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
  13 //**********************************************************************************************************************
  14 vector<string> SffInfoCommand::setParameters(){
  15         try {
  16                 CommandParameter psff("sff", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(psff);
  17                 CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(paccnos);
  18                 CommandParameter psfftxt("sfftxt", "String", "", "", "", "", "",false,false); parameters.push_back(psfftxt);
  19                 CommandParameter pflow("flow", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pflow);
  20                 CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(ptrim);
  21                 CommandParameter pfasta("fasta", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pfasta);
  22                 CommandParameter pqfile("name", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pqfile);
  23                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  24                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  25
  26                 vector<string> myArray;
  27                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "SffInfoCommand", "setParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 string SffInfoCommand::getHelpString(){
  37         try {
  38                 string helpString = "";
  39                 helpString += "The sffinfo command reads a sff file and extracts the sequence data, or you can use it to parse a sfftxt file.\n";
  40                 helpString += "The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n";
  41                 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";
  42                 helpString += "The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n";
  43                 helpString += "The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n";
  44                 helpString += "The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=False. \n";
  45                 helpString += "The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n";
  46                 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";
  47                 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";
  48                 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";
  49                 helpString += "Example sffinfo(sff=mySffFile.sff, trim=F).\n";
  50                 helpString += "Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n";
  51                 return helpString;
  52         }
  53         catch(exception& e) {
  54                 m->errorOut(e, "SffInfoCommand", "getHelpString");
  55                 exit(1);
  56         }
  57 }
  58
  59
  60 //**********************************************************************************************************************
  61 SffInfoCommand::SffInfoCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["fasta"] = tempOutNames;
  67                 outputTypes["flow"] = tempOutNames;
  68                 outputTypes["sfftxt"] = tempOutNames;
  69                 outputTypes["qfile"] = tempOutNames;
  70         }
  71         catch(exception& e) {
  72                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
  73                 exit(1);
  74         }
  75 }
  76 //**********************************************************************************************************************
  77
  78 SffInfoCommand::SffInfoCommand(string option)  {
  79         try {
  80                 abort = false; calledHelp = false;
  81                 hasAccnos = false;
  82
  83                 //allow user to run help
  84                 if(option == "help") { help(); abort = true; calledHelp = true; }
  85
  86                 else {
  87                         //valid paramters for this command
  88                         vector<string> myArray = setParameters();
  89
  90                         OptionParser parser(option);
  91                         map<string, string> parameters = parser.getParameters();
  92
  93                         ValidParameters validParameter;
  94                         //check to make sure all parameters are valid for command
  95                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  96                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  97                         }
  98
  99                         //initialize outputTypes
 100                         vector<string> tempOutNames;
 101                         outputTypes["fasta"] = tempOutNames;
 102                         outputTypes["flow"] = tempOutNames;
 103                         outputTypes["sfftxt"] = tempOutNames;
 104                         outputTypes["qfile"] = tempOutNames;
 105
 106                         //if the user changes the output directory command factory will send this info to us in the output parameter
 107                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 108
 109                         //if the user changes the input directory command factory will send this info to us in the output parameter
 110                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }
 111
 112                         sffFilename = validParameter.validFile(parameters, "sff", false);
 113                         if (sffFilename == "not found") { sffFilename = "";  }
 114                         else {
 115                                 m->splitAtDash(sffFilename, filenames);
 116
 117                                 //go through files and make sure they are good, if not, then disregard them
 118                                 for (int i = 0; i < filenames.size(); i++) {
 119                                         bool ignore = false;
 120                                         if (filenames[i] == "current") {
 121                                                 filenames[i] = m->getSFFFile();
 122                                                 if (filenames[i] != "") {  m->mothurOut("Using " + filenames[i] + " as input file for the sff parameter where you had given current."); m->mothurOutEndLine(); }
 123                                                 else {
 124                                                         m->mothurOut("You have no current sfffile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 125                                                         //erase from file list
 126                                                         filenames.erase(filenames.begin()+i);
 127                                                         i--;
 128                                                 }
 129                                         }
 130
 131                                         if (!ignore) {
 132                                                 if (inputDir != "") {
 133                                                         string path = m->hasPath(filenames[i]);
 134                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 135                                                         if (path == "") {       filenames[i] = inputDir + filenames[i];         }
 136                                                 }
 137
 138                                                 ifstream in;
 139                                                 int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
 140
 141                                                 //if you can't open it, try default location
 142                                                 if (ableToOpen == 1) {
 143                                                         if (m->getDefaultPath() != "") { //default path is set
 144                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
 145                                                                 m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 146                                                                 ifstream in2;
 147                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 148                                                                 in2.close();
 149                                                                 filenames[i] = tryPath;
 150                                                         }
 151                                                 }
 152
 153                                                 //if you can't open it, try default location
 154                                                 if (ableToOpen == 1) {
 155                                                         if (m->getOutputDir() != "") { //default path is set
 156                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(filenames[i]);
 157                                                                 m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 158                                                                 ifstream in2;
 159                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 160                                                                 in2.close();
 161                                                                 filenames[i] = tryPath;
 162                                                         }
 163                                                 }
 164
 165                                                 in.close();
 166
 167                                                 if (ableToOpen == 1) {
 168                                                         m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 169                                                         //erase from file list
 170                                                         filenames.erase(filenames.begin()+i);
 171                                                         i--;
 172                                                 }
 173                                         }
 174                                 }
 175
 176                                 //make sure there is at least one valid file left
 177                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 178                         }
 179
 180                         accnosName = validParameter.validFile(parameters, "accnos", false);
 181                         if (accnosName == "not found") { accnosName = "";  }
 182                         else {
 183                                 hasAccnos = true;
 184                                 m->splitAtDash(accnosName, accnosFileNames);
 185
 186                                 //go through files and make sure they are good, if not, then disregard them
 187                                 for (int i = 0; i < accnosFileNames.size(); i++) {
 188                                         bool ignore = false;
 189                                         if (accnosFileNames[i] == "current") {
 190                                                 accnosFileNames[i] = m->getAccnosFile();
 191                                                 if (accnosFileNames[i] != "") {  m->mothurOut("Using " + accnosFileNames[i] + " as input file for the accnos parameter where you had given current."); m->mothurOutEndLine(); }
 192                                                 else {
 193                                                         m->mothurOut("You have no current accnosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 194                                                         //erase from file list
 195                                                         accnosFileNames.erase(accnosFileNames.begin()+i);
 196                                                         i--;
 197                                                 }
 198                                         }
 199
 200                                         if (!ignore) {
 201
 202                                                 if (inputDir != "") {
 203                                                         string path = m->hasPath(accnosFileNames[i]);
 204                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 205                                                         if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }
 206                                                 }
 207
 208                                                 ifstream in;
 209                                                 int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
 210
 211                                                 //if you can't open it, try default location
 212                                                 if (ableToOpen == 1) {
 213                                                         if (m->getDefaultPath() != "") { //default path is set
 214                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
 215                                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 216                                                                 ifstream in2;
 217                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 218                                                                 in2.close();
 219                                                                 accnosFileNames[i] = tryPath;
 220                                                         }
 221                                                 }
 222                                                 //if you can't open it, try default location
 223                                                 if (ableToOpen == 1) {
 224                                                         if (m->getOutputDir() != "") { //default path is set
 225                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
 226                                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 227                                                                 ifstream in2;
 228                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 229                                                                 in2.close();
 230                                                                 accnosFileNames[i] = tryPath;
 231                                                         }
 232                                                 }
 233                                                 in.close();
 234
 235                                                 if (ableToOpen == 1) {
 236                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 237                                                         //erase from file list
 238                                                         accnosFileNames.erase(accnosFileNames.begin()+i);
 239                                                         i--;
 240                                                 }
 241                                         }
 242                                 }
 243
 244                                 //make sure there is at least one valid file left
 245                                 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 246                         }
 247
 248                         if (hasAccnos) {
 249                                 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(); }
 250                         }
 251
 252                         string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }
 253                         qual = m->isTrue(temp);
 254
 255                         temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
 256                         fasta = m->isTrue(temp);
 257
 258                         temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }
 259                         flow = m->isTrue(temp);
 260
 261                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
 262                         trim = m->isTrue(temp);
 263
 264                         temp = validParameter.validFile(parameters, "sfftxt", false);
 265                         if (temp == "not found")        {       temp = "F";      sfftxt = false; sfftxtFilename = "";           }
 266                         else if (m->isTrue(temp))       {       sfftxt = true;          sfftxtFilename = "";                            }
 267                         else {
 268                                 //you are a filename
 269                                 if (inputDir != "") {
 270                                         map<string,string>::iterator it = parameters.find("sfftxt");
 271                                         //user has given a template file
 272                                         if(it != parameters.end()){
 273                                                 string path = m->hasPath(it->second);
 274                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 275                                                 if (path == "") {       parameters["sfftxt"] = inputDir + it->second;           }
 276                                         }
 277                                 }
 278
 279                                 sfftxtFilename = validParameter.validFile(parameters, "sfftxt", true);
 280                                 if (sfftxtFilename == "not found") { sfftxtFilename = "";  }
 281                                 else if (sfftxtFilename == "not open") { sfftxtFilename = "";  }
 282                         }
 283
 284                         if ((sfftxtFilename == "") && (filenames.size() == 0)) {
 285                                 //if there is a current fasta file, use it
 286                                 string filename = m->getSFFFile();
 287                                 if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
 288                                 else {  m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true;  }
 289                         }
 290                 }
 291         }
 292         catch(exception& e) {
 293                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 294                 exit(1);
 295         }
 296 }
 297 //**********************************************************************************************************************
 298 int SffInfoCommand::execute(){
 299         try {
 300
 301                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 302
 303                 for (int s = 0; s < filenames.size(); s++) {
 304
 305                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 306
 307                         int start = time(NULL);
 308
 309                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 310
 311                         string accnos = "";
 312                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 313
 314                         int numReads = extractSffInfo(filenames[s], accnos);
 315
 316                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 317                 }
 318
 319                 if (sfftxtFilename != "") {  parseSffTxt(); }
 320
 321                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 322
 323                 //set fasta file as new current fastafile
 324                 string current = "";
 325                 itTypes = outputTypes.find("fasta");
 326                 if (itTypes != outputTypes.end()) {
 327                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 328                 }
 329
 330                 itTypes = outputTypes.find("qfile");
 331                 if (itTypes != outputTypes.end()) {
 332                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 333                 }
 334
 335                 itTypes = outputTypes.find("flow");
 336                 if (itTypes != outputTypes.end()) {
 337                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
 338                 }
 339
 340                 //report output filenames
 341                 m->mothurOutEndLine();
 342                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 343                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 344                 m->mothurOutEndLine();
 345
 346                 return 0;
 347         }
 348         catch(exception& e) {
 349                 m->errorOut(e, "SffInfoCommand", "execute");
 350                 exit(1);
 351         }
 352 }
 353 //**********************************************************************************************************************
 354 int SffInfoCommand::extractSffInfo(string input, string accnos){
 355         try {
 356
 357                 if (outputDir == "") {  outputDir += m->hasPath(input); }
 358
 359                 if (accnos != "")       {  readAccnosFile(accnos);  }
 360                 else                            {       seqNames.clear();               }
 361
 362                 ofstream outSfftxt, outFasta, outQual, outFlow;
 363                 string outFastaFileName, outQualFileName;
 364                 string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
 365                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
 366                 if (trim) {
 367                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
 368                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
 369                 }else{
 370                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
 371                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
 372                 }
 373
 374                 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); }
 375                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 376                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
 377                 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);  }
 378
 379                 ifstream in;
 380                 in.open(input.c_str(), ios::binary);
 381
 382                 CommonHeader header;
 383                 readCommonHeader(in, header);
 384
 385                 int count = 0;
 386                 mycount = 0;
 387
 388                 //check magic number and version
 389                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 390                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 391
 392                 //print common header
 393                 if (sfftxt) {   printCommonHeader(outSfftxt, header);           }
 394                 if (flow)       {       outFlow << header.numFlowsPerRead << endl;      }
 395
 396                 //read through the sff file
 397                 while (!in.eof()) {
 398
 399                         bool print = true;
 400
 401                         //read header
 402                         Header readheader;
 403                         readHeader(in, readheader);
 404
 405                         //read data
 406                         seqRead read;
 407                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 408
 409                         //if you have provided an accosfile and this seq is not in it, then dont print
 410                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 411
 412                         //print
 413                         if (print) {
 414                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 415                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 416                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 417                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 418                         }
 419
 420                         count++;
 421                         mycount++;
 422
 423                         //report progress
 424                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 425
 426                         if (m->control_pressed) { count = 0; break;   }
 427
 428                         if (count >= header.numReads) { break; }
 429                 }
 430
 431                 //report progress
 432                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 433
 434                 in.close();
 435
 436                 if (sfftxt) {  outSfftxt.close();       }
 437                 if (fasta)      {  outFasta.close();    }
 438                 if (qual)       {  outQual.close();             }
 439                 if (flow)       {  outFlow.close();             }
 440
 441                 return count;
 442         }
 443         catch(exception& e) {
 444                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 445                 exit(1);
 446         }
 447 }
 448 //**********************************************************************************************************************
 449 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 450         try {
 451
 452                 if (!in.eof()) {
 453
 454                         //read magic number
 455                         char buffer[4];
 456                         in.read(buffer, 4);
 457                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 458
 459                         //read version
 460                         char buffer9[4];
 461                         in.read(buffer9, 4);
 462                         header.version = "";
 463                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 464
 465                         //read offset
 466                         char buffer2 [8];
 467                         in.read(buffer2, 8);
 468                         header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
 469
 470                         //read index length
 471                         char buffer3 [4];
 472                         in.read(buffer3, 4);
 473                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 474
 475                         //read num reads
 476                         char buffer4 [4];
 477                         in.read(buffer4, 4);
 478                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 479
 480                         //read header length
 481                         char buffer5 [2];
 482                         in.read(buffer5, 2);
 483                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 484
 485                         //read key length
 486                         char buffer6 [2];
 487                         in.read(buffer6, 2);
 488                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 489
 490                         //read number of flow reads
 491                         char buffer7 [2];
 492                         in.read(buffer7, 2);
 493                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 494
 495                         //read format code
 496                         char buffer8 [1];
 497                         in.read(buffer8, 1);
 498                         header.flogramFormatCode = (int)(buffer8[0]);
 499
 500                         //read flow chars
 501                         char* tempBuffer = new char[header.numFlowsPerRead];
 502                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 503                         header.flowChars = tempBuffer;
 504                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 505                         delete[] tempBuffer;
 506
 507                         //read key
 508                         char* tempBuffer2 = new char[header.keyLength];
 509                         in.read(&(*tempBuffer2), header.keyLength);
 510                         header.keySequence = tempBuffer2;
 511                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 512                         delete[] tempBuffer2;
 513
 514                         /* Pad to 8 chars */
 515                         unsigned long int spotInFile = in.tellg();
 516                         unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
 517                         in.seekg(spot);
 518
 519                 }else{
 520                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 521                 }
 522
 523                 return 0;
 524         }
 525         catch(exception& e) {
 526                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 527                 exit(1);
 528         }
 529 }
 530 //**********************************************************************************************************************
 531 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 532         try {
 533
 534                 if (!in.eof()) {
 535
 536                         //read header length
 537                         char buffer [2];
 538                         in.read(buffer, 2);
 539                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 540
 541                         //read name length
 542                         char buffer2 [2];
 543                         in.read(buffer2, 2);
 544                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 545
 546                         //read num bases
 547                         char buffer3 [4];
 548                         in.read(buffer3, 4);
 549                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 550
 551                         //read clip qual left
 552                         char buffer4 [2];
 553                         in.read(buffer4, 2);
 554                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 555                         header.clipQualLeft = 5;
 556
 557                         //read clip qual right
 558                         char buffer5 [2];
 559                         in.read(buffer5, 2);
 560                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 561
 562                         //read clipAdapterLeft
 563                         char buffer6 [2];
 564                         in.read(buffer6, 2);
 565                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 566
 567                         //read clipAdapterRight
 568                         char buffer7 [2];
 569                         in.read(buffer7, 2);
 570                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 571
 572                         //read name
 573                         char* tempBuffer = new char[header.nameLength];
 574                         in.read(&(*tempBuffer), header.nameLength);
 575                         header.name = tempBuffer;
 576                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 577                         delete[] tempBuffer;
 578
 579                         //extract info from name
 580                         decodeName(header.timestamp, header.region, header.xy, header.name);
 581
 582                         /* Pad to 8 chars */
 583                         unsigned long int spotInFile = in.tellg();
 584                         unsigned long int spot = (spotInFile + 7)& ~7;
 585                         in.seekg(spot);
 586
 587                 }else{
 588                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 589                 }
 590
 591                 return 0;
 592         }
 593         catch(exception& e) {
 594                 m->errorOut(e, "SffInfoCommand", "readHeader");
 595                 exit(1);
 596         }
 597 }
 598 //**********************************************************************************************************************
 599 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 600         try {
 601
 602                 if (!in.eof()) {
 603
 604                         //read flowgram
 605                         read.flowgram.resize(numFlowReads);
 606                         for (int i = 0; i < numFlowReads; i++) {
 607                                 char buffer [2];
 608                                 in.read(buffer, 2);
 609                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 610                         }
 611
 612                         //read flowIndex
 613                         read.flowIndex.resize(numBases);
 614                         for (int i = 0; i < numBases; i++) {
 615                                 char temp[1];
 616                                 in.read(temp, 1);
 617                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 618                         }
 619
 620                         //read bases
 621                         char* tempBuffer = new char[numBases];
 622                         in.read(&(*tempBuffer), numBases);
 623                         read.bases = tempBuffer;
 624                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 625                         delete[] tempBuffer;
 626
 627                         //read qual scores
 628                         read.qualScores.resize(numBases);
 629                         for (int i = 0; i < numBases; i++) {
 630                                 char temp[1];
 631                                 in.read(temp, 1);
 632                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 633                         }
 634
 635                         /* Pad to 8 chars */
 636                         unsigned long int spotInFile = in.tellg();
 637                         unsigned long int spot = (spotInFile + 7)& ~7;
 638                         in.seekg(spot);
 639
 640                 }else{
 641                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 642                 }
 643
 644                 return 0;
 645         }
 646         catch(exception& e) {
 647                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 648                 exit(1);
 649         }
 650 }
 651 //**********************************************************************************************************************
 652 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
 653         try {
 654
 655                 if (name.length() >= 6) {
 656                         string time = name.substr(0, 6);
 657                         unsigned int timeNum = m->fromBase36(time);
 658
 659                         int q1 = timeNum / 60;
 660                         int sec = timeNum - 60 * q1;
 661                         int q2 = q1 / 60;
 662                         int minute = q1 - 60 * q2;
 663                         int q3 = q2 / 24;
 664                         int hr = q2 - 24 * q3;
 665                         int q4 = q3 / 32;
 666                         int day = q3 - 32 * q4;
 667                         int q5 = q4 / 13;
 668                         int mon = q4 - 13 * q5;
 669                         int year = 2000 + q5;
 670
 671                         timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
 672                 }
 673
 674                 if (name.length() >= 9) {
 675                         region = name.substr(7, 2);
 676
 677                         string xyNum = name.substr(9);
 678                         unsigned int myXy = m->fromBase36(xyNum);
 679                         int x = myXy >> 12;
 680                         int y = myXy & 4095;
 681
 682                         xy = toString(x) + "_" + toString(y);
 683                 }
 684
 685                 return 0;
 686         }
 687         catch(exception& e) {
 688                 m->errorOut(e, "SffInfoCommand", "decodeName");
 689                 exit(1);
 690         }
 691 }
 692 //**********************************************************************************************************************
 693 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 694         try {
 695
 696                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 697                 out << "Version: " << header.version << endl;
 698                 out << "Index Offset: " << header.indexOffset << endl;
 699                 out << "Index Length: " << header.indexLength << endl;
 700                 out << "Number of Reads: " << header.numReads << endl;
 701                 out << "Header Length: " << header.headerLength << endl;
 702                 out << "Key Length: " << header.keyLength << endl;
 703                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 704                 out << "Format Code: " << header.flogramFormatCode << endl;
 705                 out << "Flow Chars: " << header.flowChars << endl;
 706                 out << "Key Sequence: " << header.keySequence << endl << endl;
 707
 708                 return 0;
 709         }
 710         catch(exception& e) {
 711                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 712                 exit(1);
 713         }
 714 }
 715 //**********************************************************************************************************************
 716 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 717         try {
 718
 719                 out << ">" << header.name << endl;
 720                 out << "Run Prefix: " << header.timestamp << endl;
 721                 out << "Region #:  " << header.region << endl;
 722                 out << "XY Location: " << header.xy << endl << endl;
 723
 724                 out << "Run Name:  " << endl;
 725                 out << "Analysis Name:  " << endl;
 726                 out << "Full Path: " << endl << endl;
 727
 728                 out << "Read Header Len: " << header.headerLength << endl;
 729                 out << "Name Length: " << header.nameLength << endl;
 730                 out << "# of Bases: " << header.numBases << endl;
 731                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 732                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 733                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 734                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 735
 736                 return 0;
 737         }
 738         catch(exception& e) {
 739                 m->errorOut(e, "SffInfoCommand", "printHeader");
 740                 exit(1);
 741         }
 742 }
 743
 744 //**********************************************************************************************************************
 745 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
 746         try {
 747
 748                 out << "Flowgram: ";
 749                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 750
 751                 out << endl <<  "Flow Indexes: ";
 752                 int sum = 0;
 753                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 754
 755                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 756                 if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
 757                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 758                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 759                 for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
 760
 761                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 762                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 763
 764
 765                 out << endl << endl;
 766
 767                 return 0;
 768         }
 769         catch(exception& e) {
 770                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 771                 exit(1);
 772         }
 773 }
 774 //**********************************************************************************************************************
 775 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 776         try {
 777
 778                 string seq = read.bases;
 779
 780                 if (trim) {
 781                         if(header.clipQualRight < header.clipQualLeft){
 782                                 seq = "NNNN";
 783                         }
 784                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 785                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 786                         }
 787                         else {
 788                                 seq = seq.substr(header.clipQualLeft-1);
 789                         }
 790                 }else{
 791                         //if you wanted the sfftxt then you already converted the bases to the right case
 792                         if (!sfftxt) {
 793                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 794                                 if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
 795                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 796                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
 797                                 for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 798                         }
 799                 }
 800
 801                 out << ">" << header.name  << " xy=" << header.xy << endl;
 802                 out << seq << endl;
 803
 804                 return 0;
 805         }
 806         catch(exception& e) {
 807                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 808                 exit(1);
 809         }
 810 }
 811
 812 //**********************************************************************************************************************
 813 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 814         try {
 815
 816                 if (trim) {
 817                         if(header.clipQualRight < header.clipQualLeft){
 818                                 out << ">" << header.name << " xy=" << header.xy << endl;
 819                                 out << "0\t0\t0\t0";
 820                         }
 821                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 822                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 823                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
 824                         }
 825                         else{
 826                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 827                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
 828                         }
 829                 }else{
 830                         out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
 831                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 832                 }
 833
 834                 out << endl;
 835
 836                 return 0;
 837         }
 838         catch(exception& e) {
 839                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 840                 exit(1);
 841         }
 842 }
 843
 844 //**********************************************************************************************************************
 845 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 846         try {
 847                 if(header.clipQualRight > header.clipQualLeft){
 848
 849                         int rightIndex = 0;
 850                         for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];     }
 851
 852                         out << header.name << ' ' << rightIndex;
 853                         for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
 854                         out << endl;
 855                 }
 856
 857
 858                 return 0;
 859         }
 860         catch(exception& e) {
 861                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 862                 exit(1);
 863         }
 864 }
 865 //**********************************************************************************************************************
 866 int SffInfoCommand::readAccnosFile(string filename) {
 867         try {
 868                 //remove old names
 869                 seqNames.clear();
 870
 871                 ifstream in;
 872                 m->openInputFile(filename, in);
 873                 string name;
 874
 875                 while(!in.eof()){
 876                         in >> name; m->gobble(in);
 877
 878                         seqNames.insert(name);
 879
 880                         if (m->control_pressed) { seqNames.clear(); break; }
 881                 }
 882                 in.close();
 883
 884                 return 0;
 885         }
 886         catch(exception& e) {
 887                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 888                 exit(1);
 889         }
 890 }
 891 //**********************************************************************************************************************
 892 int SffInfoCommand::parseSffTxt() {
 893         try {
 894
 895                 ifstream inSFF;
 896                 m->openInputFile(sfftxtFilename, inSFF);
 897
 898                 if (outputDir == "") {  outputDir += m->hasPath(sfftxtFilename); }
 899
 900                 //output file names
 901                 ofstream outFasta, outQual, outFlow;
 902                 string outFastaFileName, outQualFileName;
 903                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "flow";
 904                 if (trim) {
 905                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "fasta";
 906                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "qual";
 907                 }else{
 908                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.fasta";
 909                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(sfftxtFilename)) + "raw.qual";
 910                 }
 911
 912                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 913                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
 914                 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);  }
 915
 916                 //read common header
 917                 string commonHeader = m->getline(inSFF);
 918                 string magicNumber = m->getline(inSFF);
 919                 string version = m->getline(inSFF);
 920                 string indexOffset = m->getline(inSFF);
 921                 string indexLength = m->getline(inSFF);
 922                 int numReads = parseHeaderLineToInt(inSFF);
 923                 string headerLength = m->getline(inSFF);
 924                 string keyLength = m->getline(inSFF);
 925                 int numFlows = parseHeaderLineToInt(inSFF);
 926                 string flowgramCode = m->getline(inSFF);
 927                 string flowChars = m->getline(inSFF);
 928                 string keySequence = m->getline(inSFF);
 929                 m->gobble(inSFF);
 930
 931                 string seqName;
 932
 933                 if (flow)       {       outFlow << numFlows << endl;    }
 934
 935                 for(int i=0;i<numReads;i++){
 936
 937                         //sanity check
 938                         if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
 939
 940                         Header header;
 941
 942                         //parse read header
 943                         inSFF >> seqName;
 944                         seqName = seqName.substr(1);
 945                         m->gobble(inSFF);
 946                         header.name = seqName;
 947
 948                         string runPrefix = parseHeaderLineToString(inSFF);              header.timestamp = runPrefix;
 949                         string regionNumber = parseHeaderLineToString(inSFF);   header.region = regionNumber;
 950                         string xyLocation = parseHeaderLineToString(inSFF);             header.xy = xyLocation;
 951                         m->gobble(inSFF);
 952
 953                         string runName = parseHeaderLineToString(inSFF);
 954                         string analysisName = parseHeaderLineToString(inSFF);
 955                         string fullPath = parseHeaderLineToString(inSFF);
 956                         m->gobble(inSFF);
 957
 958                         string readHeaderLen = parseHeaderLineToString(inSFF);  convert(readHeaderLen, header.headerLength);
 959                         string nameLength = parseHeaderLineToString(inSFF);             convert(nameLength, header.nameLength);
 960                         int numBases = parseHeaderLineToInt(inSFF);                             header.numBases = numBases;
 961                         string clipQualLeft = parseHeaderLineToString(inSFF);   convert(clipQualLeft, header.clipQualLeft);
 962                         int clipQualRight = parseHeaderLineToInt(inSFF);                header.clipQualRight = clipQualRight;
 963                         string clipAdapLeft = parseHeaderLineToString(inSFF);   convert(clipAdapLeft, header.clipAdapterLeft);
 964                         string clipAdapRight = parseHeaderLineToString(inSFF);  convert(clipAdapRight, header.clipAdapterRight);
 965                         m->gobble(inSFF);
 966
 967                         seqRead read;
 968
 969                         //parse read
 970                         vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows);      read.flowgram = flowVector;
 971                         vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
 972
 973                         //adjust for print
 974                         vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
 975                         for (int j = 1; j < flowIndices.size(); j++) {   flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]);   }
 976                         read.flowIndex = flowIndicesAdjusted;
 977
 978                         string bases = parseHeaderLineToString(inSFF);                                                                          read.bases = bases;
 979                         vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases);       read.qualScores = qualityScores;
 980                         m->gobble(inSFF);
 981
 982                         //if you have provided an accosfile and this seq is not in it, then dont print
 983                         bool print = true;
 984                         if (seqNames.size() != 0) {   if (seqNames.count(header.name) == 0) { print = false; }  }
 985
 986                         //print
 987                         if (print) {
 988                                 if (fasta)      {       printFastaSeqData(outFasta, read, header);      }
 989                                 if (qual)       {       printQualSeqData(outQual, read, header);        }
 990                                 if (flow)       {       printFlowSeqData(outFlow, read, header);        }
 991                         }
 992
 993                         //report progress
 994                         if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
 995
 996                         if (m->control_pressed) {  break;  }
 997                 }
 998
 999                 //report progress
1000                 if (!m->control_pressed) {   if((numReads) % 10000 != 0){       m->mothurOut(toString(numReads)); m->mothurOutEndLine();                }  }
1001
1002                 inSFF.close();
1003
1004                 if (fasta)      {  outFasta.close();    }
1005                 if (qual)       {  outQual.close();             }
1006                 if (flow)       {  outFlow.close();             }
1007
1008                 return 0;
1009         }
1010         catch(exception& e) {
1011                 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
1012                 exit(1);
1013         }
1014 }
1015 //**********************************************************************************************************************
1016
1017 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
1018         try {
1019                 int number;
1020
1021                 while (!file.eof())     {
1022
1023                         char c = file.get();
1024                         if (c == ':'){
1025                                 file >> number;
1026                                 break;
1027                         }
1028
1029                 }
1030                 m->gobble(file);
1031                 return number;
1032         }
1033         catch(exception& e) {
1034                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
1035                 exit(1);
1036         }
1037
1038 }
1039
1040 //**********************************************************************************************************************
1041
1042 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
1043         try {
1044                 string text;
1045
1046                 while (!file.eof())     {
1047                         char c = file.get();
1048
1049                         if (c == ':'){
1050                                 //m->gobble(file);
1051                                 //text = m->getline(file);
1052                                 file >> text;
1053                                 break;
1054                         }
1055                 }
1056                 m->gobble(file);
1057
1058                 return text;
1059         }
1060         catch(exception& e) {
1061                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
1062                 exit(1);
1063         }
1064 }
1065
1066 //**********************************************************************************************************************
1067
1068 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
1069         try {
1070                 vector<unsigned short> floatVector(length);
1071
1072                 while (!file.eof())     {
1073                         char c = file.get();
1074                         if (c == ':'){
1075                                 float temp;
1076                                 for(int i=0;i<length;i++){
1077                                         file >> temp;
1078                                         floatVector[i] = temp * 100;
1079                                 }
1080                                 break;
1081                         }
1082                 }
1083                 m->gobble(file);
1084                 return floatVector;
1085         }
1086         catch(exception& e) {
1087                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
1088                 exit(1);
1089         }
1090 }
1091
1092 //**********************************************************************************************************************
1093
1094 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
1095         try {
1096                 vector<unsigned int> intVector(length);
1097
1098                 while (!file.eof())     {
1099                         char c = file.get();
1100                         if (c == ':'){
1101                                 for(int i=0;i<length;i++){
1102                                         file >> intVector[i];
1103                                 }
1104                                 break;
1105                         }
1106                 }
1107                 m->gobble(file);
1108                 return intVector;
1109         }
1110         catch(exception& e) {
1111                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
1112                 exit(1);
1113         }
1114 }
1115
1116 //**********************************************************************************************************************
1117
1118
1119
1120