sffinfocommand.cpp

   1 /*
   2  *  sffinfocommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 7/7/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "sffinfocommand.h"
  11 #include "endiannessmacros.h"
  12 #include "trimoligos.h"
  13 #include "sequence.hpp"
  14 #include "qualityscores.h"
  15
  16 //**********************************************************************************************************************
  17 vector<string> SffInfoCommand::setParameters(){
  18         try {
  19                 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(psff);
  20         CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(poligos);
  21                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
  22                 CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "","",false,false); parameters.push_back(psfftxt);
  23                 CommandParameter pflow("flow", "Boolean", "", "T", "", "", "","flow",false,false); parameters.push_back(pflow);
  24                 CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim);
  25                 CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "","fasta",false,false); parameters.push_back(pfasta);
  26                 CommandParameter pqfile("qfile", "Boolean", "", "T", "", "", "","qfile",false,false); parameters.push_back(pqfile);
  27         CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ppdiffs);
  28                 CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pbdiffs);
  29         CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
  30                 CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
  31         CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
  32                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  33                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  34
  35                 vector<string> myArray;
  36                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  37                 return myArray;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "SffInfoCommand", "setParameters");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 string SffInfoCommand::getHelpString(){
  46         try {
  47                 string helpString = "";
  48                 helpString += "The sffinfo command reads a sff file and extracts the sequence data, or you can use it to parse a sfftxt file.\n";
  49                 helpString += "The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, oligos, bdiffs, tdiffs, ldiffs, sdiffs, pdiffs and trim. sff is required. \n";
  50                 helpString += "The sff parameter allows you to enter the sff file you would like to extract data from.  You may enter multiple files by separating them by -'s.\n";
  51                 helpString += "The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n";
  52                 helpString += "The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n";
  53         helpString += "The oligos parameter allows you to provide an oligos file to split your sff file into separate sff files by barcode. \n";
  54         helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
  55                 helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
  56                 helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
  57         helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
  58                 helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
  59                 helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=True. \n";
  60                 helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n";
  61                 helpString += "If you want to parse an existing sfftxt file into flow, fasta and quality file, enter the file name using the sfftxt parameter. \n";
  62                 helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values.  Default=True. \n";
  63                 helpString += "The accnos parameter allows you to provide a accnos file containing the names of the sequences you would like extracted. You may enter multiple files by separating them by -'s. \n";
  64                 helpString += "Example sffinfo(sff=mySffFile.sff, trim=F).\n";
  65                 helpString += "Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n";
  66                 return helpString;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "SffInfoCommand", "getHelpString");
  70                 exit(1);
  71         }
  72 }
  73
  74 //**********************************************************************************************************************
  75 string SffInfoCommand::getOutputPattern(string type) {
  76     try {
  77         string pattern = "";
  78
  79         if (type == "fasta")            {   pattern =  "[filename],fasta-[filename],[tag],fasta";   }
  80         else if (type == "flow")    {   pattern =  "[filename],flow";   }
  81         else if (type == "sfftxt")        {   pattern =  "[filename],sff.txt";   }
  82         else if (type == "sff")        {   pattern =  "[filename],[group],sff";   }
  83         else if (type == "qfile")       {   pattern =  "[filename],qual-[filename],[tag],qual";   }
  84         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  85
  86         return pattern;
  87     }
  88     catch(exception& e) {
  89         m->errorOut(e, "SffInfoCommand", "getOutputPattern");
  90         exit(1);
  91     }
  92 }
  93 //**********************************************************************************************************************
  94 SffInfoCommand::SffInfoCommand(){
  95         try {
  96                 abort = true; calledHelp = true;
  97                 setParameters();
  98                 vector<string> tempOutNames;
  99                 outputTypes["fasta"] = tempOutNames;
 100                 outputTypes["flow"] = tempOutNames;
 101                 outputTypes["sfftxt"] = tempOutNames;
 102                 outputTypes["qfile"] = tempOutNames;
 103         outputTypes["sff"] = tempOutNames;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 107                 exit(1);
 108         }
 109 }
 110 //**********************************************************************************************************************
 111
 112 SffInfoCommand::SffInfoCommand(string option)  {
 113         try {
 114                 abort = false; calledHelp = false;
 115                 hasAccnos = false; hasOligos = false;
 116         split = 1;
 117
 118                 //allow user to run help
 119                 if(option == "help") { help(); abort = true; calledHelp = true; }
 120                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 121
 122                 else {
 123                         //valid paramters for this command
 124                         vector<string> myArray = setParameters();
 125
 126                         OptionParser parser(option);
 127                         map<string, string> parameters = parser.getParameters();
 128
 129                         ValidParameters validParameter;
 130                         //check to make sure all parameters are valid for command
 131                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
 132                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
 133                         }
 134
 135                         //initialize outputTypes
 136                         vector<string> tempOutNames;
 137                         outputTypes["fasta"] = tempOutNames;
 138                         outputTypes["flow"] = tempOutNames;
 139                         outputTypes["sfftxt"] = tempOutNames;
 140                         outputTypes["qfile"] = tempOutNames;
 141             outputTypes["sff"] = tempOutNames;
 142
 143                         //if the user changes the output directory command factory will send this info to us in the output parameter
 144                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 145
 146                         //if the user changes the input directory command factory will send this info to us in the output parameter
 147                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }
 148
 149                         sffFilename = validParameter.validFile(parameters, "sff", false);
 150                         if (sffFilename == "not found") { sffFilename = "";  }
 151                         else {
 152                                 m->splitAtDash(sffFilename, filenames);
 153
 154                                 //go through files and make sure they are good, if not, then disregard them
 155                                 for (int i = 0; i < filenames.size(); i++) {
 156                                         bool ignore = false;
 157                                         if (filenames[i] == "current") {
 158                                                 filenames[i] = m->getSFFFile();
 159                                                 if (filenames[i] != "") {  m->mothurOut("Using " + filenames[i] + " as input file for the sff parameter where you had given current."); m->mothurOutEndLine(); }
 160                                                 else {
 161                                                         m->mothurOut("You have no current sfffile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 162                                                         //erase from file list
 163                                                         filenames.erase(filenames.begin()+i);
 164                                                         i--;
 165                                                 }
 166                                         }
 167
 168                                         if (!ignore) {
 169                                                 if (inputDir != "") {
 170                                                         string path = m->hasPath(filenames[i]);
 171                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 172                                                         if (path == "") {       filenames[i] = inputDir + filenames[i];         }
 173                                                 }
 174
 175                                                 ifstream in;
 176                                                 int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
 177
 178                                                 //if you can't open it, try default location
 179                                                 if (ableToOpen == 1) {
 180                                                         if (m->getDefaultPath() != "") { //default path is set
 181                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
 182                                                                 m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 183                                                                 ifstream in2;
 184                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 185                                                                 in2.close();
 186                                                                 filenames[i] = tryPath;
 187                                                         }
 188                                                 }
 189
 190                                                 //if you can't open it, try default location
 191                                                 if (ableToOpen == 1) {
 192                                                         if (m->getOutputDir() != "") { //default path is set
 193                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(filenames[i]);
 194                                                                 m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 195                                                                 ifstream in2;
 196                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 197                                                                 in2.close();
 198                                                                 filenames[i] = tryPath;
 199                                                         }
 200                                                 }
 201
 202                                                 in.close();
 203
 204                                                 if (ableToOpen == 1) {
 205                                                         m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 206                                                         //erase from file list
 207                                                         filenames.erase(filenames.begin()+i);
 208                                                         i--;
 209                                                 }else { m->setSFFFile(filenames[i]); }
 210                                         }
 211                                 }
 212
 213                                 //make sure there is at least one valid file left
 214                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 215                         }
 216
 217                         accnosName = validParameter.validFile(parameters, "accnos", false);
 218                         if (accnosName == "not found") { accnosName = "";  }
 219                         else {
 220                                 hasAccnos = true;
 221                                 m->splitAtDash(accnosName, accnosFileNames);
 222
 223                                 //go through files and make sure they are good, if not, then disregard them
 224                                 for (int i = 0; i < accnosFileNames.size(); i++) {
 225                                         bool ignore = false;
 226                                         if (accnosFileNames[i] == "current") {
 227                                                 accnosFileNames[i] = m->getAccnosFile();
 228                                                 if (accnosFileNames[i] != "") {  m->mothurOut("Using " + accnosFileNames[i] + " as input file for the accnos parameter where you had given current."); m->mothurOutEndLine(); }
 229                                                 else {
 230                                                         m->mothurOut("You have no current accnosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 231                                                         //erase from file list
 232                                                         accnosFileNames.erase(accnosFileNames.begin()+i);
 233                                                         i--;
 234                                                 }
 235                                         }
 236
 237                                         if (!ignore) {
 238
 239                                                 if (inputDir != "") {
 240                                                         string path = m->hasPath(accnosFileNames[i]);
 241                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 242                                                         if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }
 243                                                 }
 244
 245                                                 ifstream in;
 246                                                 int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
 247
 248                                                 //if you can't open it, try default location
 249                                                 if (ableToOpen == 1) {
 250                                                         if (m->getDefaultPath() != "") { //default path is set
 251                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
 252                                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 253                                                                 ifstream in2;
 254                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 255                                                                 in2.close();
 256                                                                 accnosFileNames[i] = tryPath;
 257                                                         }
 258                                                 }
 259                                                 //if you can't open it, try default location
 260                                                 if (ableToOpen == 1) {
 261                                                         if (m->getOutputDir() != "") { //default path is set
 262                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
 263                                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 264                                                                 ifstream in2;
 265                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 266                                                                 in2.close();
 267                                                                 accnosFileNames[i] = tryPath;
 268                                                         }
 269                                                 }
 270                                                 in.close();
 271
 272                                                 if (ableToOpen == 1) {
 273                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 274                                                         //erase from file list
 275                                                         accnosFileNames.erase(accnosFileNames.begin()+i);
 276                                                         i--;
 277                                                 }
 278                                         }
 279                                 }
 280
 281                                 //make sure there is at least one valid file left
 282                                 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 283                         }
 284
 285             oligosfile = validParameter.validFile(parameters, "oligos", false);
 286                         if (oligosfile == "not found") { oligosfile = "";  }
 287                         else {
 288                                 hasOligos = true;
 289                                 m->splitAtDash(oligosfile, oligosFileNames);
 290
 291                                 //go through files and make sure they are good, if not, then disregard them
 292                                 for (int i = 0; i < oligosFileNames.size(); i++) {
 293                                         bool ignore = false;
 294                                         if (oligosFileNames[i] == "current") {
 295                                                 oligosFileNames[i] = m->getOligosFile();
 296                                                 if (oligosFileNames[i] != "") {  m->mothurOut("Using " + oligosFileNames[i] + " as input file for the accnos parameter where you had given current."); m->mothurOutEndLine(); }
 297                                                 else {
 298                                                         m->mothurOut("You have no current oligosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 299                                                         //erase from file list
 300                                                         oligosFileNames.erase(oligosFileNames.begin()+i);
 301                                                         i--;
 302                                                 }
 303                                         }
 304
 305                                         if (!ignore) {
 306
 307                                                 if (inputDir != "") {
 308                                                         string path = m->hasPath(oligosFileNames[i]);
 309                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 310                                                         if (path == "") {       oligosFileNames[i] = inputDir + oligosFileNames[i];             }
 311                                                 }
 312
 313                                                 ifstream in;
 314                                                 int ableToOpen = m->openInputFile(oligosFileNames[i], in, "noerror");
 315
 316                                                 //if you can't open it, try default location
 317                                                 if (ableToOpen == 1) {
 318                                                         if (m->getDefaultPath() != "") { //default path is set
 319                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(oligosFileNames[i]);
 320                                                                 m->mothurOut("Unable to open " + oligosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 321                                                                 ifstream in2;
 322                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 323                                                                 in2.close();
 324                                                                 oligosFileNames[i] = tryPath;
 325                                                         }
 326                                                 }
 327                                                 //if you can't open it, try default location
 328                                                 if (ableToOpen == 1) {
 329                                                         if (m->getOutputDir() != "") { //default path is set
 330                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(oligosFileNames[i]);
 331                                                                 m->mothurOut("Unable to open " + oligosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 332                                                                 ifstream in2;
 333                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 334                                                                 in2.close();
 335                                                                 oligosFileNames[i] = tryPath;
 336                                                         }
 337                                                 }
 338                                                 in.close();
 339
 340                                                 if (ableToOpen == 1) {
 341                                                         m->mothurOut("Unable to open " + oligosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 342                                                         //erase from file list
 343                                                         oligosFileNames.erase(oligosFileNames.begin()+i);
 344                                                         i--;
 345                                                 }
 346                                         }
 347                                 }
 348
 349                                 //make sure there is at least one valid file left
 350                                 if (oligosFileNames.size() == 0) { m->mothurOut("no valid oligos files."); m->mothurOutEndLine(); abort = true; }
 351                         }
 352
 353                         if (hasOligos) {
 354                 split = 2;
 355                                 if (oligosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a oligos file, you must have one for each sff file."); m->mothurOutEndLine(); }
 356                         }
 357
 358                         if (hasAccnos) {
 359                                 if (accnosFileNames.size() != filenames.size()) { abort = true; m->mothurOut("If you provide a accnos file, you must have one for each sff file."); m->mothurOutEndLine(); }
 360                         }
 361
 362                         string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }
 363                         qual = m->isTrue(temp);
 364
 365                         temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
 366                         fasta = m->isTrue(temp);
 367
 368                         temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "T";                             }
 369                         flow = m->isTrue(temp);
 370
 371                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
 372                         trim = m->isTrue(temp);
 373
 374             temp = validParameter.validFile(parameters, "bdiffs", false);               if (temp == "not found") { temp = "0"; }
 375                         m->mothurConvert(temp, bdiffs);
 376
 377                         temp = validParameter.validFile(parameters, "pdiffs", false);           if (temp == "not found") { temp = "0"; }
 378                         m->mothurConvert(temp, pdiffs);
 379
 380             temp = validParameter.validFile(parameters, "ldiffs", false);               if (temp == "not found") { temp = "0"; }
 381                         m->mothurConvert(temp, ldiffs);
 382
 383             temp = validParameter.validFile(parameters, "sdiffs", false);               if (temp == "not found") { temp = "0"; }
 384                         m->mothurConvert(temp, sdiffs);
 385
 386                         temp = validParameter.validFile(parameters, "tdiffs", false);           if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs;  temp = toString(tempTotal); }
 387                         m->mothurConvert(temp, tdiffs);
 388
 389                         if(tdiffs == 0){        tdiffs = bdiffs + pdiffs + ldiffs + sdiffs;     }
 390
 391                         temp = validParameter.validFile(parameters, "sfftxt", false);
 392                         if (temp == "not found")        {       temp = "F";      sfftxt = false; sfftxtFilename = "";           }
 393                         else if (m->isTrue(temp))       {       sfftxt = true;          sfftxtFilename = "";                            }
 394                         else {
 395                                 //you are a filename
 396                                 if (inputDir != "") {
 397                                         map<string,string>::iterator it = parameters.find("sfftxt");
 398                                         //user has given a template file
 399                                         if(it != parameters.end()){
 400                                                 string path = m->hasPath(it->second);
 401                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 402                                                 if (path == "") {       parameters["sfftxt"] = inputDir + it->second;           }
 403                                         }
 404                                 }
 405
 406                                 sfftxtFilename = validParameter.validFile(parameters, "sfftxt", true);
 407                                 if (sfftxtFilename == "not found") { sfftxtFilename = "";  }
 408                                 else if (sfftxtFilename == "not open") { sfftxtFilename = "";  }
 409                         }
 410
 411                         if ((sfftxtFilename == "") && (filenames.size() == 0)) {
 412                                 //if there is a current sff file, use it
 413                                 string filename = m->getSFFFile();
 414                                 if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
 415                                 else {  m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true;  }
 416                         }
 417
 418
 419                 }
 420         }
 421         catch(exception& e) {
 422                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 423                 exit(1);
 424         }
 425 }
 426 //**********************************************************************************************************************
 427 int SffInfoCommand::execute(){
 428         try {
 429                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 430
 431                 for (int s = 0; s < filenames.size(); s++) {
 432
 433                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
 434
 435                         int start = time(NULL);
 436
 437             filenames[s] = m->getFullPathName(filenames[s]);
 438                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 439
 440                         string accnos = "";
 441                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 442
 443             string oligos = "";
 444             if (hasOligos) { oligos = oligosFileNames[s]; }
 445
 446                         int numReads = extractSffInfo(filenames[s], accnos, oligos);
 447
 448                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 449                 }
 450
 451                 if (sfftxtFilename != "") {  parseSffTxt(); }
 452
 453                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
 454
 455                 //set fasta file as new current fastafile
 456                 string current = "";
 457                 itTypes = outputTypes.find("fasta");
 458                 if (itTypes != outputTypes.end()) {
 459                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 460                 }
 461
 462                 itTypes = outputTypes.find("qfile");
 463                 if (itTypes != outputTypes.end()) {
 464                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 465                 }
 466
 467                 itTypes = outputTypes.find("flow");
 468                 if (itTypes != outputTypes.end()) {
 469                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
 470                 }
 471
 472                 //report output filenames
 473                 m->mothurOutEndLine();
 474                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 475                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 476                 m->mothurOutEndLine();
 477
 478                 return 0;
 479         }
 480         catch(exception& e) {
 481                 m->errorOut(e, "SffInfoCommand", "execute");
 482                 exit(1);
 483         }
 484 }
 485 //**********************************************************************************************************************
 486 int SffInfoCommand::extractSffInfo(string input, string accnos, string oligos){
 487         try {
 488                 currentFileName = input;
 489                 if (outputDir == "") {  outputDir += m->hasPath(input); }
 490
 491                 if (accnos != "")       {  readAccnosFile(accnos);  }
 492                 else                            {       seqNames.clear();               }
 493
 494         if (oligos != "")   {   readOligos(oligos);  split = 2;   }
 495
 496                 ofstream outSfftxt, outFasta, outQual, outFlow;
 497                 string outFastaFileName, outQualFileName;
 498         string rootName = outputDir + m->getRootName(m->getSimpleName(input));
 499         if(rootName.find_last_of(".") == rootName.npos){ rootName += "."; }
 500
 501         map<string, string> variables;
 502                 variables["[filename]"] = rootName;
 503                 string sfftxtFileName = getOutputFileName("sfftxt",variables);
 504                 string outFlowFileName = getOutputFileName("flow",variables);
 505                 if (!trim) { variables["[tag]"] = "raw"; }
 506                 outFastaFileName = getOutputFileName("fasta",variables);
 507         outQualFileName = getOutputFileName("qfile",variables);
 508
 509                 if (sfftxt) { m->openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName);  outputTypes["sfftxt"].push_back(sfftxtFileName); }
 510                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 511                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
 512                 if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
 513
 514                 ifstream in;
 515                 in.open(input.c_str(), ios::binary);
 516
 517                 CommonHeader header;
 518                 readCommonHeader(in, header);
 519
 520                 int count = 0;
 521                 mycount = 0;
 522
 523                 //check magic number and version
 524                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 525                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 526
 527                 //print common header
 528                 if (sfftxt) {   printCommonHeader(outSfftxt, header);           }
 529                 if (flow)       {       outFlow << header.numFlowsPerRead << endl;      }
 530
 531                 //read through the sff file
 532                 while (!in.eof()) {
 533
 534                         bool print = true;
 535
 536                         //read data
 537                         seqRead read;  Header readheader;
 538                         readSeqData(in, read, header.numFlowsPerRead, readheader);
 539             bool okay = sanityCheck(readheader, read);
 540             if (!okay) { break; }
 541
 542                         //if you have provided an accosfile and this seq is not in it, then dont print
 543                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 544
 545                         //print
 546                         if (print) {
 547                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 548                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 549                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 550                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 551                         }
 552
 553                         count++;
 554                         mycount++;
 555
 556                         //report progress
 557                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 558
 559                         if (m->control_pressed) { count = 0; break;   }
 560
 561                         if (count >= header.numReads) { break; }
 562             //if (count >= 100) { break; }
 563                 }
 564
 565                 //report progress
 566                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 567
 568                 in.close();
 569
 570                 if (sfftxt) {  outSfftxt.close();       }
 571                 if (fasta)      {  outFasta.close();    }
 572                 if (qual)       {  outQual.close();             }
 573                 if (flow)       {  outFlow.close();             }
 574
 575         if (split > 1) {
 576             //create new common headers for each file with the correct number of reads
 577             adjustCommonHeader(header);
 578
 579                         map<string, string>::iterator it;
 580                         set<string> namesToRemove;
 581                         for(int i=0;i<filehandles.size();i++){
 582                                 for(int j=0;j<filehandles[0].size();j++){
 583                                         if (filehandles[i][j] != "") {
 584                                                 if (namesToRemove.count(filehandles[i][j]) == 0) {
 585                                                         if(m->isBlank(filehandles[i][j])){
 586                                                                 m->mothurRemove(filehandles[i][j]);
 587                                 m->mothurRemove(filehandlesHeaders[i][j]);
 588                                                                 namesToRemove.insert(filehandles[i][j]);
 589                             }
 590                                                 }
 591                                         }
 592                                 }
 593                         }
 594
 595             //append new header to reads
 596             for (int i = 0; i < filehandles.size(); i++) {
 597                 for (int j = 0; j < filehandles[i].size(); j++) {
 598                     m->appendFiles(filehandles[i][j], filehandlesHeaders[i][j]);
 599                     m->renameFile(filehandlesHeaders[i][j], filehandles[i][j]);
 600                     m->mothurRemove(filehandlesHeaders[i][j]);
 601                     if (numSplitReads[i][j] == 0) { m->mothurRemove(filehandles[i][j]); }
 602                 }
 603             }
 604
 605                         //remove names for outputFileNames, just cleans up the output
 606                         for(int i = 0; i < outputNames.size(); i++) {
 607                 if (namesToRemove.count(outputNames[i]) != 0) {
 608                     outputNames.erase(outputNames.begin()+i);
 609                     i--;
 610                 }
 611             }
 612
 613             if(m->isBlank(noMatchFile)){  m->mothurRemove(noMatchFile); }
 614             else { outputNames.push_back(noMatchFile); outputTypes["sff"].push_back(noMatchFile); }
 615         }
 616
 617                 return count;
 618         }
 619         catch(exception& e) {
 620                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 621                 exit(1);
 622         }
 623 }
 624 //**********************************************************************************************************************
 625 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 626         try {
 627
 628                 if (!in.eof()) {
 629
 630                         //read magic number
 631                         char buffer[4];
 632                         in.read(buffer, 4);
 633                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 634
 635                         //read version
 636                         char buffer9[4];
 637                         in.read(buffer9, 4);
 638                         header.version = "";
 639                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i]));  }
 640
 641                         //read offset
 642                         char buffer2 [8];
 643                         in.read(buffer2, 8);
 644                         header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
 645
 646                         //read index length
 647                         char buffer3 [4];
 648                         in.read(buffer3, 4);
 649                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 650
 651                         //read num reads
 652                         char buffer4 [4];
 653                         in.read(buffer4, 4);
 654                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 655
 656             if (m->debug) { m->mothurOut("[DEBUG]: numReads = " + toString(header.numReads) + "\n"); }
 657
 658                         //read header length
 659                         char buffer5 [2];
 660                         in.read(buffer5, 2);
 661                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 662
 663                         //read key length
 664                         char buffer6 [2];
 665                         in.read(buffer6, 2);
 666                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 667
 668                         //read number of flow reads
 669                         char buffer7 [2];
 670                         in.read(buffer7, 2);
 671                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 672
 673                         //read format code
 674                         char buffer8 [1];
 675                         in.read(buffer8, 1);
 676                         header.flogramFormatCode = (int)(buffer8[0]);
 677
 678                         //read flow chars
 679                         char* tempBuffer = new char[header.numFlowsPerRead];
 680                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 681                         header.flowChars = tempBuffer;
 682                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 683                         delete[] tempBuffer;
 684
 685                         //read key
 686                         char* tempBuffer2 = new char[header.keyLength];
 687                         in.read(&(*tempBuffer2), header.keyLength);
 688                         header.keySequence = tempBuffer2;
 689                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 690                         delete[] tempBuffer2;
 691
 692                         /* Pad to 8 chars */
 693                         unsigned long long spotInFile = in.tellg();
 694                         unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 695                         in.seekg(spot);
 696
 697         }else{
 698                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 699                 }
 700
 701                 return 0;
 702
 703         }
 704         catch(exception& e) {
 705                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 706                 exit(1);
 707         }
 708 }
 709 //**********************************************************************************************************************
 710 int SffInfoCommand::adjustCommonHeader(CommonHeader header){
 711         try {
 712
 713         char* mybuffer = new char[4];
 714         ifstream in;
 715         in.open(currentFileName.c_str(), ios::binary);
 716
 717         //magic number
 718         in.read(mybuffer,4);
 719         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 720             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 721                 ofstream out;
 722                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 723                 out.write(mybuffer, in.gcount());
 724                 out.close();
 725             }
 726         }
 727         delete[] mybuffer;
 728
 729         //version
 730         mybuffer = new char[4];
 731         in.read(mybuffer,4);
 732         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 733             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 734                 ofstream out;
 735                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 736                 out.write(mybuffer, in.gcount());
 737                 out.close();
 738             }
 739         }
 740         delete[] mybuffer;
 741
 742         //offset
 743         mybuffer = new char[8];
 744         in.read(mybuffer,8);
 745         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 746             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 747                 unsigned long long offset = 0;
 748                 char* thisbuffer = new char[8];
 749                 thisbuffer[0] = (offset >> 56) & 0xFF;
 750                 thisbuffer[1] = (offset >> 48) & 0xFF;
 751                 thisbuffer[2] = (offset >> 40) & 0xFF;
 752                 thisbuffer[3] = (offset >> 32) & 0xFF;
 753                 thisbuffer[4] = (offset >> 24) & 0xFF;
 754                 thisbuffer[5] = (offset >> 16) & 0xFF;
 755                 thisbuffer[6] = (offset >> 8) & 0xFF;
 756                 thisbuffer[7] = offset & 0xFF;
 757                 ofstream out;
 758                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 759                 out.write(thisbuffer, 8);
 760                 out.close();
 761             }
 762         }
 763         delete[] mybuffer;
 764
 765
 766         //read index length
 767                 mybuffer = new char[4];
 768         in.read(mybuffer,4);
 769         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 770             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 771                 ofstream out;
 772                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 773                 unsigned int offset = 0;
 774                 char* thisbuffer = new char[4];
 775                 thisbuffer[0] = (offset >> 24) & 0xFF;
 776                 thisbuffer[1] = (offset >> 16) & 0xFF;
 777                 thisbuffer[2] = (offset >> 8) & 0xFF;
 778                 thisbuffer[3] = offset & 0xFF;
 779                 out.write(thisbuffer, 4);
 780                 out.close();
 781             }
 782         }
 783         delete[] mybuffer;
 784
 785         //change num reads
 786         mybuffer = new char[4];
 787         in.read(mybuffer,4);
 788         delete[] mybuffer;
 789         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 790             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 791                 ofstream out;
 792                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 793                 //convert number of reads to 4 byte char*
 794                 char* thisbuffer = new char[4];
 795                 if ((m->findEdianness()) == "BIG_ENDIAN") {
 796                     thisbuffer[0] = (numSplitReads[i][j] >> 24) & 0xFF;
 797                     thisbuffer[1] = (numSplitReads[i][j] >> 16) & 0xFF;
 798                     thisbuffer[2] = (numSplitReads[i][j] >> 8) & 0xFF;
 799                     thisbuffer[3] = numSplitReads[i][j] & 0xFF;
 800                 }else {
 801                     thisbuffer[0] = numSplitReads[i][j] & 0xFF;
 802                     thisbuffer[1] = (numSplitReads[i][j] >> 8) & 0xFF;
 803                     thisbuffer[2] = (numSplitReads[i][j] >> 16) & 0xFF;
 804                     thisbuffer[3] = (numSplitReads[i][j] >> 24) & 0xFF;
 805                  }
 806                 out.write(thisbuffer, 4);
 807                 out.close();
 808                 delete[] thisbuffer;
 809             }
 810         }
 811
 812         //read header length
 813         mybuffer = new char[2];
 814         in.read(mybuffer,2);
 815         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 816             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 817                 ofstream out;
 818                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 819                 out.write(mybuffer, in.gcount());
 820                 out.close();
 821             }
 822         }
 823         delete[] mybuffer;
 824
 825         //read key length
 826         mybuffer = new char[2];
 827         in.read(mybuffer,2);
 828         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 829             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 830                 ofstream out;
 831                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 832                 out.write(mybuffer, in.gcount());
 833                 out.close();
 834             }
 835         }
 836         delete[] mybuffer;
 837
 838         //read number of flow reads
 839         mybuffer = new char[2];
 840         in.read(mybuffer,2);
 841         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 842             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 843                 ofstream out;
 844                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 845                 out.write(mybuffer, in.gcount());
 846                 out.close();
 847             }
 848         }
 849         delete[] mybuffer;
 850
 851         //read format code
 852         mybuffer = new char[1];
 853         in.read(mybuffer,1);
 854         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 855             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 856                 ofstream out;
 857                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 858                 out.write(mybuffer, in.gcount());
 859                 out.close();
 860             }
 861         }
 862         delete[] mybuffer;
 863
 864         //read flow chars
 865         mybuffer = new char[header.numFlowsPerRead];
 866         in.read(mybuffer,header.numFlowsPerRead);
 867         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 868             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 869                 ofstream out;
 870                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 871                 out.write(mybuffer, in.gcount());
 872                 out.close();
 873             }
 874         }
 875         delete[] mybuffer;
 876
 877         //read key
 878         mybuffer = new char[header.keyLength];
 879         in.read(mybuffer,header.keyLength);
 880         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 881             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 882                 ofstream out;
 883                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 884                 out.write(mybuffer, in.gcount());
 885                 out.close();
 886             }
 887         }
 888         delete[] mybuffer;
 889
 890
 891         /* Pad to 8 chars */
 892         unsigned long long spotInFile = in.tellg();
 893         unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 894         in.seekg(spot);
 895
 896         mybuffer = new char[spot-spotInFile];
 897         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 898             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 899                 ofstream out;
 900                 m->openOutputFileBinaryAppend(filehandlesHeaders[i][j], out);
 901                 out.write(mybuffer, spot-spotInFile);
 902                 out.close();
 903             }
 904         }
 905         delete[] mybuffer;
 906         in.close();
 907                 return 0;
 908
 909         }
 910         catch(exception& e) {
 911                 m->errorOut(e, "SffInfoCommand", "adjustCommonHeader");
 912                 exit(1);
 913         }
 914 }
 915 //**********************************************************************************************************************
 916 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, Header& header){
 917         try {
 918         unsigned long long startSpotInFile = in.tellg();
 919                 if (!in.eof()) {
 920
 921             /*****************************************/
 922             //read header
 923
 924             //read header length
 925                         char buffer [2];
 926                         in.read(buffer, 2);
 927                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 928
 929                         //read name length
 930                         char buffer2 [2];
 931                         in.read(buffer2, 2);
 932                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 933
 934                         //read num bases
 935                         char buffer3 [4];
 936                         in.read(buffer3, 4);
 937                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 938
 939
 940                         //read clip qual left
 941                         char buffer4 [2];
 942                         in.read(buffer4, 2);
 943                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 944                         header.clipQualLeft = 5;
 945
 946
 947                         //read clip qual right
 948                         char buffer5 [2];
 949                         in.read(buffer5, 2);
 950                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 951
 952
 953                         //read clipAdapterLeft
 954                         char buffer6 [2];
 955                         in.read(buffer6, 2);
 956                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 957
 958
 959                         //read clipAdapterRight
 960                         char buffer7 [2];
 961                         in.read(buffer7, 2);
 962                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 963
 964
 965                         //read name
 966                         char* tempBuffer = new char[header.nameLength];
 967                         in.read(&(*tempBuffer), header.nameLength);
 968                         header.name = tempBuffer;
 969                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 970
 971                         delete[] tempBuffer;
 972
 973                         //extract info from name
 974                         decodeName(header.timestamp, header.region, header.xy, header.name);
 975
 976                         /* Pad to 8 chars */
 977                         unsigned long long spotInFile = in.tellg();
 978                         unsigned long long spot = (spotInFile + 7)& ~7;
 979                         in.seekg(spot);
 980
 981             /*****************************************/
 982             //sequence read
 983
 984                         //read flowgram
 985                         read.flowgram.resize(numFlowReads);
 986                         for (int i = 0; i < numFlowReads; i++) {
 987                                 char buffer [2];
 988                                 in.read(buffer, 2);
 989                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 990                         }
 991
 992                         //read flowIndex
 993                         read.flowIndex.resize(header.numBases);
 994                         for (int i = 0; i < header.numBases; i++) {
 995                                 char temp[1];
 996                                 in.read(temp, 1);
 997                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 998                         }
 999
1000                         //read bases
1001                         char* tempBuffer6 = new char[header.numBases];
1002                         in.read(&(*tempBuffer6), header.numBases);
1003                         read.bases = tempBuffer6;
1004                         if (read.bases.length() > header.numBases) { read.bases = read.bases.substr(0, header.numBases);  }
1005                         delete[] tempBuffer6;
1006
1007                         //read qual scores
1008                         read.qualScores.resize(header.numBases);
1009                         for (int i = 0; i < header.numBases; i++) {
1010                                 char temp[1];
1011                                 in.read(temp, 1);
1012                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
1013                         }
1014
1015                         /* Pad to 8 chars */
1016                         spotInFile = in.tellg();
1017                         spot = (spotInFile + 7)& ~7;
1018                         in.seekg(spot);
1019
1020             if (split > 1) {
1021                 char * mybuffer;
1022                 mybuffer = new char [spot-startSpotInFile];
1023                 ifstream in2;
1024                 in2.open(currentFileName.c_str(), ios::binary);
1025                 in2.seekg(startSpotInFile);
1026                 in2.read(mybuffer,spot-startSpotInFile);
1027                 in2.close();
1028
1029                 int barcodeIndex, primerIndex;
1030                 int trashCodeLength = findGroup(header, read, barcodeIndex, primerIndex);
1031
1032                 if(trashCodeLength == 0){
1033                     //cout << header.name << " length = " << spot << '\t' << startSpotInFile << '\t' << in2.gcount() << endl;
1034
1035                     ofstream out;
1036                     m->openOutputFileBinaryAppend(filehandles[barcodeIndex][primerIndex], out);
1037                     out.write(mybuffer, in2.gcount());
1038                     out.close();
1039                     numSplitReads[barcodeIndex][primerIndex]++;
1040                                 }
1041                                 else{
1042                                         ofstream out;
1043                     m->openOutputFileBinaryAppend(noMatchFile, out);
1044                     out.write(mybuffer, in2.gcount());
1045                     out.close();
1046                                 }
1047                                 delete[] mybuffer;
1048                         }
1049                 }else{
1050                         m->mothurOut("Error reading."); m->mothurOutEndLine();
1051                 }
1052
1053                 return 0;
1054         }
1055         catch(exception& e) {
1056                 m->errorOut(e, "SffInfoCommand", "readSeqData");
1057                 exit(1);
1058         }
1059 }
1060 //**********************************************************************************************************************
1061 int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& primer) {
1062         try {
1063         //find group read belongs to
1064         TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
1065
1066         int success = 1;
1067         string trashCode = "";
1068         int currentSeqsDiffs = 0;
1069
1070         string seq = read.bases;
1071
1072         if (trim) {
1073             if(header.clipQualRight < header.clipQualLeft){
1074                 if (header.clipQualRight == 0) { //don't trim right
1075                     seq = seq.substr(header.clipQualLeft-1);
1076                 }else {
1077                     seq = "NNNN";
1078                 }
1079             }
1080             else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
1081                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
1082             }
1083             else {
1084                 seq = seq.substr(header.clipQualLeft-1);
1085             }
1086         }else{
1087             //if you wanted the sfftxt then you already converted the bases to the right case
1088             if (!sfftxt) {
1089                 int endValue = header.clipQualRight;
1090                 //make the bases you want to clip lowercase and the bases you want to keep upper case
1091                 if(endValue == 0){      endValue = seq.length();        }
1092                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
1093                 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++)  {   seq[i] = toupper(seq[i]);  }
1094                 for (int i = (endValue-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
1095             }
1096         }
1097
1098         Sequence currSeq(header.name, seq);
1099         QualityScores currQual;
1100
1101         if(numLinkers != 0){
1102             success = trimOligos.stripLinker(currSeq, currQual);
1103             if(success > ldiffs)                {       trashCode += 'k';       }
1104             else{ currentSeqsDiffs += success;  }
1105
1106         }
1107
1108         if(barcodes.size() != 0){
1109             success = trimOligos.stripBarcode(currSeq, currQual, barcode);
1110             if(success > bdiffs)                {       trashCode += 'b';       }
1111             else{ currentSeqsDiffs += success;  }
1112         }
1113
1114         if(numSpacers != 0){
1115             success = trimOligos.stripSpacer(currSeq, currQual);
1116             if(success > sdiffs)                {       trashCode += 's';       }
1117             else{ currentSeqsDiffs += success;  }
1118
1119         }
1120
1121         if(numFPrimers != 0){
1122             success = trimOligos.stripForward(currSeq, currQual, primer, true);
1123             if(success > pdiffs)                {       trashCode += 'f';       }
1124             else{ currentSeqsDiffs += success;  }
1125         }
1126
1127         if (currentSeqsDiffs > tdiffs)  {       trashCode += 't';   }
1128
1129         if(revPrimer.size() != 0){
1130             success = trimOligos.stripReverse(currSeq, currQual);
1131             if(!success)                                {       trashCode += 'r';       }
1132         }
1133
1134
1135         return trashCode.length();
1136     }
1137         catch(exception& e) {
1138                 m->errorOut(e, "SffInfoCommand", "findGroup");
1139                 exit(1);
1140         }
1141 }
1142 //**********************************************************************************************************************
1143 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
1144         try {
1145
1146                 if (name.length() >= 6) {
1147                         string time = name.substr(0, 6);
1148                         unsigned int timeNum = m->fromBase36(time);
1149
1150                         int q1 = timeNum / 60;
1151                         int sec = timeNum - 60 * q1;
1152                         int q2 = q1 / 60;
1153                         int minute = q1 - 60 * q2;
1154                         int q3 = q2 / 24;
1155                         int hr = q2 - 24 * q3;
1156                         int q4 = q3 / 32;
1157                         int day = q3 - 32 * q4;
1158                         int q5 = q4 / 13;
1159                         int mon = q4 - 13 * q5;
1160                         int year = 2000 + q5;
1161
1162                         timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
1163                 }
1164
1165                 if (name.length() >= 9) {
1166                         region = name.substr(7, 2);
1167
1168                         string xyNum = name.substr(9);
1169                         unsigned int myXy = m->fromBase36(xyNum);
1170                         int x = myXy >> 12;
1171                         int y = myXy & 4095;
1172
1173                         xy = toString(x) + "_" + toString(y);
1174                 }
1175
1176                 return 0;
1177         }
1178         catch(exception& e) {
1179                 m->errorOut(e, "SffInfoCommand", "decodeName");
1180                 exit(1);
1181         }
1182 }
1183 //**********************************************************************************************************************
1184 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
1185         try {
1186
1187                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
1188                 out << "Version: " << header.version << endl;
1189                 out << "Index Offset: " << header.indexOffset << endl;
1190                 out << "Index Length: " << header.indexLength << endl;
1191                 out << "Number of Reads: " << header.numReads << endl;
1192                 out << "Header Length: " << header.headerLength << endl;
1193                 out << "Key Length: " << header.keyLength << endl;
1194                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
1195                 out << "Format Code: " << header.flogramFormatCode << endl;
1196                 out << "Flow Chars: " << header.flowChars << endl;
1197                 out << "Key Sequence: " << header.keySequence << endl << endl;
1198
1199                 return 0;
1200         }
1201         catch(exception& e) {
1202                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
1203                 exit(1);
1204         }
1205 }
1206 //**********************************************************************************************************************
1207 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
1208         try {
1209
1210                 out << ">" << header.name << endl;
1211                 out << "Run Prefix: " << header.timestamp << endl;
1212                 out << "Region #:  " << header.region << endl;
1213                 out << "XY Location: " << header.xy << endl << endl;
1214
1215                 out << "Run Name:  " << endl;
1216                 out << "Analysis Name:  " << endl;
1217                 out << "Full Path: " << endl << endl;
1218
1219                 out << "Read Header Len: " << header.headerLength << endl;
1220                 out << "Name Length: " << header.nameLength << endl;
1221                 out << "# of Bases: " << header.numBases << endl;
1222                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
1223                 out << "Clip Qual Right: " << header.clipQualRight << endl;
1224                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
1225                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
1226
1227                 return 0;
1228         }
1229         catch(exception& e) {
1230                 m->errorOut(e, "SffInfoCommand", "printHeader");
1231                 exit(1);
1232         }
1233 }
1234 //**********************************************************************************************************************
1235 bool SffInfoCommand::sanityCheck(Header& header, seqRead& read) {
1236         try {
1237         bool okay = true;
1238         string message = "[WARNING]: Your sff file may be corrupted! Sequence: " + header.name + "\n";
1239
1240         if (header.clipQualLeft > read.bases.length()) {
1241             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
1242         }
1243         if (header.clipQualRight > read.bases.length()) {
1244             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
1245         }
1246         if (header.clipQualLeft > read.qualScores.size()) {
1247             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
1248         }
1249         if (header.clipQualRight > read.qualScores.size()) {
1250             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
1251         }
1252
1253         if (okay == false) {
1254             m->mothurOut(message); m->mothurOutEndLine();
1255         }
1256
1257                 return okay;
1258         }
1259         catch(exception& e) {
1260                 m->errorOut(e, "SffInfoCommand", "sanityCheck");
1261                 exit(1);
1262         }
1263 }
1264 //**********************************************************************************************************************
1265 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
1266         try {
1267                 out << "Flowgram: ";
1268                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
1269
1270                 out << endl <<  "Flow Indexes: ";
1271                 int sum = 0;
1272                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
1273
1274                 //make the bases you want to clip lowercase and the bases you want to keep upper case
1275         int endValue = header.clipQualRight;
1276                 if(endValue == 0){      endValue = read.bases.length(); }
1277                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
1278                 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
1279                 for (int i = (endValue-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
1280
1281                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
1282                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
1283
1284
1285                 out << endl << endl;
1286
1287                 return 0;
1288         }
1289         catch(exception& e) {
1290                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
1291                 exit(1);
1292         }
1293 }
1294 //**********************************************************************************************************************
1295 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
1296         try {
1297                 string seq = read.bases;
1298
1299         if (trim) {
1300                         if(header.clipQualRight < header.clipQualLeft){
1301                                 if (header.clipQualRight == 0) { //don't trim right
1302                     seq = seq.substr(header.clipQualLeft-1);
1303                 }else {
1304                     seq = "NNNN";
1305                 }
1306                         }
1307                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
1308                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
1309                         }
1310                         else {
1311                                 seq = seq.substr(header.clipQualLeft-1);
1312                         }
1313                 }else{
1314                         //if you wanted the sfftxt then you already converted the bases to the right case
1315                         if (!sfftxt) {
1316                 int endValue = header.clipQualRight;
1317                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
1318                                 if(endValue == 0){      endValue = seq.length();        }
1319                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
1320                                 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++)  {   seq[i] = toupper(seq[i]);  }
1321                                 for (int i = (endValue-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
1322                         }
1323                 }
1324
1325                 out << ">" << header.name  << " xy=" << header.xy << endl;
1326                 out << seq << endl;
1327
1328                 return 0;
1329         }
1330         catch(exception& e) {
1331                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
1332                 exit(1);
1333         }
1334 }
1335
1336 //**********************************************************************************************************************
1337 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
1338         try {
1339
1340                 if (trim) {
1341                         if(header.clipQualRight < header.clipQualLeft){
1342                 if (header.clipQualRight == 0) { //don't trim right
1343                     out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
1344                     for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';       }
1345                 }else {
1346                     out << ">" << header.name << " xy=" << header.xy << endl;
1347                     out << "0\t0\t0\t0";
1348                 }
1349                         }
1350                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
1351                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
1352                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
1353                         }
1354                         else{
1355                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
1356                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
1357                         }
1358                 }else{
1359                         out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
1360                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
1361                 }
1362
1363                 out << endl;
1364
1365                 return 0;
1366         }
1367         catch(exception& e) {
1368                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
1369                 exit(1);
1370         }
1371 }
1372
1373 //**********************************************************************************************************************
1374 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
1375         try {
1376
1377         int endValue = header.clipQualRight;
1378         if (header.clipQualRight == 0) {
1379             endValue = read.flowIndex.size();
1380             if (m->debug) { m->mothurOut("[DEBUG]: " + header.name + " has clipQualRight=0.\n"); }
1381         }
1382         if(endValue > header.clipQualLeft){
1383
1384             int rightIndex = 0;
1385             for (int i = 0; i < endValue; i++) {  rightIndex +=  read.flowIndex[i];      }
1386
1387             out << header.name << ' ' << rightIndex;
1388             for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
1389             out << endl;
1390         }
1391
1392
1393                 return 0;
1394         }
1395         catch(exception& e) {
1396                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
1397                 exit(1);
1398         }
1399 }
1400 //**********************************************************************************************************************
1401 int SffInfoCommand::readAccnosFile(string filename) {
1402         try {
1403                 //remove old names
1404                 seqNames.clear();
1405
1406                 ifstream in;
1407                 m->openInputFile(filename, in);
1408                 string name;
1409
1410                 while(!in.eof()){
1411                         in >> name; m->gobble(in);
1412
1413                         seqNames.insert(name);
1414
1415                         if (m->control_pressed) { seqNames.clear(); break; }
1416                 }
1417                 in.close();
1418
1419                 return 0;
1420         }
1421         catch(exception& e) {
1422                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
1423                 exit(1);
1424         }
1425 }
1426 //**********************************************************************************************************************
1427 int SffInfoCommand::parseSffTxt() {
1428         try {
1429
1430                 ifstream inSFF;
1431                 m->openInputFile(sfftxtFilename, inSFF);
1432
1433                 if (outputDir == "") {  outputDir += m->hasPath(sfftxtFilename); }
1434
1435                 //output file names
1436                 ofstream outFasta, outQual, outFlow;
1437                 string outFastaFileName, outQualFileName;
1438                 string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
1439                 if (fileRoot.length() > 0) {
1440                         //rip off last .
1441                         fileRoot = fileRoot.substr(0, fileRoot.length()-1);
1442                         fileRoot = m->getRootName(fileRoot);
1443                 }
1444
1445         map<string, string> variables;
1446                 variables["[filename]"] = fileRoot;
1447                 string sfftxtFileName = getOutputFileName("sfftxt",variables);
1448                 string outFlowFileName = getOutputFileName("flow",variables);
1449                 if (!trim) { variables["[tag]"] = "raw"; }
1450                 outFastaFileName = getOutputFileName("fasta",variables);
1451         outQualFileName = getOutputFileName("qfile",variables);
1452
1453                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
1454                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
1455                 if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outFlow.setf(ios::fixed, ios::floatfield); outFlow.setf(ios::showpoint); outputTypes["flow"].push_back(outFlowFileName);  }
1456
1457                 //read common header
1458                 string commonHeader = m->getline(inSFF);
1459                 string magicNumber = m->getline(inSFF);
1460                 string version = m->getline(inSFF);
1461                 string indexOffset = m->getline(inSFF);
1462                 string indexLength = m->getline(inSFF);
1463                 int numReads = parseHeaderLineToInt(inSFF);
1464                 string headerLength = m->getline(inSFF);
1465                 string keyLength = m->getline(inSFF);
1466                 int numFlows = parseHeaderLineToInt(inSFF);
1467                 string flowgramCode = m->getline(inSFF);
1468                 string flowChars = m->getline(inSFF);
1469                 string keySequence = m->getline(inSFF);
1470                 m->gobble(inSFF);
1471
1472                 string seqName;
1473
1474                 if (flow)       {       outFlow << numFlows << endl;    }
1475
1476                 for(int i=0;i<numReads;i++){
1477
1478                         //sanity check
1479                         if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
1480
1481                         Header header;
1482
1483                         //parse read header
1484                         inSFF >> seqName;
1485                         seqName = seqName.substr(1);
1486                         m->gobble(inSFF);
1487                         header.name = seqName;
1488
1489                         string runPrefix = parseHeaderLineToString(inSFF);              header.timestamp = runPrefix;
1490                         string regionNumber = parseHeaderLineToString(inSFF);   header.region = regionNumber;
1491                         string xyLocation = parseHeaderLineToString(inSFF);             header.xy = xyLocation;
1492                         m->gobble(inSFF);
1493
1494                         string runName = parseHeaderLineToString(inSFF);
1495                         string analysisName = parseHeaderLineToString(inSFF);
1496                         string fullPath = parseHeaderLineToString(inSFF);
1497                         m->gobble(inSFF);
1498
1499                         string readHeaderLen = parseHeaderLineToString(inSFF);  convert(readHeaderLen, header.headerLength);
1500                         string nameLength = parseHeaderLineToString(inSFF);             convert(nameLength, header.nameLength);
1501                         int numBases = parseHeaderLineToInt(inSFF);                             header.numBases = numBases;
1502                         string clipQualLeft = parseHeaderLineToString(inSFF);   convert(clipQualLeft, header.clipQualLeft);
1503                         int clipQualRight = parseHeaderLineToInt(inSFF);                header.clipQualRight = clipQualRight;
1504                         string clipAdapLeft = parseHeaderLineToString(inSFF);   convert(clipAdapLeft, header.clipAdapterLeft);
1505                         string clipAdapRight = parseHeaderLineToString(inSFF);  convert(clipAdapRight, header.clipAdapterRight);
1506                         m->gobble(inSFF);
1507
1508                         seqRead read;
1509
1510                         //parse read
1511                         vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows);      read.flowgram = flowVector;
1512                         vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
1513
1514                         //adjust for print
1515                         vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
1516                         for (int j = 1; j < flowIndices.size(); j++) {   flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]);   }
1517                         read.flowIndex = flowIndicesAdjusted;
1518
1519                         string bases = parseHeaderLineToString(inSFF);                                                                          read.bases = bases;
1520                         vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases);       read.qualScores = qualityScores;
1521                         m->gobble(inSFF);
1522
1523                         //if you have provided an accosfile and this seq is not in it, then dont print
1524                         bool print = true;
1525                         if (seqNames.size() != 0) {   if (seqNames.count(header.name) == 0) { print = false; }  }
1526
1527                         //print
1528                         if (print) {
1529                                 if (fasta)      {       printFastaSeqData(outFasta, read, header);      }
1530                                 if (qual)       {       printQualSeqData(outQual, read, header);        }
1531                                 if (flow)       {       printFlowSeqData(outFlow, read, header);        }
1532                         }
1533
1534                         //report progress
1535                         if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
1536
1537                         if (m->control_pressed) {  break;  }
1538                 }
1539
1540                 //report progress
1541                 if (!m->control_pressed) {   if((numReads) % 10000 != 0){       m->mothurOut(toString(numReads)); m->mothurOutEndLine();                }  }
1542
1543                 inSFF.close();
1544
1545                 if (fasta)      {  outFasta.close();    }
1546                 if (qual)       {  outQual.close();             }
1547                 if (flow)       {  outFlow.close();             }
1548
1549                 return 0;
1550         }
1551         catch(exception& e) {
1552                 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
1553                 exit(1);
1554         }
1555 }
1556 //**********************************************************************************************************************
1557
1558 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
1559         try {
1560                 int number;
1561
1562                 while (!file.eof())     {
1563
1564                         char c = file.get();
1565                         if (c == ':'){
1566                                 file >> number;
1567                                 break;
1568                         }
1569
1570                 }
1571                 m->gobble(file);
1572                 return number;
1573         }
1574         catch(exception& e) {
1575                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
1576                 exit(1);
1577         }
1578
1579 }
1580
1581 //**********************************************************************************************************************
1582
1583 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
1584         try {
1585                 string text;
1586
1587                 while (!file.eof())     {
1588                         char c = file.get();
1589
1590                         if (c == ':'){
1591                                 //m->gobble(file);
1592                                 //text = m->getline(file);
1593                                 file >> text;
1594                                 break;
1595                         }
1596                 }
1597                 m->gobble(file);
1598
1599                 return text;
1600         }
1601         catch(exception& e) {
1602                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
1603                 exit(1);
1604         }
1605 }
1606
1607 //**********************************************************************************************************************
1608
1609 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
1610         try {
1611                 vector<unsigned short> floatVector(length);
1612
1613                 while (!file.eof())     {
1614                         char c = file.get();
1615                         if (c == ':'){
1616                                 float temp;
1617                                 for(int i=0;i<length;i++){
1618                                         file >> temp;
1619                                         floatVector[i] = temp * 100;
1620                                 }
1621                                 break;
1622                         }
1623                 }
1624                 m->gobble(file);
1625                 return floatVector;
1626         }
1627         catch(exception& e) {
1628                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
1629                 exit(1);
1630         }
1631 }
1632
1633 //**********************************************************************************************************************
1634
1635 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
1636         try {
1637                 vector<unsigned int> intVector(length);
1638
1639                 while (!file.eof())     {
1640                         char c = file.get();
1641                         if (c == ':'){
1642                                 for(int i=0;i<length;i++){
1643                                         file >> intVector[i];
1644                                 }
1645                                 break;
1646                         }
1647                 }
1648                 m->gobble(file);
1649                 return intVector;
1650         }
1651         catch(exception& e) {
1652                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
1653                 exit(1);
1654         }
1655 }
1656 //***************************************************************************************************************
1657
1658 bool SffInfoCommand::readOligos(string oligoFile){
1659         try {
1660         filehandles.clear();
1661         numSplitReads.clear();
1662         filehandlesHeaders.clear();
1663
1664                 ifstream inOligos;
1665                 m->openInputFile(oligoFile, inOligos);
1666
1667                 string type, oligo, group;
1668
1669                 int indexPrimer = 0;
1670                 int indexBarcode = 0;
1671
1672                 while(!inOligos.eof()){
1673
1674                         inOligos >> type;
1675
1676                         if(type[0] == '#'){
1677                                 while (!inOligos.eof()) {       char c = inOligos.get();  if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
1678                                 m->gobble(inOligos);
1679                         }
1680                         else{
1681                                 m->gobble(inOligos);
1682                                 //make type case insensitive
1683                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
1684
1685                                 inOligos >> oligo;
1686
1687                                 for(int i=0;i<oligo.length();i++){
1688                                         oligo[i] = toupper(oligo[i]);
1689                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
1690                                 }
1691
1692                                 if(type == "FORWARD"){
1693                                         group = "";
1694
1695                                         // get rest of line in case there is a primer name
1696                                         while (!inOligos.eof()) {
1697                                                 char c = inOligos.get();
1698                                                 if (c == 10 || c == 13 || c == -1){     break;  }
1699                                                 else if (c == 32 || c == 9){;} //space or tab
1700                                                 else {  group += c;  }
1701                                         }
1702
1703                                         //check for repeat barcodes
1704                                         map<string, int>::iterator itPrime = primers.find(oligo);
1705                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
1706
1707                                         primers[oligo]=indexPrimer; indexPrimer++;
1708                                         primerNameVector.push_back(group);
1709                                 }else if(type == "REVERSE"){
1710                                         //Sequence oligoRC("reverse", oligo);
1711                                         //oligoRC.reverseComplement();
1712                     string oligoRC = reverseOligo(oligo);
1713                                         revPrimer.push_back(oligoRC);
1714                                 }
1715                                 else if(type == "BARCODE"){
1716                                         inOligos >> group;
1717
1718                                         //check for repeat barcodes
1719                                         map<string, int>::iterator itBar = barcodes.find(oligo);
1720                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
1721
1722                                         barcodes[oligo]=indexBarcode; indexBarcode++;
1723                                         barcodeNameVector.push_back(group);
1724                                 }else if(type == "LINKER"){
1725                                         linker.push_back(oligo);
1726                                 }else if(type == "SPACER"){
1727                                         spacer.push_back(oligo);
1728                                 }
1729                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
1730                         }
1731                         m->gobble(inOligos);
1732                 }
1733                 inOligos.close();
1734
1735                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ split = 1;      }
1736
1737                 //add in potential combos
1738                 if(barcodeNameVector.size() == 0){
1739                         barcodes[""] = 0;
1740                         barcodeNameVector.push_back("");
1741                 }
1742
1743                 if(primerNameVector.size() == 0){
1744                         primers[""] = 0;
1745                         primerNameVector.push_back("");
1746                 }
1747
1748                 filehandles.resize(barcodeNameVector.size());
1749                 for(int i=0;i<filehandles.size();i++){
1750                         filehandles[i].assign(primerNameVector.size(), "");
1751                 }
1752
1753                 if(split > 1){
1754                         set<string> uniqueNames; //used to cleanup outputFileNames
1755                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1756                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1757
1758                                         string primerName = primerNameVector[itPrimer->second];
1759                                         string barcodeName = barcodeNameVector[itBar->second];
1760
1761                                         string comboGroupName = "";
1762                                         string fastaFileName = "";
1763                                         string qualFileName = "";
1764                                         string nameFileName = "";
1765
1766                                         if(primerName == ""){
1767                                                 comboGroupName = barcodeNameVector[itBar->second];
1768                                         }
1769                                         else{
1770                                                 if(barcodeName == ""){
1771                                                         comboGroupName = primerNameVector[itPrimer->second];
1772                                                 }
1773                                                 else{
1774                                                         comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
1775                                                 }
1776                                         }
1777
1778                                         ofstream temp;
1779                     map<string, string> variables;
1780                     variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
1781                     variables["[group]"] = comboGroupName;
1782                                         string thisFilename = getOutputFileName("sff",variables);
1783                                         if (uniqueNames.count(thisFilename) == 0) {
1784                                                 outputNames.push_back(thisFilename);
1785                                                 outputTypes["sff"].push_back(thisFilename);
1786                                                 uniqueNames.insert(thisFilename);
1787                                         }
1788
1789                                         filehandles[itBar->second][itPrimer->second] = thisFilename;
1790                                         temp.open(thisFilename.c_str(), ios::binary);           temp.close();
1791                                 }
1792                         }
1793                 }
1794                 numFPrimers = primers.size();
1795         numLinkers = linker.size();
1796         numSpacers = spacer.size();
1797         map<string, string> variables;
1798         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
1799         variables["[group]"] = "scrap";
1800                 noMatchFile = getOutputFileName("sff",variables);
1801         m->mothurRemove(noMatchFile);
1802
1803                 bool allBlank = true;
1804                 for (int i = 0; i < barcodeNameVector.size(); i++) {
1805                         if (barcodeNameVector[i] != "") {
1806                                 allBlank = false;
1807                                 break;
1808                         }
1809                 }
1810                 for (int i = 0; i < primerNameVector.size(); i++) {
1811                         if (primerNameVector[i] != "") {
1812                                 allBlank = false;
1813                                 break;
1814                         }
1815                 }
1816
1817         filehandlesHeaders.resize(filehandles.size());
1818         numSplitReads.resize(filehandles.size());
1819         for (int i = 0; i < filehandles.size(); i++) {
1820             numSplitReads[i].resize(filehandles[i].size(), 0);
1821             for (int j = 0; j < filehandles[i].size(); j++) {
1822                 filehandlesHeaders[i].push_back(filehandles[i][j]+"headers");
1823             }
1824         }
1825
1826                 if (allBlank) {
1827                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a split the sff file."); m->mothurOutEndLine();
1828                         split = 1;
1829                         return false;
1830                 }
1831
1832                 return true;
1833
1834         }
1835         catch(exception& e) {
1836                 m->errorOut(e, "SffInfoCommand", "readOligos");
1837                 exit(1);
1838         }
1839 }
1840 //********************************************************************/
1841 string SffInfoCommand::reverseOligo(string oligo){
1842         try {
1843         string reverse = "";
1844
1845         for(int i=oligo.length()-1;i>=0;i--){
1846
1847             if(oligo[i] == 'A')         {       reverse += 'T'; }
1848             else if(oligo[i] == 'T'){   reverse += 'A'; }
1849             else if(oligo[i] == 'U'){   reverse += 'A'; }
1850
1851             else if(oligo[i] == 'G'){   reverse += 'C'; }
1852             else if(oligo[i] == 'C'){   reverse += 'G'; }
1853
1854             else if(oligo[i] == 'R'){   reverse += 'Y'; }
1855             else if(oligo[i] == 'Y'){   reverse += 'R'; }
1856
1857             else if(oligo[i] == 'M'){   reverse += 'K'; }
1858             else if(oligo[i] == 'K'){   reverse += 'M'; }
1859
1860             else if(oligo[i] == 'W'){   reverse += 'W'; }
1861             else if(oligo[i] == 'S'){   reverse += 'S'; }
1862
1863             else if(oligo[i] == 'B'){   reverse += 'V'; }
1864             else if(oligo[i] == 'V'){   reverse += 'B'; }
1865
1866             else if(oligo[i] == 'D'){   reverse += 'H'; }
1867             else if(oligo[i] == 'H'){   reverse += 'D'; }
1868
1869             else                                                {       reverse += 'N'; }
1870         }
1871
1872
1873         return reverse;
1874     }
1875         catch(exception& e) {
1876                 m->errorOut(e, "SffInfoCommand", "reverseOligo");
1877                 exit(1);
1878         }
1879 }
1880
1881 //**********************************************************************************************************************
1882
1883
1884
1885