aligncommand.cpp

   1 /*
   2  *  aligncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 5/15/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  *      This version of nast does everything I think that the greengenes nast server does and then some.  I have added the
   9  *      feature of allowing users to define their database, kmer size for searching, alignment penalty values and alignment
  10  *      method.  This latter feature is perhaps most significant.  nastPlus enables a user to use either a Needleman-Wunsch
  11  *      (non-affine gap penalty) or Gotoh (affine gap penalty) pairwise alignment algorithm.  This is significant because it
  12  *      allows for a global alignment and not the local alignment provided by bLAst.  Furthermore, it has the potential to
  13  *      provide a better alignment because of the banding method employed by blast (I'm not sure about this).
  14  *
  15  */
  16
  17 #include "aligncommand.h"
  18 #include "sequence.hpp"
  19
  20 #include "gotohoverlap.hpp"
  21 #include "needlemanoverlap.hpp"
  22 #include "blastalign.hpp"
  23 #include "noalign.hpp"
  24
  25 #include "nast.hpp"
  26 #include "nastreport.hpp"
  27
  28
  29 //**********************************************************************************************************************
  30
  31 AlignCommand::AlignCommand(string option){
  32         try {
  33                 //              globaldata = GlobalData::getInstance();
  34                 abort = false;
  35
  36                 //allow user to run help
  37                 if(option == "help") { help(); abort = true; }
  38
  39                 else {
  40
  41                         //valid paramters for this command
  42                         string AlignArray[] =  {"template","candidate","search","ksize","align","match","mismatch","gapopen","gapextend", "processors","flip","threshold","outputdir","inputdir"};
  43                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  44
  45                         OptionParser parser(option);
  46                         map<string, string> parameters = parser.getParameters();
  47
  48                         ValidParameters validParameter;
  49                         map<string, string>::iterator it;
  50
  51                         //check to make sure all parameters are valid for command
  52                         for (it = parameters.begin(); it != parameters.end(); it++) {
  53                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  54                         }
  55
  56                         //if the user changes the output directory command factory will send this info to us in the output parameter
  57                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  58
  59                         //if the user changes the input directory command factory will send this info to us in the output parameter
  60                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  61                         if (inputDir == "not found"){   inputDir = "";          }
  62                         else {
  63                                 string path;
  64                                 it = parameters.find("template");
  65                                 //user has given a template file
  66                                 if(it != parameters.end()){
  67                                         path = hasPath(it->second);
  68                                         //if the user has not given a path then, add inputdir. else leave path alone.
  69                                         if (path == "") {       parameters["template"] = inputDir + it->second;         }
  70                                 }
  71                         }
  72
  73                         //check for required parameters
  74                         templateFileName = validParameter.validFile(parameters, "template", true);
  75                         if (templateFileName == "not found") {
  76                                 mothurOut("template is a required parameter for the align.seqs command.");
  77                                 mothurOutEndLine();
  78                                 abort = true;
  79                         }else if (templateFileName == "not open") { abort = true; }
  80
  81                         candidateFileName = validParameter.validFile(parameters, "candidate", false);
  82                         if (candidateFileName == "not found") { mothurOut("candidate is a required parameter for the align.seqs command."); mothurOutEndLine(); abort = true;  }
  83                         else {
  84                                 splitAtDash(candidateFileName, candidateFileNames);
  85
  86                                 //go through files and make sure they are good, if not, then disregard them
  87                                 for (int i = 0; i < candidateFileNames.size(); i++) {
  88                                         if (inputDir != "") {
  89                                                 string path = hasPath(candidateFileNames[i]);
  90                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  91                                                 if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
  92                                         }
  93
  94                                         int ableToOpen;
  95                                         ifstream in;
  96                                         ableToOpen = openInputFile(candidateFileNames[i], in);
  97                                         if (ableToOpen == 1) {
  98                                                 mothurOut(candidateFileNames[i] + " will be disregarded."); mothurOutEndLine();
  99                                                 //erase from file list
 100                                                 candidateFileNames.erase(candidateFileNames.begin()+i);
 101                                                 i--;
 102                                         }
 103                                         in.close();
 104                                 }
 105
 106                                 //make sure there is at least one valid file left
 107                                 if (candidateFileNames.size() == 0) { mothurOut("no valid files."); mothurOutEndLine(); abort = true; }
 108                         }
 109
 110
 111                         //check for optional parameter and set defaults
 112                         // ...at some point should added some additional type checking...
 113                         string temp;
 114                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 115                         convert(temp, kmerSize);
 116
 117                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 118                         convert(temp, match);
 119
 120                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 121                         convert(temp, misMatch);
 122
 123                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 124                         convert(temp, gapOpen);
 125
 126                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 127                         convert(temp, gapExtend);
 128
 129                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = "1";                             }
 130                         convert(temp, processors);
 131
 132                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 133                         flip = isTrue(temp);
 134
 135                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 136                         convert(temp, threshold);
 137
 138                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 139
 140                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 141                 }
 142
 143         }
 144         catch(exception& e) {
 145                 errorOut(e, "AlignCommand", "AlignCommand");
 146                 exit(1);
 147         }
 148 }
 149
 150 //**********************************************************************************************************************
 151
 152 AlignCommand::~AlignCommand(){
 153
 154         if (abort == false) {
 155                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 156                 delete templateDB;
 157                 delete alignment;
 158         }
 159 }
 160
 161 //**********************************************************************************************************************
 162
 163 void AlignCommand::help(){
 164         try {
 165                 mothurOut("The align.seqs command reads a file containing sequences and creates an alignment file and a report file.\n");
 166                 mothurOut("The align.seqs command parameters are template, candidate, search, ksize, align, match, mismatch, gapopen and gapextend.\n");
 167                 mothurOut("The template and candidate parameters are required. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta \n");
 168                 mothurOut("The search parameter allows you to specify the method to find most similar template.  Your options are: suffix, kmer and blast. The default is kmer.\n");
 169                 mothurOut("The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.\n");
 170                 mothurOut("The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.\n");
 171                 mothurOut("The match parameter allows you to specify the bonus for having the same base. The default is 1.0.\n");
 172                 mothurOut("The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.\n");
 173                 mothurOut("The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n");
 174                 mothurOut("The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.\n");
 175                 mothurOut("The flip parameter is used to specify whether or not you want mothur to try the reverse complement if a sequence falls below the threshold.  The default is false.\n");
 176                 mothurOut("The threshold is used to specify a cutoff at which an alignment is deemed 'bad' and the reverse complement may be tried. The default threshold is 0.50, meaning 50% of the bases are removed in the alignment.\n");
 177                 mothurOut("If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.\n");
 178                 mothurOut("The default for the threshold parameter is 0.50, meaning at least 50% of the bases must remain or the sequence is reported as potentially reversed.\n");
 179                 mothurOut("The align.seqs command should be in the following format: \n");
 180                 mothurOut("align.seqs(template=yourTemplateFile, candidate=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty) \n");
 181                 mothurOut("Example align.seqs(candidate=candidate.fasta, template=core.filtered, align=kmer, search=gotoh, ksize=8, match=2.0, mismatch=3.0, gapopen=-2.0, gapextend=-1.0)\n");
 182                 mothurOut("Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).\n\n");
 183         }
 184         catch(exception& e) {
 185                 errorOut(e, "AlignCommand", "help");
 186                 exit(1);
 187         }
 188 }
 189
 190
 191 //**********************************************************************************************************************
 192
 193 int AlignCommand::execute(){
 194         try {
 195                 if (abort == true) {    return 0;       }
 196
 197                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch);
 198                 int longestBase = templateDB->getLongestBase();
 199
 200                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 201                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 202                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 203                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 204                 else {
 205                         mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 206                         mothurOutEndLine();
 207                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 208                 }
 209
 210                 for (int s = 0; s < candidateFileNames.size(); s++) {
 211                         mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); mothurOutEndLine();
 212
 213                         if (outputDir == "") {  outputDir += hasPath(candidateFileNames[s]); }
 214                         string alignFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align";
 215                         string reportFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "align.report";
 216                         string accnosFileName = outputDir + getRootName(getSimpleName(candidateFileNames[s])) + "flip.accnos";
 217
 218                         int numFastaSeqs = 0;
 219                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 220                         int start = time(NULL);
 221
 222 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 223                         if(processors == 1){
 224                                 ifstream inFASTA;
 225                                 openInputFile(candidateFileNames[s], inFASTA);
 226                                 numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 227                                 inFASTA.close();
 228
 229                                 lines.push_back(new linePair(0, numFastaSeqs));
 230
 231                                 driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 232
 233                                 //delete accnos file if its blank else report to user
 234                                 if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  }
 235                                 else {
 236                                         mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 237                                         if (!flip) {
 238                                                 mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 239                                         }else{  mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 240                                         mothurOutEndLine();
 241                                 }
 242                         }
 243                         else{
 244                                 vector<int> positions;
 245                                 processIDS.resize(0);
 246
 247                                 ifstream inFASTA;
 248                                 openInputFile(candidateFileNames[s], inFASTA);
 249
 250                                 string input;
 251                                 while(!inFASTA.eof()){
 252                                         input = getline(inFASTA);
 253                                         if (input.length() != 0) {
 254                                                 if(input[0] == '>'){    long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  }
 255                                         }
 256                                 }
 257                                 inFASTA.close();
 258
 259                                 numFastaSeqs = positions.size();
 260
 261                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 262
 263                                 for (int i = 0; i < processors; i++) {
 264                                         long int startPos = positions[ i * numSeqsPerProcessor ];
 265                                         if(i == processors - 1){
 266                                                 numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;
 267                                         }
 268                                         lines.push_back(new linePair(startPos, numSeqsPerProcessor));
 269                                 }
 270
 271                                 createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 272
 273                                 rename((alignFileName + toString(processIDS[0]) + ".temp").c_str(), alignFileName.c_str());
 274                                 rename((reportFileName + toString(processIDS[0]) + ".temp").c_str(), reportFileName.c_str());
 275
 276                                 //append alignment and report files
 277                                 for(int i=1;i<processors;i++){
 278                                         appendAlignFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 279                                         remove((alignFileName + toString(processIDS[i]) + ".temp").c_str());
 280
 281                                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 282                                         remove((reportFileName + toString(processIDS[i]) + ".temp").c_str());
 283                                 }
 284
 285                                 vector<string> nonBlankAccnosFiles;
 286                                 //delete blank accnos files generated with multiple processes
 287                                 for(int i=0;i<processors;i++){
 288                                         if (!(isBlank(accnosFileName + toString(processIDS[i]) + ".temp"))) {
 289                                                 nonBlankAccnosFiles.push_back(accnosFileName + toString(processIDS[i]) + ".temp");
 290                                         }else { remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());  }
 291                                 }
 292
 293                                 //append accnos files
 294                                 if (nonBlankAccnosFiles.size() != 0) {
 295                                         rename(nonBlankAccnosFiles[0].c_str(), accnosFileName.c_str());
 296
 297                                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 298                                                 appendAlignFiles(nonBlankAccnosFiles[h], accnosFileName);
 299                                                 remove(nonBlankAccnosFiles[h].c_str());
 300                                         }
 301                                         mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 302                                         if (!flip) {
 303                                                 mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 304                                         }else{  mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 305                                         mothurOutEndLine();
 306                                 }
 307                         }
 308 #else
 309                         ifstream inFASTA;
 310                         openInputFile(candidateFileNames[s], inFASTA);
 311                         numFastaSeqs=count(istreambuf_iterator<char>(inFASTA),istreambuf_iterator<char>(), '>');
 312                         inFASTA.close();
 313
 314                         lines.push_back(new linePair(0, numFastaSeqs));
 315
 316                         driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 317
 318                         //delete accnos file if its blank else report to user
 319                         if (isBlank(accnosFileName)) {  remove(accnosFileName.c_str());  }
 320                         else {
 321                                 mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 322                                 if (!flip) {
 323                                         mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 324                                 }else{  mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 325                                 mothurOutEndLine();
 326                         }
 327
 328 #endif
 329
 330
 331
 332                         mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 333                         mothurOutEndLine();
 334                         mothurOutEndLine();
 335                 }
 336
 337                 return 0;
 338         }
 339         catch(exception& e) {
 340                 errorOut(e, "AlignCommand", "execute");
 341                 exit(1);
 342         }
 343 }
 344
 345 //**********************************************************************************************************************
 346
 347 int AlignCommand::driver(linePair* line, string alignFName, string reportFName, string accnosFName, string filename){
 348         try {
 349                 ofstream alignmentFile;
 350                 openOutputFile(alignFName, alignmentFile);
 351
 352                 ofstream accnosFile;
 353                 openOutputFile(accnosFName, accnosFile);
 354
 355                 NastReport report(reportFName);
 356
 357                 ifstream inFASTA;
 358                 openInputFile(filename, inFASTA);
 359
 360                 inFASTA.seekg(line->start);
 361
 362                 for(int i=0;i<line->numSeqs;i++){
 363
 364                         Sequence* candidateSeq = new Sequence(inFASTA);  gobble(inFASTA);
 365                         int origNumBases = candidateSeq->getNumBases();
 366                         string originalUnaligned = candidateSeq->getUnaligned();
 367                         int numBasesNeeded = origNumBases * threshold;
 368
 369                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 370                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 371                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 372                                 }
 373
 374                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 375                                 Sequence* templateSeq = &temp;
 376
 377                                 float searchScore = templateDB->getSearchScore();
 378
 379                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 380                                 Sequence* copy;
 381
 382                                 Nast* nast2;
 383                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 384                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 385                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 386                                                                                                 //so this bool tells you if you need to delete it
 387
 388                                 //if there is a possibility that this sequence should be reversed
 389                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 390
 391                                         string wasBetter = "";
 392                                         //if the user wants you to try the reverse
 393                                         if (flip) {
 394                                                 //get reverse compliment
 395                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 396                                                 copy->reverseComplement();
 397
 398                                                 //rerun alignment
 399                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 400                                                 Sequence* templateSeq2 = &temp2;
 401
 402                                                 searchScore = templateDB->getSearchScore();
 403
 404                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 405
 406                                                 //check if any better
 407                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 408                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 409                                                         templateSeq = templateSeq2;
 410                                                         delete nast;
 411                                                         nast = nast2;
 412                                                         needToDeleteCopy = true;
 413                                                 }else{
 414                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 415                                                         delete nast2;
 416                                                         delete copy;
 417                                                 }
 418                                         }
 419
 420                                         //create accnos file with names
 421                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 422                                 }
 423
 424                                 report.setCandidate(candidateSeq);
 425                                 report.setTemplate(templateSeq);
 426                                 report.setSearchParameters(search, searchScore);
 427                                 report.setAlignmentParameters(align, alignment);
 428                                 report.setNastParameters(*nast);
 429
 430                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 431
 432                                 report.print();
 433                                 delete nast;
 434                                 if (needToDeleteCopy) {   delete copy;   }
 435                         }
 436                         delete candidateSeq;
 437
 438                         //report progress
 439                         if((i+1) % 100 == 0){   mothurOut(toString(i+1)); mothurOutEndLine();           }
 440                 }
 441                 //report progress
 442                 if((line->numSeqs) % 100 != 0){ mothurOut(toString(line->numSeqs)); mothurOutEndLine();         }
 443
 444                 alignmentFile.close();
 445                 inFASTA.close();
 446                 accnosFile.close();
 447
 448                 return 1;
 449         }
 450         catch(exception& e) {
 451                 errorOut(e, "AlignCommand", "driver");
 452                 exit(1);
 453         }
 454 }
 455
 456 /**************************************************************************************************/
 457
 458 void AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 459         try {
 460 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 461                 int process = 0;
 462                 //              processIDS.resize(0);
 463
 464                 //loop through and create all the processes you want
 465                 while (process != processors) {
 466                         int pid = fork();
 467
 468                         if (pid > 0) {
 469                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 470                                 process++;
 471                         }else if (pid == 0){
 472                                 driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 473                                 exit(0);
 474                         }else { mothurOut("unable to spawn the necessary processes."); mothurOutEndLine(); exit(0); }
 475                 }
 476
 477                 //force parent to wait until all the processes are done
 478                 for (int i=0;i<processors;i++) {
 479                         int temp = processIDS[i];
 480                         wait(&temp);
 481                 }
 482 #endif
 483         }
 484         catch(exception& e) {
 485                 errorOut(e, "AlignCommand", "createProcesses");
 486                 exit(1);
 487         }
 488 }
 489
 490 /**************************************************************************************************/
 491
 492 void AlignCommand::appendAlignFiles(string temp, string filename) {
 493         try{
 494
 495                 ofstream output;
 496                 ifstream input;
 497                 openOutputFileAppend(filename, output);
 498                 openInputFile(temp, input);
 499
 500                 while(char c = input.get()){
 501                         if(input.eof())         {       break;                  }
 502                         else                            {       output << c;    }
 503                 }
 504
 505                 input.close();
 506                 output.close();
 507         }
 508         catch(exception& e) {
 509                 errorOut(e, "AlignCommand", "appendAlignFiles");
 510                 exit(1);
 511         }
 512 }
 513 //**********************************************************************************************************************
 514
 515 void AlignCommand::appendReportFiles(string temp, string filename) {
 516         try{
 517
 518                 ofstream output;
 519                 ifstream input;
 520                 openOutputFileAppend(filename, output);
 521                 openInputFile(temp, input);
 522
 523                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
 524
 525                 while(char c = input.get()){
 526                         if(input.eof())         {       break;                  }
 527                         else                            {       output << c;    }
 528                 }
 529
 530                 input.close();
 531                 output.close();
 532         }
 533         catch(exception& e) {
 534                 errorOut(e, "AlignCommand", "appendReportFiles");
 535                 exit(1);
 536         }
 537 }
 538
 539 //**********************************************************************************************************************