chimeraslayercommand.cpp

   1 /*
   2  *  chimeraslayercommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/31/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "chimeraslayercommand.h"
  11 #include "chimeraslayer.h"
  12 #include "deconvolutecommand.h"
  13
  14 //**********************************************************************************************************************
  15 vector<string> ChimeraSlayerCommand::setParameters(){
  16         try {
  17                 CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate);
  18                 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
  19                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
  20                 CommandParameter pwindow("window", "Number", "", "50", "", "", "",false,false); parameters.push_back(pwindow);
  21                 CommandParameter pksize("ksize", "Number", "", "7", "", "", "",false,false); parameters.push_back(pksize);
  22                 CommandParameter pmatch("match", "Number", "", "5.0", "", "", "",false,false); parameters.push_back(pmatch);
  23                 CommandParameter pmismatch("mismatch", "Number", "", "-4.0", "", "", "",false,false); parameters.push_back(pmismatch);
  24                 CommandParameter pminsim("minsim", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminsim);
  25                 CommandParameter pmincov("mincov", "Number", "", "70", "", "", "",false,false); parameters.push_back(pmincov);
  26                 CommandParameter pminsnp("minsnp", "Number", "", "100", "", "", "",false,false); parameters.push_back(pminsnp);
  27                 CommandParameter pminbs("minbs", "Number", "", "90", "", "", "",false,false); parameters.push_back(pminbs);
  28                 CommandParameter psearch("search", "Multiple", "kmer-blast-distance", "distance", "", "", "",false,false); parameters.push_back(psearch);
  29                 CommandParameter pinclude("include", "Multiple", "greater-greaterequal-all", "greater", "", "", "",false,false); parameters.push_back(pinclude);
  30                 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
  31                 CommandParameter prealign("realign", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prealign);
  32                 CommandParameter ptrim("trim", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ptrim);
  33                 CommandParameter psplit("split", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(psplit);
  34                 CommandParameter pnumwanted("numwanted", "Number", "", "15", "", "", "",false,false); parameters.push_back(pnumwanted);
  35                 CommandParameter piters("iters", "Number", "", "100", "", "", "",false,false); parameters.push_back(piters);
  36                 CommandParameter pdivergence("divergence", "Number", "", "1.007", "", "", "",false,false); parameters.push_back(pdivergence);
  37                 CommandParameter pparents("parents", "Number", "", "3", "", "", "",false,false); parameters.push_back(pparents);
  38                 CommandParameter pincrement("increment", "Number", "", "5", "", "", "",false,false); parameters.push_back(pincrement);
  39                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  40                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  41
  42                 vector<string> myArray;
  43                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  44                 return myArray;
  45         }
  46         catch(exception& e) {
  47                 m->errorOut(e, "ChimeraSlayerCommand", "setParameters");
  48                 exit(1);
  49         }
  50 }
  51 //**********************************************************************************************************************
  52 string ChimeraSlayerCommand::getHelpString(){
  53         try {
  54                 string helpString = "";
  55                 helpString += "The chimera.slayer command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n";
  56                 helpString += "This command was modeled after the chimeraSlayer written by the Broad Institute.\n";
  57                 helpString += "The chimera.slayer command parameters are fasta, name, template, processors, trim, ksize, window, match, mismatch, divergence. minsim, mincov, minbs, minsnp, parents, search, iters, increment and numwanted.\n"; //realign,
  58                 helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n";
  59                 helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n";
  60                 helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n";
  61                 helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n";
  62                 helpString += "The include parameter is used when template=self and allows you to choose which sequences will make up the \"template\". Options are greater, greaterequal and all, default=greater, meaning sequences with greater abundance than the query sequence. \n";
  63                 helpString += "The processors parameter allows you to specify how many processors you would like to use.  The default is 1. \n";
  64 #ifdef USE_MPI
  65                 helpString += "When using MPI, the processors parameter is set to the number of MPI processes running. \n";
  66 #endif
  67                 helpString += "The trim parameter allows you to output a new fasta file containing your sequences with the chimeric ones trimmed to include only their longest piece, default=F. \n";
  68                 helpString += "The split parameter allows you to check both pieces of non-chimeric sequence for chimeras, thus looking for trimeras and quadmeras. default=F. \n";
  69                 helpString += "The window parameter allows you to specify the window size for searching for chimeras, default=50. \n";
  70                 helpString += "The increment parameter allows you to specify how far you move each window while finding chimeric sequences, default=5.\n";
  71                 helpString += "The numwanted parameter allows you to specify how many sequences you would each query sequence compared with, default=15.\n";
  72                 helpString += "The ksize parameter allows you to input kmersize, default is 7, used if search is kmer. \n";
  73                 helpString += "The match parameter allows you to reward matched bases in blast search, default is 5. \n";
  74                 helpString += "The parents parameter allows you to select the number of potential parents to investigate from the numwanted best matches after rating them, default is 3. \n";
  75                 helpString += "The mismatch parameter allows you to penalize mismatched bases in blast search, default is -4. \n";
  76                 helpString += "The divergence parameter allows you to set a cutoff for chimera determination, default is 1.007. \n";
  77                 helpString += "The iters parameter allows you to specify the number of bootstrap iters to do with the chimeraslayer method, default=100.\n";
  78                 helpString += "The minsim parameter allows you to specify a minimum similarity with the parent fragments, default=90. \n";
  79                 helpString += "The mincov parameter allows you to specify minimum coverage by closest matches found in template. Default is 70, meaning 70%. \n";
  80                 helpString += "The minbs parameter allows you to specify minimum bootstrap support for calling a sequence chimeric. Default is 90, meaning 90%. \n";
  81                 helpString += "The minsnp parameter allows you to specify percent of SNPs to sample on each side of breakpoint for computing bootstrap support (default: 100) \n";
  82                 helpString += "The search parameter allows you to specify search method for finding the closest parent. Choices are distance, blast, and kmer, default distance. \n";
  83                 helpString += "The realign parameter allows you to realign the query to the potential parents. Choices are true or false, default false.  \n";
  84                 helpString += "The chimera.slayer command should be in the following format: \n";
  85                 helpString += "chimera.slayer(fasta=yourFastaFile, reference=yourTemplate, search=yourSearch) \n";
  86                 helpString += "Example: chimera.slayer(fasta=AD.align, reference=core_set_aligned.imputed.fasta, search=kmer) \n";
  87                 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFastaFile).\n";
  88                 return helpString;
  89         }
  90         catch(exception& e) {
  91                 m->errorOut(e, "ChimeraSlayerCommand", "getHelpString");
  92                 exit(1);
  93         }
  94 }
  95 //**********************************************************************************************************************
  96 ChimeraSlayerCommand::ChimeraSlayerCommand(){
  97         try {
  98                 abort = true; calledHelp = true;
  99                 setParameters();
 100                 vector<string> tempOutNames;
 101                 outputTypes["chimera"] = tempOutNames;
 102                 outputTypes["accnos"] = tempOutNames;
 103                 outputTypes["fasta"] = tempOutNames;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 107                 exit(1);
 108         }
 109 }
 110 //***************************************************************************************************************
 111 ChimeraSlayerCommand::ChimeraSlayerCommand(string option)  {
 112         try {
 113                 abort = false; calledHelp = false;
 114
 115                 //allow user to run help
 116                 if(option == "help") { help(); abort = true; calledHelp = true; }
 117
 118                 else {
 119                         vector<string> myArray = setParameters();
 120
 121                         OptionParser parser(option);
 122                         map<string,string> parameters = parser.getParameters();
 123
 124                         ValidParameters validParameter("chimera.slayer");
 125                         map<string,string>::iterator it;
 126
 127                         //check to make sure all parameters are valid for command
 128                         for (it = parameters.begin(); it != parameters.end(); it++) {
 129                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 130                         }
 131
 132                         vector<string> tempOutNames;
 133                         outputTypes["chimera"] = tempOutNames;
 134                         outputTypes["accnos"] = tempOutNames;
 135                         outputTypes["fasta"] = tempOutNames;
 136
 137                         //if the user changes the input directory command factory will send this info to us in the output parameter
 138                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 139                         if (inputDir == "not found"){   inputDir = "";          }
 140
 141                         //check for required parameters
 142                         fastafile = validParameter.validFile(parameters, "fasta", false);
 143                         if (fastafile == "not found") {
 144                                 //if there is a current fasta file, use it
 145                                 string filename = m->getFastaFile();
 146                                 if (filename != "") { fastaFileNames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
 147                                 else {  m->mothurOut("You have no current fastafile and the fasta parameter is required."); m->mothurOutEndLine(); abort = true; }
 148                         }else {
 149                                 m->splitAtDash(fastafile, fastaFileNames);
 150
 151                                 //go through files and make sure they are good, if not, then disregard them
 152                                 for (int i = 0; i < fastaFileNames.size(); i++) {
 153                                         if (inputDir != "") {
 154                                                 string path = m->hasPath(fastaFileNames[i]);
 155                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 156                                                 if (path == "") {       fastaFileNames[i] = inputDir + fastaFileNames[i];               }
 157                                         }
 158
 159                                         int ableToOpen;
 160                                         ifstream in;
 161
 162                                         ableToOpen = m->openInputFile(fastaFileNames[i], in, "noerror");
 163
 164                                         //if you can't open it, try default location
 165                                         if (ableToOpen == 1) {
 166                                                 if (m->getDefaultPath() != "") { //default path is set
 167                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(fastaFileNames[i]);
 168                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 169                                                         ifstream in2;
 170                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 171                                                         in2.close();
 172                                                         fastaFileNames[i] = tryPath;
 173                                                 }
 174                                         }
 175
 176                                         if (ableToOpen == 1) {
 177                                                 if (m->getOutputDir() != "") { //default path is set
 178                                                         string tryPath = m->getOutputDir() + m->getSimpleName(fastaFileNames[i]);
 179                                                         m->mothurOut("Unable to open " + fastaFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 180                                                         ifstream in2;
 181                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 182                                                         in2.close();
 183                                                         fastaFileNames[i] = tryPath;
 184                                                 }
 185                                         }
 186
 187                                         in.close();
 188
 189                                         if (ableToOpen == 1) {
 190                                                 m->mothurOut("Unable to open " + fastaFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 191                                                 //erase from file list
 192                                                 fastaFileNames.erase(fastaFileNames.begin()+i);
 193                                                 i--;
 194                                         }
 195                                 }
 196
 197                                 //make sure there is at least one valid file left
 198                                 if (fastaFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid files."); m->mothurOutEndLine(); abort = true; }
 199                         }
 200
 201
 202                         //check for required parameters
 203                         bool hasName = true;
 204                         namefile = validParameter.validFile(parameters, "name", false);
 205                         if (namefile == "not found") { namefile = "";  hasName = false; }
 206                         else {
 207                                 m->splitAtDash(namefile, nameFileNames);
 208
 209                                 //go through files and make sure they are good, if not, then disregard them
 210                                 for (int i = 0; i < nameFileNames.size(); i++) {
 211                                         if (inputDir != "") {
 212                                                 string path = m->hasPath(nameFileNames[i]);
 213                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 214                                                 if (path == "") {       nameFileNames[i] = inputDir + nameFileNames[i];         }
 215                                         }
 216
 217                                         int ableToOpen;
 218                                         ifstream in;
 219
 220                                         ableToOpen = m->openInputFile(nameFileNames[i], in, "noerror");
 221
 222                                         //if you can't open it, try default location
 223                                         if (ableToOpen == 1) {
 224                                                 if (m->getDefaultPath() != "") { //default path is set
 225                                                         string tryPath = m->getDefaultPath() + m->getSimpleName(nameFileNames[i]);
 226                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 227                                                         ifstream in2;
 228                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 229                                                         in2.close();
 230                                                         nameFileNames[i] = tryPath;
 231                                                 }
 232                                         }
 233
 234                                         if (ableToOpen == 1) {
 235                                                 if (m->getOutputDir() != "") { //default path is set
 236                                                         string tryPath = m->getOutputDir() + m->getSimpleName(nameFileNames[i]);
 237                                                         m->mothurOut("Unable to open " + nameFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 238                                                         ifstream in2;
 239                                                         ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 240                                                         in2.close();
 241                                                         nameFileNames[i] = tryPath;
 242                                                 }
 243                                         }
 244
 245                                         in.close();
 246
 247                                         if (ableToOpen == 1) {
 248                                                 m->mothurOut("Unable to open " + nameFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 249                                                 //erase from file list
 250                                                 nameFileNames.erase(nameFileNames.begin()+i);
 251                                                 i--;
 252                                         }
 253                                 }
 254
 255                                 //make sure there is at least one valid file left
 256                                 if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; }
 257                         }
 258
 259                         if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; }
 260
 261                         //if the user changes the output directory command factory will send this info to us in the output parameter
 262                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
 263
 264
 265                         string path;
 266                         it = parameters.find("reference");
 267                         //user has given a template file
 268                         if(it != parameters.end()){
 269                                 if (it->second == "self") { templatefile = "self"; }
 270                                 else {
 271                                         path = m->hasPath(it->second);
 272                                         //if the user has not given a path then, add inputdir. else leave path alone.
 273                                         if (path == "") {       parameters["reference"] = inputDir + it->second;                }
 274
 275                                         templatefile = validParameter.validFile(parameters, "reference", true);
 276                                         if (templatefile == "not open") { abort = true; }
 277                                         else if (templatefile == "not found") { templatefile = "";  m->mothurOut("reference is a required parameter for the chimera.slayer command."); m->mothurOutEndLine(); abort = true;  }
 278                                 }
 279                         }
 280
 281                         string temp = validParameter.validFile(parameters, "processors", false);        if (temp == "not found"){       temp = m->getProcessors();      }
 282                         m->setProcessors(temp);
 283                         convert(temp, processors);
 284
 285                         includeAbunds = validParameter.validFile(parameters, "include", false);         if (includeAbunds == "not found") { includeAbunds = "greater"; }
 286                         if ((includeAbunds != "greater") && (includeAbunds != "greaterequal") && (includeAbunds != "all")) { includeAbunds = "greater"; m->mothurOut("Invalid include setting. options are greater, greaterequal or all. using greater."); m->mothurOutEndLine(); }
 287
 288                         temp = validParameter.validFile(parameters, "ksize", false);                    if (temp == "not found") { temp = "7"; }
 289                         convert(temp, ksize);
 290
 291                         temp = validParameter.validFile(parameters, "window", false);                   if (temp == "not found") { temp = "50"; }
 292                         convert(temp, window);
 293
 294                         temp = validParameter.validFile(parameters, "match", false);                    if (temp == "not found") { temp = "5"; }
 295                         convert(temp, match);
 296
 297                         temp = validParameter.validFile(parameters, "mismatch", false);                 if (temp == "not found") { temp = "-4"; }
 298                         convert(temp, mismatch);
 299
 300                         temp = validParameter.validFile(parameters, "divergence", false);               if (temp == "not found") { temp = "1.007"; }
 301                         convert(temp, divR);
 302
 303                         temp = validParameter.validFile(parameters, "minsim", false);                   if (temp == "not found") { temp = "90"; }
 304                         convert(temp, minSimilarity);
 305
 306                         temp = validParameter.validFile(parameters, "mincov", false);                   if (temp == "not found") { temp = "70"; }
 307                         convert(temp, minCoverage);
 308
 309                         temp = validParameter.validFile(parameters, "minbs", false);                    if (temp == "not found") { temp = "90"; }
 310                         convert(temp, minBS);
 311
 312                         temp = validParameter.validFile(parameters, "minsnp", false);                   if (temp == "not found") { temp = "100"; }
 313                         convert(temp, minSNP);
 314
 315                         temp = validParameter.validFile(parameters, "parents", false);                  if (temp == "not found") { temp = "3"; }
 316                         convert(temp, parents);
 317
 318                         temp = validParameter.validFile(parameters, "realign", false);                  if (temp == "not found") { temp = "f"; }
 319                         realign = m->isTrue(temp);
 320
 321                         temp = validParameter.validFile(parameters, "trim", false);                             if (temp == "not found") { temp = "f"; }
 322                         trim = m->isTrue(temp);
 323
 324                         temp = validParameter.validFile(parameters, "split", false);                            if (temp == "not found") { temp = "f"; }
 325                         trimera = m->isTrue(temp);
 326
 327                         search = validParameter.validFile(parameters, "search", false);                 if (search == "not found") { search = "distance"; }
 328
 329                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "100"; }
 330                         convert(temp, iters);
 331
 332                         temp = validParameter.validFile(parameters, "increment", false);                if (temp == "not found") { temp = "5"; }
 333                         convert(temp, increment);
 334
 335                         temp = validParameter.validFile(parameters, "numwanted", false);                if (temp == "not found") { temp = "15"; }
 336                         convert(temp, numwanted);
 337
 338                         if ((search != "distance") && (search != "blast") && (search != "kmer")) { m->mothurOut(search + " is not a valid search."); m->mothurOutEndLine(); abort = true;  }
 339                 }
 340         }
 341         catch(exception& e) {
 342                 m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
 343                 exit(1);
 344         }
 345 }
 346 //***************************************************************************************************************
 347
 348 int ChimeraSlayerCommand::execute(){
 349         try{
 350
 351                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 352
 353                 for (int s = 0; s < fastaFileNames.size(); s++) {
 354
 355                         m->mothurOut("Checking sequences from " + fastaFileNames[s] + " ..." ); m->mothurOutEndLine();
 356
 357                         int start = time(NULL);
 358
 359                         if (templatefile != "self") { //you want to run slayer with a refernce template
 360                                 chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 361                         }else {
 362                                 if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one
 363                                         chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFileNames[s], search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 364                                 }else {
 365
 366                                         m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
 367
 368                                         //use unique.seqs to create new name and fastafile
 369                                         string inputString = "fasta=" + fastaFileNames[s];
 370                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 371                                         m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine();
 372
 373                                         Command* uniqueCommand = new DeconvoluteCommand(inputString);
 374                                         uniqueCommand->execute();
 375
 376                                         map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 377
 378                                         delete uniqueCommand;
 379
 380                                         m->mothurOut("/******************************************/"); m->mothurOutEndLine();
 381
 382                                         string nameFile = filenames["name"][0];
 383                                         fastaFileNames[s] = filenames["fasta"][0];
 384
 385                                         chimera = new ChimeraSlayer(fastaFileNames[s], templatefile, trim, nameFile, search, includeAbunds, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign);
 386                                 }
 387                         }
 388
 389                         if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]);  }//if user entered a file with a path then preserve it
 390                         string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimera";
 391                         string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.accnos";
 392                         string trimFastaFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s]))  + "slayer.fasta";
 393
 394                         if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) {        remove(outputNames[j].c_str()); }  return 0;    }
 395
 396                         if (chimera->getUnaligned()) {
 397                                 m->mothurOut("Your template sequences are different lengths, please correct."); m->mothurOutEndLine();
 398                                 delete chimera;
 399                                 return 0;
 400                         }
 401                         templateSeqsLength = chimera->getLength();
 402
 403                 #ifdef USE_MPI
 404                         int pid, numSeqsPerProcessor;
 405                                 int tag = 2001;
 406                                 vector<unsigned long int> MPIPos;
 407
 408                                 MPI_Status status;
 409                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 410                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 411
 412                                 MPI_File inMPI;
 413                                 MPI_File outMPI;
 414                                 MPI_File outMPIAccnos;
 415                                 MPI_File outMPIFasta;
 416
 417                                 int outMode=MPI_MODE_CREATE|MPI_MODE_WRONLY;
 418                                 int inMode=MPI_MODE_RDONLY;
 419
 420                                 char outFilename[1024];
 421                                 strcpy(outFilename, outputFileName.c_str());
 422
 423                                 char outAccnosFilename[1024];
 424                                 strcpy(outAccnosFilename, accnosFileName.c_str());
 425
 426                                 char outFastaFilename[1024];
 427                                 strcpy(outFastaFilename, trimFastaFileName.c_str());
 428
 429                                 char inFileName[1024];
 430                                 strcpy(inFileName, fastaFileNames[s].c_str());
 431
 432                                 MPI_File_open(MPI_COMM_WORLD, inFileName, inMode, MPI_INFO_NULL, &inMPI);  //comm, filename, mode, info, filepointer
 433                                 MPI_File_open(MPI_COMM_WORLD, outFilename, outMode, MPI_INFO_NULL, &outMPI);
 434                                 MPI_File_open(MPI_COMM_WORLD, outAccnosFilename, outMode, MPI_INFO_NULL, &outMPIAccnos);
 435                                 if (trim) { MPI_File_open(MPI_COMM_WORLD, outFastaFilename, outMode, MPI_INFO_NULL, &outMPIFasta); }
 436
 437                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) {  MPI_File_close(&outMPIFasta);  } MPI_File_close(&outMPIAccnos); for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }   delete chimera; return 0;  }
 438
 439                                 if (pid == 0) { //you are the root process
 440                                         m->mothurOutEndLine();
 441                                         m->mothurOut("Only reporting sequence supported by " + toString(minBS) + "% of bootstrapped results.");
 442                                         m->mothurOutEndLine();
 443
 444                                         string outTemp = "Name\tLeftParent\tRightParent\tDivQLAQRB\tPerIDQLAQRB\tBootStrapA\tDivQLBQRA\tPerIDQLBQRA\tBootStrapB\tFlag\tLeftWindow\tRightWindow\n";
 445
 446                                         //print header
 447                                         int length = outTemp.length();
 448                                         char* buf2 = new char[length];
 449                                         memcpy(buf2, outTemp.c_str(), length);
 450
 451                                         MPI_File_write_shared(outMPI, buf2, length, MPI_CHAR, &status);
 452                                         delete buf2;
 453
 454                                         MPIPos = m->setFilePosFasta(fastaFileNames[s], numSeqs); //fills MPIPos, returns numSeqs
 455
 456                                         //send file positions to all processes
 457                                         for(int i = 1; i < processors; i++) {
 458                                                 MPI_Send(&numSeqs, 1, MPI_INT, i, tag, MPI_COMM_WORLD);
 459                                                 MPI_Send(&MPIPos[0], (numSeqs+1), MPI_LONG, i, tag, MPI_COMM_WORLD);
 460                                         }
 461
 462                                         //figure out how many sequences you have to align
 463                                         numSeqsPerProcessor = numSeqs / processors;
 464                                         int startIndex =  pid * numSeqsPerProcessor;
 465                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 466
 467                                         //do your part
 468                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 469
 470                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  remove(outputFileName.c_str());  remove(accnosFileName.c_str());  delete chimera; return 0;  }
 471
 472                                 }else{ //you are a child process
 473                                         MPI_Recv(&numSeqs, 1, MPI_INT, 0, tag, MPI_COMM_WORLD, &status);
 474                                         MPIPos.resize(numSeqs+1);
 475                                         MPI_Recv(&MPIPos[0], (numSeqs+1), MPI_LONG, 0, tag, MPI_COMM_WORLD, &status);
 476
 477                                         //figure out how many sequences you have to align
 478                                         numSeqsPerProcessor = numSeqs / processors;
 479                                         int startIndex =  pid * numSeqsPerProcessor;
 480                                         if(pid == (processors - 1)){    numSeqsPerProcessor = numSeqs - pid * numSeqsPerProcessor;      }
 481
 482                                         //do your part
 483                                         driverMPI(startIndex, numSeqsPerProcessor, inMPI, outMPI, outMPIAccnos, outMPIFasta, MPIPos);
 484
 485                                         if (m->control_pressed) { outputTypes.clear();  MPI_File_close(&inMPI);  MPI_File_close(&outMPI); if (trim) { MPI_File_close(&outMPIFasta); }  MPI_File_close(&outMPIAccnos);  for (int j = 0; j < outputNames.size(); j++) {   remove(outputNames[j].c_str()); }  delete chimera; return 0;  }
 486                                 }
 487
 488                                 //close files
 489                                 MPI_File_close(&inMPI);
 490                                 MPI_File_close(&outMPI);
 491                                 MPI_File_close(&outMPIAccnos);
 492                                 if (trim) { MPI_File_close(&outMPIFasta); }
 493                                 MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 494
 495                 #else
 496                         ofstream outHeader;
 497                         string tempHeader = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "slayer.chimeras.tempHeader";
 498                         m->openOutputFile(tempHeader, outHeader);
 499
 500                         chimera->printHeader(outHeader);
 501                         outHeader.close();
 502
 503                         vector<unsigned long int> positions = m->divideFile(fastaFileNames[s], processors);
 504
 505                         for (int i = 0; i < (positions.size()-1); i++) {
 506                                 lines.push_back(new linePair(positions[i], positions[(i+1)]));
 507                         }
 508
 509                         //break up file
 510                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 511                                 if(processors == 1){
 512                                         numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 513
 514                                         if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {      remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 515
 516                                 }else{
 517                                         processIDS.resize(0);
 518
 519                                         numSeqs = createProcesses(outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 520
 521                                         rename((outputFileName + toString(processIDS[0]) + ".temp").c_str(), outputFileName.c_str());
 522                                         rename((accnosFileName + toString(processIDS[0]) + ".temp").c_str(), accnosFileName.c_str());
 523                                         if (trim) {  rename((trimFastaFileName + toString(processIDS[0]) + ".temp").c_str(), trimFastaFileName.c_str()); }
 524
 525                                         //append output files
 526                                         for(int i=1;i<processors;i++){
 527                                                 m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
 528                                                 remove((outputFileName + toString(processIDS[i]) + ".temp").c_str());
 529                                         }
 530
 531                                         //append output files
 532                                         for(int i=1;i<processors;i++){
 533                                                 m->appendFiles((accnosFileName + toString(processIDS[i]) + ".temp"), accnosFileName);
 534                                                 remove((accnosFileName + toString(processIDS[i]) + ".temp").c_str());
 535                                         }
 536
 537                                         if (trim) {
 538                                                 for(int i=1;i<processors;i++){
 539                                                         m->appendFiles((trimFastaFileName + toString(processIDS[i]) + ".temp"), trimFastaFileName);
 540                                                         remove((trimFastaFileName + toString(processIDS[i]) + ".temp").c_str());
 541                                                 }
 542                                         }
 543
 544                                         if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {  remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 545                                 }
 546
 547                         #else
 548                                 numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName, trimFastaFileName);
 549
 550                                 if (m->control_pressed) { outputTypes.clear(); if (trim) { remove(trimFastaFileName.c_str()); } remove(outputFileName.c_str()); remove(tempHeader.c_str()); remove(accnosFileName.c_str()); for (int j = 0; j < outputNames.size(); j++) {      remove(outputNames[j].c_str()); } for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear(); delete chimera; return 0; }
 551
 552                         #endif
 553
 554                         m->appendFiles(outputFileName, tempHeader);
 555
 556                         remove(outputFileName.c_str());
 557                         rename(tempHeader.c_str(), outputFileName.c_str());
 558
 559                 #endif
 560                         delete chimera;
 561
 562
 563                         for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
 564
 565                         outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 566                         outputNames.push_back(accnosFileName); outputTypes["accnos"].push_back(accnosFileName);
 567                         if (trim) {  outputNames.push_back(trimFastaFileName); outputTypes["fasta"].push_back(trimFastaFileName); }
 568
 569                         m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
 570                 }
 571
 572                 //set accnos file as new current accnosfile
 573                 string current = "";
 574                 itTypes = outputTypes.find("accnos");
 575                 if (itTypes != outputTypes.end()) {
 576                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 577                 }
 578
 579                 if (trim) {
 580                         itTypes = outputTypes.find("fasta");
 581                         if (itTypes != outputTypes.end()) {
 582                                 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 583                         }
 584                 }
 585
 586                 m->mothurOutEndLine();
 587                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 588                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 589                 m->mothurOutEndLine();
 590
 591                 return 0;
 592
 593         }
 594         catch(exception& e) {
 595                 m->errorOut(e, "ChimeraSlayerCommand", "execute");
 596                 exit(1);
 597         }
 598 }
 599 //**********************************************************************************************************************
 600
 601 int ChimeraSlayerCommand::driver(linePair* filePos, string outputFName, string filename, string accnos, string fasta){
 602         try {
 603                 ofstream out;
 604                 m->openOutputFile(outputFName, out);
 605
 606                 ofstream out2;
 607                 m->openOutputFile(accnos, out2);
 608
 609                 ofstream out3;
 610                 if (trim) {  m->openOutputFile(fasta, out3); }
 611
 612                 ifstream inFASTA;
 613                 m->openInputFile(filename, inFASTA);
 614
 615                 inFASTA.seekg(filePos->start);
 616
 617                 bool done = false;
 618                 int count = 0;
 619
 620                 while (!done) {
 621
 622                         if (m->control_pressed) {       out.close(); out2.close(); if (trim) { out3.close(); } inFASTA.close(); return 1;       }
 623
 624                         Sequence* candidateSeq = new Sequence(inFASTA);  m->gobble(inFASTA);
 625                         string candidateAligned = candidateSeq->getAligned();
 626
 627                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 628
 629                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 630                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 631                                 }else{
 632                                         //find chimeras
 633                                         chimera->getChimeras(candidateSeq);
 634
 635                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 636
 637                                         //if you are not chimeric, then check each half
 638                                         data_results wholeResults = chimera->getResults();
 639
 640                                         //determine if we need to split
 641                                         bool isChimeric = false;
 642
 643                                         if (wholeResults.flag == "yes") {
 644                                                 string chimeraFlag = "no";
 645                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
 646                                                    ||
 647                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
 648
 649
 650                                                 if (chimeraFlag == "yes") {
 651                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
 652                                                 }
 653                                         }
 654
 655                                         if ((!isChimeric) && trimera) {
 656
 657                                                 //split sequence in half by bases
 658                                                 string leftQuery, rightQuery;
 659                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
 660                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
 661
 662                                                 //run chimeraSlayer on each piece
 663                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
 664                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
 665
 666                                                 //find chimeras
 667                                                 chimera->getChimeras(left);
 668                                                 data_results leftResults = chimera->getResults();
 669
 670                                                 chimera->getChimeras(right);
 671                                                 data_results rightResults = chimera->getResults();
 672
 673                                                 //if either piece is chimeric then report
 674                                                 Sequence* trimmed = chimera->print(out, out2, leftResults, rightResults);
 675                                                 if (trim) { trimmed->printSequence(out3); delete trimmed; }
 676
 677                                                 delete left; delete right;
 678
 679                                         }else { //already chimeric
 680                                                 //print results
 681                                                 Sequence* trimmed = chimera->print(out, out2);
 682                                                 if (trim) { trimmed->printSequence(out3); delete trimmed; }
 683                                         }
 684
 685
 686                                 }
 687                                 count++;
 688                         }
 689                         delete candidateSeq;
 690
 691                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 692                                 unsigned long int pos = inFASTA.tellg();
 693                                 if ((pos == -1) || (pos >= filePos->end)) { break; }
 694                         #else
 695                                 if (inFASTA.eof()) { break; }
 696                         #endif
 697
 698                         //report progress
 699                         if((count) % 100 == 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 700                 }
 701                 //report progress
 702                 if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();         }
 703
 704                 out.close();
 705                 out2.close();
 706                 if (trim) { out3.close(); }
 707                 inFASTA.close();
 708
 709                 return count;
 710         }
 711         catch(exception& e) {
 712                 m->errorOut(e, "ChimeraSlayerCommand", "driver");
 713                 exit(1);
 714         }
 715 }
 716 //**********************************************************************************************************************
 717 #ifdef USE_MPI
 718 int ChimeraSlayerCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File& outMPI, MPI_File& outAccMPI, MPI_File& outFastaMPI, vector<unsigned long int>& MPIPos){
 719         try {
 720                 MPI_Status status;
 721                 int pid;
 722                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 723
 724                 for(int i=0;i<num;i++){
 725
 726                         if (m->control_pressed) {       return 1;       }
 727
 728                         //read next sequence
 729                         int length = MPIPos[start+i+1] - MPIPos[start+i];
 730
 731                         char* buf4 = new char[length];
 732                         MPI_File_read_at(inMPI, MPIPos[start+i], buf4, length, MPI_CHAR, &status);
 733
 734                         string tempBuf = buf4;
 735                         if (tempBuf.length() > length) { tempBuf = tempBuf.substr(0, length);  }
 736                         istringstream iss (tempBuf,istringstream::in);
 737
 738                         delete buf4;
 739
 740                         Sequence* candidateSeq = new Sequence(iss);  m->gobble(iss);
 741                         string candidateAligned = candidateSeq->getAligned();
 742
 743                         if (candidateSeq->getName() != "") { //incase there is a commented sequence at the end of a file
 744
 745                                 if (candidateSeq->getAligned().length() != templateSeqsLength) {
 746                                         m->mothurOut(candidateSeq->getName() + " is not the same length as the template sequences. Skipping."); m->mothurOutEndLine();
 747                                 }else{
 748
 749                                         //find chimeras
 750                                         chimera->getChimeras(candidateSeq);
 751
 752                                         if (m->control_pressed) {       delete candidateSeq; return 1;  }
 753
 754                                         //if you are not chimeric, then check each half
 755                                         data_results wholeResults = chimera->getResults();
 756
 757                                         //determine if we need to split
 758                                         bool isChimeric = false;
 759
 760                                         if (wholeResults.flag == "yes") {
 761                                                 string chimeraFlag = "no";
 762                                                 if(  (wholeResults.results[0].bsa >= minBS && wholeResults.results[0].divr_qla_qrb >= divR)
 763                                                    ||
 764                                                    (wholeResults.results[0].bsb >= minBS && wholeResults.results[0].divr_qlb_qra >= divR) ) { chimeraFlag = "yes"; }
 765
 766
 767                                                 if (chimeraFlag == "yes") {
 768                                                         if ((wholeResults.results[0].bsa >= minBS) || (wholeResults.results[0].bsb >= minBS)) { isChimeric = true; }
 769                                                 }
 770                                         }
 771
 772                                         if ((!isChimeric) && trimera) {
 773                                                 //split sequence in half by bases
 774                                                 string leftQuery, rightQuery;
 775                                                 Sequence tempSeq(candidateSeq->getName(), candidateAligned);
 776                                                 divideInHalf(tempSeq, leftQuery, rightQuery);
 777
 778                                                 //run chimeraSlayer on each piece
 779                                                 Sequence* left = new Sequence(candidateSeq->getName(), leftQuery);
 780                                                 Sequence* right = new Sequence(candidateSeq->getName(), rightQuery);
 781
 782                                                 //find chimeras
 783                                                 chimera->getChimeras(left);
 784                                                 data_results leftResults = chimera->getResults();
 785
 786                                                 chimera->getChimeras(right);
 787                                                 data_results rightResults = chimera->getResults();
 788
 789                                                 //if either piece is chimeric then report
 790                                                 Sequence* trimmed = chimera->print(outMPI, outAccMPI, leftResults, rightResults);
 791                                                 if (trim) {
 792                                                         string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
 793                                                         delete trimmed;
 794
 795                                                         //write to accnos file
 796                                                         int length = outputString.length();
 797                                                         char* buf2 = new char[length];
 798                                                         memcpy(buf2, outputString.c_str(), length);
 799
 800                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 801                                                         delete buf2;
 802                                                 }
 803
 804                                                 delete left; delete right;
 805
 806                                         }else {
 807                                                 //print results
 808                                                 Sequence* trimmed = chimera->print(outMPI, outAccMPI);
 809
 810                                                 if (trim) {
 811                                                         string outputString = ">" + trimmed->getName() + "\n" + trimmed->getAligned() + "\n";
 812                                                         delete trimmed;
 813
 814                                                         //write to accnos file
 815                                                         int length = outputString.length();
 816                                                         char* buf2 = new char[length];
 817                                                         memcpy(buf2, outputString.c_str(), length);
 818
 819                                                         MPI_File_write_shared(outFastaMPI, buf2, length, MPI_CHAR, &status);
 820                                                         delete buf2;
 821                                                 }
 822                                         }
 823
 824                                 }
 825                         }
 826                         delete candidateSeq;
 827
 828                         //report progress
 829                         if((i+1) % 100 == 0){  cout << "Processing sequence: " << (i+1) << endl;        m->mothurOutJustToLog("Processing sequence: " + toString(i+1) + "\n");          }
 830                 }
 831                 //report progress
 832                 if(num % 100 != 0){             cout << "Processing sequence: " << num << endl; m->mothurOutJustToLog("Processing sequence: " + toString(num) + "\n");  }
 833
 834
 835                 return 0;
 836         }
 837         catch(exception& e) {
 838                 m->errorOut(e, "ChimeraSlayerCommand", "driverMPI");
 839                 exit(1);
 840         }
 841 }
 842 #endif
 843
 844 /**************************************************************************************************/
 845
 846 int ChimeraSlayerCommand::createProcesses(string outputFileName, string filename, string accnos, string fasta) {
 847         try {
 848 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 849                 int process = 0;
 850                 int num = 0;
 851
 852                 //loop through and create all the processes you want
 853                 while (process != processors) {
 854                         int pid = fork();
 855
 856                         if (pid > 0) {
 857                                 processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 858                                 process++;
 859                         }else if (pid == 0){
 860                                 num = driver(lines[process], outputFileName + toString(getpid()) + ".temp", filename, accnos + toString(getpid()) + ".temp", fasta + toString(getpid()) + ".temp");
 861
 862                                 //pass numSeqs to parent
 863                                 ofstream out;
 864                                 string tempFile = outputFileName + toString(getpid()) + ".num.temp";
 865                                 m->openOutputFile(tempFile, out);
 866                                 out << num << endl;
 867                                 out.close();
 868
 869                                 exit(0);
 870                         }else {
 871                                 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
 872                                 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
 873                                 exit(0);
 874                         }
 875                 }
 876
 877                 //force parent to wait until all the processes are done
 878                 for (int i=0;i<processors;i++) {
 879                         int temp = processIDS[i];
 880                         wait(&temp);
 881                 }
 882
 883                 for (int i = 0; i < processIDS.size(); i++) {
 884                         ifstream in;
 885                         string tempFile =  outputFileName + toString(processIDS[i]) + ".num.temp";
 886                         m->openInputFile(tempFile, in);
 887                         if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
 888                         in.close(); remove(tempFile.c_str());
 889                 }
 890
 891                 return num;
 892 #endif
 893         }
 894         catch(exception& e) {
 895                 m->errorOut(e, "ChimeraSlayerCommand", "createProcesses");
 896                 exit(1);
 897         }
 898 }
 899
 900 /**************************************************************************************************/
 901
 902 int ChimeraSlayerCommand::divideInHalf(Sequence querySeq, string& leftQuery, string& rightQuery) {
 903         try {
 904
 905                 string queryUnAligned = querySeq.getUnaligned();
 906                 int numBases = int(queryUnAligned.length() * 0.5);
 907
 908                 string queryAligned = querySeq.getAligned();
 909                 leftQuery = querySeq.getAligned();
 910                 rightQuery = querySeq.getAligned();
 911
 912                 int baseCount = 0;
 913                 int leftSpot = 0;
 914                 for (int i = 0; i < queryAligned.length(); i++) {
 915                         //if you are a base
 916                         if (isalpha(queryAligned[i])) {
 917                                 baseCount++;
 918                         }
 919
 920                         //if you have half
 921                         if (baseCount >= numBases) {  leftSpot = i; break; } //first half
 922                 }
 923
 924                 //blank out right side
 925                 for (int i = leftSpot; i < leftQuery.length(); i++) { leftQuery[i] = '.'; }
 926
 927                 //blank out left side
 928                 for (int i = 0; i < leftSpot; i++) { rightQuery[i] = '.'; }
 929
 930                 return 0;
 931
 932         }
 933         catch(exception& e) {
 934                 m->errorOut(e, "ChimeraSlayerCommand", "divideInHalf");
 935                 exit(1);
 936         }
 937 }
 938
 939 /**************************************************************************************************/
 940