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                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 576                                 Sequence* templateSeq = &temp;
 577
 578                                 float searchScore = templateDB->getSearchScore();
 579
 580                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 581
 582                                 Sequence* copy;
 583
 584                                 Nast* nast2;
 585                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 586                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 587                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 588                                                                                                 //so this bool tells you if you need to delete it
 589
 590                                 //if there is a possibility that this sequence should be reversed
 591                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 592
 593                                         string wasBetter =  "";
 594                                         //if the user wants you to try the reverse
 595                                         if (flip) {
 596
 597                                                 //get reverse compliment
 598                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 599                                                 copy->reverseComplement();
 600
 601                                                 //rerun alignment
 602                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 603                                                 Sequence* templateSeq2 = &temp2;
 604
 605                                                 searchScore = templateDB->getSearchScore();
 606
 607                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 608
 609                                                 //check if any better
 610                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 611                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 612                                                         templateSeq = templateSeq2;
 613                                                         delete nast;
 614                                                         nast = nast2;
 615                                                         needToDeleteCopy = true;
 616                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 617                                                 }else{
 618                                                         wasBetter = "\treverse complement did NOT produce a better alignment so it was not used, please check sequence.";
 619                                                         delete nast2;
 620                                                         delete copy;
 621                                                 }
 622                                         }
 623
 624                                         //create accnos file with names
 625                                         accnosFile << candidateSeq->getName() << wasBetter << endl;
 626                                 }
 627
 628                                 report.setTemplate(templateSeq);
 629                                 report.setSearchParameters(search, searchScore);
 630                                 report.setAlignmentParameters(align, alignment);
 631                                 report.setNastParameters(*nast);
 632
 633                                 alignmentFile << '>' << candidateSeq->getName() << '\n' << candidateSeq->getAligned() << endl;
 634
 635                                 report.print();
 636                                 delete nast;
 637                                 if (needToDeleteCopy) {   delete copy;   }
 638
 639                                 count++;
 640                         }
 641                         delete candidateSeq;
 642
 643                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 644                                 unsigned long long pos = inFASTA.tellg();
 645                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 646                         #else
 647                                 if (inFASTA.eof()) { break; }
 648                         #endif
 649
 650                         //report progress
 651                         if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 652
 653                 }
 654                 //report progress
 655                 if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
 656
 657                 delete alignment;
 658                 alignmentFile.close();
 659                 inFASTA.close();
 660                 accnosFile.close();
 661
 662                 return count;
 663         }
 664         catch(exception& e) {
 665                 m->errorOut(e, "AlignCommand", "driver");
 666                 exit(1);
 667         }
 668 }
 669 //**********************************************************************************************************************
 670 #ifdef USE_MPI
 671 int AlignCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& alignFile, MPI_File& reportFile, MPI_File& accnosFile, vector<unsigned long long>& MPIPos){
 672         try {
 673                 string outputString = "";
 674                 MPI_Status statusReport;
 675                 MPI_Status statusAlign;
 676                 MPI_Status statusAccnos;
 677                 MPI_Status status;
 678                 int pid;
 679                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 680
 681                 NastReport report;
 682
 683                 if (pid == 0) {
 684                         outputString = report.getHeaders();
 685                         int length = outputString.length();
 686
 687                         char* buf = new char[length];
 688                         memcpy(buf, outputString.c_str(), length);
 689
 690                         MPI_File_write_shared(reportFile, buf, length, MPI_CHAR, &statusReport);
 691
 692             delete buf;
 693                 }
 694
 695                 Alignment* alignment;
 696                 int longestBase = templateDB->getLongestBase();
 697                 if(align == "gotoh")                    {       alignment = new GotohOverlap(gapOpen, gapExtend, match, misMatch, longestBase);                 }
 698                 else if(align == "needleman")   {       alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);                                }
 699                 else if(align == "blast")               {       alignment = new BlastAlignment(gapOpen, gapExtend, match, misMatch);            }
 700                 else if(align == "noalign")             {       alignment = new NoAlign();                                                                                                      }
 701                 else {
 702                         m->mothurOut(align + " is not a valid alignment option. I will run the command using needleman.");
 703                         m->mothurOutEndLine();
 704                         alignment = new NeedlemanOverlap(gapOpen, match, misMatch, longestBase);
 705                 }
 706
 707
 708                 for(int i=0;i<num;i++){
 709
 710                         if (m->control_pressed) { delete alignment; return 0; }
 711
 712                         //read next sequence
 713                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 714
 715                         char* buf4 = new char[length];
 716                         //memcpy(buf4, outputString.c_str(), length);
 717
 718                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 719
 720                         string tempBuf = buf4;
 721
 722                         delete buf4;
 723
 724                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 725
 726                         istringstream iss (tempBuf,istringstream::in);
 727
 728                         Sequence* candidateSeq = new Sequence(iss);
 729                         report.setCandidate(candidateSeq);
 730
 731                         int origNumBases = candidateSeq->getNumBases();
 732                         string originalUnaligned = candidateSeq->getUnaligned();
 733                         int numBasesNeeded = origNumBases * threshold;
 734
 735                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 736                                 if (candidateSeq->getUnaligned().length() > alignment->getnRows()) {
 737                                         alignment->resize(candidateSeq->getUnaligned().length()+1);
 738                                 }
 739
 740                                 Sequence temp = templateDB->findClosestSequence(candidateSeq);
 741                                 Sequence* templateSeq = &temp;
 742
 743                                 float searchScore = templateDB->getSearchScore();
 744
 745                                 Nast* nast = new Nast(alignment, candidateSeq, templateSeq);
 746                                 Sequence* copy;
 747
 748                                 Nast* nast2;
 749                                 bool needToDeleteCopy = false;  //this is needed in case you have you enter the ifs below
 750                                                                                                 //since nast does not make a copy of hte sequence passed, and it is used by the reporter below
 751                                                                                                 //you can't delete the copy sequence til after you report, but you may choose not to create it in the first place
 752                                                                                                 //so this bool tells you if you need to delete it
 753
 754                                 //if there is a possibility that this sequence should be reversed
 755                                 if (candidateSeq->getNumBases() < numBasesNeeded) {
 756
 757                                         string wasBetter = "";
 758                                         //if the user wants you to try the reverse
 759                                         if (flip) {
 760                                                 //get reverse compliment
 761                                                 copy = new Sequence(candidateSeq->getName(), originalUnaligned);
 762                                                 copy->reverseComplement();
 763
 764                                                 //rerun alignment
 765                                                 Sequence temp2 = templateDB->findClosestSequence(copy);
 766                                                 Sequence* templateSeq2 = &temp2;
 767
 768                                                 searchScore = templateDB->getSearchScore();
 769
 770                                                 nast2 = new Nast(alignment, copy, templateSeq2);
 771
 772                                                 //check if any better
 773                                                 if (copy->getNumBases() > candidateSeq->getNumBases()) {
 774                                                         candidateSeq->setAligned(copy->getAligned());  //use reverse compliments alignment since its better
 775                                                         templateSeq = templateSeq2;
 776                                                         delete nast;
 777                                                         nast = nast2;
 778                                                         needToDeleteCopy = true;
 779                                                         wasBetter = "\treverse complement produced a better alignment, so mothur used the reverse complement.";
 780                                                 }else{
 781                                                         wasBetter = "\treverse complement did NOT produce a better alignment, please check sequence.";
 782                                                         delete nast2;
 783                                                         delete copy;
 784                                                 }
 785                                         }
 786
 787                                         //create accnos file with names
 788                                         outputString = candidateSeq->getName() + wasBetter + "\n";
 789
 790                                         //send results to parent
 791                                         int length = outputString.length();
 792
 793                                         char* buf = new char[length];
 794                                         memcpy(buf, outputString.c_str(), length);
 795
 796                                         MPI_File_write_shared(accnosFile, buf, length, MPI_CHAR, &statusAccnos);
 797                                         delete buf;
 798                                         MPIWroteAccnos = true;
 799                                 }
 800
 801                                 report.setTemplate(templateSeq);
 802                                 report.setSearchParameters(search, searchScore);
 803                                 report.setAlignmentParameters(align, alignment);
 804                                 report.setNastParameters(*nast);
 805
 806                                 outputString =  ">" + candidateSeq->getName() + "\n" + candidateSeq->getAligned() + "\n";
 807
 808                                 //send results to parent
 809                                 int length = outputString.length();
 810                                 char* buf2 = new char[length];
 811                                 memcpy(buf2, outputString.c_str(), length);
 812
 813                                 MPI_File_write_shared(alignFile, buf2, length, MPI_CHAR, &statusAlign);
 814
 815                                 delete buf2;
 816
 817                                 outputString = report.getReport();
 818
 819                                 //send results to parent
 820                                 length = outputString.length();
 821                                 char* buf3 = new char[length];
 822                                 memcpy(buf3, outputString.c_str(), length);
 823
 824                                 MPI_File_write_shared(reportFile, buf3, length, MPI_CHAR, &statusReport);
 825
 826                                 delete buf3;
 827                                 delete nast;
 828                                 if (needToDeleteCopy) {   delete copy;   }
 829                         }
 830                         delete candidateSeq;
 831
 832                         //report progress
 833                         if((i+1) % 100 == 0){   cout << (toString(i+1)) << endl;                }
 834                 }
 835                 //report progress
 836                 if((num) % 100 != 0){   cout << (toString(num)) << endl;                }
 837
 838                 return 1;
 839         }
 840         catch(exception& e) {
 841                 m->errorOut(e, "AlignCommand", "driverMPI");
 842                 exit(1);
 843         }
 844 }
 845 #endif
 846 /**************************************************************************************************/
 847
 848 int AlignCommand::createProcesses(string alignFileName, string reportFileName, string accnosFName, string filename) {
 849         try {
 850                 int num = 0;
 851                 processIDS.resize(0);
 852 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 853                 int process = 1;
 854
 855                 //loop through and create all the processes you want
 856                 while (process != processors) {
 857                         int pid = fork();
 858
 859                         if (pid > 0) {
 860                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 861                                 process++;
 862                         }else if (pid == 0){
 863                                 num = driver(lines[process], alignFileName + toString(getpid()) + ".temp", reportFileName + toString(getpid()) + ".temp", accnosFName + toString(getpid()) + ".temp", filename);
 864
 865                                 //pass numSeqs to parent
 866                                 ofstream out;
 867                                 string tempFile = alignFileName + toString(getpid()) + ".num.temp";
 868                                 m->openOutputFile(tempFile, out);
 869                                 out << num << endl;
 870                                 out.close();
 871
 872                                 exit(0);
 873                         }else {
 874                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 875                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 876                                 exit(0);
 877                         }
 878                 }
 879
 880                 //do my part
 881                 num = driver(lines[0], alignFileName, reportFileName, accnosFName, filename);
 882
 883                 //force parent to wait until all the processes are done
 884                 for (int i=0;i<processIDS.size();i++) {
 885                         int temp = processIDS[i];
 886                         wait(&temp);
 887                 }
 888
 889                 vector<string> nonBlankAccnosFiles;
 890                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 891                 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
 892
 893                 for (int i = 0; i < processIDS.size(); i++) {
 894                         ifstream in;
 895                         string tempFile =  alignFileName + toString(processIDS[i]) + ".num.temp";
 896                         m->openInputFile(tempFile, in);
 897                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 898                         in.close(); m->mothurRemove(tempFile);
 899
 900                         m->appendFiles((alignFileName + toString(processIDS[i]) + ".temp"), alignFileName);
 901                         m->mothurRemove((alignFileName + toString(processIDS[i]) + ".temp"));
 902
 903                         appendReportFiles((reportFileName + toString(processIDS[i]) + ".temp"), reportFileName);
 904                         m->mothurRemove((reportFileName + toString(processIDS[i]) + ".temp"));
 905
 906                         if (!(m->isBlank(accnosFName + toString(processIDS[i]) + ".temp"))) {
 907                                 nonBlankAccnosFiles.push_back(accnosFName + toString(processIDS[i]) + ".temp");
 908                         }else { m->mothurRemove((accnosFName + toString(processIDS[i]) + ".temp"));  }
 909
 910                 }
 911
 912                 //append accnos files
 913                 if (nonBlankAccnosFiles.size() != 0) {
 914                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 915
 916                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 917                                 m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
 918                                 m->mothurRemove(nonBlankAccnosFiles[h]);
 919                         }
 920                 }else { //recreate the accnosfile if needed
 921                         ofstream out;
 922                         m->openOutputFile(accnosFName, out);
 923                         out.close();
 924                 }
 925 #else
 926                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 927                 //Windows version shared memory, so be careful when passing variables through the alignData struct.
 928                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 929                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 930
 931                 vector<alignData*> pDataArray;
 932                 DWORD   dwThreadIdArray[processors-1];
 933                 HANDLE  hThreadArray[processors-1];
 934
 935                 //Create processor worker threads.
 936                 for( int i=0; i<processors-1; i++ ){
 937                         //copy templateDb
 938                         //AlignmentDB* tempDB = new AlignmentDB(*templateDB);
 939
 940                         // Allocate memory for thread data.
 941                         string extension = "";
 942                         if (i != 0) { extension = toString(i) + ".temp"; }
 943
 944                         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);
 945                         pDataArray.push_back(tempalign);
 946                         processIDS.push_back(i);
 947
 948                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 949                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 950                         hThreadArray[i] = CreateThread(NULL, 0, MyAlignThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 951                 }
 952
 953                 //need to check for line ending error
 954                 ifstream inFASTA;
 955                 m->openInputFile(filename, inFASTA);
 956                 inFASTA.seekg(lines[processors-1]->start-1);
 957                 char c = inFASTA.peek();
 958
 959                 if (c != '>') { //we need to move back
 960                         lines[processors-1]->start--;
 961                 }
 962
 963                 //using the main process as a worker saves time and memory
 964                 //do my part - do last piece because windows is looking for eof
 965                 num = driver(lines[processors-1], (alignFileName + toString(processors-1) + ".temp"), (reportFileName + toString(processors-1) + ".temp"), (accnosFName + toString(processors-1) + ".temp"), filename);
 966
 967                 //Wait until all threads have terminated.
 968                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 969
 970                 //Close all thread handles and free memory allocations.
 971                 for(int i=0; i < pDataArray.size(); i++){
 972                         num += pDataArray[i]->count;
 973                         CloseHandle(hThreadArray[i]);
 974                         delete pDataArray[i];
 975                 }
 976
 977                 vector<string> nonBlankAccnosFiles;
 978                 if (!(m->isBlank(accnosFName))) { nonBlankAccnosFiles.push_back(accnosFName); }
 979                 else { m->mothurRemove(accnosFName); } //remove so other files can be renamed to it
 980
 981                 for (int i = 1; i < processors; i++) {
 982                         m->appendFiles((alignFileName + toString(i) + ".temp"), alignFileName);
 983                         m->mothurRemove((alignFileName + toString(i) + ".temp"));
 984
 985                         appendReportFiles((reportFileName + toString(i) + ".temp"), reportFileName);
 986                         m->mothurRemove((reportFileName + toString(i) + ".temp"));
 987
 988                         if (!(m->isBlank(accnosFName + toString(i) + ".temp"))) {
 989                                 nonBlankAccnosFiles.push_back(accnosFName + toString(i) + ".temp");
 990                         }else { m->mothurRemove((accnosFName + toString(i) + ".temp"));  }
 991                 }
 992
 993                 //append accnos files
 994                 if (nonBlankAccnosFiles.size() != 0) {
 995                         rename(nonBlankAccnosFiles[0].c_str(), accnosFName.c_str());
 996
 997                         for (int h=1; h < nonBlankAccnosFiles.size(); h++) {
 998                                 m->appendFiles(nonBlankAccnosFiles[h], accnosFName);
 999                                 m->mothurRemove(nonBlankAccnosFiles[h]);
1000                         }
1001                 }else { //recreate the accnosfile if needed
1002                         ofstream out;
1003                         m->openOutputFile(accnosFName, out);
1004                         out.close();
1005                 }
1006 #endif
1007
1008                 return num;
1009         }
1010         catch(exception& e) {
1011                 m->errorOut(e, "AlignCommand", "createProcesses");
1012                 exit(1);
1013         }
1014 }
1015 //**********************************************************************************************************************
1016
1017 void AlignCommand::appendReportFiles(string temp, string filename) {
1018         try{
1019
1020                 ofstream output;
1021                 ifstream input;
1022                 m->openOutputFileAppend(filename, output);
1023                 m->openInputFile(temp, input);
1024
1025                 while (!input.eof())    {       char c = input.get(); if (c == 10 || c == 13){  break;  }       } // get header line
1026
1027         char buffer[4096];
1028         while (!input.eof()) {
1029             input.read(buffer, 4096);
1030             output.write(buffer, input.gcount());
1031         }
1032
1033                 input.close();
1034                 output.close();
1035         }
1036         catch(exception& e) {
1037                 m->errorOut(e, "AlignCommand", "appendReportFiles");
1038                 exit(1);
1039         }
1040 }
1041 //**********************************************************************************************************************