slayer.cpp

   1 /*
   2  *  slayer.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 9/25/09.
   6  *  Copyright 2009 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "slayer.h"
  11
  12 /***********************************************************************/
  13 Slayer::Slayer(int win, int increment, int parentThreshold, float div, int i, int snp, int mi) :
  14                 minBS(mi), windowSize(win), windowStep(increment), parentFragmentThreshold(parentThreshold), divRThreshold(div), iters(i), percentSNPSample(snp){ m = MothurOut::getInstance(); }
  15 /***********************************************************************/
  16 string Slayer::getResults(Sequence query, vector<Sequence> refSeqs) {
  17         try {
  18                 vector<data_struct> all; all.clear();
  19                 myQuery = query;
  20
  21                 for (int i = 0; i < refSeqs.size(); i++) {
  22
  23                         for (int j = i+1; j < refSeqs.size(); j++) {
  24
  25                                 if (m->control_pressed) { return "no";  }
  26
  27                                 //make copies of query and each parent because runBellerophon removes gaps and messes them up
  28                                 Sequence q(query.getName(), query.getAligned());
  29                                 Sequence leftParent(refSeqs[i].getName(), refSeqs[i].getAligned());
  30                                 Sequence rightParent(refSeqs[j].getName(), refSeqs[j].getAligned());
  31
  32                                 //cout << q->getName() << endl << q->getAligned() << endl << endl;
  33                                 //cout << leftParent.getName() << '\t' << leftParent.getAligned().length() << endl << endl;
  34                                 //cout << rightParent.getName() << '\t' << rightParent.getAligned().length() << endl << endl;
  35                                 //cout << q.getName() << '\t' << q.getAligned().length() << endl << endl;
  36                                 //cout << rightParent->getName() << endl << rightParent->getAligned() << endl << endl;
  37                                 //cout << " length = " << rightParent->getAligned().length() << endl;
  38
  39                                 map<int, int> spots;  //map from spot in original sequence to spot in filtered sequence for query and both parents
  40                                 vector<data_struct> divs = runBellerophon(q, leftParent, rightParent, spots);
  41
  42                                 if (m->control_pressed) { return "no"; }
  43 //                              cout << "examining:\t" << refSeqs[i]->getName() << '\t' << refSeqs[j]->getName() << endl;
  44                                 vector<data_struct> selectedDivs;
  45                                 for (int k = 0; k < divs.size(); k++) {
  46
  47                                         vector<snps> snpsLeft = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winLStart, divs[k].winLEnd);
  48                                         vector<snps> snpsRight = getSNPS(divs[k].parentA.getAligned(), divs[k].querySeq.getAligned(), divs[k].parentB.getAligned(), divs[k].winRStart, divs[k].winREnd);
  49
  50                                         if (m->control_pressed) {  return "no"; }
  51
  52                                         int numSNPSLeft = snpsLeft.size();
  53                                         int numSNPSRight = snpsRight.size();
  54
  55 //                                      cout << numSNPSLeft << '\t' << numSNPSRight << endl;
  56                                         //require at least 4 SNPs on each side of the break
  57                                         if ((numSNPSLeft >= 4) && (numSNPSRight >= 4)) {
  58
  59                                                 float BS_A, BS_B;
  60                                                 bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, iters);
  61
  62                                                 if (m->control_pressed) { return "no"; }
  63
  64                                                 divs[k].bsa = BS_A;
  65                                                 divs[k].bsb = BS_B;
  66                                                 divs[k].bsMax = max(BS_A, BS_B);
  67                                                 divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
  68
  69
  70                                                 //are we within 10 points of the bootstrap cutoff?
  71 //                                              if ((divs[k].bsMax >= (minBS-10)) && (iters < 1000)) {
  72 //                                                      bootstrapSNPS(snpsLeft, snpsRight, BS_A, BS_B, 1000);
  73 //
  74 //                                                      if (m->control_pressed) { delete q; delete leftParent; delete rightParent; return "no"; }
  75 //
  76 //                                                      divs[k].bsa = BS_A;
  77 //                                                      divs[k].bsb = BS_B;
  78 //                                                      divs[k].bsMax = max(BS_A, BS_B);
  79 //                                                      divs[k].chimeraMax = max(divs[k].qla_qrb, divs[k].qlb_qra);
  80 //                                              }
  81
  82                                                 //so results reflect orignal alignment
  83                                                 divs[k].winLStart = spots[divs[k].winLStart];
  84                                                 divs[k].winLEnd = spots[divs[k].winLEnd];
  85                                                 divs[k].winRStart = spots[divs[k].winRStart];
  86                                                 divs[k].winREnd = spots[divs[k].winREnd];
  87
  88                                                 selectedDivs.push_back(divs[k]);
  89                                         }
  90                                 }
  91
  92                                 //save selected
  93                                 for (int mi = 0; mi < selectedDivs.size(); mi++) {  all.push_back(selectedDivs[mi]);    }
  94                         }
  95                 }
  96
  97
  98                 // compute bootstrap support
  99                 if (all.size() > 0) {
 100                         //sort them
 101                         sort(all.begin(), all.end(), compareDataStruct);
 102                         reverse(all.begin(), all.end());
 103
 104                         outputResults = all;
 105                         return "yes";
 106                 }else {
 107                         outputResults = all;
 108                         return "no";
 109                 }
 110         }
 111         catch(exception& e) {
 112                 m->errorOut(e, "Slayer", "getResults");
 113                 exit(1);
 114         }
 115 }
 116 /***********************************************************************/
 117 vector<data_struct> Slayer::runBellerophon(Sequence q, Sequence pA, Sequence pB, map<int, int>& spots) {
 118         try{
 119
 120                 vector<data_struct> data;
 121
 122                 //vertical filter
 123                 //cout << q.getName() << endl << q.getAligned() << endl << endl;
 124                 //cout << pA.getName() << endl << pA.getUnaligned() << endl << endl;
 125                 //cout << pB.getName() << endl << pB.getUnaligned() << endl << endl;
 126
 127                 //maps spot in new alignment to spot in alignment before filter
 128                 spots = verticalFilter(q, pA, pB);  //fills baseSpots
 129
 130                 //get these to avoid numerous function calls
 131                 string query = q.getAligned();
 132                 string parentA = pA.getAligned();
 133                 string parentB = pB.getAligned();
 134                 int length = query.length();
 135 //cout << q.getName() << endl << q.getAligned() << endl << endl;
 136 //cout << pA.getName() << endl << pA.getUnaligned() << endl << endl;
 137 //cout << pB.getName() << endl << pB.getUnaligned() << endl << endl;
 138 //cout << " length = " << length << endl;
 139
 140                 //check window size
 141                 if (length < (2*windowSize+windowStep)) {
 142 //                      m->mothurOut("Your window size is too large for " + q->getName() + ". I will make the window size " + toString(length/4) + " which is 1/4 the filtered length."); m->mothurOutEndLine();
 143                         windowSize = length / 4;
 144                 }
 145
 146                 for (int i = windowSize-1; i <= (length - windowSize); i += windowStep) {
 147
 148                         if (m->control_pressed) { return data; }
 149
 150                         int breakpoint = i;
 151                         int leftLength = breakpoint + 1;
 152                         int rightLength = length - leftLength;
 153
 154                         float QLA = computePercentID(query, parentA, 0, breakpoint);
 155                         float QRB = computePercentID(query, parentB, breakpoint+1, length-1);
 156
 157                         float QLB = computePercentID(query, parentB, 0, breakpoint);
 158                         float QRA = computePercentID(query, parentA, breakpoint+1, length-1);
 159
 160                         float LAB = computePercentID(parentA, parentB, 0, breakpoint);
 161                         float RAB = computePercentID(parentA, parentB, breakpoint+1, length-1);
 162
 163                         float AB = ((LAB*leftLength) + (RAB*rightLength)) / (float) length;
 164                         float QA = ((QLA*leftLength) + (QRA*rightLength)) / (float) length;
 165                         float QB = ((QLB*leftLength) + (QRB*rightLength)) / (float) length;
 166
 167                         float QLA_QRB = ((QLA*leftLength) + (QRB*rightLength)) / (float) length;
 168                         float QLB_QRA = ((QLB*leftLength) + (QRA*rightLength)) / (float) length;
 169
 170                         //in original and not used
 171                         //float avgQA_QB = ((QA*leftLength) + (QB*rightLength)) / (float) length;
 172
 173                         float divR_QLA_QRB = min((QLA_QRB/QA), (QLA_QRB/QB));
 174                         float divR_QLB_QRA = min((QLB_QRA/QA), (QLB_QRA/QB));
 175
 176
 177                         //cout << q->getName() << '\t';
 178                         //cout << pA->getName() << '\t';
 179                         //cout << pB->getName() << '\t';
 180                     //cout << "bp: " << breakpoint << " CHIM_TYPE_A\t" << divR_QLA_QRB << "\tQLA: " << QLA << "\tQRB: " << QRB << "\tQLA_QRB: " << QLA_QRB;
 181                         //cout << "\tCHIM_TYPE_B\t" << divR_QLB_QRA << "\tQLB: " << QLB << "\tQRA: " << QRA << "\tQLB_QRA: " << QLB_QRA << endl;
 182 //cout << leftLength << '\t' << rightLength << '\t' << QLA << '\t' << QRB << '\t' << QLB << '\t' << QRA  << '\t' << LAB << '\t' << RAB << '\t' << AB << '\t' << QA << '\t' << QB << '\t' << QLA_QRB << '\t' <<  QLB_QRA <<    endl;
 183
 184 //cout << divRThreshold << endl;
 185 //cout << breakpoint << '\t' << divR_QLA_QRB << '\t' << divR_QLB_QRA << endl;
 186                         //is one of them above the
 187                         if (divR_QLA_QRB >= divRThreshold || divR_QLB_QRA >= divRThreshold) {
 188
 189                                 if (((QLA_QRB > QA) && (QLA_QRB > QB) && (QLA >= parentFragmentThreshold) && (QRB >= parentFragmentThreshold))  ||
 190                                         ((QLB_QRA > QA) && (QLB_QRA > QB) && (QLB >=parentFragmentThreshold) && (QRA >= parentFragmentThreshold)))  {
 191
 192                                         data_struct member;
 193
 194                                         member.divr_qla_qrb = divR_QLA_QRB;
 195                                         member.divr_qlb_qra = divR_QLB_QRA;
 196                                         member.qla_qrb = QLA_QRB;
 197                                         member.qlb_qra = QLB_QRA;
 198                                         member.qla = QLA;
 199                                         member.qrb = QRB;
 200                                         member.ab = AB;
 201                                         member.qa = QA;
 202                                         member.qb = QB;
 203                                         member.lab = LAB;
 204                                         member.rab = RAB;
 205                                         member.qra = QRA;
 206                                         member.qlb = QLB;
 207                                         member.winLStart = 0;
 208                                         member.winLEnd = breakpoint;
 209                                         member.winRStart = breakpoint+1;
 210                                         member.winREnd = length-1;
 211                                         member.querySeq = q;
 212                                         member.parentA = pA;
 213                                         member.parentB = pB;
 214                                         member.bsa = 0;
 215                                         member.bsb = 0;
 216                                         member.bsMax = 0;
 217                                         member.chimeraMax = 0;
 218
 219                                         data.push_back(member);
 220
 221                                 }//if
 222                         }//if
 223                 }//for
 224
 225
 226                 return data;
 227
 228         }
 229         catch(exception& e) {
 230                 m->errorOut(e, "Slayer", "runBellerophon");
 231                 exit(1);
 232         }
 233 }
 234 /***********************************************************************/
 235 vector<snps> Slayer::getSNPS(string parentA, string query, string parentB, int left, int right) {
 236         try {
 237
 238                 vector<snps> data;
 239
 240                 for (int i = left; i <= right; i++) {
 241
 242                         char A = parentA[i];
 243                         char Q = query[i];
 244                         char B = parentB[i];
 245
 246                         if ((A != Q) || (B != Q)) {
 247
 248                                 //ensure not neighboring a gap. change to 12/09 release of chimeraSlayer - not sure what this adds, but it eliminates alot of SNPS
 249
 250
 251                                 if (
 252                                         //did query loose a base here during filter??
 253                                         ( i == 0 || abs (baseSpots[0][i] - baseSpots[0][i-1]) == 1) &&
 254                                         ( i == query.length()-1 || abs (baseSpots[0][i] - baseSpots[0][i+1]) == 1)
 255                                         &&
 256                                         //did parentA loose a base here during filter??
 257                                         ( i == 0 || abs (baseSpots[1][i] - baseSpots[1][i-1]) == 1) &&
 258                                         ( i == parentA.length()-1 || abs (baseSpots[1][i] - baseSpots[1][i+1]) == 1)
 259                                         &&
 260                                         //did parentB loose a base here during filter??
 261                                         ( i == 0 || abs (baseSpots[2][i] - baseSpots[2][i-1]) == 1) &&
 262                                         ( i == parentB.length()-1 || abs (baseSpots[2][i] - baseSpots[2][i+1]) == 1)
 263                                         )
 264                                 {
 265                                         snps member;
 266                                         member.queryChar = Q;
 267                                         member.parentAChar = A;
 268                                         member.parentBChar = B;
 269                                         data.push_back(member);
 270                                 }
 271                         }
 272                 }
 273
 274                 return data;
 275
 276         }
 277         catch(exception& e) {
 278                 m->errorOut(e, "Slayer", "getSNPS");
 279                 exit(1);
 280         }
 281 }
 282 /***********************************************************************/
 283 int Slayer::bootstrapSNPS(vector<snps> left, vector<snps> right, float& BSA, float& BSB, int numIters) {
 284         try {
 285
 286                 srand((unsigned)time( NULL ));
 287
 288                 int count_A = 0; // sceneario QLA,QRB supported
 289                 int count_B = 0; // sceneario QLB,QRA supported
 290
 291                 int numLeft = max(1, int(left.size() * percentSNPSample/(float)100 + 0.5));
 292                 int numRight = max(1, int(right.size() * percentSNPSample/(float)100 + 0.5));
 293
 294                 for (int i = 0; i < numIters; i++) {
 295                         //random sampling with replacement.
 296
 297                         if (m->control_pressed) { return 0;  }
 298
 299                         vector<snps> selectedLeft;
 300
 301                         for (int j = 0; j < numLeft; j++) {
 302                                 int index = int(rand() % left.size());
 303                                 selectedLeft.push_back(left[index]);
 304                         }
 305
 306                         vector<snps> selectedRight;
 307                         for (int j = 0; j < numRight; j++) {
 308                                 int index = int(rand() % right.size());
 309                                 selectedRight.push_back(right[index]);
 310                         }
 311
 312                         /* A  ------------------------------------------
 313                         #       QLA                     QRA
 314                         # Q  ------------------------------------------
 315                         #                      |
 316                         #                      |
 317                         # Q  ------------------------------------------
 318                         #       QLB                     QRB
 319                         # B  ------------------------------------------ */
 320
 321
 322                         float QLA = snpQA(selectedLeft);
 323                         float QRA = snpQA(selectedRight);
 324
 325                         float QLB = snpQB(selectedLeft);
 326                         float QRB = snpQB(selectedRight);
 327
 328                         //in original - not used - not sure why?
 329                         //float ALB = snpAB(selectedLeft);
 330                         //float ARB = snpAB(selectedRight);
 331
 332                         if ((QLA > QLB) && (QRB > QRA)) {
 333                                 count_A++;
 334                         }
 335
 336                         if ((QLB > QLA) && (QRA > QRB)) {
 337                                 count_B++;
 338                         }
 339
 340 //cout << "selected left snp: \n";
 341 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentAChar;  }
 342 //cout << endl;
 343 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].queryChar;  }
 344 //cout << endl;
 345 //for (int j = 0; j < selectedLeft.size(); j++) {  cout << selectedLeft[j].parentBChar;  }
 346 //cout << endl;
 347 //cout << "selected right snp: \n";
 348 //for (int j = 0; j < selectedRight.size(); j++) {  cout << selectedRight[j].parentAChar;  }
 349 //cout << endl;
 350 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].queryChar;  }
 351 //cout << endl;
 352 //for (int i = 0; i < selectedRight.size(); i++) {  cout << selectedRight[i].parentBChar;  }
 353 //cout << endl;
 354                 }
 355
 356
 357                 //cout << count_A << '\t' << count_B << endl;
 358
 359                 BSA = (float) count_A / (float) numIters * 100;
 360                 BSB = (float) count_B / (float) numIters * 100;
 361 //cout << "bsa = " << BSA << " bsb = " << BSB << endl;
 362
 363                 return 0;
 364
 365         }
 366         catch(exception& e) {
 367                 m->errorOut(e, "Slayer", "bootstrapSNPS");
 368                 exit(1);
 369         }
 370 }
 371 /***********************************************************************/
 372 float Slayer::snpQA(vector<snps> data) {
 373         try {
 374
 375                 int numIdentical = 0;
 376
 377                 for (int i = 0; i < data.size(); i++) {
 378                         if (data[i].parentAChar == data[i].queryChar) {
 379                                 numIdentical++;
 380                         }
 381                 }
 382
 383                 float percentID = (numIdentical / (float) data.size()) * 100;
 384
 385                 return percentID;
 386         }
 387         catch(exception& e) {
 388                 m->errorOut(e, "Slayer", "snpQA");
 389                 exit(1);
 390         }
 391 }
 392 /***********************************************************************/
 393 float Slayer::snpQB(vector<snps> data) {
 394         try {
 395
 396                 int numIdentical = 0;
 397
 398                 for (int i = 0; i < data.size(); i++) {
 399                         if (data[i].parentBChar == data[i].queryChar) {
 400                                 numIdentical++;
 401                         }
 402                 }
 403
 404                 float percentID = (numIdentical / (float) data.size()) * 100;
 405
 406                 return percentID;
 407
 408         }
 409         catch(exception& e) {
 410                 m->errorOut(e, "Slayer", "snpQB");
 411                 exit(1);
 412         }
 413 }
 414 /***********************************************************************/
 415 float Slayer::snpAB(vector<snps> data) {
 416         try {
 417                 int numIdentical = 0;
 418
 419                 for (int i = 0; i < data.size(); i++) {
 420                         if (data[i].parentAChar == data[i].parentBChar) {
 421                                 numIdentical++;
 422                         }
 423                 }
 424
 425                 float percentID = (numIdentical / (float) data.size()) * 100;
 426
 427                 return percentID;
 428
 429         }
 430         catch(exception& e) {
 431                 m->errorOut(e, "Slayer", "snpAB");
 432                 exit(1);
 433         }
 434 }
 435 /***********************************************************************/
 436 float Slayer::computePercentID(string queryAlign, string chimera, int left, int right) {
 437         try {
 438
 439                 int numIdentical = 0;
 440                 int countA = 0;
 441                 int countB = 0;
 442                 for (int i = left; i <= right; i++) {
 443                         if (((queryAlign[i] != 'G') && (queryAlign[i] != 'T') && (queryAlign[i] != 'A') && (queryAlign[i] != 'C')&& (queryAlign[i] != '.') && (queryAlign[i] != '-')) ||
 444                                 ((chimera[i] != 'G') && (chimera[i] != 'T') && (chimera[i] != 'A') && (chimera[i] != 'C')&& (chimera[i] != '.') && (chimera[i] != '-'))) {}
 445                         else {
 446
 447                                 bool charA = false; bool charB = false;
 448                                 if ((queryAlign[i] == 'G') || (queryAlign[i] == 'T') || (queryAlign[i] == 'A') || (queryAlign[i] == 'C')) { charA = true; }
 449                                 if ((chimera[i] == 'G') || (chimera[i] == 'T') || (chimera[i] == 'A') || (chimera[i] == 'C')) { charB = true; }
 450
 451                                 if (charA || charB) {
 452
 453                                         if (charA) { countA++; }
 454                                         if (charB) { countB++; }
 455
 456                                         if (queryAlign[i] == chimera[i]) {
 457                                                 numIdentical++;
 458                                         }
 459                                 }
 460                         }
 461
 462                 }
 463
 464                 float numBases = (countA + countB) /(float) 2;
 465
 466                 if (numBases == 0) { return 0; }
 467
 468                 float percentIdentical = (numIdentical/(float)numBases) * 100;
 469
 470                 return percentIdentical;
 471
 472         }
 473         catch(exception& e) {
 474                 m->errorOut(e, "Slayer", "computePercentID");
 475                 exit(1);
 476         }
 477 }
 478 /***********************************************************************/
 479 //remove columns that contain any gaps
 480 map<int, int> Slayer::verticalFilter(Sequence& q, Sequence& pA, Sequence& pB) {
 481         try {
 482                 //find baseSpots
 483                 baseSpots.clear();
 484                 baseSpots.resize(3);  //query, parentA, parentB
 485
 486                 vector<int> gaps;       gaps.resize(q.getAligned().length(), 0);
 487
 488                 string filterString = (string(q.getAligned().length(), '1'));
 489
 490                 string seqAligned = q.getAligned();
 491                 for (int j = 0; j < seqAligned.length(); j++) {
 492                         //if this spot is a gap
 493                         if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
 494                 }
 495
 496                 seqAligned = pA.getAligned();
 497                 for (int j = 0; j < seqAligned.length(); j++) {
 498                         //if this spot is a gap
 499                         if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
 500                 }
 501
 502                 seqAligned = pB.getAligned();
 503                 for (int j = 0; j < seqAligned.length(); j++) {
 504                         //if this spot is a gap
 505                         if ((seqAligned[j] == '-') || (seqAligned[j] == '.') || (toupper(seqAligned[j]) == 'N'))        {   gaps[j]++;  }
 506                 }
 507
 508
 509                 //zero out spot where any sequences have blanks
 510                 int numColRemoved = 0;
 511                 int count = 0;
 512                 map<int, int> maskMap; maskMap.clear();
 513
 514                 for(int i = 0; i < q.getAligned().length(); i++){
 515                         if(gaps[i] != 0)        {       filterString[i] = '0';  numColRemoved++;  }
 516                         else {
 517                                 maskMap[count] = i;
 518                                 count++;
 519                         }
 520                 }
 521
 522                 seqAligned = q.getAligned();
 523                 string newAligned = "";
 524
 525                 int baseCount = 0;
 526                 count = 0;
 527                 for (int j = 0; j < seqAligned.length(); j++) {
 528                         //are you a base
 529                         if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
 530
 531                         //if this spot is not a gap
 532                         if (filterString[j] == '1') {
 533                                 newAligned += seqAligned[j];
 534                                 baseSpots[0][count] = baseCount;
 535                                 count++;
 536                         }
 537                 }
 538
 539                 q.setAligned(newAligned);
 540
 541                 seqAligned = pA.getAligned();
 542                 newAligned = "";
 543
 544                 baseCount = 0;
 545                 count = 0;
 546                 for (int j = 0; j < seqAligned.length(); j++) {
 547                         //are you a base
 548                         if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
 549
 550                         //if this spot is not a gap
 551                         if (filterString[j] == '1') {
 552                                 newAligned += seqAligned[j];
 553                                 baseSpots[1][count] = baseCount;
 554                                 count++;
 555                         }
 556                 }
 557
 558                 pA.setAligned(newAligned);
 559
 560                 seqAligned = pB.getAligned();
 561                 newAligned = "";
 562
 563                 baseCount = 0;
 564                 count = 0;
 565                 for (int j = 0; j < seqAligned.length(); j++) {
 566                         //are you a base
 567                         if ((seqAligned[j] != '-') && (seqAligned[j] != '.') && (toupper(seqAligned[j]) != 'N'))        { baseCount++; }
 568
 569                         //if this spot is not a gap
 570                         if (filterString[j] == '1') {
 571                                 newAligned += seqAligned[j];
 572                                 baseSpots[2][count] = baseCount;
 573                                 count++;
 574                         }
 575                 }
 576
 577                 pB.setAligned(newAligned);
 578
 579
 580                 return maskMap;
 581         }
 582         catch(exception& e) {
 583                 m->errorOut(e, "Slayer", "verticalFilter");
 584                 exit(1);
 585         }
 586 }
 587 /***********************************************************************/