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                 }
 563
 564                 //report progress
 565                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 566
 567                 in.close();
 568
 569                 if (sfftxt) {  outSfftxt.close();       }
 570                 if (fasta)      {  outFasta.close();    }
 571                 if (qual)       {  outQual.close();             }
 572                 if (flow)       {  outFlow.close();             }
 573
 574         if (split > 1) {
 575             //create new common headers for each file with the correct number of reads
 576             adjustCommonHeader(header);
 577
 578                         map<string, string>::iterator it;
 579                         set<string> namesToRemove;
 580                         for(int i=0;i<filehandles.size();i++){
 581                                 for(int j=0;j<filehandles[0].size();j++){
 582                                         if (filehandles[i][j] != "") {
 583                                                 if (namesToRemove.count(filehandles[i][j]) == 0) {
 584                                                         if(m->isBlank(filehandles[i][j])){
 585                                                                 m->mothurRemove(filehandles[i][j]);
 586                                 m->mothurRemove(filehandlesHeaders[i][j]);
 587                                                                 namesToRemove.insert(filehandles[i][j]);
 588                             }
 589                                                 }
 590                                         }
 591                                 }
 592                         }
 593
 594             //append new header to reads
 595             for (int i = 0; i < filehandles.size(); i++) {
 596                 for (int j = 0; j < filehandles[i].size(); j++) {
 597                     m->appendFiles(filehandles[i][j], filehandlesHeaders[i][j]);
 598                     m->renameFile(filehandlesHeaders[i][j], filehandles[i][j]);
 599                     m->mothurRemove(filehandlesHeaders[i][j]);
 600                     if (numSplitReads[i][j] == 0) { m->mothurRemove(filehandles[i][j]); }
 601                 }
 602             }
 603
 604                         //remove names for outputFileNames, just cleans up the output
 605                         for(int i = 0; i < outputNames.size(); i++) {
 606                 if (namesToRemove.count(outputNames[i]) != 0) {
 607                     outputNames.erase(outputNames.begin()+i);
 608                     i--;
 609                 }
 610             }
 611
 612             if(m->isBlank(noMatchFile)){  m->mothurRemove(noMatchFile); }
 613             else { outputNames.push_back(noMatchFile); outputTypes["sff"].push_back(noMatchFile); }
 614         }
 615
 616                 return count;
 617         }
 618         catch(exception& e) {
 619                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 620                 exit(1);
 621         }
 622 }
 623 //**********************************************************************************************************************
 624 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 625         try {
 626
 627                 if (!in.eof()) {
 628
 629                         //read magic number
 630                         char buffer[4];
 631                         in.read(buffer, 4);
 632                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 633
 634                         //read version
 635                         char buffer9[4];
 636                         in.read(buffer9, 4);
 637                         header.version = "";
 638                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i]));  }
 639
 640                         //read offset
 641                         char buffer2 [8];
 642                         in.read(buffer2, 8);
 643                         header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
 644
 645                         //read index length
 646                         char buffer3 [4];
 647                         in.read(buffer3, 4);
 648                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 649
 650                         //read num reads
 651                         char buffer4 [4];
 652                         in.read(buffer4, 4);
 653                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 654
 655                         //read header length
 656                         char buffer5 [2];
 657                         in.read(buffer5, 2);
 658                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 659
 660                         //read key length
 661                         char buffer6 [2];
 662                         in.read(buffer6, 2);
 663                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 664
 665                         //read number of flow reads
 666                         char buffer7 [2];
 667                         in.read(buffer7, 2);
 668                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 669
 670                         //read format code
 671                         char buffer8 [1];
 672                         in.read(buffer8, 1);
 673                         header.flogramFormatCode = (int)(buffer8[0]);
 674
 675                         //read flow chars
 676                         char* tempBuffer = new char[header.numFlowsPerRead];
 677                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 678                         header.flowChars = tempBuffer;
 679                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 680                         delete[] tempBuffer;
 681
 682                         //read key
 683                         char* tempBuffer2 = new char[header.keyLength];
 684                         in.read(&(*tempBuffer2), header.keyLength);
 685                         header.keySequence = tempBuffer2;
 686                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 687                         delete[] tempBuffer2;
 688
 689                         /* Pad to 8 chars */
 690                         unsigned long long spotInFile = in.tellg();
 691                         unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 692                         in.seekg(spot);
 693
 694         }else{
 695                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 696                 }
 697
 698                 return 0;
 699
 700         }
 701         catch(exception& e) {
 702                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 703                 exit(1);
 704         }
 705 }
 706 //**********************************************************************************************************************
 707 int SffInfoCommand::adjustCommonHeader(CommonHeader header){
 708         try {
 709
 710         char* mybuffer = new char[4];
 711         ifstream in;
 712         in.open(currentFileName.c_str(), ios::binary);
 713
 714         //magic number
 715         in.read(mybuffer,4);
 716         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 717             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 718                 ofstream out;
 719                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 720                 out.write(mybuffer, in.gcount());
 721                 out.close();
 722             }
 723         }
 724         delete[] mybuffer;
 725
 726         //version
 727         mybuffer = new char[4];
 728         in.read(mybuffer,4);
 729         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 730             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 731                 ofstream out;
 732                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 733                 out.write(mybuffer, in.gcount());
 734                 out.close();
 735             }
 736         }
 737         delete[] mybuffer;
 738
 739         //offset
 740         mybuffer = new char[8];
 741         in.read(mybuffer,8);
 742         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 743             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 744                 ofstream out;
 745                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 746                 out.write(mybuffer, in.gcount());
 747                 out.close();
 748             }
 749         }
 750         delete[] mybuffer;
 751
 752
 753         //read index length
 754                 mybuffer = new char[4];
 755         in.read(mybuffer,4);
 756         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 757             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 758                 ofstream out;
 759                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 760                 out.write(mybuffer, in.gcount());
 761                 out.close();
 762             }
 763         }
 764         delete[] mybuffer;
 765
 766         //change num reads
 767         mybuffer = new char[4];
 768         in.read(mybuffer,4);
 769         delete[] mybuffer;
 770         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 771             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 772                 ofstream out;
 773                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 774                 //convert number of reads to 4 byte char*
 775                 char* thisbuffer = new char[4];
 776                 thisbuffer[0] = (numSplitReads[i][j] >> 24) & 0xFF;
 777                 thisbuffer[1] = (numSplitReads[i][j] >> 16) & 0xFF;
 778                 thisbuffer[2] = (numSplitReads[i][j] >> 8) & 0xFF;
 779                 thisbuffer[3] = numSplitReads[i][j] & 0xFF;
 780                 out.write(thisbuffer, 4);
 781                 out.close();
 782                 delete[] thisbuffer;
 783             }
 784         }
 785
 786         //read header length
 787         mybuffer = new char[2];
 788         in.read(mybuffer,2);
 789         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 790             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 791                 ofstream out;
 792                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 793                 out.write(mybuffer, in.gcount());
 794                 out.close();
 795             }
 796         }
 797         delete[] mybuffer;
 798
 799         //read key length
 800         mybuffer = new char[2];
 801         in.read(mybuffer,2);
 802         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 803             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 804                 ofstream out;
 805                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 806                 out.write(mybuffer, in.gcount());
 807                 out.close();
 808             }
 809         }
 810         delete[] mybuffer;
 811
 812         //read number of flow reads
 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->openOutputFileAppend(filehandlesHeaders[i][j], out);
 819                 out.write(mybuffer, in.gcount());
 820                 out.close();
 821             }
 822         }
 823         delete[] mybuffer;
 824
 825         //read format code
 826         mybuffer = new char[1];
 827         in.read(mybuffer,1);
 828         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 829             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 830                 ofstream out;
 831                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 832                 out.write(mybuffer, in.gcount());
 833                 out.close();
 834             }
 835         }
 836         delete[] mybuffer;
 837
 838         //read flow chars
 839         mybuffer = new char[header.numFlowsPerRead];
 840         in.read(mybuffer,header.numFlowsPerRead);
 841         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 842             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 843                 ofstream out;
 844                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 845                 out.write(mybuffer, in.gcount());
 846                 out.close();
 847             }
 848         }
 849         delete[] mybuffer;
 850
 851         //read key
 852         mybuffer = new char[header.keyLength];
 853         in.read(mybuffer,header.keyLength);
 854         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 855             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 856                 ofstream out;
 857                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 858                 out.write(mybuffer, in.gcount());
 859                 out.close();
 860             }
 861         }
 862         delete[] mybuffer;
 863
 864
 865         /* Pad to 8 chars */
 866         unsigned long long spotInFile = in.tellg();
 867         unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 868         in.seekg(spot);
 869
 870         mybuffer = new char[spot-spotInFile];
 871         for (int i = 0; i < filehandlesHeaders.size(); i++) {
 872             for (int j = 0; j < filehandlesHeaders[i].size(); j++) {
 873                 ofstream out;
 874                 m->openOutputFileAppend(filehandlesHeaders[i][j], out);
 875                 out.write(mybuffer, spot-spotInFile);
 876                 out.close();
 877             }
 878         }
 879         delete[] mybuffer;
 880         in.close();
 881                 return 0;
 882
 883         }
 884         catch(exception& e) {
 885                 m->errorOut(e, "SffInfoCommand", "adjustCommonHeader");
 886                 exit(1);
 887         }
 888 }
 889 //**********************************************************************************************************************
 890 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, Header& header){
 891         try {
 892         unsigned long long startSpotInFile = in.tellg();
 893                 if (!in.eof()) {
 894
 895             /*****************************************/
 896             //read header
 897
 898             //read header length
 899                         char buffer [2];
 900                         in.read(buffer, 2);
 901                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 902
 903                         //read name length
 904                         char buffer2 [2];
 905                         in.read(buffer2, 2);
 906                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 907
 908                         //read num bases
 909                         char buffer3 [4];
 910                         in.read(buffer3, 4);
 911                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 912
 913                         //read clip qual left
 914                         char buffer4 [2];
 915                         in.read(buffer4, 2);
 916                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 917                         header.clipQualLeft = 5;
 918
 919                         //read clip qual right
 920                         char buffer5 [2];
 921                         in.read(buffer5, 2);
 922                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 923
 924                         //read clipAdapterLeft
 925                         char buffer6 [2];
 926                         in.read(buffer6, 2);
 927                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 928
 929                         //read clipAdapterRight
 930                         char buffer7 [2];
 931                         in.read(buffer7, 2);
 932                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 933
 934                         //read name
 935                         char* tempBuffer = new char[header.nameLength];
 936                         in.read(&(*tempBuffer), header.nameLength);
 937                         header.name = tempBuffer;
 938                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 939                         delete[] tempBuffer;
 940
 941                         //extract info from name
 942                         decodeName(header.timestamp, header.region, header.xy, header.name);
 943
 944                         /* Pad to 8 chars */
 945                         unsigned long long spotInFile = in.tellg();
 946                         unsigned long long spot = (spotInFile + 7)& ~7;
 947                         in.seekg(spot);
 948
 949             /*****************************************/
 950             //sequence read
 951
 952                         //read flowgram
 953                         read.flowgram.resize(numFlowReads);
 954                         for (int i = 0; i < numFlowReads; i++) {
 955                                 char buffer [2];
 956                                 in.read(buffer, 2);
 957                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 958                         }
 959
 960                         //read flowIndex
 961                         read.flowIndex.resize(header.numBases);
 962                         for (int i = 0; i < header.numBases; i++) {
 963                                 char temp[1];
 964                                 in.read(temp, 1);
 965                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 966                         }
 967
 968                         //read bases
 969                         char* tempBuffer6 = new char[header.numBases];
 970                         in.read(&(*tempBuffer6), header.numBases);
 971                         read.bases = tempBuffer6;
 972                         if (read.bases.length() > header.numBases) { read.bases = read.bases.substr(0, header.numBases);  }
 973                         delete[] tempBuffer6;
 974
 975                         //read qual scores
 976                         read.qualScores.resize(header.numBases);
 977                         for (int i = 0; i < header.numBases; i++) {
 978                                 char temp[1];
 979                                 in.read(temp, 1);
 980                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 981                         }
 982
 983                         /* Pad to 8 chars */
 984                         spotInFile = in.tellg();
 985                         spot = (spotInFile + 7)& ~7;
 986                         in.seekg(spot);
 987
 988             if (split > 1) {
 989                 char * mybuffer;
 990                 mybuffer = new char [spot-startSpotInFile];
 991                 ifstream in2;
 992                 m->openInputFile(currentFileName, in2);
 993                 in2.seekg(startSpotInFile);
 994                 in2.read(mybuffer,spot-startSpotInFile);
 995                 in2.close();
 996
 997                 int barcodeIndex, primerIndex;
 998                 int trashCodeLength = findGroup(header, read, barcodeIndex, primerIndex);
 999
1000                 if(trashCodeLength == 0){
1001                     ofstream out;
1002                     m->openOutputFileAppend(filehandles[barcodeIndex][primerIndex], out);
1003                     out.write(mybuffer, in2.gcount());
1004                     out.close();
1005                     delete[] mybuffer;
1006                     numSplitReads[barcodeIndex][primerIndex]++;
1007                                 }
1008                                 else{
1009                                         ofstream out;
1010                     m->openOutputFileAppend(noMatchFile, out);
1011                     out.write(mybuffer, in2.gcount());
1012                     out.close();
1013                     delete[] mybuffer;
1014                                 }
1015
1016                         }
1017                 }else{
1018                         m->mothurOut("Error reading."); m->mothurOutEndLine();
1019                 }
1020
1021                 return 0;
1022         }
1023         catch(exception& e) {
1024                 m->errorOut(e, "SffInfoCommand", "readSeqData");
1025                 exit(1);
1026         }
1027 }
1028 //**********************************************************************************************************************
1029 int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& primer) {
1030         try {
1031         //find group read belongs to
1032         TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
1033
1034         int success = 1;
1035         string trashCode = "";
1036         int currentSeqsDiffs = 0;
1037
1038         string seq = read.bases;
1039
1040         if (trim) {
1041             if(header.clipQualRight < header.clipQualLeft){
1042                 if (header.clipQualRight == 0) { //don't trim right
1043                     seq = seq.substr(header.clipQualLeft-1);
1044                 }else {
1045                     seq = "NNNN";
1046                 }
1047             }
1048             else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
1049                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
1050             }
1051             else {
1052                 seq = seq.substr(header.clipQualLeft-1);
1053             }
1054         }else{
1055             //if you wanted the sfftxt then you already converted the bases to the right case
1056             if (!sfftxt) {
1057                 int endValue = header.clipQualRight;
1058                 //make the bases you want to clip lowercase and the bases you want to keep upper case
1059                 if(endValue == 0){      endValue = seq.length();        }
1060                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
1061                 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++)  {   seq[i] = toupper(seq[i]);  }
1062                 for (int i = (endValue-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
1063             }
1064         }
1065
1066         Sequence currSeq(header.name, seq);
1067         QualityScores currQual;
1068
1069         if(numLinkers != 0){
1070             success = trimOligos.stripLinker(currSeq, currQual);
1071             if(success > ldiffs)                {       trashCode += 'k';       }
1072             else{ currentSeqsDiffs += success;  }
1073
1074         }
1075
1076         if(barcodes.size() != 0){
1077             success = trimOligos.stripBarcode(currSeq, currQual, barcode);
1078             if(success > bdiffs)                {       trashCode += 'b';       }
1079             else{ currentSeqsDiffs += success;  }
1080         }
1081
1082         if(numSpacers != 0){
1083             success = trimOligos.stripSpacer(currSeq, currQual);
1084             if(success > sdiffs)                {       trashCode += 's';       }
1085             else{ currentSeqsDiffs += success;  }
1086
1087         }
1088
1089         if(numFPrimers != 0){
1090             success = trimOligos.stripForward(currSeq, currQual, primer, true);
1091             if(success > pdiffs)                {       trashCode += 'f';       }
1092             else{ currentSeqsDiffs += success;  }
1093         }
1094
1095         if (currentSeqsDiffs > tdiffs)  {       trashCode += 't';   }
1096
1097         if(revPrimer.size() != 0){
1098             success = trimOligos.stripReverse(currSeq, currQual);
1099             if(!success)                                {       trashCode += 'r';       }
1100         }
1101
1102
1103         return trashCode.length();
1104     }
1105         catch(exception& e) {
1106                 m->errorOut(e, "SffInfoCommand", "findGroup");
1107                 exit(1);
1108         }
1109 }
1110 //**********************************************************************************************************************
1111 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
1112         try {
1113
1114                 if (name.length() >= 6) {
1115                         string time = name.substr(0, 6);
1116                         unsigned int timeNum = m->fromBase36(time);
1117
1118                         int q1 = timeNum / 60;
1119                         int sec = timeNum - 60 * q1;
1120                         int q2 = q1 / 60;
1121                         int minute = q1 - 60 * q2;
1122                         int q3 = q2 / 24;
1123                         int hr = q2 - 24 * q3;
1124                         int q4 = q3 / 32;
1125                         int day = q3 - 32 * q4;
1126                         int q5 = q4 / 13;
1127                         int mon = q4 - 13 * q5;
1128                         int year = 2000 + q5;
1129
1130                         timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
1131                 }
1132
1133                 if (name.length() >= 9) {
1134                         region = name.substr(7, 2);
1135
1136                         string xyNum = name.substr(9);
1137                         unsigned int myXy = m->fromBase36(xyNum);
1138                         int x = myXy >> 12;
1139                         int y = myXy & 4095;
1140
1141                         xy = toString(x) + "_" + toString(y);
1142                 }
1143
1144                 return 0;
1145         }
1146         catch(exception& e) {
1147                 m->errorOut(e, "SffInfoCommand", "decodeName");
1148                 exit(1);
1149         }
1150 }
1151 //**********************************************************************************************************************
1152 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
1153         try {
1154
1155                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
1156                 out << "Version: " << header.version << endl;
1157                 out << "Index Offset: " << header.indexOffset << endl;
1158                 out << "Index Length: " << header.indexLength << endl;
1159                 out << "Number of Reads: " << header.numReads << endl;
1160                 out << "Header Length: " << header.headerLength << endl;
1161                 out << "Key Length: " << header.keyLength << endl;
1162                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
1163                 out << "Format Code: " << header.flogramFormatCode << endl;
1164                 out << "Flow Chars: " << header.flowChars << endl;
1165                 out << "Key Sequence: " << header.keySequence << endl << endl;
1166
1167                 return 0;
1168         }
1169         catch(exception& e) {
1170                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
1171                 exit(1);
1172         }
1173 }
1174 //**********************************************************************************************************************
1175 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
1176         try {
1177
1178                 out << ">" << header.name << endl;
1179                 out << "Run Prefix: " << header.timestamp << endl;
1180                 out << "Region #:  " << header.region << endl;
1181                 out << "XY Location: " << header.xy << endl << endl;
1182
1183                 out << "Run Name:  " << endl;
1184                 out << "Analysis Name:  " << endl;
1185                 out << "Full Path: " << endl << endl;
1186
1187                 out << "Read Header Len: " << header.headerLength << endl;
1188                 out << "Name Length: " << header.nameLength << endl;
1189                 out << "# of Bases: " << header.numBases << endl;
1190                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
1191                 out << "Clip Qual Right: " << header.clipQualRight << endl;
1192                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
1193                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
1194
1195                 return 0;
1196         }
1197         catch(exception& e) {
1198                 m->errorOut(e, "SffInfoCommand", "printHeader");
1199                 exit(1);
1200         }
1201 }
1202 //**********************************************************************************************************************
1203 bool SffInfoCommand::sanityCheck(Header& header, seqRead& read) {
1204         try {
1205         bool okay = true;
1206         string message = "[WARNING]: Your sff file may be corrupted! Sequence: " + header.name + "\n";
1207
1208         if (header.clipQualLeft > read.bases.length()) {
1209             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
1210         }
1211         if (header.clipQualRight > read.bases.length()) {
1212             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.bases.length()) + " bases.\n";
1213         }
1214         if (header.clipQualLeft > read.qualScores.size()) {
1215             okay = false; message += "Clip Qual Left = " + toString(header.clipQualLeft) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
1216         }
1217         if (header.clipQualRight > read.qualScores.size()) {
1218             okay = false; message += "Clip Qual Right = " + toString(header.clipQualRight) + ", but we only read " + toString(read.qualScores.size()) + " quality scores.\n";
1219         }
1220
1221         if (okay == false) {
1222             m->mothurOut(message); m->mothurOutEndLine();
1223         }
1224
1225                 return okay;
1226         }
1227         catch(exception& e) {
1228                 m->errorOut(e, "SffInfoCommand", "sanityCheck");
1229                 exit(1);
1230         }
1231 }
1232 //**********************************************************************************************************************
1233 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
1234         try {
1235                 out << "Flowgram: ";
1236                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
1237
1238                 out << endl <<  "Flow Indexes: ";
1239                 int sum = 0;
1240                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
1241
1242                 //make the bases you want to clip lowercase and the bases you want to keep upper case
1243         int endValue = header.clipQualRight;
1244                 if(endValue == 0){      endValue = read.bases.length(); }
1245                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
1246                 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
1247                 for (int i = (endValue-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
1248
1249                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
1250                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
1251
1252
1253                 out << endl << endl;
1254
1255                 return 0;
1256         }
1257         catch(exception& e) {
1258                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
1259                 exit(1);
1260         }
1261 }
1262 //**********************************************************************************************************************
1263 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
1264         try {
1265                 string seq = read.bases;
1266
1267         if (trim) {
1268                         if(header.clipQualRight < header.clipQualLeft){
1269                                 if (header.clipQualRight == 0) { //don't trim right
1270                     seq = seq.substr(header.clipQualLeft-1);
1271                 }else {
1272                     seq = "NNNN";
1273                 }
1274                         }
1275                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
1276                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
1277                         }
1278                         else {
1279                                 seq = seq.substr(header.clipQualLeft-1);
1280                         }
1281                 }else{
1282                         //if you wanted the sfftxt then you already converted the bases to the right case
1283                         if (!sfftxt) {
1284                 int endValue = header.clipQualRight;
1285                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
1286                                 if(endValue == 0){      endValue = seq.length();        }
1287                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
1288                                 for (int i = (header.clipQualLeft-1); i < (endValue-1); i++)  {   seq[i] = toupper(seq[i]);  }
1289                                 for (int i = (endValue-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
1290                         }
1291                 }
1292
1293                 out << ">" << header.name  << " xy=" << header.xy << endl;
1294                 out << seq << endl;
1295
1296                 return 0;
1297         }
1298         catch(exception& e) {
1299                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
1300                 exit(1);
1301         }
1302 }
1303
1304 //**********************************************************************************************************************
1305 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
1306         try {
1307
1308                 if (trim) {
1309                         if(header.clipQualRight < header.clipQualLeft){
1310                 if (header.clipQualRight == 0) { //don't trim right
1311                     out << ">" << header.name << " xy=" << header.xy << " length=" << (read.qualScores.size()-header.clipQualLeft) << endl;
1312                     for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';       }
1313                 }else {
1314                     out << ">" << header.name << " xy=" << header.xy << endl;
1315                     out << "0\t0\t0\t0";
1316                 }
1317                         }
1318                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
1319                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
1320                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
1321                         }
1322                         else{
1323                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
1324                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
1325                         }
1326                 }else{
1327                         out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
1328                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
1329                 }
1330
1331                 out << endl;
1332
1333                 return 0;
1334         }
1335         catch(exception& e) {
1336                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
1337                 exit(1);
1338         }
1339 }
1340
1341 //**********************************************************************************************************************
1342 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
1343         try {
1344
1345         int endValue = header.clipQualRight;
1346         if (header.clipQualRight == 0) {
1347             endValue = read.flowIndex.size();
1348             if (m->debug) { m->mothurOut("[DEBUG]: " + header.name + " has clipQualRight=0.\n"); }
1349         }
1350         if(endValue > header.clipQualLeft){
1351
1352             int rightIndex = 0;
1353             for (int i = 0; i < endValue; i++) {  rightIndex +=  read.flowIndex[i];      }
1354
1355             out << header.name << ' ' << rightIndex;
1356             for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
1357             out << endl;
1358         }
1359
1360
1361                 return 0;
1362         }
1363         catch(exception& e) {
1364                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
1365                 exit(1);
1366         }
1367 }
1368 //**********************************************************************************************************************
1369 int SffInfoCommand::readAccnosFile(string filename) {
1370         try {
1371                 //remove old names
1372                 seqNames.clear();
1373
1374                 ifstream in;
1375                 m->openInputFile(filename, in);
1376                 string name;
1377
1378                 while(!in.eof()){
1379                         in >> name; m->gobble(in);
1380
1381                         seqNames.insert(name);
1382
1383                         if (m->control_pressed) { seqNames.clear(); break; }
1384                 }
1385                 in.close();
1386
1387                 return 0;
1388         }
1389         catch(exception& e) {
1390                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
1391                 exit(1);
1392         }
1393 }
1394 //**********************************************************************************************************************
1395 int SffInfoCommand::parseSffTxt() {
1396         try {
1397
1398                 ifstream inSFF;
1399                 m->openInputFile(sfftxtFilename, inSFF);
1400
1401                 if (outputDir == "") {  outputDir += m->hasPath(sfftxtFilename); }
1402
1403                 //output file names
1404                 ofstream outFasta, outQual, outFlow;
1405                 string outFastaFileName, outQualFileName;
1406                 string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
1407                 if (fileRoot.length() > 0) {
1408                         //rip off last .
1409                         fileRoot = fileRoot.substr(0, fileRoot.length()-1);
1410                         fileRoot = m->getRootName(fileRoot);
1411                 }
1412
1413         map<string, string> variables;
1414                 variables["[filename]"] = fileRoot;
1415                 string sfftxtFileName = getOutputFileName("sfftxt",variables);
1416                 string outFlowFileName = getOutputFileName("flow",variables);
1417                 if (!trim) { variables["[tag]"] = "raw"; }
1418                 outFastaFileName = getOutputFileName("fasta",variables);
1419         outQualFileName = getOutputFileName("qfile",variables);
1420
1421                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
1422                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
1423                 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);  }
1424
1425                 //read common header
1426                 string commonHeader = m->getline(inSFF);
1427                 string magicNumber = m->getline(inSFF);
1428                 string version = m->getline(inSFF);
1429                 string indexOffset = m->getline(inSFF);
1430                 string indexLength = m->getline(inSFF);
1431                 int numReads = parseHeaderLineToInt(inSFF);
1432                 string headerLength = m->getline(inSFF);
1433                 string keyLength = m->getline(inSFF);
1434                 int numFlows = parseHeaderLineToInt(inSFF);
1435                 string flowgramCode = m->getline(inSFF);
1436                 string flowChars = m->getline(inSFF);
1437                 string keySequence = m->getline(inSFF);
1438                 m->gobble(inSFF);
1439
1440                 string seqName;
1441
1442                 if (flow)       {       outFlow << numFlows << endl;    }
1443
1444                 for(int i=0;i<numReads;i++){
1445
1446                         //sanity check
1447                         if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
1448
1449                         Header header;
1450
1451                         //parse read header
1452                         inSFF >> seqName;
1453                         seqName = seqName.substr(1);
1454                         m->gobble(inSFF);
1455                         header.name = seqName;
1456
1457                         string runPrefix = parseHeaderLineToString(inSFF);              header.timestamp = runPrefix;
1458                         string regionNumber = parseHeaderLineToString(inSFF);   header.region = regionNumber;
1459                         string xyLocation = parseHeaderLineToString(inSFF);             header.xy = xyLocation;
1460                         m->gobble(inSFF);
1461
1462                         string runName = parseHeaderLineToString(inSFF);
1463                         string analysisName = parseHeaderLineToString(inSFF);
1464                         string fullPath = parseHeaderLineToString(inSFF);
1465                         m->gobble(inSFF);
1466
1467                         string readHeaderLen = parseHeaderLineToString(inSFF);  convert(readHeaderLen, header.headerLength);
1468                         string nameLength = parseHeaderLineToString(inSFF);             convert(nameLength, header.nameLength);
1469                         int numBases = parseHeaderLineToInt(inSFF);                             header.numBases = numBases;
1470                         string clipQualLeft = parseHeaderLineToString(inSFF);   convert(clipQualLeft, header.clipQualLeft);
1471                         int clipQualRight = parseHeaderLineToInt(inSFF);                header.clipQualRight = clipQualRight;
1472                         string clipAdapLeft = parseHeaderLineToString(inSFF);   convert(clipAdapLeft, header.clipAdapterLeft);
1473                         string clipAdapRight = parseHeaderLineToString(inSFF);  convert(clipAdapRight, header.clipAdapterRight);
1474                         m->gobble(inSFF);
1475
1476                         seqRead read;
1477
1478                         //parse read
1479                         vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows);      read.flowgram = flowVector;
1480                         vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
1481
1482                         //adjust for print
1483                         vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
1484                         for (int j = 1; j < flowIndices.size(); j++) {   flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]);   }
1485                         read.flowIndex = flowIndicesAdjusted;
1486
1487                         string bases = parseHeaderLineToString(inSFF);                                                                          read.bases = bases;
1488                         vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases);       read.qualScores = qualityScores;
1489                         m->gobble(inSFF);
1490
1491                         //if you have provided an accosfile and this seq is not in it, then dont print
1492                         bool print = true;
1493                         if (seqNames.size() != 0) {   if (seqNames.count(header.name) == 0) { print = false; }  }
1494
1495                         //print
1496                         if (print) {
1497                                 if (fasta)      {       printFastaSeqData(outFasta, read, header);      }
1498                                 if (qual)       {       printQualSeqData(outQual, read, header);        }
1499                                 if (flow)       {       printFlowSeqData(outFlow, read, header);        }
1500                         }
1501
1502                         //report progress
1503                         if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
1504
1505                         if (m->control_pressed) {  break;  }
1506                 }
1507
1508                 //report progress
1509                 if (!m->control_pressed) {   if((numReads) % 10000 != 0){       m->mothurOut(toString(numReads)); m->mothurOutEndLine();                }  }
1510
1511                 inSFF.close();
1512
1513                 if (fasta)      {  outFasta.close();    }
1514                 if (qual)       {  outQual.close();             }
1515                 if (flow)       {  outFlow.close();             }
1516
1517                 return 0;
1518         }
1519         catch(exception& e) {
1520                 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
1521                 exit(1);
1522         }
1523 }
1524 //**********************************************************************************************************************
1525
1526 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
1527         try {
1528                 int number;
1529
1530                 while (!file.eof())     {
1531
1532                         char c = file.get();
1533                         if (c == ':'){
1534                                 file >> number;
1535                                 break;
1536                         }
1537
1538                 }
1539                 m->gobble(file);
1540                 return number;
1541         }
1542         catch(exception& e) {
1543                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
1544                 exit(1);
1545         }
1546
1547 }
1548
1549 //**********************************************************************************************************************
1550
1551 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
1552         try {
1553                 string text;
1554
1555                 while (!file.eof())     {
1556                         char c = file.get();
1557
1558                         if (c == ':'){
1559                                 //m->gobble(file);
1560                                 //text = m->getline(file);
1561                                 file >> text;
1562                                 break;
1563                         }
1564                 }
1565                 m->gobble(file);
1566
1567                 return text;
1568         }
1569         catch(exception& e) {
1570                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
1571                 exit(1);
1572         }
1573 }
1574
1575 //**********************************************************************************************************************
1576
1577 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
1578         try {
1579                 vector<unsigned short> floatVector(length);
1580
1581                 while (!file.eof())     {
1582                         char c = file.get();
1583                         if (c == ':'){
1584                                 float temp;
1585                                 for(int i=0;i<length;i++){
1586                                         file >> temp;
1587                                         floatVector[i] = temp * 100;
1588                                 }
1589                                 break;
1590                         }
1591                 }
1592                 m->gobble(file);
1593                 return floatVector;
1594         }
1595         catch(exception& e) {
1596                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
1597                 exit(1);
1598         }
1599 }
1600
1601 //**********************************************************************************************************************
1602
1603 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
1604         try {
1605                 vector<unsigned int> intVector(length);
1606
1607                 while (!file.eof())     {
1608                         char c = file.get();
1609                         if (c == ':'){
1610                                 for(int i=0;i<length;i++){
1611                                         file >> intVector[i];
1612                                 }
1613                                 break;
1614                         }
1615                 }
1616                 m->gobble(file);
1617                 return intVector;
1618         }
1619         catch(exception& e) {
1620                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
1621                 exit(1);
1622         }
1623 }
1624 //***************************************************************************************************************
1625
1626 bool SffInfoCommand::readOligos(string oligoFile){
1627         try {
1628         filehandles.clear();
1629         numSplitReads.clear();
1630         filehandlesHeaders.clear();
1631
1632                 ifstream inOligos;
1633                 m->openInputFile(oligoFile, inOligos);
1634
1635                 string type, oligo, group;
1636
1637                 int indexPrimer = 0;
1638                 int indexBarcode = 0;
1639
1640                 while(!inOligos.eof()){
1641
1642                         inOligos >> type;
1643
1644                         if(type[0] == '#'){
1645                                 while (!inOligos.eof()) {       char c = inOligos.get();  if (c == 10 || c == 13){      break;  }       } // get rest of line if there's any crap there
1646                                 m->gobble(inOligos);
1647                         }
1648                         else{
1649                                 m->gobble(inOligos);
1650                                 //make type case insensitive
1651                                 for(int i=0;i<type.length();i++){       type[i] = toupper(type[i]);  }
1652
1653                                 inOligos >> oligo;
1654
1655                                 for(int i=0;i<oligo.length();i++){
1656                                         oligo[i] = toupper(oligo[i]);
1657                                         if(oligo[i] == 'U')     {       oligo[i] = 'T'; }
1658                                 }
1659
1660                                 if(type == "FORWARD"){
1661                                         group = "";
1662
1663                                         // get rest of line in case there is a primer name
1664                                         while (!inOligos.eof()) {
1665                                                 char c = inOligos.get();
1666                                                 if (c == 10 || c == 13 || c == -1){     break;  }
1667                                                 else if (c == 32 || c == 9){;} //space or tab
1668                                                 else {  group += c;  }
1669                                         }
1670
1671                                         //check for repeat barcodes
1672                                         map<string, int>::iterator itPrime = primers.find(oligo);
1673                                         if (itPrime != primers.end()) { m->mothurOut("primer " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
1674
1675                                         primers[oligo]=indexPrimer; indexPrimer++;
1676                                         primerNameVector.push_back(group);
1677                                 }else if(type == "REVERSE"){
1678                                         //Sequence oligoRC("reverse", oligo);
1679                                         //oligoRC.reverseComplement();
1680                     string oligoRC = reverseOligo(oligo);
1681                                         revPrimer.push_back(oligoRC);
1682                                 }
1683                                 else if(type == "BARCODE"){
1684                                         inOligos >> group;
1685
1686                                         //check for repeat barcodes
1687                                         map<string, int>::iterator itBar = barcodes.find(oligo);
1688                                         if (itBar != barcodes.end()) { m->mothurOut("barcode " + oligo + " is in your oligos file already."); m->mothurOutEndLine();  }
1689
1690                                         barcodes[oligo]=indexBarcode; indexBarcode++;
1691                                         barcodeNameVector.push_back(group);
1692                                 }else if(type == "LINKER"){
1693                                         linker.push_back(oligo);
1694                                 }else if(type == "SPACER"){
1695                                         spacer.push_back(oligo);
1696                                 }
1697                                 else{   m->mothurOut("[WARNING]: " + type + " is not recognized as a valid type. Choices are forward, reverse, and barcode. Ignoring " + oligo + "."); m->mothurOutEndLine(); }
1698                         }
1699                         m->gobble(inOligos);
1700                 }
1701                 inOligos.close();
1702
1703                 if(barcodeNameVector.size() == 0 && primerNameVector[0] == ""){ split = 1;      }
1704
1705                 //add in potential combos
1706                 if(barcodeNameVector.size() == 0){
1707                         barcodes[""] = 0;
1708                         barcodeNameVector.push_back("");
1709                 }
1710
1711                 if(primerNameVector.size() == 0){
1712                         primers[""] = 0;
1713                         primerNameVector.push_back("");
1714                 }
1715
1716                 filehandles.resize(barcodeNameVector.size());
1717                 for(int i=0;i<filehandles.size();i++){
1718                         filehandles[i].assign(primerNameVector.size(), "");
1719                 }
1720
1721                 if(split > 1){
1722                         set<string> uniqueNames; //used to cleanup outputFileNames
1723                         for(map<string, int>::iterator itBar = barcodes.begin();itBar != barcodes.end();itBar++){
1724                                 for(map<string, int>::iterator itPrimer = primers.begin();itPrimer != primers.end(); itPrimer++){
1725
1726                                         string primerName = primerNameVector[itPrimer->second];
1727                                         string barcodeName = barcodeNameVector[itBar->second];
1728
1729                                         string comboGroupName = "";
1730                                         string fastaFileName = "";
1731                                         string qualFileName = "";
1732                                         string nameFileName = "";
1733
1734                                         if(primerName == ""){
1735                                                 comboGroupName = barcodeNameVector[itBar->second];
1736                                         }
1737                                         else{
1738                                                 if(barcodeName == ""){
1739                                                         comboGroupName = primerNameVector[itPrimer->second];
1740                                                 }
1741                                                 else{
1742                                                         comboGroupName = barcodeNameVector[itBar->second] + "." + primerNameVector[itPrimer->second];
1743                                                 }
1744                                         }
1745
1746                                         ofstream temp;
1747                     map<string, string> variables;
1748                     variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
1749                     variables["[group]"] = comboGroupName;
1750                                         string thisFilename = getOutputFileName("sff",variables);
1751                                         if (uniqueNames.count(thisFilename) == 0) {
1752                                                 outputNames.push_back(thisFilename);
1753                                                 outputTypes["sff"].push_back(thisFilename);
1754                                                 uniqueNames.insert(thisFilename);
1755                                         }
1756
1757                                         filehandles[itBar->second][itPrimer->second] = thisFilename;
1758                                         m->openOutputFile(thisFilename, temp);          temp.close();
1759                                 }
1760                         }
1761                 }
1762                 numFPrimers = primers.size();
1763         numLinkers = linker.size();
1764         numSpacers = spacer.size();
1765         map<string, string> variables;
1766         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(currentFileName));
1767         variables["[group]"] = "scrap";
1768                 noMatchFile = getOutputFileName("sff",variables);
1769         m->mothurRemove(noMatchFile);
1770
1771                 bool allBlank = true;
1772                 for (int i = 0; i < barcodeNameVector.size(); i++) {
1773                         if (barcodeNameVector[i] != "") {
1774                                 allBlank = false;
1775                                 break;
1776                         }
1777                 }
1778                 for (int i = 0; i < primerNameVector.size(); i++) {
1779                         if (primerNameVector[i] != "") {
1780                                 allBlank = false;
1781                                 break;
1782                         }
1783                 }
1784
1785         filehandlesHeaders.resize(filehandles.size());
1786         numSplitReads.resize(filehandles.size());
1787         for (int i = 0; i < filehandles.size(); i++) {
1788             numSplitReads[i].resize(filehandles[i].size(), 0);
1789             for (int j = 0; j < filehandles[i].size(); j++) {
1790                 filehandlesHeaders[i].push_back(filehandles[i][j]+"headers");
1791             }
1792         }
1793
1794                 if (allBlank) {
1795                         m->mothurOut("[WARNING]: your oligos file does not contain any group names.  mothur will not create a split the sff file."); m->mothurOutEndLine();
1796                         split = 1;
1797                         return false;
1798                 }
1799
1800                 return true;
1801
1802         }
1803         catch(exception& e) {
1804                 m->errorOut(e, "SffInfoCommand", "readOligos");
1805                 exit(1);
1806         }
1807 }
1808 //********************************************************************/
1809 string SffInfoCommand::reverseOligo(string oligo){
1810         try {
1811         string reverse = "";
1812
1813         for(int i=oligo.length()-1;i>=0;i--){
1814
1815             if(oligo[i] == 'A')         {       reverse += 'T'; }
1816             else if(oligo[i] == 'T'){   reverse += 'A'; }
1817             else if(oligo[i] == 'U'){   reverse += 'A'; }
1818
1819             else if(oligo[i] == 'G'){   reverse += 'C'; }
1820             else if(oligo[i] == 'C'){   reverse += 'G'; }
1821
1822             else if(oligo[i] == 'R'){   reverse += 'Y'; }
1823             else if(oligo[i] == 'Y'){   reverse += 'R'; }
1824
1825             else if(oligo[i] == 'M'){   reverse += 'K'; }
1826             else if(oligo[i] == 'K'){   reverse += 'M'; }
1827
1828             else if(oligo[i] == 'W'){   reverse += 'W'; }
1829             else if(oligo[i] == 'S'){   reverse += 'S'; }
1830
1831             else if(oligo[i] == 'B'){   reverse += 'V'; }
1832             else if(oligo[i] == 'V'){   reverse += 'B'; }
1833
1834             else if(oligo[i] == 'D'){   reverse += 'H'; }
1835             else if(oligo[i] == 'H'){   reverse += 'D'; }
1836
1837             else                                                {       reverse += 'N'; }
1838         }
1839
1840
1841         return reverse;
1842     }
1843         catch(exception& e) {
1844                 m->errorOut(e, "SffInfoCommand", "reverseOligo");
1845                 exit(1);
1846         }
1847 }
1848
1849 //**********************************************************************************************************************
1850
1851
1852
1853