screenseqscommand.cpp

   1 /*
   2  *  screenseqscommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Pat Schloss on 6/3/09.
   6  *  Copyright 2009 Patrick D. Schloss. All rights reserved.
   7  *
   8  */
   9
  10 #include "screenseqscommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14 vector<string> ScreenSeqsCommand::setParameters(){
  15         try {
  16                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  18                 CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup);
  19                 CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pqfile);
  20                 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(palignreport);
  21                 CommandParameter ptax("taxonomy", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(ptax);
  22                 CommandParameter pstart("start", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pstart);
  23                 CommandParameter pend("end", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pend);
  24                 CommandParameter pmaxambig("maxambig", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxambig);
  25                 CommandParameter pmaxhomop("maxhomop", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxhomop);
  26                 CommandParameter pminlength("minlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pminlength);
  27                 CommandParameter pmaxlength("maxlength", "Number", "", "-1", "", "", "",false,false); parameters.push_back(pmaxlength);
  28                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  29                 CommandParameter pcriteria("criteria", "Number", "", "90", "", "", "",false,false); parameters.push_back(pcriteria);
  30                 CommandParameter poptimize("optimize", "Multiple", "none-start-end-maxambig-maxhomop-minlength-maxlength", "none", "", "", "",true,false); parameters.push_back(poptimize);
  31                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  32                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  33
  34                 vector<string> myArray;
  35                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  36                 return myArray;
  37         }
  38         catch(exception& e) {
  39                 m->errorOut(e, "ScreenSeqsCommand", "setParameters");
  40                 exit(1);
  41         }
  42 }
  43 //**********************************************************************************************************************
  44 string ScreenSeqsCommand::getHelpString(){
  45         try {
  46                 string helpString = "";
  47                 helpString += "The screen.seqs command reads a fastafile and creates .....\n";
  48                 helpString += "The screen.seqs command parameters are fasta, start, end, maxambig, maxhomop, minlength, maxlength, name, group, qfile, alignreport, taxonomy, optimize, criteria and processors.\n";
  49                 helpString += "The fasta parameter is required.\n";
  50                 helpString += "The alignreport and taxonomy parameters allow you to remove bad seqs from taxonomy and alignreport files.\n";
  51                 helpString += "The start parameter .... The default is -1.\n";
  52                 helpString += "The end parameter .... The default is -1.\n";
  53                 helpString += "The maxambig parameter allows you to set the maximum number of ambigious bases allowed. The default is -1.\n";
  54                 helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
  55                 helpString += "The minlength parameter allows you to set and minimum sequence length. \n";
  56                 helpString += "The maxlength parameter allows you to set and maximum sequence length. \n";
  57                 helpString += "The processors parameter allows you to specify the number of processors to use while running the command. The default is 1.\n";
  58                 helpString += "The optimize and criteria parameters allow you set the start, end, maxabig, maxhomop, minlength and maxlength parameters relative to your set of sequences .\n";
  59                 helpString += "For example optimize=start-end, criteria=90, would set the start and end values to the position 90% of your sequences started and ended.\n";
  60                 helpString += "The name parameter allows you to provide a namesfile, and the group parameter allows you to provide a groupfile.\n";
  61                 helpString += "The screen.seqs command should be in the following format: \n";
  62                 helpString += "screen.seqs(fasta=yourFastaFile, name=youNameFile, group=yourGroupFIle, start=yourStart, end=yourEnd, maxambig=yourMaxambig,  \n";
  63                 helpString += "maxhomop=yourMaxhomop, minlength=youMinlength, maxlength=yourMaxlength)  \n";
  64                 helpString += "Example screen.seqs(fasta=abrecovery.fasta, name=abrecovery.names, group=abrecovery.groups, start=..., end=..., maxambig=..., maxhomop=..., minlength=..., maxlength=...).\n";
  65                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
  66                 return helpString;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "ScreenSeqsCommand", "getHelpString");
  70                 exit(1);
  71         }
  72 }
  73 //**********************************************************************************************************************
  74 ScreenSeqsCommand::ScreenSeqsCommand(){
  75         try {
  76                 abort = true; calledHelp = true;
  77                 setParameters();
  78                 vector<string> tempOutNames;
  79                 outputTypes["fasta"] = tempOutNames;
  80                 outputTypes["name"] = tempOutNames;
  81                 outputTypes["group"] = tempOutNames;
  82                 outputTypes["alignreport"] = tempOutNames;
  83                 outputTypes["accnos"] = tempOutNames;
  84                 outputTypes["qfile"] = tempOutNames;
  85                 outputTypes["taxonomy"] = tempOutNames;
  86         }
  87         catch(exception& e) {
  88                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
  89                 exit(1);
  90         }
  91 }
  92 //***************************************************************************************************************
  93
  94 ScreenSeqsCommand::ScreenSeqsCommand(string option)  {
  95         try {
  96                 abort = false; calledHelp = false;
  97
  98                 //allow user to run help
  99                 if(option == "help") { help(); abort = true; calledHelp = true; }
 100                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 101
 102                 else {
 103                         vector<string> myArray = setParameters();
 104
 105                         OptionParser parser(option);
 106                         map<string,string> parameters = parser.getParameters();
 107
 108                         ValidParameters validParameter("screen.seqs");
 109                         map<string,string>::iterator it;
 110
 111                         //check to make sure all parameters are valid for command
 112                         for (it = parameters.begin(); it != parameters.end(); it++) {
 113                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 114                         }
 115
 116                         //initialize outputTypes
 117                         vector<string> tempOutNames;
 118                         outputTypes["fasta"] = tempOutNames;
 119                         outputTypes["name"] = tempOutNames;
 120                         outputTypes["group"] = tempOutNames;
 121                         outputTypes["alignreport"] = tempOutNames;
 122                         outputTypes["accnos"] = tempOutNames;
 123                         outputTypes["qfile"] = tempOutNames;
 124                         outputTypes["taxonomy"] = tempOutNames;
 125
 126                         //if the user changes the input directory command factory will send this info to us in the output parameter
 127                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 128                         if (inputDir == "not found"){   inputDir = "";          }
 129                         else {
 130                                 string path;
 131                                 it = parameters.find("fasta");
 132                                 //user has given a template file
 133                                 if(it != parameters.end()){
 134                                         path = m->hasPath(it->second);
 135                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                         if (path == "") {       parameters["fasta"] = inputDir + it->second;            }
 137                                 }
 138
 139                                 it = parameters.find("group");
 140                                 //user has given a template file
 141                                 if(it != parameters.end()){
 142                                         path = m->hasPath(it->second);
 143                                         //if the user has not given a path then, add inputdir. else leave path alone.
 144                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
 145                                 }
 146
 147                                 it = parameters.find("name");
 148                                 //user has given a template file
 149                                 if(it != parameters.end()){
 150                                         path = m->hasPath(it->second);
 151                                         //if the user has not given a path then, add inputdir. else leave path alone.
 152                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 153                                 }
 154
 155                                 it = parameters.find("alignreport");
 156                                 //user has given a template file
 157                                 if(it != parameters.end()){
 158                                         path = m->hasPath(it->second);
 159                                         //if the user has not given a path then, add inputdir. else leave path alone.
 160                                         if (path == "") {       parameters["alignreport"] = inputDir + it->second;              }
 161                                 }
 162
 163                                 it = parameters.find("qfile");
 164                                 //user has given a template file
 165                                 if(it != parameters.end()){
 166                                         path = m->hasPath(it->second);
 167                                         //if the user has not given a path then, add inputdir. else leave path alone.
 168                                         if (path == "") {       parameters["qfile"] = inputDir + it->second;            }
 169                                 }
 170
 171                                 it = parameters.find("taxonomy");
 172                                 //user has given a template file
 173                                 if(it != parameters.end()){
 174                                         path = m->hasPath(it->second);
 175                                         //if the user has not given a path then, add inputdir. else leave path alone.
 176                                         if (path == "") {       parameters["taxonomy"] = inputDir + it->second;         }
 177                                 }
 178                         }
 179
 180                         //check for required parameters
 181                         fastafile = validParameter.validFile(parameters, "fasta", true);
 182                         if (fastafile == "not found") {
 183                                 fastafile = m->getFastaFile();
 184                                 if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 185                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 186                         }
 187                         else if (fastafile == "not open") { abort = true; }
 188                         else { m->setFastaFile(fastafile); }
 189
 190                         groupfile = validParameter.validFile(parameters, "group", true);
 191                         if (groupfile == "not open") { abort = true; }
 192                         else if (groupfile == "not found") { groupfile = ""; }
 193                         else { m->setGroupFile(groupfile); }
 194
 195                         qualfile = validParameter.validFile(parameters, "qfile", true);
 196                         if (qualfile == "not open") { abort = true; }
 197                         else if (qualfile == "not found") { qualfile = ""; }
 198                         else { m->setQualFile(qualfile); }
 199
 200                         namefile = validParameter.validFile(parameters, "name", true);
 201                         if (namefile == "not open") { namefile = ""; abort = true; }
 202                         else if (namefile == "not found") { namefile = ""; }
 203                         else { m->setNameFile(namefile); }
 204
 205                         alignreport = validParameter.validFile(parameters, "alignreport", true);
 206                         if (alignreport == "not open") { abort = true; }
 207                         else if (alignreport == "not found") { alignreport = ""; }
 208
 209                         taxonomy = validParameter.validFile(parameters, "taxonomy", true);
 210                         if (taxonomy == "not open") { abort = true; }
 211                         else if (taxonomy == "not found") { taxonomy = ""; }
 212
 213                         //if the user changes the output directory command factory will send this info to us in the output parameter
 214                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
 215                                 outputDir = "";
 216                                 outputDir += m->hasPath(fastafile); //if user entered a file with a path then preserve it
 217                         }
 218
 219                         //check for optional parameter and set defaults
 220                         // ...at some point should added some additional type checking...
 221                         string temp;
 222                         temp = validParameter.validFile(parameters, "start", false);            if (temp == "not found") { temp = "-1"; }
 223                         m->mothurConvert(temp, startPos);
 224
 225                         temp = validParameter.validFile(parameters, "end", false);                      if (temp == "not found") { temp = "-1"; }
 226                         m->mothurConvert(temp, endPos);
 227
 228                         temp = validParameter.validFile(parameters, "maxambig", false);         if (temp == "not found") { temp = "-1"; }
 229                         m->mothurConvert(temp, maxAmbig);
 230
 231                         temp = validParameter.validFile(parameters, "maxhomop", false);         if (temp == "not found") { temp = "-1"; }
 232                         m->mothurConvert(temp, maxHomoP);
 233
 234                         temp = validParameter.validFile(parameters, "minlength", false);        if (temp == "not found") { temp = "-1"; }
 235                         m->mothurConvert(temp, minLength);
 236
 237                         temp = validParameter.validFile(parameters, "maxlength", false);        if (temp == "not found") { temp = "-1"; }
 238                         m->mothurConvert(temp, maxLength);
 239
 240                         temp = validParameter.validFile(parameters, "processors", false);       if (temp == "not found"){       temp = m->getProcessors();      }
 241                         m->setProcessors(temp);
 242                         m->mothurConvert(temp, processors);
 243
 244                         temp = validParameter.validFile(parameters, "optimize", false); //optimizing trumps the optimized values original value
 245                         if (temp == "not found"){       temp = "none";          }
 246                         m->splitAtDash(temp, optimize);
 247
 248                         //check for invalid optimize options
 249                         set<string> validOptimizers;
 250                         validOptimizers.insert("none"); validOptimizers.insert("start"); validOptimizers.insert("end"); validOptimizers.insert("maxambig"); validOptimizers.insert("maxhomop"); validOptimizers.insert("minlength"); validOptimizers.insert("maxlength");
 251                         for (int i = 0; i < optimize.size(); i++) {
 252                                 if (validOptimizers.count(optimize[i]) == 0) {
 253                                         m->mothurOut(optimize[i] + " is not a valid optimizer. Valid options are start, end, maxambig, maxhomop, minlength and maxlength."); m->mothurOutEndLine();
 254                                         optimize.erase(optimize.begin()+i);
 255                                         i--;
 256                                 }
 257                         }
 258
 259                         if (optimize.size() == 1) { if (optimize[0] == "none") { optimize.clear(); } }
 260
 261                         temp = validParameter.validFile(parameters, "criteria", false); if (temp == "not found"){       temp = "90";                            }
 262                         m->mothurConvert(temp, criteria);
 263
 264                         if (namefile == "") {
 265                                 vector<string> files; files.push_back(fastafile);
 266                                 parser.getNameFile(files);
 267                         }
 268                 }
 269
 270         }
 271         catch(exception& e) {
 272                 m->errorOut(e, "ScreenSeqsCommand", "ScreenSeqsCommand");
 273                 exit(1);
 274         }
 275 }
 276 //***************************************************************************************************************
 277
 278 int ScreenSeqsCommand::execute(){
 279         try{
 280
 281                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 282
 283                 //if the user want to optimize we need to know the 90% mark
 284                 vector<unsigned long long> positions;
 285                 if (optimize.size() != 0) {  //get summary is paralellized so we need to divideFile, no need to do this step twice so I moved it here
 286                         //use the namefile to optimize correctly
 287                         if (namefile != "") { nameMap = m->readNames(namefile); }
 288                         getSummary(positions);
 289                 }
 290                 else {
 291                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 292                 positions = m->divideFile(fastafile, processors);
 293                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
 294                         #else
 295                 if(processors == 1){ lines.push_back(linePair(0, 1000));  }
 296                 else {
 297                     int numFastaSeqs = 0;
 298                     positions = m->setFilePosFasta(fastafile, numFastaSeqs);
 299
 300                     //figure out how many sequences you have to process
 301                     int numSeqsPerProcessor = numFastaSeqs / processors;
 302                     for (int i = 0; i < processors; i++) {
 303                         int startIndex =  i * numSeqsPerProcessor;
 304                         if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 305                         lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 306                     }
 307                 }
 308                         #endif
 309                 }
 310
 311                 string goodSeqFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "good" + m->getExtension(fastafile);
 312                 string badAccnosFile =  outputDir + m->getRootName(m->getSimpleName(fastafile)) + "bad.accnos";
 313
 314                 int numFastaSeqs = 0;
 315                 set<string> badSeqNames;
 316                 int start = time(NULL);
 317
 318 #ifdef USE_MPI
 319                         int pid, numSeqsPerProcessor;
 320                         int tag = 2001;
 321                         vector<unsigned long long> MPIPos;
 322
 323                         MPI_Status status;
 324                         MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 325                         MPI_Comm_size(MPI_COMM_WORLD, &processors);
 326
 327                         MPI_File inMPI;
 328                         MPI_File outMPIGood;
 329                         MPI_File outMPIBadAccnos;
 330
 331                         int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 332                         int inMode=MPI_MODE_RDONLY;
 333
 334                         char outGoodFilename[1024];
 335                         strcpy(outGoodFilename, goodSeqFile.c_str());
 336
 337                         char outBadAccnosFilename[1024];
 338                         strcpy(outBadAccnosFilename, badAccnosFile.c_str());
 339
 340                         char inFileName[1024];
 341                         strcpy(inFileName, fastafile.c_str());
 342
 343                         MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 344                         MPI_File_open(MPI_COMM_WORLD, outGoodFilename, outMode, MPI_INFO_NULL, &outMPIGood);
 345                         MPI_File_open(MPI_COMM_WORLD, outBadAccnosFilename, outMode, MPI_INFO_NULL, &outMPIBadAccnos);
 346
 347                         if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood); MPI_File_close(&outMPIBadAccnos); return 0; }
 348
 349                         if (pid == 0) { //you are the root process
 350
 351                                 MPIPos = m->setFilePosFasta(fastafile, numFastaSeqs); //fills MPIPos, returns numSeqs
 352
 353                                 //send file positions to all processes
 354                                 for(int i = 1; i < processors; i++) {
 355                                         MPI_Send(&numFastaSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 356                                         MPI_Send(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 357                                 }
 358
 359                                 //figure out how many sequences you have to align
 360                                 numSeqsPerProcessor = numFastaSeqs / processors;
 361                                 int startIndex =  pid * numSeqsPerProcessor;
 362                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 363
 364                                 //align your part
 365                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 366
 367                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos);  return 0; }
 368
 369                                 for (int i = 1; i < processors; i++) {
 370                                         //get bad lists
 371                                         int badSize;
 372                                         MPI_Recv(&badSize, 1, MPI_INT, i, tag, MPI_COMM_WORLD, &status);
 373                                 }
 374                         }else{ //you are a child process
 375                                 MPI_Recv(&numFastaSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 376                                 MPIPos.resize(numFastaSeqs+1);
 377                                 MPI_Recv(&MPIPos[0], (numFastaSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 378
 379                                 //figure out how many sequences you have to align
 380                                 numSeqsPerProcessor = numFastaSeqs / processors;
 381                                 int startIndex =  pid * numSeqsPerProcessor;
 382                                 if(pid == (processors - 1)){    numSeqsPerProcessor = numFastaSeqs - pid * numSeqsPerProcessor;         }
 383
 384                                 //align your part
 385                                 driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPIGood, outMPIBadAccnos, MPIPos, badSeqNames);
 386
 387                                 if (m->control_pressed) { MPI_File_close(&inMPI);  MPI_File_close(&outMPIGood);  MPI_File_close(&outMPIBadAccnos); return 0; }
 388
 389                                 //send bad list
 390                                 int badSize = badSeqNames.size();
 391                                 MPI_Send(&badSize, 1, MPI_INT, 0, tag, MPI_COMM_WORLD);
 392                         }
 393
 394                         //close files
 395                         MPI_File_close(&inMPI);
 396                         MPI_File_close(&outMPIGood);
 397                         MPI_File_close(&outMPIBadAccnos);
 398                         MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 399
 400 #else
 401
 402         //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 403                         if(processors == 1){
 404                                 numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 405                         }else{
 406                                 numFastaSeqs = createProcesses(goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 407             }
 408         //#else
 409         //              numFastaSeqs = driver(lines[0], goodSeqFile, badAccnosFile, fastafile, badSeqNames);
 410         //#endif
 411             if (m->control_pressed) { m->mothurRemove(goodSeqFile); return 0; }
 412 #endif
 413
 414                 #ifdef USE_MPI
 415                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 416
 417                         if (pid == 0) { //only one process should fix files
 418
 419                                 //read accnos file with all names in it, process 0 just has its names
 420                                 MPI_File inMPIAccnos;
 421                                 MPI_Offset size;
 422
 423                                 char inFileName[1024];
 424                                 strcpy(inFileName, badAccnosFile.c_str());
 425
 426                                 MPI_File_open(MPI_COMM_SELF, inFileName, inMode, MPI_INFO_NULL, &inMPIAccnos);  //comm, filename, mode, info, filepointer
 427                                 MPI_File_get_size(inMPIAccnos, &size);
 428
 429                                 char* buffer = new char[size];
 430                                 MPI_File_read(inMPIAccnos, buffer, size, MPI_CHAR, &status);
 431
 432                                 string tempBuf = buffer;
 433                                 if (tempBuf.length() > size) { tempBuf = tempBuf.substr(0, size);  }
 434                                 istringstream iss (tempBuf,istringstream::in);
 435
 436                                 delete buffer;
 437                                 MPI_File_close(&inMPIAccnos);
 438
 439                                 badSeqNames.clear();
 440                                 string tempName;
 441                                 while (!iss.eof()) {
 442                                         iss >> tempName; m->gobble(iss);
 443                                         badSeqNames.insert(tempName);
 444                                 }
 445                 #endif
 446
 447                 if(namefile != "" && groupfile != "")   {
 448                         screenNameGroupFile(badSeqNames);
 449                         if (m->control_pressed) {  m->mothurRemove(goodSeqFile); return 0; }
 450                 }else if(namefile != "")        {
 451                         screenNameGroupFile(badSeqNames);
 452                         if (m->control_pressed) {  m->mothurRemove(goodSeqFile);  return 0; }
 453                 }else if(groupfile != "")                               {       screenGroupFile(badSeqNames);           }       // this screens just the group
 454
 455                 if (m->control_pressed) { m->mothurRemove(goodSeqFile);  return 0; }
 456
 457                 if(alignreport != "")                                   {       screenAlignReport(badSeqNames);         }
 458                 if(qualfile != "")                                              {       screenQual(badSeqNames);                        }
 459                 if(taxonomy != "")                                              {       screenTaxonomy(badSeqNames);            }
 460
 461                 if (m->control_pressed) { m->mothurRemove(goodSeqFile);  return 0; }
 462
 463                 #ifdef USE_MPI
 464                         }
 465                 #endif
 466
 467                 m->mothurOutEndLine();
 468                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 469                 m->mothurOut(goodSeqFile); m->mothurOutEndLine();       outputTypes["fasta"].push_back(goodSeqFile);
 470                 m->mothurOut(badAccnosFile); m->mothurOutEndLine();      outputTypes["accnos"].push_back(badAccnosFile);
 471                 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
 472                 m->mothurOutEndLine();
 473                 m->mothurOutEndLine();
 474
 475                 //set fasta file as new current fastafile
 476                 string current = "";
 477                 itTypes = outputTypes.find("fasta");
 478                 if (itTypes != outputTypes.end()) {
 479                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 480                 }
 481
 482                 itTypes = outputTypes.find("name");
 483                 if (itTypes != outputTypes.end()) {
 484                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
 485                 }
 486
 487                 itTypes = outputTypes.find("group");
 488                 if (itTypes != outputTypes.end()) {
 489                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
 490                 }
 491
 492                 itTypes = outputTypes.find("qfile");
 493                 if (itTypes != outputTypes.end()) {
 494                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 495                 }
 496
 497                 itTypes = outputTypes.find("taxonomy");
 498                 if (itTypes != outputTypes.end()) {
 499                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
 500                 }
 501
 502                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to screen " + toString(numFastaSeqs) + " sequences.");
 503                 m->mothurOutEndLine();
 504
 505                 return 0;
 506         }
 507         catch(exception& e) {
 508                 m->errorOut(e, "ScreenSeqsCommand", "execute");
 509                 exit(1);
 510         }
 511 }
 512
 513 //***************************************************************************************************************
 514
 515 int ScreenSeqsCommand::screenNameGroupFile(set<string> badSeqNames){
 516         try {
 517                 ifstream inputNames;
 518                 m->openInputFile(namefile, inputNames);
 519                 set<string> badSeqGroups;
 520                 string seqName, seqList, group;
 521                 set<string>::iterator it;
 522
 523                 string goodNameFile = outputDir + m->getRootName(m->getSimpleName(namefile)) + "good" + m->getExtension(namefile);
 524                 outputNames.push_back(goodNameFile);  outputTypes["name"].push_back(goodNameFile);
 525
 526                 ofstream goodNameOut;   m->openOutputFile(goodNameFile, goodNameOut);
 527
 528                 while(!inputNames.eof()){
 529                         if (m->control_pressed) { goodNameOut.close();  inputNames.close(); m->mothurRemove(goodNameFile);  return 0; }
 530
 531                         inputNames >> seqName >> seqList;
 532                         it = badSeqNames.find(seqName);
 533
 534                         if(it != badSeqNames.end()){
 535                                 badSeqNames.erase(it);
 536
 537                                 if(namefile != ""){
 538                                         int start = 0;
 539                                         for(int i=0;i<seqList.length();i++){
 540                                                 if(seqList[i] == ','){
 541                                                         badSeqGroups.insert(seqList.substr(start,i-start));
 542                                                         start = i+1;
 543                                                 }
 544                                         }
 545                                         badSeqGroups.insert(seqList.substr(start,seqList.length()-start));
 546                                 }
 547                         }
 548                         else{
 549                                 goodNameOut << seqName << '\t' << seqList << endl;
 550                         }
 551                         m->gobble(inputNames);
 552                 }
 553                 inputNames.close();
 554                 goodNameOut.close();
 555
 556                 //we were unable to remove some of the bad sequences
 557                 if (badSeqNames.size() != 0) {
 558                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 559                                 m->mothurOut("Your namefile does not include the sequence " + *it + " please correct.");
 560                                 m->mothurOutEndLine();
 561                         }
 562                 }
 563
 564                 if(groupfile != ""){
 565
 566                         ifstream inputGroups;
 567                         m->openInputFile(groupfile, inputGroups);
 568
 569                         string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 570                         outputNames.push_back(goodGroupFile);   outputTypes["group"].push_back(goodGroupFile);
 571
 572                         ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 573
 574                         while(!inputGroups.eof()){
 575                                 if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodNameFile);  m->mothurRemove(goodGroupFile); return 0; }
 576
 577                                 inputGroups >> seqName >> group;
 578
 579                                 it = badSeqGroups.find(seqName);
 580
 581                                 if(it != badSeqGroups.end()){
 582                                         badSeqGroups.erase(it);
 583                                 }
 584                                 else{
 585                                         goodGroupOut << seqName << '\t' << group << endl;
 586                                 }
 587                                 m->gobble(inputGroups);
 588                         }
 589                         inputGroups.close();
 590                         goodGroupOut.close();
 591
 592                         //we were unable to remove some of the bad sequences
 593                         if (badSeqGroups.size() != 0) {
 594                                 for (it = badSeqGroups.begin(); it != badSeqGroups.end(); it++) {
 595                                         m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 596                                         m->mothurOutEndLine();
 597                                 }
 598                         }
 599                 }
 600
 601
 602                 return 0;
 603
 604         }
 605         catch(exception& e) {
 606                 m->errorOut(e, "ScreenSeqsCommand", "screenNameGroupFile");
 607                 exit(1);
 608         }
 609 }
 610 //***************************************************************************************************************
 611 int ScreenSeqsCommand::getSummary(vector<unsigned long long>& positions){
 612         try {
 613
 614                 vector<int> startPosition;
 615                 vector<int> endPosition;
 616                 vector<int> seqLength;
 617                 vector<int> ambigBases;
 618                 vector<int> longHomoPolymer;
 619
 620         vector<unsigned long long> positions;
 621 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 622                 positions = m->divideFile(fastafile, processors);
 623                 for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
 624 #else
 625                 if(processors == 1){ lines.push_back(linePair(0, 1000));  }
 626         else {
 627             int numFastaSeqs = 0;
 628             positions = m->setFilePosFasta(fastafile, numFastaSeqs);
 629
 630             //figure out how many sequences you have to process
 631             int numSeqsPerProcessor = numFastaSeqs / processors;
 632             for (int i = 0; i < processors; i++) {
 633                 int startIndex =  i * numSeqsPerProcessor;
 634                 if(i == (processors - 1)){      numSeqsPerProcessor = numFastaSeqs - i * numSeqsPerProcessor;   }
 635                 lines.push_back(linePair(positions[startIndex], numSeqsPerProcessor));
 636             }
 637         }
 638 #endif
 639
 640 #ifdef USE_MPI
 641                 int pid;
 642                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 643
 644                 if (pid == 0) {
 645                         driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 646 #else
 647                 int numSeqs = 0;
 648                 //#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 649                         if(processors == 1){
 650                                 numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 651                         }else{
 652                                 numSeqs = createProcessesCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile);
 653                         }
 654
 655                         if (m->control_pressed) {  return 0; }
 656                 //#else
 657                 //      numSeqs = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 658                 //      if (m->control_pressed) {  return 0; }
 659                 //#endif
 660 #endif
 661                 sort(startPosition.begin(), startPosition.end());
 662                 sort(endPosition.begin(), endPosition.end());
 663                 sort(seqLength.begin(), seqLength.end());
 664                 sort(ambigBases.begin(), ambigBases.end());
 665                 sort(longHomoPolymer.begin(), longHomoPolymer.end());
 666
 667                 //numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
 668                 int criteriaPercentile  = int(startPosition.size() * (criteria / (float) 100));
 669
 670                 for (int i = 0; i < optimize.size(); i++) {
 671                         if (optimize[i] == "start") { startPos = startPosition[criteriaPercentile]; m->mothurOut("Optimizing start to " + toString(startPos) + "."); m->mothurOutEndLine(); }
 672                         else if (optimize[i] == "end") { int endcriteriaPercentile = int(endPosition.size() * ((100 - criteria) / (float) 100));  endPos = endPosition[endcriteriaPercentile]; m->mothurOut("Optimizing end to " + toString(endPos) + "."); m->mothurOutEndLine();}
 673                         else if (optimize[i] == "maxambig") { maxAmbig = ambigBases[criteriaPercentile]; m->mothurOut("Optimizing maxambig to " + toString(maxAmbig) + "."); m->mothurOutEndLine(); }
 674                         else if (optimize[i] == "maxhomop") { maxHomoP = longHomoPolymer[criteriaPercentile]; m->mothurOut("Optimizing maxhomop to " + toString(maxHomoP) + "."); m->mothurOutEndLine(); }
 675                         else if (optimize[i] == "minlength") { int mincriteriaPercentile = int(seqLength.size() * ((100 - criteria) / (float) 100)); minLength = seqLength[mincriteriaPercentile]; m->mothurOut("Optimizing minlength to " + toString(minLength) + "."); m->mothurOutEndLine(); }
 676                         else if (optimize[i] == "maxlength") { maxLength = seqLength[criteriaPercentile]; m->mothurOut("Optimizing maxlength to " + toString(maxLength) + "."); m->mothurOutEndLine(); }
 677                 }
 678
 679 #ifdef USE_MPI
 680                 }
 681
 682                 MPI_Status status;
 683                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 684                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 685
 686                 if (pid == 0) {
 687                         //send file positions to all processes
 688                         for(int i = 1; i < processors; i++) {
 689                                 MPI_Send(&startPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 690                                 MPI_Send(&endPos, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 691                                 MPI_Send(&maxAmbig, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 692                                 MPI_Send(&maxHomoP, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 693                                 MPI_Send(&minLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 694                                 MPI_Send(&maxLength, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 695                         }
 696                 }else {
 697                         MPI_Recv(&startPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 698                         MPI_Recv(&endPos, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 699                         MPI_Recv(&maxAmbig, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 700                         MPI_Recv(&maxHomoP, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 701                         MPI_Recv(&minLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 702                         MPI_Recv(&maxLength, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 703                 }
 704                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 705 #endif
 706                 return 0;
 707         }
 708         catch(exception& e) {
 709                 m->errorOut(e, "ScreenSeqsCommand", "getSummary");
 710                 exit(1);
 711         }
 712 }
 713 /**************************************************************************************/
 714 int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename, linePair filePos) {
 715         try {
 716
 717                 ifstream in;
 718                 m->openInputFile(filename, in);
 719
 720                 in.seekg(filePos.start);
 721
 722                 bool done = false;
 723                 int count = 0;
 724
 725                 while (!done) {
 726
 727                         if (m->control_pressed) { in.close(); return 1; }
 728
 729                         Sequence current(in); m->gobble(in);
 730
 731                         if (current.getName() != "") {
 732                                 int num = 1;
 733                                 if (namefile != "") {
 734                                         //make sure this sequence is in the namefile, else error
 735                                         map<string, int>::iterator it = nameMap.find(current.getName());
 736
 737                                         if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 738                                         else { num = it->second; }
 739                                 }
 740
 741                                 //for each sequence this sequence represents
 742                                 for (int i = 0; i < num; i++) {
 743                                         startPosition.push_back(current.getStartPos());
 744                                         endPosition.push_back(current.getEndPos());
 745                                         seqLength.push_back(current.getNumBases());
 746                                         ambigBases.push_back(current.getAmbigBases());
 747                                         longHomoPolymer.push_back(current.getLongHomoPolymer());
 748                                 }
 749
 750                                 count++;
 751                         }
 752                         //if((count) % 100 == 0){       m->mothurOut("Optimizing sequence: " + toString(count)); m->mothurOutEndLine();         }
 753                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 754                                 unsigned long long pos = in.tellg();
 755                                 if ((pos == -1) || (pos >= filePos.end)) { break; }
 756                         #else
 757                                 if (in.eof()) { break; }
 758                         #endif
 759
 760                 }
 761
 762                 in.close();
 763
 764                 return count;
 765         }
 766         catch(exception& e) {
 767                 m->errorOut(e, "ScreenSeqsCommand", "driverCreateSummary");
 768                 exit(1);
 769         }
 770 }
 771 /**************************************************************************************************/
 772 int ScreenSeqsCommand::createProcessesCreateSummary(vector<int>& startPosition, vector<int>& endPosition, vector<int>& seqLength, vector<int>& ambigBases, vector<int>& longHomoPolymer, string filename) {
 773         try {
 774
 775         int process = 1;
 776                 int num = 0;
 777                 vector<int> processIDS;
 778
 779 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 780
 781                 //loop through and create all the processes you want
 782                 while (process != processors) {
 783                         int pid = fork();
 784
 785                         if (pid > 0) {
 786                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 787                                 process++;
 788                         }else if (pid == 0){
 789                                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[process]);
 790
 791                                 //pass numSeqs to parent
 792                                 ofstream out;
 793                                 string tempFile = fastafile + toString(getpid()) + ".num.temp";
 794                                 m->openOutputFile(tempFile, out);
 795
 796                                 out << num << endl;
 797                                 out << startPosition.size() << endl;
 798                                 for (int k = 0; k < startPosition.size(); k++)          {               out << startPosition[k] << '\t'; }  out << endl;
 799                                 for (int k = 0; k < endPosition.size(); k++)            {               out << endPosition[k] << '\t'; }  out << endl;
 800                                 for (int k = 0; k < seqLength.size(); k++)                      {               out << seqLength[k] << '\t'; }  out << endl;
 801                                 for (int k = 0; k < ambigBases.size(); k++)                     {               out << ambigBases[k] << '\t'; }  out << endl;
 802                                 for (int k = 0; k < longHomoPolymer.size(); k++)        {               out << longHomoPolymer[k] << '\t'; }  out << endl;
 803
 804                                 out.close();
 805
 806                                 exit(0);
 807                         }else {
 808                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 809                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 810                                 exit(0);
 811                         }
 812                 }
 813
 814                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[0]);
 815
 816                 //force parent to wait until all the processes are done
 817                 for (int i=0;i<processIDS.size();i++) {
 818                         int temp = processIDS[i];
 819                         wait(&temp);
 820                 }
 821
 822                 //parent reads in and combine Filter info
 823                 for (int i = 0; i < processIDS.size(); i++) {
 824                         string tempFilename = fastafile + toString(processIDS[i]) + ".num.temp";
 825                         ifstream in;
 826                         m->openInputFile(tempFilename, in);
 827
 828                         int temp, tempNum;
 829                         in >> tempNum; m->gobble(in); num += tempNum;
 830                         in >> tempNum; m->gobble(in);
 831                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; startPosition.push_back(temp);              }               m->gobble(in);
 832                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; endPosition.push_back(temp);                }               m->gobble(in);
 833                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; seqLength.push_back(temp);                  }               m->gobble(in);
 834                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; ambigBases.push_back(temp);                 }               m->gobble(in);
 835                         for (int k = 0; k < tempNum; k++)                       {               in >> temp; longHomoPolymer.push_back(temp);    }               m->gobble(in);
 836
 837                         in.close();
 838                         m->mothurRemove(tempFilename);
 839                 }
 840
 841
 842 #else
 843         //////////////////////////////////////////////////////////////////////////////////////////////////////
 844                 //Windows version shared memory, so be careful when passing variables through the seqSumData struct.
 845                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
 846                 //Taking advantage of shared memory to allow both threads to add info to vectors.
 847                 //////////////////////////////////////////////////////////////////////////////////////////////////////
 848
 849                 vector<sumData*> pDataArray;
 850                 DWORD   dwThreadIdArray[processors-1];
 851                 HANDLE  hThreadArray[processors-1];
 852
 853                 //Create processor worker threads.
 854                 for( int i=0; i<processors-1; i++ ){
 855
 856                         // Allocate memory for thread data.
 857                         sumData* tempSum = new sumData(filename, m, lines[i].start, lines[i].end, namefile, nameMap);
 858                         pDataArray.push_back(tempSum);
 859
 860                         //MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
 861                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
 862                         hThreadArray[i] = CreateThread(NULL, 0, MySumThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
 863                 }
 864
 865         //do your part
 866                 num = driverCreateSummary(startPosition, endPosition, seqLength, ambigBases, longHomoPolymer, fastafile, lines[processors-1]);
 867
 868                 //Wait until all threads have terminated.
 869                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
 870
 871                 //Close all thread handles and free memory allocations.
 872                 for(int i=0; i < pDataArray.size(); i++){
 873                         num += pDataArray[i]->count;
 874             for (int k = 0; k < pDataArray[i]->startPosition.size(); k++) {     startPosition.push_back(pDataArray[i]->startPosition[k]);       }
 875                         for (int k = 0; k < pDataArray[i]->endPosition.size(); k++) {   endPosition.push_back(pDataArray[i]->endPosition[k]);       }
 876             for (int k = 0; k < pDataArray[i]->seqLength.size(); k++) { seqLength.push_back(pDataArray[i]->seqLength[k]);       }
 877             for (int k = 0; k < pDataArray[i]->ambigBases.size(); k++) {        ambigBases.push_back(pDataArray[i]->ambigBases[k]);       }
 878             for (int k = 0; k < pDataArray[i]->longHomoPolymer.size(); k++) {   longHomoPolymer.push_back(pDataArray[i]->longHomoPolymer[k]);       }
 879                         CloseHandle(hThreadArray[i]);
 880                         delete pDataArray[i];
 881                 }
 882
 883 #endif
 884         return num;
 885         }
 886         catch(exception& e) {
 887                 m->errorOut(e, "ScreenSeqsCommand", "createProcessesCreateSummary");
 888                 exit(1);
 889         }
 890 }
 891
 892 //***************************************************************************************************************
 893
 894 int ScreenSeqsCommand::screenGroupFile(set<string> badSeqNames){
 895         try {
 896                 ifstream inputGroups;
 897                 m->openInputFile(groupfile, inputGroups);
 898                 string seqName, group;
 899                 set<string>::iterator it;
 900
 901                 string goodGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "good" + m->getExtension(groupfile);
 902                 outputNames.push_back(goodGroupFile);  outputTypes["group"].push_back(goodGroupFile);
 903                 ofstream goodGroupOut;  m->openOutputFile(goodGroupFile, goodGroupOut);
 904
 905                 while(!inputGroups.eof()){
 906                         if (m->control_pressed) { goodGroupOut.close(); inputGroups.close(); m->mothurRemove(goodGroupFile); return 0; }
 907
 908                         inputGroups >> seqName >> group;
 909                         it = badSeqNames.find(seqName);
 910
 911                         if(it != badSeqNames.end()){
 912                                 badSeqNames.erase(it);
 913                         }
 914                         else{
 915                                 goodGroupOut << seqName << '\t' << group << endl;
 916                         }
 917                         m->gobble(inputGroups);
 918                 }
 919
 920                 if (m->control_pressed) { goodGroupOut.close();  inputGroups.close(); m->mothurRemove(goodGroupFile);  return 0; }
 921
 922                 //we were unable to remove some of the bad sequences
 923                 if (badSeqNames.size() != 0) {
 924                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 925                                 m->mothurOut("Your groupfile does not include the sequence " + *it + " please correct.");
 926                                 m->mothurOutEndLine();
 927                         }
 928                 }
 929
 930                 inputGroups.close();
 931                 goodGroupOut.close();
 932
 933                 if (m->control_pressed) { m->mothurRemove(goodGroupFile);   }
 934
 935                 return 0;
 936
 937         }
 938         catch(exception& e) {
 939                 m->errorOut(e, "ScreenSeqsCommand", "screenGroupFile");
 940                 exit(1);
 941         }
 942 }
 943
 944 //***************************************************************************************************************
 945
 946 int ScreenSeqsCommand::screenAlignReport(set<string> badSeqNames){
 947         try {
 948                 ifstream inputAlignReport;
 949                 m->openInputFile(alignreport, inputAlignReport);
 950                 string seqName, group;
 951                 set<string>::iterator it;
 952
 953                 string goodAlignReportFile = outputDir + m->getRootName(m->getSimpleName(alignreport)) + "good" + m->getExtension(alignreport);
 954                 outputNames.push_back(goodAlignReportFile);  outputTypes["alignreport"].push_back(goodAlignReportFile);
 955                 ofstream goodAlignReportOut;    m->openOutputFile(goodAlignReportFile, goodAlignReportOut);
 956
 957                 while (!inputAlignReport.eof()) {               //      need to copy header
 958                         char c = inputAlignReport.get();
 959                         goodAlignReportOut << c;
 960                         if (c == 10 || c == 13){        break;  }
 961                 }
 962
 963                 while(!inputAlignReport.eof()){
 964                         if (m->control_pressed) { goodAlignReportOut.close(); inputAlignReport.close(); m->mothurRemove(goodAlignReportFile); return 0; }
 965
 966                         inputAlignReport >> seqName;
 967                         it = badSeqNames.find(seqName);
 968                         string line;
 969                         while (!inputAlignReport.eof()) {               //      need to copy header
 970                                 char c = inputAlignReport.get();
 971                                 line += c;
 972                                 if (c == 10 || c == 13){        break;  }
 973                         }
 974
 975                         if(it != badSeqNames.end()){
 976                                 badSeqNames.erase(it);
 977                         }
 978                         else{
 979                                 goodAlignReportOut << seqName << '\t' << line;
 980                         }
 981                         m->gobble(inputAlignReport);
 982                 }
 983
 984                 if (m->control_pressed) { goodAlignReportOut.close();  inputAlignReport.close(); m->mothurRemove(goodAlignReportFile);  return 0; }
 985
 986                 //we were unable to remove some of the bad sequences
 987                 if (badSeqNames.size() != 0) {
 988                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
 989                                 m->mothurOut("Your alignreport file does not include the sequence " + *it + " please correct.");
 990                                 m->mothurOutEndLine();
 991                         }
 992                 }
 993
 994                 inputAlignReport.close();
 995                 goodAlignReportOut.close();
 996
 997                 if (m->control_pressed) {  m->mothurRemove(goodAlignReportFile);  return 0; }
 998
 999                 return 0;
1000
1001         }
1002         catch(exception& e) {
1003                 m->errorOut(e, "ScreenSeqsCommand", "screenAlignReport");
1004                 exit(1);
1005         }
1006
1007 }
1008 //***************************************************************************************************************
1009
1010 int ScreenSeqsCommand::screenTaxonomy(set<string> badSeqNames){
1011         try {
1012                 ifstream input;
1013                 m->openInputFile(taxonomy, input);
1014                 string seqName, tax;
1015                 set<string>::iterator it;
1016
1017                 string goodTaxFile = outputDir + m->getRootName(m->getSimpleName(taxonomy)) + "good" + m->getExtension(taxonomy);
1018                 outputNames.push_back(goodTaxFile);  outputTypes["taxonomy"].push_back(goodTaxFile);
1019                 ofstream goodTaxOut;    m->openOutputFile(goodTaxFile, goodTaxOut);
1020
1021                 while(!input.eof()){
1022                         if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
1023
1024                         input >> seqName >> tax;
1025                         it = badSeqNames.find(seqName);
1026
1027                         if(it != badSeqNames.end()){ badSeqNames.erase(it); }
1028                         else{
1029                                 goodTaxOut << seqName << '\t' << tax << endl;
1030                         }
1031                         m->gobble(input);
1032                 }
1033
1034                 if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
1035
1036                 //we were unable to remove some of the bad sequences
1037                 if (badSeqNames.size() != 0) {
1038                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1039                                 m->mothurOut("Your taxonomy file does not include the sequence " + *it + " please correct.");
1040                                 m->mothurOutEndLine();
1041                         }
1042                 }
1043
1044                 input.close();
1045                 goodTaxOut.close();
1046
1047                 if (m->control_pressed) {  m->mothurRemove(goodTaxFile);  return 0; }
1048
1049                 return 0;
1050
1051         }
1052         catch(exception& e) {
1053                 m->errorOut(e, "ScreenSeqsCommand", "screenTaxonomy");
1054                 exit(1);
1055         }
1056
1057 }
1058 //***************************************************************************************************************
1059
1060 int ScreenSeqsCommand::screenQual(set<string> badSeqNames){
1061         try {
1062                 ifstream in;
1063                 m->openInputFile(qualfile, in);
1064                 set<string>::iterator it;
1065
1066                 string goodQualFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "good" + m->getExtension(qualfile);
1067                 outputNames.push_back(goodQualFile);  outputTypes["qfile"].push_back(goodQualFile);
1068                 ofstream goodQual;      m->openOutputFile(goodQualFile, goodQual);
1069
1070                 while(!in.eof()){
1071
1072                         if (m->control_pressed) { goodQual.close(); in.close(); m->mothurRemove(goodQualFile); return 0; }
1073
1074                         string saveName = "";
1075                         string name = "";
1076                         string scores = "";
1077
1078                         in >> name;
1079
1080                         if (name.length() != 0) {
1081                                 saveName = name.substr(1);
1082                                 while (!in.eof())       {
1083                                         char c = in.get();
1084                                         if (c == 10 || c == 13){        break;  }
1085                                         else { name += c; }
1086                                 }
1087                                 m->gobble(in);
1088                         }
1089
1090                         while(in){
1091                                 char letter= in.get();
1092                                 if(letter == '>'){      in.putback(letter);     break;  }
1093                                 else{ scores += letter; }
1094                         }
1095
1096                         m->gobble(in);
1097
1098                         it = badSeqNames.find(saveName);
1099
1100                         if(it != badSeqNames.end()){
1101                                 badSeqNames.erase(it);
1102                         }else{
1103                                 goodQual << name << endl << scores;
1104                         }
1105
1106                         m->gobble(in);
1107                 }
1108
1109                 in.close();
1110                 goodQual.close();
1111
1112                 //we were unable to remove some of the bad sequences
1113                 if (badSeqNames.size() != 0) {
1114                         for (it = badSeqNames.begin(); it != badSeqNames.end(); it++) {
1115                                 m->mothurOut("Your qual file does not include the sequence " + *it + " please correct.");
1116                                 m->mothurOutEndLine();
1117                         }
1118                 }
1119
1120                 if (m->control_pressed) {  m->mothurRemove(goodQualFile);  return 0; }
1121
1122                 return 0;
1123
1124         }
1125         catch(exception& e) {
1126                 m->errorOut(e, "ScreenSeqsCommand", "screenQual");
1127                 exit(1);
1128         }
1129
1130 }
1131 //**********************************************************************************************************************
1132
1133 int ScreenSeqsCommand::driver(linePair filePos, string goodFName, string badAccnosFName, string filename, set<string>& badSeqNames){
1134         try {
1135                 ofstream goodFile;
1136                 m->openOutputFile(goodFName, goodFile);
1137
1138                 ofstream badAccnosFile;
1139                 m->openOutputFile(badAccnosFName, badAccnosFile);
1140
1141                 ifstream inFASTA;
1142                 m->openInputFile(filename, inFASTA);
1143
1144                 inFASTA.seekg(filePos.start);
1145
1146                 bool done = false;
1147                 int count = 0;
1148
1149                 while (!done) {
1150
1151                         if (m->control_pressed) {  return 0; }
1152
1153                         Sequence currSeq(inFASTA); m->gobble(inFASTA);
1154                         if (currSeq.getName() != "") {
1155                                 bool goodSeq = 1;               //      innocent until proven guilty
1156                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1157                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1158                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1159                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1160                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1161                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1162
1163                                 if(goodSeq == 1){
1164                                         currSeq.printSequence(goodFile);
1165                                 }
1166                                 else{
1167                                         badAccnosFile << currSeq.getName() << endl;
1168                                         badSeqNames.insert(currSeq.getName());
1169                                 }
1170                         count++;
1171                         }
1172
1173                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1174                                 unsigned long long pos = inFASTA.tellg();
1175                                 if ((pos == -1) || (pos >= filePos.end)) { break; }
1176                         #else
1177                                 if (inFASTA.eof()) { break; }
1178                         #endif
1179
1180                         //report progress
1181                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1182                 }
1183                 //report progress
1184                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
1185
1186
1187                 goodFile.close();
1188                 inFASTA.close();
1189                 badAccnosFile.close();
1190
1191                 return count;
1192         }
1193         catch(exception& e) {
1194                 m->errorOut(e, "ScreenSeqsCommand", "driver");
1195                 exit(1);
1196         }
1197 }
1198 //**********************************************************************************************************************
1199 #ifdef USE_MPI
1200 int ScreenSeqsCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& goodFile, MPI_File& badAccnosFile, vector<unsigned long long>& MPIPos, set<string>& badSeqNames){
1201         try {
1202                 string outputString = "";
1203                 MPI_Status statusGood;
1204                 MPI_Status statusBadAccnos;
1205                 MPI_Status status;
1206                 int pid;
1207                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
1208
1209                 for(int i=0;i<num;i++){
1210
1211                         if (m->control_pressed) {  return 0; }
1212
1213                         //read next sequence
1214                         int length = MPIPos[start+i+1] - MPIPos[start+i];
1215
1216                         char* buf4 = new char[length];
1217                         memcpy(buf4, outputString.c_str(), length);
1218
1219                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
1220
1221                         string tempBuf = buf4;  delete buf4;
1222                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
1223                         istringstream iss (tempBuf,istringstream::in);
1224
1225                         Sequence currSeq(iss);
1226
1227                         //process seq
1228                         if (currSeq.getName() != "") {
1229                                 bool goodSeq = 1;               //      innocent until proven guilty
1230                                 if(goodSeq == 1 && startPos != -1 && startPos < currSeq.getStartPos())                  {       goodSeq = 0;    }
1231                                 if(goodSeq == 1 && endPos != -1 && endPos > currSeq.getEndPos())                                {       goodSeq = 0;    }
1232                                 if(goodSeq == 1 && maxAmbig != -1 && maxAmbig < currSeq.getAmbigBases())                {       goodSeq = 0;    }
1233                                 if(goodSeq == 1 && maxHomoP != -1 && maxHomoP < currSeq.getLongHomoPolymer())   {       goodSeq = 0;    }
1234                                 if(goodSeq == 1 && minLength != -1 && minLength > currSeq.getNumBases())                {       goodSeq = 0;    }
1235                                 if(goodSeq == 1 && maxLength != -1 && maxLength < currSeq.getNumBases())                {       goodSeq = 0;    }
1236
1237                                 if(goodSeq == 1){
1238                                         outputString =  ">" + currSeq.getName() + "\n" + currSeq.getAligned() + "\n";
1239
1240                                         //print good seq
1241                                         length = outputString.length();
1242                                         char* buf2 = new char[length];
1243                                         memcpy(buf2, outputString.c_str(), length);
1244
1245                                         MPI_File_write_shared(goodFile, buf2, length, MPI_CHAR, &statusGood);
1246                                         delete buf2;
1247                                 }
1248                                 else{
1249
1250                                         badSeqNames.insert(currSeq.getName());
1251
1252                                         //write to bad accnos file
1253                                         outputString = currSeq.getName() + "\n";
1254
1255                                         length = outputString.length();
1256                                         char* buf3 = new char[length];
1257                                         memcpy(buf3, outputString.c_str(), length);
1258
1259                                         MPI_File_write_shared(badAccnosFile, buf3, length, MPI_CHAR, &statusBadAccnos);
1260                                         delete buf3;
1261                                 }
1262                         }
1263
1264                         //report progress
1265                         if((i) % 100 == 0){     m->mothurOut("Processing sequence: " + toString(i)); m->mothurOutEndLine();             }
1266                 }
1267
1268                 return 1;
1269         }
1270         catch(exception& e) {
1271                 m->errorOut(e, "ScreenSeqsCommand", "driverMPI");
1272                 exit(1);
1273         }
1274 }
1275 #endif
1276 /**************************************************************************************************/
1277
1278 int ScreenSeqsCommand::createProcesses(string goodFileName, string badAccnos, string filename, set<string>& badSeqNames) {
1279         try {
1280
1281         vector<int> processIDS;
1282         int process = 1;
1283                 int num = 0;
1284
1285 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
1286
1287                 //loop through and create all the processes you want
1288                 while (process != processors) {
1289                         int pid = fork();
1290
1291                         if (pid > 0) {
1292                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
1293                                 process++;
1294                         }else if (pid == 0){
1295                                 num = driver(lines[process], goodFileName + toString(getpid()) + ".temp", badAccnos + toString(getpid()) + ".temp", filename, badSeqNames);
1296
1297                                 //pass numSeqs to parent
1298                                 ofstream out;
1299                                 string tempFile = filename + toString(getpid()) + ".num.temp";
1300                                 m->openOutputFile(tempFile, out);
1301                                 out << num << endl;
1302                                 out.close();
1303
1304                                 exit(0);
1305                         }else {
1306                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
1307                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
1308                                 exit(0);
1309                         }
1310                 }
1311
1312         num = driver(lines[0], goodFileName, badAccnos, filename, badSeqNames);
1313
1314                 //force parent to wait until all the processes are done
1315                 for (int i=0;i<processIDS.size();i++) {
1316                         int temp = processIDS[i];
1317                         wait(&temp);
1318                 }
1319
1320                 for (int i = 0; i < processIDS.size(); i++) {
1321                         ifstream in;
1322                         string tempFile =  filename + toString(processIDS[i]) + ".num.temp";
1323                         m->openInputFile(tempFile, in);
1324                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
1325                         in.close(); m->mothurRemove(tempFile);
1326
1327             m->appendFiles((goodFileName + toString(processIDS[i]) + ".temp"), goodFileName);
1328             m->mothurRemove((goodFileName + toString(processIDS[i]) + ".temp"));
1329
1330             m->appendFiles((badAccnos + toString(processIDS[i]) + ".temp"), badAccnos);
1331             m->mothurRemove((badAccnos + toString(processIDS[i]) + ".temp"));
1332                 }
1333
1334         //read badSeqs in because root process doesnt know what other "bad" seqs the children found
1335         ifstream inBad;
1336         int ableToOpen = m->openInputFile(badAccnos, inBad, "no error");
1337
1338         if (ableToOpen == 0) {
1339             badSeqNames.clear();
1340             string tempName;
1341             while (!inBad.eof()) {
1342                 inBad >> tempName; m->gobble(inBad);
1343                 badSeqNames.insert(tempName);
1344             }
1345             inBad.close();
1346         }
1347 #else
1348
1349         //////////////////////////////////////////////////////////////////////////////////////////////////////
1350                 //Windows version shared memory, so be careful when passing variables through the sumScreenData struct.
1351                 //Above fork() will clone, so memory is separate, but that's not the case with windows,
1352                 //Taking advantage of shared memory to allow both threads to add info to badSeqNames.
1353                 //////////////////////////////////////////////////////////////////////////////////////////////////////
1354
1355                 vector<sumScreenData*> pDataArray;
1356                 DWORD   dwThreadIdArray[processors-1];
1357                 HANDLE  hThreadArray[processors-1];
1358
1359                 //Create processor worker threads.
1360                 for( int i=0; i<processors-1; i++ ){
1361
1362             string extension = "";
1363             if (i!=0) {extension += toString(i) + ".temp"; processIDS.push_back(i); }
1364
1365                         // Allocate memory for thread data.
1366                         sumScreenData* tempSum = new sumScreenData(startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, filename, m, lines[i].start, lines[i].end,goodFileName+extension, badAccnos+extension, &badSeqNames);
1367                         pDataArray.push_back(tempSum);
1368
1369                         //default security attributes, thread function name, argument to thread function, use default creation flags, returns the thread identifier
1370                         hThreadArray[i] = CreateThread(NULL, 0, MySumScreenThreadFunction, pDataArray[i], 0, &dwThreadIdArray[i]);
1371                 }
1372
1373         //do your part
1374         num = driver(lines[processors-1], (goodFileName+toString(processors-1)+".temp"), (badAccnos+toString(processors-1)+".temp"), filename, badSeqNames);
1375         processIDS.push_back(processors-1);
1376
1377                 //Wait until all threads have terminated.
1378                 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
1379
1380                 //Close all thread handles and free memory allocations.
1381                 for(int i=0; i < pDataArray.size(); i++){
1382                         num += pDataArray[i]->count;
1383                         CloseHandle(hThreadArray[i]);
1384                         delete pDataArray[i];
1385                 }
1386
1387         for (int i = 0; i < processIDS.size(); i++) {
1388             m->appendFiles((goodFileName + toString(processIDS[i]) + ".temp"), goodFileName);
1389             m->mothurRemove((goodFileName + toString(processIDS[i]) + ".temp"));
1390
1391             m->appendFiles((badAccnos + toString(processIDS[i]) + ".temp"), badAccnos);
1392             m->mothurRemove((badAccnos + toString(processIDS[i]) + ".temp"));
1393                 }
1394
1395 #endif
1396
1397         return num;
1398
1399         }
1400         catch(exception& e) {
1401                 m->errorOut(e, "ScreenSeqsCommand", "createProcesses");
1402                 exit(1);
1403         }
1404 }
1405
1406 //***************************************************************************************************************
1407
1408