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 "referencedb.h"
  19
  20 //**********************************************************************************************************************
  21 vector<string> AlignCommand::setParameters(){
  22         try {
  23                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  24                 CommandParameter pcandidate("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pcandidate);
  25                 CommandParameter psearch("search", "Multiple", "kmer-blast-suffix", "kmer", "", "", "",false,false); parameters.push_back(psearch);
  26                 CommandParameter pksize("ksize", "Number", "", "8", "", "", "",false,false); parameters.push_back(pksize);
  27                 CommandParameter pmatch("match", "Number", "", "1.0", "", "", "",false,false); parameters.push_back(pmatch);
  28                 CommandParameter palign("align", "Multiple", "needleman-gotoh-blast-noalign", "needleman", "", "", "",false,false); parameters.push_back(palign);
  29                 CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pmismatch);
  30                 CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "",false,false); parameters.push_back(pgapopen);
  31                 CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "",false,false); parameters.push_back(pgapextend);
  32                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  33                 CommandParameter pflip("flip", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflip);
  34                 CommandParameter psave("save", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psave);
  35                 CommandParameter pthreshold("threshold", "Number", "", "0.50", "", "", "",false,false); parameters.push_back(pthreshold);
  36                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  37                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  38
  39                 vector<string> myArray;
  40                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  41                 return myArray;
  42         }
  43         catch(exception& e) {
  44                 m->errorOut(e, "AlignCommand", "setParameters");
  45                 exit(1);
  46         }
  47 }
  48 //**********************************************************************************************************************
  49 string AlignCommand::getHelpString(){
  50         try {
  51                 string helpString = "";
  52                 helpString += "The align.seqs command reads a file containing sequences and creates an alignment file and a report file.";
  53                 helpString += "The align.seqs command parameters are reference, fasta, search, ksize, align, match, mismatch, gapopen, gapextend and processors.";
  54                 helpString += "The reference and fasta parameters are required. You may leave fasta blank if you have a valid fasta file. You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amzon.fasta.";
  55                 helpString += "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.";
  56                 helpString += "The align parameter allows you to specify the alignment method to use.  Your options are: gotoh, needleman, blast and noalign. The default is needleman.";
  57                 helpString += "The ksize parameter allows you to specify the kmer size for finding most similar template to candidate.  The default is 8.";
  58                 helpString += "The match parameter allows you to specify the bonus for having the same base. The default is 1.0.";
  59                 helpString += "The mistmatch parameter allows you to specify the penalty for having different bases.  The default is -1.0.";
  60                 helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.";
  61                 helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment.  The default is -1.0.";
  62                 helpString += "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.";
  63                 helpString += "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.";
  64                 helpString += "If the flip parameter is set to true the reverse complement of the sequence is aligned and the better alignment is reported.";
  65                 helpString += "If the save parameter is set to true the reference sequences will be saved in memory, to clear them later you can use the clear.memory command. Default=f.";
  66                 helpString += "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.";
  67                 helpString += "The align.seqs command should be in the following format:";
  68                 helpString += "align.seqs(reference=yourTemplateFile, fasta=yourCandidateFile, align=yourAlignmentMethod, search=yourSearchmethod, ksize=yourKmerSize, match=yourMatchBonus, mismatch=yourMismatchpenalty, gapopen=yourGapopenPenalty, gapextend=yourGapExtendPenalty)";
  69                 helpString += "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)";
  70                 helpString += "Note: No spaces between parameter labels (i.e. candidate), '=' and parameters (i.e.yourFastaFile).";
  71                 return helpString;
  72         }
  73         catch(exception& e) {
  74                 m->errorOut(e, "AlignCommand", "getHelpString");
  75                 exit(1);
  76         }
  77 }
  78 //**********************************************************************************************************************
  79 string AlignCommand::getOutputFileNameTag(string type, string inputName=""){
  80         try {
  81         string tag = "";
  82                 map<string, vector<string> >::iterator it;
  83
  84         //is this a type this command creates
  85         it = outputTypes.find(type);
  86         if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
  87         else {
  88             if (type == "fasta") {  tag = "align"; }
  89             else if (type == "alignreport") {  tag = "align.report"; }
  90             else if (type == "accnos") {  tag = "flip.accnos"; }
  91             else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
  92         }
  93         return tag;
  94         }
  95         catch(exception& e) {
  96                 m->errorOut(e, "AlignCommand", "getOutputFileName");
  97                 exit(1);
  98         }
  99 }
 100
 101 //**********************************************************************************************************************
 102 AlignCommand::AlignCommand(){
 103         try {
 104                 abort = true; calledHelp = true;
 105                 setParameters();
 106                 vector<string> tempOutNames;
 107                 outputTypes["fasta"] = tempOutNames;
 108                 outputTypes["alignreport"] = tempOutNames;
 109                 outputTypes["accnos"] = tempOutNames;
 110         }
 111         catch(exception& e) {
 112                 m->errorOut(e, "AlignCommand", "AlignCommand");
 113                 exit(1);
 114         }
 115 }
 116 //**********************************************************************************************************************
 117 AlignCommand::AlignCommand(string option)  {
 118         try {
 119                 abort = false; calledHelp = false;
 120                 ReferenceDB* rdb = ReferenceDB::getInstance();
 121
 122                 //allow user to run help
 123                 if(option == "help") { help(); abort = true; calledHelp = true;}
 124                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 125
 126                 else {
 127                         vector<string> myArray = setParameters();
 128
 129                         OptionParser parser(option);
 130                         map<string, string> parameters = parser.getParameters();
 131
 132                         ValidParameters validParameter("align.seqs");
 133                         map<string, string>::iterator it;
 134
 135                         //check to make sure all parameters are valid for command
 136                         for (it = parameters.begin(); it != parameters.end(); it++) {
 137                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 138                         }
 139
 140                         //initialize outputTypes
 141                         vector<string> tempOutNames;
 142                         outputTypes["fasta"] = tempOutNames;
 143                         outputTypes["alignreport"] = tempOutNames;
 144                         outputTypes["accnos"] = tempOutNames;
 145
 146                         //if the user changes the output directory command factory will send this info to us in the output parameter
 147                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 148
 149
 150                         //if the user changes the input directory command factory will send this info to us in the output parameter
 151                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 152
 153                         if (inputDir == "not found"){   inputDir = "";          }
 154                         else {
 155                                 string path;
 156
 157                                 it = parameters.find("reference");
 158
 159                                 //user has given a template file
 160                                 if(it != parameters.end()){
 161                                         path = m->hasPath(it->second);
 162                                         //if the user has not given a path then, add inputdir. else leave path alone.
 163                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 164                                 }
 165                         }
 166
 167                         candidateFileName = validParameter.validFile(parameters, "fasta", false);
 168                         if (candidateFileName == "not found") {
 169                                 //if there is a current fasta file, use it
 170                                 string filename = m->getFastaFile();
 171                                 if (filename != "") { candidateFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 172                                 else {  m->mothurOut("You have no current fastafile and the candidate parameter is required."); m->mothurOutEndLine(); abort = true; }
 173                         }else {
 174                                 m->splitAtDash(candidateFileName, candidateFileNames);
 175
 176                                 //go through files and make sure they are good, if not, then disregard them
 177                                 for (int i = 0; i < candidateFileNames.size(); i++) {
 178                                         //candidateFileNames[i] = m->getFullPathName(candidateFileNames[i]);
 179
 180                                         bool ignore = false;
 181                                         if (candidateFileNames[i] == "current") {
 182                                                 candidateFileNames[i] = m->getFastaFile();
 183                                                 if (candidateFileNames[i] != "") {  m->mothurOut("Using " + candidateFileNames[i] + " as input file for the fasta parameter where you had given current."); m->mothurOutEndLine(); }
 184                                                 else {
 185                                                         m->mothurOut("You have no current fastafile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 186                                                         //erase from file list
 187                                                         candidateFileNames.erase(candidateFileNames.begin()+i);
 188                                                         i--;
 189                                                 }
 190                                         }
 191
 192                                         if (!ignore) {
 193
 194                                                 if (inputDir != "") {
 195                                                         string path = m->hasPath(candidateFileNames[i]);
 196                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 197                                                         if (path == "") {       candidateFileNames[i] = inputDir + candidateFileNames[i];               }
 198                                                 }
 199
 200                                                 int ableToOpen;
 201                                                 ifstream in;
 202                                                 ableToOpen = m->openInputFile(candidateFileNames[i], in, "noerror");
 203                                                 in.close();
 204
 205                                                 //if you can't open it, try default location
 206                                                 if (ableToOpen == 1) {
 207                                                         if (m->getDefaultPath() != "") { //default path is set
 208                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(candidateFileNames[i]);
 209                                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 210                                                                 ifstream in2;
 211                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 212                                                                 in2.close();
 213                                                                 candidateFileNames[i] = tryPath;
 214                                                         }
 215                                                 }
 216
 217                                                 //if you can't open it, try output location
 218                                                 if (ableToOpen == 1) {
 219                                                         if (m->getOutputDir() != "") { //default path is set
 220                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(candidateFileNames[i]);
 221                                                                 m->mothurOut("Unable to open " + candidateFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 222                                                                 ifstream in2;
 223                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 224                                                                 in2.close();
 225                                                                 candidateFileNames[i] = tryPath;
 226                                                         }
 227                                                 }
 228
 229
 230
 231                                                 if (ableToOpen == 1) {
 232                                                         m->mothurOut("Unable to open " + candidateFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 233                                                         //erase from file list
 234                                                         candidateFileNames.erase(candidateFileNames.begin()+i);
 235                                                         i--;
 236                                                 }else {
 237                                                         m->setFastaFile(candidateFileNames[i]);
 238                                                 }
 239                                         }
 240                                 }
 241
 242                                 //make sure there is at least one valid file left
 243                                 if (candidateFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 244                         }
 245
 246                         //check for optional parameter and set defaults
 247                         // ...at some point should added some additional type checking...
 248                         string temp;
 249                         temp = validParameter.validFile(parameters, "ksize", false);            if (temp == "not found"){       temp = "8";                             }
 250                         m->mothurConvert(temp, kmerSize);
 251
 252                         temp = validParameter.validFile(parameters, "match", false);            if (temp == "not found"){       temp = "1.0";                   }
 253                         m->mothurConvert(temp, match);
 254
 255                         temp = validParameter.validFile(parameters, "mismatch", false);         if (temp == "not found"){       temp = "-1.0";                  }
 256                         m->mothurConvert(temp, misMatch);
 257
 258                         temp = validParameter.validFile(parameters, "gapopen", false);          if (temp == "not found"){       temp = "-2.0";                  }
 259                         m->mothurConvert(temp, gapOpen);
 260
 261                         temp = validParameter.validFile(parameters, "gapextend", false);        if (temp == "not found"){       temp = "-1.0";                  }
 262                         m->mothurConvert(temp, gapExtend);
 263
 264                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 265                         m->setProcessors(temp);
 266                         m->mothurConvert(temp, processors);
 267
 268                         temp = validParameter.validFile(parameters, "flip", false);                     if (temp == "not found"){       temp = "f";                             }
 269                         flip = m->isTrue(temp);
 270
 271                         temp = validParameter.validFile(parameters, "save", false);                     if (temp == "not found"){       temp = "f";                             }
 272                         save = m->isTrue(temp);
 273                         rdb->save = save;
 274                         if (save) { //clear out old references
 275                                 rdb->clearMemory();
 276                         }
 277
 278                         //this has to go after save so that if the user sets save=t and provides no reference we abort
 279                         templateFileName = validParameter.validFile(parameters, "reference", true);
 280                         if (templateFileName == "not found") {
 281                                 //check for saved reference sequences
 282                                 if (rdb->referenceSeqs.size() != 0) {
 283                                         templateFileName = "saved";
 284                                 }else {
 285                                         m->mothurOut("[ERROR]: You don't have any saved reference sequences and the reference parameter is a required for the align.seqs command.");
 286                                         m->mothurOutEndLine();
 287                                         abort = true;
 288                                 }
 289                         }else if (templateFileName == "not open") { abort = true; }
 290                         else {  if (save) {     rdb->setSavedReference(templateFileName);       }       }
 291
 292                         temp = validParameter.validFile(parameters, "threshold", false);        if (temp == "not found"){       temp = "0.50";                  }
 293                         m->mothurConvert(temp, threshold);
 294
 295                         search = validParameter.validFile(parameters, "search", false);         if (search == "not found"){     search = "kmer";                }
 296                         if ((search != "suffix") && (search != "kmer") && (search != "blast")) { m->mothurOut("invalid search option: choices are kmer, suffix or blast."); m->mothurOutEndLine(); abort=true; }
 297
 298                         align = validParameter.validFile(parameters, "align", false);           if (align == "not found"){      align = "needleman";    }
 299                         if ((align != "needleman") && (align != "gotoh") && (align != "blast") && (align != "noalign")) { m->mothurOut("invalid align option: choices are needleman, gotoh, blast or noalign."); m->mothurOutEndLine(); abort=true; }
 300
 301                 }
 302
 303         }
 304         catch(exception& e) {
 305                 m->errorOut(e, "AlignCommand", "AlignCommand");
 306                 exit(1);
 307         }
 308 }
 309 //**********************************************************************************************************************
 310 AlignCommand::~AlignCommand(){
 311
 312         if (abort == false) {
 313                 for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 314                 delete templateDB;
 315         }
 316 }
 317 //**********************************************************************************************************************
 318
 319 int AlignCommand::execute(){
 320         try {
 321                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 322
 323                 templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
 324
 325                 for (int s = 0; s < candidateFileNames.size(); s++) {
 326                         if (m->control_pressed) { outputTypes.clear(); return 0; }
 327
 328                         m->mothurOut("Aligning sequences from " + candidateFileNames[s] + " ..." ); m->mothurOutEndLine();
 329
 330                         if (outputDir == "") {  outputDir += m->hasPath(candidateFileNames[s]); }
 331                         string alignFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("fasta");
 332                         string reportFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("alignreport");
 333                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(candidateFileNames[s])) + getOutputFileNameTag("accnos");
 334                         bool hasAccnos = true;
 335
 336                         int numFastaSeqs = 0;
 337                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 338                         int start = time(NULL);
 339
 340 #ifdef USE_MPI
 341                                 int pid, numSeqsPerProcessor;
 342                                 int tag = 2001;
 343                                 vector<unsigned long long> MPIPos;
 344                                 MPIWroteAccnos = false;
 345
 346                                 MPI_Status status;
 347                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 348                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 349
 350                                 MPI_File inMPI;
 351                                 MPI_File outMPIAlign;
 352                                 MPI_File outMPIReport;
 353                                 MPI_File outMPIAccnos;
 354
 355                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 356                                 int inMode=MPI_MODE_RDONLY;
 357
 358                                 char outAlignFilename[1024];
 359                                 strcpy(outAlignFilename, alignFileName.c_str());
 360
 361                                 char outReportFilename[1024];
 362                                 strcpy(outReportFilename, reportFileName.c_str());
 363
 364                                 char outAccnosFilename[1024];
 365                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 366
 367                                 char inFileName[1024];
 368                                 strcpy(inFileName, candidateFileNames[s].c_str());
 369
 370                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 371                                 MPI_File_open(MPI_COMM_WORLD, outAlignFilename, outMode, MPI_INFO_NULL, &outMPIAlign);
 372                                 MPI_File_open(MPI_COMM_WORLD, outReportFilename, outMode, MPI_INFO_NULL, &outMPIReport);
 373                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 374
 375                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 376
 377                                 if (pid == 0) { //you are the root process
 378
 379                                         MPIPos = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs); //fills MPIPos, returns numSeqs
 380
 381                                         //send file positions to all processes
 382                                         for(int i = 1; i < processors; i++) {
 383                                                 MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 384                                                 MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 385                                         }
 386
 387                                         //figure out how many sequences you have to align
 388                                         numSeqsPerProcessor = numFastaSeqs / processors;
 389                                         int startIndex =  pid * numSeqsPerProcessor;
 390                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 391
 392                                         //align your part
 393                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 394
 395                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 396
 397                                         for (int i = 1; i < processors; i++) {
 398                                                 bool tempResult;
 399                                                 MPI_Recv(&tempResult, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 400                                                 if (tempResult != 0) { MPIWroteAccnos = true; }
 401                                         }
 402                                 }else{ //you are a child process
 403                                         MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 404                                         MPIPos.resize(numFastaSeqs+1);
 405                                         MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 406
 407
 408                                         //figure out how many sequences you have to align
 409                                         numSeqsPerProcessor = numFastaSeqs / processors;
 410                                         int startIndex =  pid * numSeqsPerProcessor;
 411                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 412
 413
 414                                         //align your part
 415                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIAlign, outMPIReport, outMPIAccnos, MPIPos);
 416
 417                                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIAlign);  MPI_File_close(&outMPIReport);  MPI_File_close(&outMPIAccnos); outputTypes.clear(); return 0; }
 418
 419                                         MPI_Send(&MPIWroteAccnos, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 420                                 }
 421
 422                                 //close files
 423                                 MPI_File_close(&inMPI);
 424                                 MPI_File_close(&outMPIAlign);
 425                                 MPI_File_close(&outMPIReport);
 426                                 MPI_File_close(&outMPIAccnos);
 427
 428                                 //delete accnos file if blank
 429                                 if (pid == 0) {
 430                                         //delete accnos file if its blank else report to user
 431                                         if (MPIWroteAccnos) {
 432                                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 433                                                 if (!flip) {
 434                                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 435                                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 436                                                 m->mothurOutEndLine();
 437                                         }else {
 438                                                 //MPI_Info info;
 439                                                 //MPI_File_delete(outAccnosFilename, info);
 440                                                 hasAccnos = false;
 441                                                 m->mothurRemove(accnosFileName);
 442                                         }
 443                                 }
 444
 445 #else
 446
 447                         vector<unsigned long long> positions;
 448                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 449                         positions = m->divideFile(candidateFileNames[s], processors);
 450                         for (int i = 0; i < (positions.size()-1); i++) {        lines.push_back(new linePair(positions[i], positions[(i+1)]));  }
 451                 #else
 452                         if (processors == 1) {
 453                                 lines.push_back(new linePair(0, 1000));
 454                         }else {
 455                                 positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs);
 456                                 if (positions.size() < processors) { processors = positions.size(); }
 457
 458                                 //figure out how many sequences you have to process
 459                                 int numSeqsPerProcessor = numFastaSeqs / processors;
 460                                 for (int i = 0; i < processors; i++) {
 461                                         int startIndex =  i * numSeqsPerProcessor;
 462                                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 463                                         lines.push_back(new linePair(positions[startIndex], numSeqsPerProcessor));
 464                                 }
 465                         }
 466                 #endif
 467
 468                         if(processors == 1){
 469                                 numFastaSeqs = driver(lines[0], alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 470                         }else{
 471                                 numFastaSeqs = createProcesses(alignFileName, reportFileName, accnosFileName, candidateFileNames[s]);
 472                         }
 473
 474                         if (m->control_pressed) { m->mothurRemove(accnosFileName); m->mothurRemove(alignFileName); m->mothurRemove(reportFileName); outputTypes.clear();  return 0; }
 475
 476                         //delete accnos file if its blank else report to user
 477                         if (m->isBlank(accnosFileName)) {  m->mothurRemove(accnosFileName);  hasAccnos = false; }
 478                         else {
 479                                 m->mothurOut("Some of you sequences generated alignments that eliminated too many bases, a list is provided in " + accnosFileName + ".");
 480                                 if (!flip) {
 481                                         m->mothurOut(" If you set the flip parameter to true mothur will try aligning the reverse compliment as well.");
 482                                 }else{  m->mothurOut(" If the reverse compliment proved to be better it was reported.");  }
 483                                 m->mothurOutEndLine();
 484                         }
 485
 486 #endif
 487
 488
 489                 #ifdef USE_MPI
 490                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 491
 492                         if (pid == 0) { //only one process should output to screen
 493                 #endif
 494
 495                         outputNames.push_back(alignFileName); outputTypes["fasta"].push_back(alignFileName);
 496                         outputNames.push_back(reportFileName); outputTypes["alignreport"].push_back(reportFileName);
 497                         if (hasAccnos)  {       outputNames.push_back(accnosFileName);  outputTypes["accnos"].push_back(accnosFileName);  }
 498
 499                 #ifdef USE_MPI
 500                         }
 501                 #endif
 502
 503                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to align " + toString(numFastaSeqs) + " sequences.");
 504                         m->mothurOutEndLine();
 505                         m->mothurOutEndLine();
 506                 }
 507
 508                 //set align file as new current fastafile
 509                 string currentFasta = "";
 510                 itTypes = outputTypes.find("fasta");
 511                 if (itTypes != outputTypes.end()) {
 512                         if ((itTypes->second).size() != 0) { currentFasta = (itTypes->second)[0]; m->setFastaFile(currentFasta); }
 513                 }
 514
 515                 m->mothurOutEndLine();
 516                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 517                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 518                 m->mothurOutEndLine();
 519
 520                 return 0;
 521         }
 522         catch(exception& e) {
 523                 m->errorOut(e, "AlignCommand", "execute");
 524                 exit(1);
 525         }
 526 }
 527
 528 //**********************************************************************************************************************
 529 int AlignCommand::driver(linePair* filePos, string alignFName, string reportFName, string accnosFName, string filename){
 530         try {
 531                 ofstream alignmentFile;
 532                 m->openOutputFile(alignFName, alignmentFile);
 533
 534                 ofstream accnosFile;
 535                 m->openOutputFile(accnosFName, accnosFile);
 536
 537                 NastReport report(reportFName);
 538
 539                 ifstream inFASTA;
 540                 m->openInputFile(filename, inFASTA);
 541
 542                 inFASTA.seekg(filePos->start);
 543
 544                 bool done = false;
 545                 int count = 0;
 546
 547                 //moved this into driver to avoid deep copies in windows paralellized version
 548                 Alignment* alignment;
 549                 int longestBase = templateDB->getLongestBase();
 550                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 551                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 552                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 553                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 554                 else {
 555                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 556                         m->mothurOutEndLine();
 557                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 558                 }
 559
 560                 while (!done) {
 561
 562                         if (m->control_pressed) {  break; }
 563
 564                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 565                         report.setCandidate(candidateSeq);
 566
 567                         int origNumBases = candidateSeq->getNumBases();
 568                         string originalUnaligned = candidateSeq->getUnaligned();
 569                         int numBasesNeeded = origNumBases * threshold;
 570
 571                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 572                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 573                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 574                                 }
 575
 576                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 577                                 Sequence* templateSeq = &temp;
 578
 579                                 float searchScore = templateDB->getSearchScore();
 580
 581                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 582
 583                                 Sequence* copy;
 584
 585                                 Nast* nast2;
 586                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 587                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 588                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 589                                                                                                 //so this bool tells you if you need to delete it
 590
 591                                 //if there is a possibility that this sequence should be reversed
 592                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 593
 594                                         string wasBetter =  "";
 595                                         //if the user wants you to try the reverse
 596                                         if (flip) {
 597
 598                                                 //get reverse compliment
 599                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 600                                                 copy->reverseComplement();
 601
 602                                                 //rerun alignment
 603                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 604                                                 Sequence* templateSeq2 = &temp2;
 605
 606                                                 searchScore = templateDB->getSearchScore();
 607
 608                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 609
 610                                                 //check if any better
 611                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 612                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 613                                                         templateSeq = templateSeq2;
 614                                                         delete nast;
 615                                                         nast = nast2;
 616                                                         needToDeleteCopy = true;
 617                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 618                                                 }else{
 619                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 620                                                         delete nast2;
 621                                                         delete copy;
 622                                                 }
 623                                         }
 624
 625                                         //create accnos file with names
 626                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 627                                 }
 628
 629                                 report.setTemplate(templateSeq);
 630                                 report.setSearchParameters(search, searchScore);
 631                                 report.setAlignmentParameters(align, alignment);
 632                                 report.setNastParameters(*nast);
 633
 634                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 635
 636                                 report.print();
 637                                 delete nast;
 638                                 if (needToDeleteCopy) {   delete copy;   }
 639
 640                                 count++;
 641                         }
 642                         delete candidateSeq;
 643
 644                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 645                                 unsigned long long pos = inFASTA.tellg();
 646                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 647                         #else
 648                                 if (inFASTA.eof()) { break; }
 649                         #endif
 650
 651                         //report progress
 652                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 653
 654                 }
 655                 //report progress
 656                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 657
 658                 delete alignment;
 659                 alignmentFile.close();
 660                 inFASTA.close();
 661                 accnosFile.close();
 662
 663                 return count;
 664         }
 665         catch(exception& e) {
 666                 m->errorOut(e, "AlignCommand", "driver");
 667                 exit(1);
 668         }
 669 }
 670 //**********************************************************************************************************************
 671 #ifdef USE_MPI
 672 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long long>& MPIPos){
 673         try {
 674                 string outputString = "";
 675                 MPI_Status statusReport;
 676                 MPI_Status statusAlign;
 677                 MPI_Status statusAccnos;
 678                 MPI_Status status;
 679                 int pid;
 680                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 681
 682                 NastReport report;
 683
 684                 if (pid == 0) {
 685                         outputString = report.getHeaders();
 686                         int length = outputString.length();
 687
 688                         char* buf = new char[length];
 689                         memcpy(buf, outputString.c_str(), length);
 690
 691                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 692
 693             delete buf;
 694                 }
 695
 696                 Alignment* alignment;
 697                 int longestBase = templateDB->getLongestBase();
 698                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 699                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 700                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 701                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 702                 else {
 703                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 704                         m->mothurOutEndLine();
 705                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 706                 }
 707
 708
 709                 for(int i=0;i<num;i++){
 710
 711                         if (m->control_pressed) { delete alignment; return 0; }
 712
 713                         //read next sequence
 714                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 715
 716                         char* buf4 = new char[length];
 717                         //memcpy(buf4, outputString.c_str(), length);
 718
 719                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 720
 721                         string tempBuf = buf4;
 722
 723                         delete buf4;
 724
 725                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 726
 727                         istringstream iss (tempBuf,istringstream::in);
 728
 729                         Sequence* candidateSeq = new Sequence(iss);
 730                         report.setCandidate(candidateSeq);
 731
 732                         int origNumBases = candidateSeq->getNumBases();
 733                         string originalUnaligned = candidateSeq->getUnaligned();
 734                         int numBasesNeeded = origNumBases * threshold;
 735
 736                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 737                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 738                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 739                                 }
 740
 741                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 742                                 Sequence* templateSeq = &temp;
 743
 744                                 float searchScore = templateDB->getSearchScore();
 745
 746                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 747                                 Sequence* copy;
 748
 749                                 Nast* nast2;
 750                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 751                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 752                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 753                                                                                                 //so this bool tells you if you need to delete it
 754
 755                                 //if there is a possibility that this sequence should be reversed
 756                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 757
 758                                         string wasBetter = "";
 759                                         //if the user wants you to try the reverse
 760                                         if (flip) {
 761                                                 //get reverse compliment
 762                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 763                                                 copy->reverseComplement();
 764
 765                                                 //rerun alignment
 766                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 767                                                 Sequence* templateSeq2 = &temp2;
 768
 769                                                 searchScore = templateDB->getSearchScore();
 770
 771                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 772
 773                                                 //check if any better
 774                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 775                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 776                                                         templateSeq = templateSeq2;
 777                                                         delete nast;
 778                                                         nast = nast2;
 779                                                         needToDeleteCopy = true;
 780                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 781                                                 }else{
 782                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 783                                                         delete nast2;
 784                                                         delete copy;
 785                                                 }
 786                                         }
 787
 788                                         //create accnos file with names
 789                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 790
 791                                         //send results to parent
 792                                         int length = outputString.length();
 793
 794                                         char* buf = new char[length];
 795                                         memcpy(buf, outputString.c_str(), length);
 796
 797                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 798                                         delete buf;
 799                                         MPIWroteAccnos = true;
 800                                 }
 801
 802                                 report.setTemplate(templateSeq);
 803                                 report.setSearchParameters(search, searchScore);
 804                                 report.setAlignmentParameters(align, alignment);
 805                                 report.setNastParameters(*nast);
 806
 807                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 808
 809                                 //send results to parent
 810                                 int length = outputString.length();
 811                                 char* buf2 = new char[length];
 812                                 memcpy(buf2, outputString.c_str(), length);
 813
 814                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 815
 816                                 delete buf2;
 817
 818                                 outputString = report.getReport();
 819
 820                                 //send results to parent
 821                                 length = outputString.length();
 822                                 char* buf3 = new char[length];
 823                                 memcpy(buf3, outputString.c_str(), length);
 824
 825                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 826
 827                                 delete buf3;
 828                                 delete nast;
 829                                 if (needToDeleteCopy) {   delete copy;   }
 830                         }
 831                         delete candidateSeq;
 832
 833                         //report progress
 834                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 835                 }
 836                 //report progress
 837                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 838
 839                 return 1;
 840         }
 841         catch(exception& e) {
 842                 m->errorOut(e, "AlignCommand", "driverMPI");
 843                 exit(1);
 844         }
 845 }
 846 #endif
 847 /**************************************************************************************************/
 848
 849 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 850         try {
 851                 int num = 0;
 852                 processIDS.resize(0);
 853 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 854                 int process = 1;
 855
 856                 //loop through and create all the processes you want
 857                 while (process != processors) {
 858                         int pid = fork();
 859
 860                         if (pid > 0) {
 861                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 862                                 process++;
 863                         }else if (pid == 0){
 864                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 865
 866                                 //pass numSeqs to parent
 867                                 ofstream out;
 868                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 869                                 m->openOutputFile(tempFile, out);
 870                                 out << num << endl;
 871                                 out.close();
 872
 873                                 exit(0);
 874                         }else {
 875                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 876                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 877                                 exit(0);
 878                         }
 879                 }
 880
 881                 //do my part
 882                 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
 883
 884                 //force parent to wait until all the processes are done
 885                 for (int i=0;i<processIDS.size();i++) {
 886                         int temp = processIDS[i];
 887                         wait(&temp);
 888                 }
 889
 890                 vector<string> nonBlankAccnosFiles;
 891                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 892                 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
 893
 894                 for (int i = 0; i < processIDS.size(); i++) {
 895                         ifstream in;
 896                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 897                         m->openInputFile(tempFile, in);
 898                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 899                         in.close(); m->mothurRemove(tempFile);
 900
 901                         m->appendFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 902                         m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
 903
 904                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 905                         m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
 906
 907                         if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
 908                                 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
 909                         }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp"));  }
 910
 911                 }
 912
 913                 //append accnos files
 914                 if (nonBlankAccnosFiles.size() != 0) {
 915                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 916
 917                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 918                                 m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
 919                                 m->mothurRemove(nonBlankAccnosFiles[h]);
 920                         }
 921                 }else { //recreate the accnosfile if needed
 922                         ofstream out;
 923                         m->openOutputFile(accnosFName, out);
 924                         out.close();
 925                 }
 926 #else
 927                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 928                 //Windows version shared memory, so be careful when passing variables through the alignData struct.
 929                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 930                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 931
 932                 vector<alignData*> pDataArray;
 933                 DWORD   dwThreadIdArray[processors-1];
 934                 HANDLE  hThreadArray[processors-1];
 935
 936                 //Create processor worker threads.
 937                 for( int i=0; i<processors-1; i++ ){
 938                         //copy templateDb
 939                         //AlignmentDB* tempDB = new AlignmentDB(*templateDB);
 940
 941                         // Allocate memory for thread data.
 942                         string extension = "";
 943                         if (i != 0) { extension = toString(i) + ".temp"; }
 944
 945                         alignData* tempalign = new alignData(templateFileName, (alignFileName + extension), (reportFileName + extension), (accnosFName + extension), filename, align, search, kmerSize, m, lines[i]->start, lines[i]->end, flip, match, misMatch, gapOpen, gapExtend, threshold, i);
 946                         pDataArray.push_back(tempalign);
 947                         processIDS.push_back(i);
 948
 949                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 950                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 951                         hThreadArray[i] = CreateThread(NULL, 0, MyAlignThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 952                 }
 953
 954                 //need to check for line ending error
 955                 ifstream inFASTA;
 956                 m->openInputFile(filename, inFASTA);
 957                 inFASTA.seekg(lines[processors-1]->start-1);
 958                 char c = inFASTA.peek();
 959
 960                 if (c != '>') { //we need to move back
 961                         lines[processors-1]->start--;
 962                 }
 963
 964                 //using the main process as a worker saves time and memory
 965                 //do my part - do last piece because windows is looking for eof
 966                 num = driver(lines[processors-1], (alignFileName + toString(processors-1) + ".temp"), (reportFileName + toString(processors-1) + ".temp"), (accnosFName + toString(processors-1) + ".temp"), filename);
 967
 968                 //Wait until all threads have terminated.
 969                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 970
 971                 //Close all thread handles and free memory allocations.
 972                 for(int i=0; i < pDataArray.size(); i++){
 973                         num += pDataArray[i]->count;
 974                         CloseHandle(hThreadArray[i]);
 975                         delete pDataArray[i];
 976                 }
 977
 978                 vector<string> nonBlankAccnosFiles;
 979                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 980                 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
 981
 982                 for (int i = 1; i < processors; i++) {
 983                         m->appendFiles((alignFileName + toString(i) + ".temp"), alignFileName);
 984                         m->mothurRemove((alignFileName + toString(i) + ".temp"));
 985
 986                         appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
 987                         m->mothurRemove((reportFileName + toString(i) + ".temp"));
 988
 989                         if (!(m->isBlank(accnosFName + toString(i) + ".temp"))) {
 990                                 nonBlankAccnosFiles.push_back(accnosFName + toString(i) + ".temp");
 991                         }else { m->mothurRemove((accnosFName + toString(i) + ".temp"));  }
 992                 }
 993
 994                 //append accnos files
 995                 if (nonBlankAccnosFiles.size() != 0) {
 996                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 997
 998                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 999                                 m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
1000                                 m->mothurRemove(nonBlankAccnosFiles[h]);
1001                         }
1002                 }else { //recreate the accnosfile if needed
1003                         ofstream out;
1004                         m->openOutputFile(accnosFName, out);
1005                         out.close();
1006                 }
1007 #endif
1008
1009                 return num;
1010         }
1011         catch(exception& e) {
1012                 m->errorOut(e, "AlignCommand", "createProcesses");
1013                 exit(1);
1014         }
1015 }
1016 //**********************************************************************************************************************
1017
1018 void AlignCommand::appendReportFiles(string temp, string filename) {
1019         try{
1020
1021                 ofstream output;
1022                 ifstream input;
1023                 m->openOutputFileAppend(filename, output);
1024                 m->openInputFile(temp, input);
1025
1026                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
1027
1028         char buffer[4096];
1029         while (!input.eof()) {
1030             input.read(buffer, 4096);
1031             output.write(buffer, input.gcount());
1032         }
1033
1034                 input.close();
1035                 output.close();
1036         }
1037         catch(exception& e) {
1038                 m->errorOut(e, "AlignCommand", "appendReportFiles");
1039                 exit(1);
1040         }
1041 }
1042 //**********************************************************************************************************************