /*
   2  *  pintail.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 7/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "pintail.h"
  11 #include "ignoregaps.h"
  12 #include "eachgapdist.h"
  13
  14 //********************************************************************************************************************
  15 //sorts lowest to highest
  16 inline bool compareQuanMembers(quanMember left, quanMember right){
  17         return (left.score < right.score);
  18 }
  19 //***************************************************************************************************************
  20
  21 Pintail::Pintail(string filename, string temp, bool f, int p, string mask, string cons, string q, int win, int inc, string o) : Chimera() {
  22         try {
  23
  24                 fastafile = filename;
  25                 templateFileName = temp; templateSeqs = readSeqs(temp);
  26                 filter = f;
  27                 processors = p;
  28                 setMask(mask);
  29                 consfile = cons;
  30                 quanfile = q;
  31                 window = win;
  32                 increment = inc;
  33                 outputDir = o;
  34
  35                 distcalculator = new eachGapDist();
  36                 decalc = new DeCalculator();
  37
  38                 doPrep();
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "Pintail", "Pintail");
  42                 exit(1);
  43         }
  44
  45 }
  46 //***************************************************************************************************************
  47
  48 Pintail::~Pintail() {
  49         try {
  50
  51                 delete distcalculator;
  52                 delete decalc;
  53         }
  54         catch(exception& e) {
  55                 m->errorOut(e, "Pintail", "~Pintail");
  56                 exit(1);
  57         }
  58 }
  59 //***************************************************************************************************************
  60 int Pintail::doPrep() {
  61         try {
  62
  63                 mergedFilterString = "";
  64                 windowSizesTemplate.resize(templateSeqs.size(), window);
  65                 quantiles.resize(100);  //one for every percent mismatch
  66                 quantilesMembers.resize(100);  //one for every percent mismatch
  67
  68                 //if the user does not enter a mask then you want to keep all the spots in the alignment
  69                 if (seqMask.length() == 0)      {       decalc->setAlignmentLength(templateSeqs[0]->getAligned().length());     }
  70                 else                                            {       decalc->setAlignmentLength(seqMask.length());                                           }
  71
  72                 decalc->setMask(seqMask);
  73
  74         #ifdef USE_MPI
  75                 //do nothing
  76         #else
  77                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  78                         //find breakup of templatefile for quantiles
  79                         if (processors == 1) {   templateLines.push_back(new linePair(0, templateSeqs.size()));  }
  80                         else {
  81                                 for (int i = 0; i < processors; i++) {
  82                                         templateLines.push_back(new linePair());
  83                                         templateLines[i]->start = int (sqrt(float(i)/float(processors)) * templateSeqs.size());
  84                                         templateLines[i]->end = int (sqrt(float(i+1)/float(processors)) * templateSeqs.size());
  85                                 }
  86                         }
  87                 #else
  88                         templateLines.push_back(new linePair(0, templateSeqs.size()));
  89                 #endif
  90         #endif
  91
  92                 m->mothurOut("Getting conservation... "); cout.flush();
  93                 if (consfile == "") {
  94                         m->mothurOut("Calculating probability of conservation for your template sequences.  This can take a while...  I will output the frequency of the highest base in each position to a .freq file so that you can input them using the conservation parameter next time you run this command.  Providing the .freq file will improve speed.    "); cout.flush();
  95                         probabilityProfile = decalc->calcFreq(templateSeqs, outputDir + getSimpleName(templateFileName));
  96                         if (m->control_pressed) {  return 0;  }
  97                         m->mothurOut("Done."); m->mothurOutEndLine();
  98                 }else                           {   probabilityProfile = readFreq();    m->mothurOut("Done.");            }
  99                 m->mothurOutEndLine();
 100
 101                 //make P into Q
 102                 for (int i = 0; i < probabilityProfile.size(); i++)  { probabilityProfile[i] = 1 - probabilityProfile[i];  }  //
 103
 104                 bool reRead = false;
 105                 //create filter if needed for later
 106                 if (filter) {
 107
 108                         //read in all query seqs
 109                         vector<Sequence*> tempQuerySeqs = readSeqs(fastafile);
 110
 111                         vector<Sequence*> temp;
 112                         //merge query seqs and template seqs
 113                         temp = templateSeqs;
 114                         for (int i = 0; i < tempQuerySeqs.size(); i++) {  temp.push_back(tempQuerySeqs[i]);  }
 115
 116                         if (seqMask != "") {
 117                             reRead = true;
 118                                 //mask templates
 119                                 for (int i = 0; i < temp.size(); i++) {
 120                                         if (m->control_pressed) {
 121                                                 for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
 122                                                 return 0;
 123                                         }
 124                                         decalc->runMask(temp[i]);
 125                                 }
 126                         }
 127
 128                         mergedFilterString = createFilter(temp, 0.5);
 129
 130                         if (m->control_pressed) {
 131                                 for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
 132                                 return 0;
 133                         }
 134
 135                         //reread template seqs
 136                         for (int i = 0; i < tempQuerySeqs.size(); i++) { delete tempQuerySeqs[i];  }
 137                 }
 138
 139
 140                 //quantiles are used to determine whether the de values found indicate a chimera
 141                 //if you have to calculate them, its time intensive because you are finding the de and deviation values for each
 142                 //combination of sequences in the template
 143                 if (quanfile != "") {
 144                         quantiles = readQuantiles();
 145                 }else {
 146                         if ((!filter) && (seqMask != "")) { //if you didn't filter but you want to mask. if you filtered then you did mask first above.
 147                                 reRead = true;
 148                                 //mask templates
 149                                 for (int i = 0; i < templateSeqs.size(); i++) {
 150                                         if (m->control_pressed) {  return 0;  }
 151                                         decalc->runMask(templateSeqs[i]);
 152                                 }
 153                         }
 154
 155                         if (filter) {
 156                                 reRead = true;
 157                                 for (int i = 0; i < templateSeqs.size(); i++) {
 158                                         if (m->control_pressed) {  return 0;  }
 159                                         runFilter(templateSeqs[i]);
 160                                 }
 161                         }
 162
 163                         m->mothurOut("Calculating quantiles for your template.  This can take a while...  I will output the quantiles to a .quan file that you can input them using the quantiles parameter next time you run this command.  Providing the .quan file will dramatically improve speed.    "); cout.flush();
 164                         if (processors == 1) {
 165                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 166                         }else {         createProcessesQuan();          }
 167
 168                         if (m->control_pressed) {  return 0;  }
 169
 170                         string noOutliers, outliers;
 171
 172                         if ((!filter) && (seqMask == "")) {
 173                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.quan";
 174                         }else if ((!filter) && (seqMask != "")) {
 175                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.masked.quan";
 176                         }else if ((filter) && (seqMask != "")) {
 177                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "masked.quan";
 178                         }else if ((filter) && (seqMask == "")) {
 179                                 noOutliers = outputDir + getRootName(getSimpleName(templateFileName)) + "pintail.filtered." + getSimpleName(getRootName(fastafile)) + "quan";
 180                         }
 181
 182                         decalc->removeObviousOutliers(quantilesMembers, templateSeqs.size());
 183
 184                         if (m->control_pressed) {  return 0;  }
 185
 186                         string outputString = "";
 187
 188                         //adjust quantiles
 189                         for (int i = 0; i < quantilesMembers.size(); i++) {
 190                                 vector<float> temp;
 191
 192                                 if (quantilesMembers[i].size() == 0) {
 193                                         //in case this is not a distance found in your template files
 194                                         for (int g = 0; g < 6; g++) {
 195                                                 temp.push_back(0.0);
 196                                         }
 197                                 }else{
 198
 199                                         sort(quantilesMembers[i].begin(), quantilesMembers[i].end(), compareQuanMembers);
 200
 201                                         //save 10%
 202                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.10)].score);
 203                                         //save 25%
 204                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.25)].score);
 205                                         //save 50%
 206                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.5)].score);
 207                                         //save 75%
 208                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.75)].score);
 209                                         //save 95%
 210                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.95)].score);
 211                                         //save 99%
 212                                         temp.push_back(quantilesMembers[i][int(quantilesMembers[i].size() * 0.99)].score);
 213
 214                                 }
 215
 216                                 //output quan value
 217                                 outputString += toString(i+1) + "\t";
 218                                 for (int u = 0; u < temp.size(); u++) {   outputString += toString(temp[u]) + "\t"; }
 219                                 outputString += "\n";
 220
 221                                 quantiles[i] = temp;
 222
 223                         }
 224
 225                         printQuanFile(noOutliers, outputString);
 226
 227                         m->mothurOut("Done."); m->mothurOutEndLine();
 228                 }
 229
 230                 if (reRead) {
 231                         for (int i = 0; i < templateSeqs.size(); i++) { delete templateSeqs[i];  }
 232                         templateSeqs.clear();
 233                         templateSeqs = readSeqs(templateFileName);
 234                 }
 235
 236
 237                 //free memory
 238                 for (int i = 0; i < templateLines.size(); i++) { delete templateLines[i];  }
 239
 240                 return 0;
 241
 242         }
 243         catch(exception& e) {
 244                 m->errorOut(e, "Pintail", "doPrep");
 245                 exit(1);
 246         }
 247 }
 248 //***************************************************************************************************************
 249 int Pintail::print(ostream& out, ostream& outAcc) {
 250         try {
 251                 int index = ceil(deviation);
 252
 253                 //is your DE value higher than the 95%
 254                 string chimera;
 255                 if (index != 0) {  //if index is 0 then its an exact match to a template seq
 256                         if (quantiles[index][4] == 0.0) {
 257                                 chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
 258                         }else {
 259                                 if (DE > quantiles[index][4])           {       chimera = "Yes";        }
 260                                 else                                                            {       chimera = "No";         }
 261                         }
 262                 }else{ chimera = "No";          }
 263
 264                 out << querySeq->getName() << '\t' << "div: " << deviation << "\tstDev: " << DE << "\tchimera flag: " << chimera << endl;
 265                 if (chimera == "Yes") {
 266                         m->mothurOut(querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera); m->mothurOutEndLine();
 267                         outAcc << querySeq->getName() << endl;
 268                 }
 269                 out << "Observed\t";
 270
 271                 for (int j = 0; j < obsDistance.size(); j++) {  out << obsDistance[j] << '\t';  }
 272                 out << endl;
 273
 274                 out << "Expected\t";
 275
 276                 for (int m = 0; m < expectedDistance.size(); m++) {  out << expectedDistance[m] << '\t';  }
 277                 out << endl;
 278
 279                 return 0;
 280
 281         }
 282         catch(exception& e) {
 283                 m->errorOut(e, "Pintail", "print");
 284                 exit(1);
 285         }
 286 }
 287 #ifdef USE_MPI
 288 //***************************************************************************************************************
 289 int Pintail::print(MPI_File& out, MPI_File& outAcc) {
 290         try {
 291                 bool results = false;
 292                 string outputString = "";
 293                 int index = ceil(deviation);
 294
 295                 //is your DE value higher than the 95%
 296                 string chimera;
 297                 if (index != 0) {  //if index is 0 then its an exact match to a template seq
 298                         if (quantiles[index][4] == 0.0) {
 299                                 chimera = "Your template does not include sequences that provide quantile values at distance " + toString(index);
 300                         }else {
 301                                 if (DE > quantiles[index][4])           {       chimera = "Yes";        }
 302                                 else                                                            {       chimera = "No";         }
 303                         }
 304                 }else{ chimera = "No";          }
 305
 306                 outputString += querySeq->getName() + "\tdiv: " + toString(deviation) + "\tstDev: " + toString(DE) + "\tchimera flag: " + chimera + "\n";
 307                 if (chimera == "Yes") {
 308                         cout << querySeq->getName() << "\tdiv: " << toString(deviation) << "\tstDev: " << toString(DE) << "\tchimera flag: " << chimera << endl;
 309                         string outAccString = querySeq->getName() + "\n";
 310
 311                         MPI_Status statusAcc;
 312                         int length = outAccString.length();
 313                         char buf[length];
 314                         strcpy(buf, outAccString.c_str());
 315
 316                         MPI_File_write_shared(outAcc, buf, length, MPI_CHAR, &statusAcc);
 317
 318                         results = true;
 319                 }
 320                 outputString += "Observed\t";
 321
 322                 for (int j = 0; j < obsDistance.size(); j++) {  outputString += toString(obsDistance[j]) + "\t";  }
 323                 outputString += "\n";
 324
 325                 outputString += "Expected\t";
 326
 327                 for (int m = 0; m < expectedDistance.size(); m++) {  outputString += toString(expectedDistance[m]) + "\t";  }
 328                 outputString += "\n";
 329
 330                 MPI_Status status;
 331                 int length = outputString.length();
 332                 char buf2[length];
 333                 strcpy(buf2, outputString.c_str());
 334
 335                 MPI_File_write_shared(out, buf2, length, MPI_CHAR, &status);
 336
 337                 return results;
 338         }
 339         catch(exception& e) {
 340                 m->errorOut(e, "Pintail", "print");
 341                 exit(1);
 342         }
 343 }
 344 #endif
 345 //***************************************************************************************************************
 346 int Pintail::getChimeras(Sequence* query) {
 347         try {
 348                 querySeq = query;
 349                 trimmed.clear();
 350                 windowSizes = window;
 351
 352                 //find pairs has to be done before a mask
 353                 bestfit = findPairs(query);
 354
 355                 if (m->control_pressed) {  return 0; }
 356
 357                 //if they mask
 358                 if (seqMask != "") {
 359                         decalc->runMask(query);
 360                         decalc->runMask(bestfit);
 361                 }
 362
 363                 if (filter) { //must be done after a mask
 364                         runFilter(query);
 365                         runFilter(bestfit);
 366                 }
 367
 368
 369                 //trim seq
 370                 decalc->trimSeqs(query, bestfit, trimmed);
 371
 372                 //find windows
 373                 it = trimmed.begin();
 374                 windowsForeachQuery = decalc->findWindows(query, it->first, it->second, windowSizes, increment);
 375
 376                 //find observed distance
 377                 obsDistance = decalc->calcObserved(query, bestfit, windowsForeachQuery, windowSizes);
 378
 379                 if (m->control_pressed) {  return 0; }
 380
 381                 Qav = decalc->findQav(windowsForeachQuery, windowSizes, probabilityProfile);
 382
 383                 if (m->control_pressed) {  return 0; }
 384
 385                 //find alpha
 386                 seqCoef = decalc->getCoef(obsDistance, Qav);
 387
 388                 //calculating expected distance
 389                 expectedDistance = decalc->calcExpected(Qav, seqCoef);
 390
 391                 if (m->control_pressed) {  return 0; }
 392
 393                 //finding de
 394                 DE = decalc->calcDE(obsDistance, expectedDistance);
 395
 396                 if (m->control_pressed) {  return 0; }
 397
 398                 //find distance between query and closest match
 399                 it = trimmed.begin();
 400                 deviation = decalc->calcDist(query, bestfit, it->first, it->second);
 401
 402                 delete bestfit;
 403
 404                 return 0;
 405         }
 406         catch(exception& e) {
 407                 m->errorOut(e, "Pintail", "getChimeras");
 408                 exit(1);
 409         }
 410 }
 411
 412 //***************************************************************************************************************
 413
 414 vector<float> Pintail::readFreq() {
 415         try {
 416                 //read in probabilities and store in vector
 417                 int pos; float num;
 418
 419                 vector<float> prob;
 420                 set<int> h = decalc->getPos();  //positions of bases in masking sequence
 421
 422         #ifdef USE_MPI
 423
 424                 MPI_File inMPI;
 425                 MPI_Offset size;
 426                 MPI_Status status;
 427
 428                 char inFileName[consfile.length()];
 429                 strcpy(inFileName, consfile.c_str());
 430
 431                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 432                 MPI_File_get_size(inMPI, &size);
 433
 434                 char buffer[size];
 435                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 436
 437                 string tempBuf = buffer;
 438
 439                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 440                 istringstream iss (tempBuf,istringstream::in);
 441
 442                 while(!iss.eof()) {
 443                         iss >> pos >> num;
 444
 445                         if (h.count(pos) > 0) {
 446                                 float Pi;
 447                                 Pi =  (num - 0.25) / 0.75;
 448
 449                                 //cannot have probability less than 0.
 450                                 if (Pi < 0) { Pi = 0.0; }
 451
 452                                 //do you want this spot
 453                                 prob.push_back(Pi);
 454                         }
 455
 456                         gobble(iss);
 457                 }
 458
 459                 MPI_File_close(&inMPI);
 460
 461         #else
 462
 463                 ifstream in;
 464                 openInputFile(consfile, in);
 465
 466                 while(!in.eof()){
 467
 468                         in >> pos >> num;
 469
 470                         if (h.count(pos) > 0) {
 471                                 float Pi;
 472                                 Pi =  (num - 0.25) / 0.75;
 473
 474                                 //cannot have probability less than 0.
 475                                 if (Pi < 0) { Pi = 0.0; }
 476
 477                                 //do you want this spot
 478                                 prob.push_back(Pi);
 479                         }
 480
 481                         gobble(in);
 482                 }
 483                 in.close();
 484
 485         #endif
 486
 487                 return prob;
 488
 489         }
 490         catch(exception& e) {
 491                 m->errorOut(e, "Pintail", "readFreq");
 492                 exit(1);
 493         }
 494 }
 495
 496 //***************************************************************************************************************
 497 //calculate the distances from each query sequence to all sequences in the template to find the closest sequence
 498 Sequence* Pintail::findPairs(Sequence* q) {
 499         try {
 500
 501                 Sequence* seqsMatches;
 502
 503                 seqsMatches = decalc->findClosest(q, templateSeqs);
 504                 return seqsMatches;
 505
 506         }
 507         catch(exception& e) {
 508                 m->errorOut(e, "Pintail", "findPairs");
 509                 exit(1);
 510         }
 511 }
 512 //**************************************************************************************************
 513 void Pintail::createProcessesQuan() {
 514         try {
 515 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 516                 int process = 0;
 517                 vector<int> processIDS;
 518
 519                 //loop through and create all the processes you want
 520                 while (process != processors) {
 521                         int pid = fork();
 522
 523                         if (pid > 0) {
 524                                 processIDS.push_back(pid);
 525                                 process++;
 526                         }else if (pid == 0){
 527
 528                                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, templateLines[process]->start, templateLines[process]->end);
 529
 530                                 //write out data to file so parent can read it
 531                                 ofstream out;
 532                                 string s = toString(getpid()) + ".temp";
 533                                 openOutputFile(s, out);
 534
 535
 536                                 //output observed distances
 537                                 for (int i = 0; i < quantilesMembers.size(); i++) {
 538                                         out << quantilesMembers[i].size() << '\t';
 539                                         for (int j = 0; j < quantilesMembers[i].size(); j++) {
 540                                                 out << quantilesMembers[i][j].score << '\t' << quantilesMembers[i][j].member1 << '\t' << quantilesMembers[i][j].member2 << '\t';
 541                                         }
 542                                         out << endl;
 543                                 }
 544
 545                                 out.close();
 546
 547                                 exit(0);
 548                         }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
 549                 }
 550
 551                 //force parent to wait until all the processes are done
 552                 for (int i=0;i<processors;i++) {
 553                         int temp = processIDS[i];
 554                         wait(&temp);
 555                 }
 556
 557                 //get data created by processes
 558                 for (int i=0;i<processors;i++) {
 559                         ifstream in;
 560                         string s = toString(processIDS[i]) + ".temp";
 561                         openInputFile(s, in);
 562
 563                         vector< vector<quanMember> > quan;
 564                         quan.resize(100);
 565
 566                         //get quantiles
 567                         for (int m = 0; m < quan.size(); m++) {
 568                                 int num;
 569                                 in >> num;
 570
 571                                 gobble(in);
 572
 573                                 vector<quanMember> q;  float w; int b, n;
 574                                 for (int j = 0; j < num; j++) {
 575                                         in >> w >> b >> n;
 576
 577                                         quanMember newMember(w, b, n);
 578                                         q.push_back(newMember);
 579                                 }
 580
 581                                 quan[m] = q;
 582                                 gobble(in);
 583                         }
 584
 585
 586                         //save quan in quantiles
 587                         for (int j = 0; j < quan.size(); j++) {
 588                                 //put all values of q[i] into quan[i]
 589                                 for (int l = 0; l < quan[j].size(); l++) {  quantilesMembers[j].push_back(quan[j][l]);   }
 590                                 //quantilesMembers[j].insert(quantilesMembers[j].begin(), quan[j].begin(), quan[j].end());
 591                         }
 592
 593                         in.close();
 594                         remove(s.c_str());
 595                 }
 596
 597 #else
 598                 quantilesMembers = decalc->getQuantiles(templateSeqs, windowSizesTemplate, window, probabilityProfile, increment, 0, templateSeqs.size());
 599 #endif
 600         }
 601         catch(exception& e) {
 602                 m->errorOut(e, "Pintail", "createProcessesQuan");
 603                 exit(1);
 604         }
 605 }
 606 //***************************************************************************************************************
 607 vector< vector<float> > Pintail::readQuantiles() {
 608         try {
 609                 int num;
 610                 float ten, twentyfive, fifty, seventyfive, ninetyfive, ninetynine;
 611
 612                 vector< vector<float> > quan;
 613                 vector <float> temp; temp.resize(6, 0);
 614
 615                 //to fill 0
 616                 quan.push_back(temp);
 617
 618         #ifdef USE_MPI
 619
 620                 MPI_File inMPI;
 621                 MPI_Offset size;
 622                 MPI_Status status;
 623
 624                 char inFileName[quanfile.length()];
 625                 strcpy(inFileName, quanfile.c_str());
 626
 627                 MPI_File_open(MPI_COMM_WORLD, inFileName, MPI_MODE_RDONLY, MPI_INFO_NULL, &inMPI);
 628                 MPI_File_get_size(inMPI, &size);
 629
 630                 char buffer[size];
 631                 MPI_File_read(inMPI, buffer, size, MPI_CHAR, &status);
 632
 633                 string tempBuf = buffer;
 634                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 635                 istringstream iss (tempBuf,istringstream::in);
 636
 637                 while(!iss.eof()) {
 638                         iss >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
 639
 640                         temp.clear();
 641
 642                         temp.push_back(ten);
 643                         temp.push_back(twentyfive);
 644                         temp.push_back(fifty);
 645                         temp.push_back(seventyfive);
 646                         temp.push_back(ninetyfive);
 647                         temp.push_back(ninetynine);
 648
 649                         quan.push_back(temp);
 650
 651                         gobble(iss);
 652                 }
 653
 654                 MPI_File_close(&inMPI);
 655
 656         #else
 657
 658                 ifstream in;
 659                 openInputFile(quanfile, in);
 660
 661                 while(!in.eof()){
 662
 663                         in >> num >> ten >> twentyfive >> fifty >> seventyfive >> ninetyfive >> ninetynine;
 664
 665                         temp.clear();
 666
 667                         temp.push_back(ten);
 668                         temp.push_back(twentyfive);
 669                         temp.push_back(fifty);
 670                         temp.push_back(seventyfive);
 671                         temp.push_back(ninetyfive);
 672                         temp.push_back(ninetynine);
 673
 674                         quan.push_back(temp);
 675
 676                         gobble(in);
 677                 }
 678                 in.close();
 679         #endif
 680
 681                 return quan;
 682
 683         }
 684         catch(exception& e) {
 685                 m->errorOut(e, "Pintail", "readQuantiles");
 686                 exit(1);
 687         }
 688 }
 689 //***************************************************************************************************************/
 690
 691 void Pintail::printQuanFile(string file, string outputString) {
 692         try {
 693
 694                 #ifdef USE_MPI
 695
 696                         MPI_File outQuan;
 697                         MPI_Status status;
 698
 699                         int pid;
 700                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 701
 702                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 703
 704                         char FileName[file.length()];
 705                         strcpy(FileName, file.c_str());
 706
 707                         if (pid == 0) {
 708                                 MPI_File_open(MPI_COMM_SELF, FileName, outMode, MPI_INFO_NULL, &outQuan);  //comm, filename, mode, info, filepointer
 709
 710                                 int length = outputString.length();
 711                                 char buf[length];
 712                                 strcpy(buf, outputString.c_str());
 713
 714                                 MPI_File_write(outQuan, buf, length, MPI_CHAR, &status);
 715
 716                                 MPI_File_close(&outQuan);
 717                         }
 718                 #else
 719                         ofstream outQuan;
 720                         openOutputFile(file, outQuan);
 721
 722                         outQuan << outputString;
 723
 724                         outQuan.close();
 725                 #endif
 726         }
 727         catch(exception& e) {
 728                 m->errorOut(e, "Pintail", "printQuanFile");
 729                 exit(1);
 730         }
 731 }
 732
 733 //***************************************************************************************************************/
 734
 735
 736