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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  86
  87                 else {
  88                         //valid paramters for this command
  89                         vector<string> myArray = setParameters();
  90
  91                         OptionParser parser(option);
  92                         map<string, string> parameters = parser.getParameters();
  93
  94                         ValidParameters validParameter;
  95                         //check to make sure all parameters are valid for command
  96                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  97                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  98                         }
  99
 100                         //initialize outputTypes
 101                         vector<string> tempOutNames;
 102                         outputTypes["fasta"] = tempOutNames;
 103                         outputTypes["flow"] = tempOutNames;
 104                         outputTypes["sfftxt"] = tempOutNames;
 105                         outputTypes["qfile"] = tempOutNames;
 106
 107                         //if the user changes the output directory command factory will send this info to us in the output parameter
 108                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
 109
 110                         //if the user changes the input directory command factory will send this info to us in the output parameter
 111                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }
 112
 113                         sffFilename = validParameter.validFile(parameters, "sff", false);
 114                         if (sffFilename == "not found") { sffFilename = "";  }
 115                         else {
 116                                 m->splitAtDash(sffFilename, filenames);
 117
 118                                 //go through files and make sure they are good, if not, then disregard them
 119                                 for (int i = 0; i < filenames.size(); i++) {
 120                                         bool ignore = false;
 121                                         if (filenames[i] == "current") {
 122                                                 filenames[i] = m->getSFFFile();
 123                                                 if (filenames[i] != "") {  m->mothurOut("Using " + filenames[i] + " as input file for the sff parameter where you had given current."); m->mothurOutEndLine(); }
 124                                                 else {
 125                                                         m->mothurOut("You have no current sfffile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 126                                                         //erase from file list
 127                                                         filenames.erase(filenames.begin()+i);
 128                                                         i--;
 129                                                 }
 130                                         }
 131
 132                                         if (!ignore) {
 133                                                 if (inputDir != "") {
 134                                                         string path = m->hasPath(filenames[i]);
 135                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 136                                                         if (path == "") {       filenames[i] = inputDir + filenames[i];         }
 137                                                 }
 138
 139                                                 ifstream in;
 140                                                 int ableToOpen = m->openInputFile(filenames[i], in, "noerror");
 141
 142                                                 //if you can't open it, try default location
 143                                                 if (ableToOpen == 1) {
 144                                                         if (m->getDefaultPath() != "") { //default path is set
 145                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(filenames[i]);
 146                                                                 m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 147                                                                 ifstream in2;
 148                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 149                                                                 in2.close();
 150                                                                 filenames[i] = tryPath;
 151                                                         }
 152                                                 }
 153
 154                                                 //if you can't open it, try default location
 155                                                 if (ableToOpen == 1) {
 156                                                         if (m->getOutputDir() != "") { //default path is set
 157                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(filenames[i]);
 158                                                                 m->mothurOut("Unable to open " + filenames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 159                                                                 ifstream in2;
 160                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 161                                                                 in2.close();
 162                                                                 filenames[i] = tryPath;
 163                                                         }
 164                                                 }
 165
 166                                                 in.close();
 167
 168                                                 if (ableToOpen == 1) {
 169                                                         m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 170                                                         //erase from file list
 171                                                         filenames.erase(filenames.begin()+i);
 172                                                         i--;
 173                                                 }else { m->setSFFFile(filenames[i]); }
 174                                         }
 175                                 }
 176
 177                                 //make sure there is at least one valid file left
 178                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 179                         }
 180
 181                         accnosName = validParameter.validFile(parameters, "accnos", false);
 182                         if (accnosName == "not found") { accnosName = "";  }
 183                         else {
 184                                 hasAccnos = true;
 185                                 m->splitAtDash(accnosName, accnosFileNames);
 186
 187                                 //go through files and make sure they are good, if not, then disregard them
 188                                 for (int i = 0; i < accnosFileNames.size(); i++) {
 189                                         bool ignore = false;
 190                                         if (accnosFileNames[i] == "current") {
 191                                                 accnosFileNames[i] = m->getAccnosFile();
 192                                                 if (accnosFileNames[i] != "") {  m->mothurOut("Using " + accnosFileNames[i] + " as input file for the accnos parameter where you had given current."); m->mothurOutEndLine(); }
 193                                                 else {
 194                                                         m->mothurOut("You have no current accnosfile, ignoring current."); m->mothurOutEndLine(); ignore=true;
 195                                                         //erase from file list
 196                                                         accnosFileNames.erase(accnosFileNames.begin()+i);
 197                                                         i--;
 198                                                 }
 199                                         }
 200
 201                                         if (!ignore) {
 202
 203                                                 if (inputDir != "") {
 204                                                         string path = m->hasPath(accnosFileNames[i]);
 205                                                         //if the user has not given a path then, add inputdir. else leave path alone.
 206                                                         if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }
 207                                                 }
 208
 209                                                 ifstream in;
 210                                                 int ableToOpen = m->openInputFile(accnosFileNames[i], in, "noerror");
 211
 212                                                 //if you can't open it, try default location
 213                                                 if (ableToOpen == 1) {
 214                                                         if (m->getDefaultPath() != "") { //default path is set
 215                                                                 string tryPath = m->getDefaultPath() + m->getSimpleName(accnosFileNames[i]);
 216                                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 217                                                                 ifstream in2;
 218                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 219                                                                 in2.close();
 220                                                                 accnosFileNames[i] = tryPath;
 221                                                         }
 222                                                 }
 223                                                 //if you can't open it, try default location
 224                                                 if (ableToOpen == 1) {
 225                                                         if (m->getOutputDir() != "") { //default path is set
 226                                                                 string tryPath = m->getOutputDir() + m->getSimpleName(accnosFileNames[i]);
 227                                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine();
 228                                                                 ifstream in2;
 229                                                                 ableToOpen = m->openInputFile(tryPath, in2, "noerror");
 230                                                                 in2.close();
 231                                                                 accnosFileNames[i] = tryPath;
 232                                                         }
 233                                                 }
 234                                                 in.close();
 235
 236                                                 if (ableToOpen == 1) {
 237                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 238                                                         //erase from file list
 239                                                         accnosFileNames.erase(accnosFileNames.begin()+i);
 240                                                         i--;
 241                                                 }
 242                                         }
 243                                 }
 244
 245                                 //make sure there is at least one valid file left
 246                                 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 247                         }
 248
 249                         if (hasAccnos) {
 250                                 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(); }
 251                         }
 252
 253                         string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }
 254                         qual = m->isTrue(temp);
 255
 256                         temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
 257                         fasta = m->isTrue(temp);
 258
 259                         temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }
 260                         flow = m->isTrue(temp);
 261
 262                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
 263                         trim = m->isTrue(temp);
 264
 265                         temp = validParameter.validFile(parameters, "sfftxt", false);
 266                         if (temp == "not found")        {       temp = "F";      sfftxt = false; sfftxtFilename = "";           }
 267                         else if (m->isTrue(temp))       {       sfftxt = true;          sfftxtFilename = "";                            }
 268                         else {
 269                                 //you are a filename
 270                                 if (inputDir != "") {
 271                                         map<string,string>::iterator it = parameters.find("sfftxt");
 272                                         //user has given a template file
 273                                         if(it != parameters.end()){
 274                                                 string path = m->hasPath(it->second);
 275                                                 //if the user has not given a path then, add inputdir. else leave path alone.
 276                                                 if (path == "") {       parameters["sfftxt"] = inputDir + it->second;           }
 277                                         }
 278                                 }
 279
 280                                 sfftxtFilename = validParameter.validFile(parameters, "sfftxt", true);
 281                                 if (sfftxtFilename == "not found") { sfftxtFilename = "";  }
 282                                 else if (sfftxtFilename == "not open") { sfftxtFilename = "";  }
 283                         }
 284
 285                         if ((sfftxtFilename == "") && (filenames.size() == 0)) {
 286                                 //if there is a current sff file, use it
 287                                 string filename = m->getSFFFile();
 288                                 if (filename != "") { filenames.push_back(filename); m->mothurOut("Using " + filename + " as input file for the sff parameter."); m->mothurOutEndLine(); }
 289                                 else {  m->mothurOut("[ERROR]: you must provide a valid sff or sfftxt file."); m->mothurOutEndLine(); abort=true;  }
 290                         }
 291                 }
 292         }
 293         catch(exception& e) {
 294                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 295                 exit(1);
 296         }
 297 }
 298 //**********************************************************************************************************************
 299 int SffInfoCommand::execute(){
 300         try {
 301
 302                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 303
 304                 for (int s = 0; s < filenames.size(); s++) {
 305
 306                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
 307
 308                         int start = time(NULL);
 309
 310                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 311
 312                         string accnos = "";
 313                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 314
 315                         int numReads = extractSffInfo(filenames[s], accnos);
 316
 317                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 318                 }
 319
 320                 if (sfftxtFilename != "") {  parseSffTxt(); }
 321
 322                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       m->mothurRemove(outputNames[i]);        } return 0; }
 323
 324                 //set fasta file as new current fastafile
 325                 string current = "";
 326                 itTypes = outputTypes.find("fasta");
 327                 if (itTypes != outputTypes.end()) {
 328                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
 329                 }
 330
 331                 itTypes = outputTypes.find("qfile");
 332                 if (itTypes != outputTypes.end()) {
 333                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setQualFile(current); }
 334                 }
 335
 336                 itTypes = outputTypes.find("flow");
 337                 if (itTypes != outputTypes.end()) {
 338                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFlowFile(current); }
 339                 }
 340
 341                 //report output filenames
 342                 m->mothurOutEndLine();
 343                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 344                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 345                 m->mothurOutEndLine();
 346
 347                 return 0;
 348         }
 349         catch(exception& e) {
 350                 m->errorOut(e, "SffInfoCommand", "execute");
 351                 exit(1);
 352         }
 353 }
 354 //**********************************************************************************************************************
 355 int SffInfoCommand::extractSffInfo(string input, string accnos){
 356         try {
 357
 358                 if (outputDir == "") {  outputDir += m->hasPath(input); }
 359
 360                 if (accnos != "")       {  readAccnosFile(accnos);  }
 361                 else                            {       seqNames.clear();               }
 362
 363                 ofstream outSfftxt, outFasta, outQual, outFlow;
 364                 string outFastaFileName, outQualFileName;
 365                 string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
 366                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
 367                 if (trim) {
 368                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
 369                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
 370                 }else{
 371                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
 372                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
 373                 }
 374
 375                 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); }
 376                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 377                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qfile"].push_back(outQualFileName);  }
 378                 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);  }
 379
 380                 ifstream in;
 381                 in.open(input.c_str(), ios::binary);
 382
 383                 CommonHeader header;
 384                 readCommonHeader(in, header);
 385
 386                 int count = 0;
 387                 mycount = 0;
 388
 389                 //check magic number and version
 390                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 391                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 392
 393                 //print common header
 394                 if (sfftxt) {   printCommonHeader(outSfftxt, header);           }
 395                 if (flow)       {       outFlow << header.numFlowsPerRead << endl;      }
 396
 397                 //read through the sff file
 398                 while (!in.eof()) {
 399
 400                         bool print = true;
 401
 402                         //read header
 403                         Header readheader;
 404                         readHeader(in, readheader);
 405
 406                         //read data
 407                         seqRead read;
 408                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 409
 410                         //if you have provided an accosfile and this seq is not in it, then dont print
 411                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 412
 413                         //print
 414                         if (print) {
 415                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 416                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 417                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 418                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 419                         }
 420
 421                         count++;
 422                         mycount++;
 423
 424                         //report progress
 425                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 426
 427                         if (m->control_pressed) { count = 0; break;   }
 428
 429                         if (count >= header.numReads) { break; }
 430                 }
 431
 432                 //report progress
 433                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 434
 435                 in.close();
 436
 437                 if (sfftxt) {  outSfftxt.close();       }
 438                 if (fasta)      {  outFasta.close();    }
 439                 if (qual)       {  outQual.close();             }
 440                 if (flow)       {  outFlow.close();             }
 441
 442                 return count;
 443         }
 444         catch(exception& e) {
 445                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 446                 exit(1);
 447         }
 448 }
 449 //**********************************************************************************************************************
 450 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 451         try {
 452
 453                 if (!in.eof()) {
 454
 455                         //read magic number
 456                         char buffer[4];
 457                         in.read(buffer, 4);
 458                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 459
 460                         //read version
 461                         char buffer9[4];
 462                         in.read(buffer9, 4);
 463                         header.version = "";
 464                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 465
 466                         //read offset
 467                         char buffer2 [8];
 468                         in.read(buffer2, 8);
 469                         header.indexOffset =  be_int8(*(unsigned long long *)(&buffer2));
 470
 471                         //read index length
 472                         char buffer3 [4];
 473                         in.read(buffer3, 4);
 474                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 475
 476                         //read num reads
 477                         char buffer4 [4];
 478                         in.read(buffer4, 4);
 479                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 480
 481                         //read header length
 482                         char buffer5 [2];
 483                         in.read(buffer5, 2);
 484                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 485
 486                         //read key length
 487                         char buffer6 [2];
 488                         in.read(buffer6, 2);
 489                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 490
 491                         //read number of flow reads
 492                         char buffer7 [2];
 493                         in.read(buffer7, 2);
 494                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 495
 496                         //read format code
 497                         char buffer8 [1];
 498                         in.read(buffer8, 1);
 499                         header.flogramFormatCode = (int)(buffer8[0]);
 500
 501                         //read flow chars
 502                         char* tempBuffer = new char[header.numFlowsPerRead];
 503                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 504                         header.flowChars = tempBuffer;
 505                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 506                         delete[] tempBuffer;
 507
 508                         //read key
 509                         char* tempBuffer2 = new char[header.keyLength];
 510                         in.read(&(*tempBuffer2), header.keyLength);
 511                         header.keySequence = tempBuffer2;
 512                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 513                         delete[] tempBuffer2;
 514
 515                         /* Pad to 8 chars */
 516                         unsigned long long spotInFile = in.tellg();
 517                         unsigned long long spot = (spotInFile + 7)& ~7;  // ~ inverts
 518                         in.seekg(spot);
 519
 520                 }else{
 521                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 522                 }
 523
 524                 return 0;
 525         }
 526         catch(exception& e) {
 527                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 528                 exit(1);
 529         }
 530 }
 531 //**********************************************************************************************************************
 532 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 533         try {
 534
 535                 if (!in.eof()) {
 536
 537                         //read header length
 538                         char buffer [2];
 539                         in.read(buffer, 2);
 540                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 541
 542                         //read name length
 543                         char buffer2 [2];
 544                         in.read(buffer2, 2);
 545                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 546
 547                         //read num bases
 548                         char buffer3 [4];
 549                         in.read(buffer3, 4);
 550                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 551
 552                         //read clip qual left
 553                         char buffer4 [2];
 554                         in.read(buffer4, 2);
 555                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 556                         header.clipQualLeft = 5;
 557
 558                         //read clip qual right
 559                         char buffer5 [2];
 560                         in.read(buffer5, 2);
 561                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 562
 563                         //read clipAdapterLeft
 564                         char buffer6 [2];
 565                         in.read(buffer6, 2);
 566                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 567
 568                         //read clipAdapterRight
 569                         char buffer7 [2];
 570                         in.read(buffer7, 2);
 571                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 572
 573                         //read name
 574                         char* tempBuffer = new char[header.nameLength];
 575                         in.read(&(*tempBuffer), header.nameLength);
 576                         header.name = tempBuffer;
 577                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 578                         delete[] tempBuffer;
 579
 580                         //extract info from name
 581                         decodeName(header.timestamp, header.region, header.xy, header.name);
 582
 583                         /* Pad to 8 chars */
 584                         unsigned long long spotInFile = in.tellg();
 585                         unsigned long long spot = (spotInFile + 7)& ~7;
 586                         in.seekg(spot);
 587
 588                 }else{
 589                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 590                 }
 591
 592                 return 0;
 593         }
 594         catch(exception& e) {
 595                 m->errorOut(e, "SffInfoCommand", "readHeader");
 596                 exit(1);
 597         }
 598 }
 599 //**********************************************************************************************************************
 600 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 601         try {
 602
 603                 if (!in.eof()) {
 604
 605                         //read flowgram
 606                         read.flowgram.resize(numFlowReads);
 607                         for (int i = 0; i < numFlowReads; i++) {
 608                                 char buffer [2];
 609                                 in.read(buffer, 2);
 610                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 611                         }
 612
 613                         //read flowIndex
 614                         read.flowIndex.resize(numBases);
 615                         for (int i = 0; i < numBases; i++) {
 616                                 char temp[1];
 617                                 in.read(temp, 1);
 618                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 619                         }
 620
 621                         //read bases
 622                         char* tempBuffer = new char[numBases];
 623                         in.read(&(*tempBuffer), numBases);
 624                         read.bases = tempBuffer;
 625                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 626                         delete[] tempBuffer;
 627
 628                         //read qual scores
 629                         read.qualScores.resize(numBases);
 630                         for (int i = 0; i < numBases; i++) {
 631                                 char temp[1];
 632                                 in.read(temp, 1);
 633                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 634                         }
 635
 636                         /* Pad to 8 chars */
 637                         unsigned long long spotInFile = in.tellg();
 638                         unsigned long long spot = (spotInFile + 7)& ~7;
 639                         in.seekg(spot);
 640
 641                 }else{
 642                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 643                 }
 644
 645                 return 0;
 646         }
 647         catch(exception& e) {
 648                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 649                 exit(1);
 650         }
 651 }
 652 //**********************************************************************************************************************
 653 int SffInfoCommand::decodeName(string& timestamp, string& region, string& xy, string name) {
 654         try {
 655
 656                 if (name.length() >= 6) {
 657                         string time = name.substr(0, 6);
 658                         unsigned int timeNum = m->fromBase36(time);
 659
 660                         int q1 = timeNum / 60;
 661                         int sec = timeNum - 60 * q1;
 662                         int q2 = q1 / 60;
 663                         int minute = q1 - 60 * q2;
 664                         int q3 = q2 / 24;
 665                         int hr = q2 - 24 * q3;
 666                         int q4 = q3 / 32;
 667                         int day = q3 - 32 * q4;
 668                         int q5 = q4 / 13;
 669                         int mon = q4 - 13 * q5;
 670                         int year = 2000 + q5;
 671
 672                         timestamp = toString(year) + "_" + toString(mon) + "_" + toString(day) + "_" + toString(hr) + "_" + toString(minute) + "_" + toString(sec);
 673                 }
 674
 675                 if (name.length() >= 9) {
 676                         region = name.substr(7, 2);
 677
 678                         string xyNum = name.substr(9);
 679                         unsigned int myXy = m->fromBase36(xyNum);
 680                         int x = myXy >> 12;
 681                         int y = myXy & 4095;
 682
 683                         xy = toString(x) + "_" + toString(y);
 684                 }
 685
 686                 return 0;
 687         }
 688         catch(exception& e) {
 689                 m->errorOut(e, "SffInfoCommand", "decodeName");
 690                 exit(1);
 691         }
 692 }
 693 //**********************************************************************************************************************
 694 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 695         try {
 696
 697                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 698                 out << "Version: " << header.version << endl;
 699                 out << "Index Offset: " << header.indexOffset << endl;
 700                 out << "Index Length: " << header.indexLength << endl;
 701                 out << "Number of Reads: " << header.numReads << endl;
 702                 out << "Header Length: " << header.headerLength << endl;
 703                 out << "Key Length: " << header.keyLength << endl;
 704                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 705                 out << "Format Code: " << header.flogramFormatCode << endl;
 706                 out << "Flow Chars: " << header.flowChars << endl;
 707                 out << "Key Sequence: " << header.keySequence << endl << endl;
 708
 709                 return 0;
 710         }
 711         catch(exception& e) {
 712                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 713                 exit(1);
 714         }
 715 }
 716 //**********************************************************************************************************************
 717 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 718         try {
 719
 720                 out << ">" << header.name << endl;
 721                 out << "Run Prefix: " << header.timestamp << endl;
 722                 out << "Region #:  " << header.region << endl;
 723                 out << "XY Location: " << header.xy << endl << endl;
 724
 725                 out << "Run Name:  " << endl;
 726                 out << "Analysis Name:  " << endl;
 727                 out << "Full Path: " << endl << endl;
 728
 729                 out << "Read Header Len: " << header.headerLength << endl;
 730                 out << "Name Length: " << header.nameLength << endl;
 731                 out << "# of Bases: " << header.numBases << endl;
 732                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 733                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 734                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 735                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 736
 737                 return 0;
 738         }
 739         catch(exception& e) {
 740                 m->errorOut(e, "SffInfoCommand", "printHeader");
 741                 exit(1);
 742         }
 743 }
 744
 745 //**********************************************************************************************************************
 746 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
 747         try {
 748
 749                 out << "Flowgram: ";
 750                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 751
 752                 out << endl <<  "Flow Indexes: ";
 753                 int sum = 0;
 754                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 755
 756                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 757                 if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
 758                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 759                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 760                 for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
 761
 762                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 763                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 764
 765
 766                 out << endl << endl;
 767
 768                 return 0;
 769         }
 770         catch(exception& e) {
 771                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 772                 exit(1);
 773         }
 774 }
 775 //**********************************************************************************************************************
 776 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 777         try {
 778
 779                 string seq = read.bases;
 780
 781                 if (trim) {
 782                         if(header.clipQualRight < header.clipQualLeft){
 783                                 seq = "NNNN";
 784                         }
 785                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 786                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 787                         }
 788                         else {
 789                                 seq = seq.substr(header.clipQualLeft-1);
 790                         }
 791                 }else{
 792                         //if you wanted the sfftxt then you already converted the bases to the right case
 793                         if (!sfftxt) {
 794                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 795                                 if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
 796                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 797                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
 798                                 for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 799                         }
 800                 }
 801
 802                 out << ">" << header.name  << " xy=" << header.xy << endl;
 803                 out << seq << endl;
 804
 805                 return 0;
 806         }
 807         catch(exception& e) {
 808                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 809                 exit(1);
 810         }
 811 }
 812
 813 //**********************************************************************************************************************
 814 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 815         try {
 816
 817                 if (trim) {
 818                         if(header.clipQualRight < header.clipQualLeft){
 819                                 out << ">" << header.name << " xy=" << header.xy << endl;
 820                                 out << "0\t0\t0\t0";
 821                         }
 822                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 823                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 824                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
 825                         }
 826                         else{
 827                                 out << ">" << header.name << " xy=" << header.xy << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 828                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
 829                         }
 830                 }else{
 831                         out << ">" << header.name << " xy=" << header.xy << " length=" << read.qualScores.size() << endl;
 832                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 833                 }
 834
 835                 out << endl;
 836
 837                 return 0;
 838         }
 839         catch(exception& e) {
 840                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 841                 exit(1);
 842         }
 843 }
 844
 845 //**********************************************************************************************************************
 846 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 847         try {
 848                 if(header.clipQualRight > header.clipQualLeft){
 849
 850                         int rightIndex = 0;
 851                         for (int i = 0; i < header.clipQualRight; i++) {  rightIndex +=  read.flowIndex[i];     }
 852
 853                         out << header.name << ' ' << rightIndex;
 854                         for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << ' ' << (read.flowgram[i]/(float)100);  }
 855                         out << endl;
 856                 }
 857
 858
 859                 return 0;
 860         }
 861         catch(exception& e) {
 862                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 863                 exit(1);
 864         }
 865 }
 866 //**********************************************************************************************************************
 867 int SffInfoCommand::readAccnosFile(string filename) {
 868         try {
 869                 //remove old names
 870                 seqNames.clear();
 871
 872                 ifstream in;
 873                 m->openInputFile(filename, in);
 874                 string name;
 875
 876                 while(!in.eof()){
 877                         in >> name; m->gobble(in);
 878
 879                         seqNames.insert(name);
 880
 881                         if (m->control_pressed) { seqNames.clear(); break; }
 882                 }
 883                 in.close();
 884
 885                 return 0;
 886         }
 887         catch(exception& e) {
 888                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 889                 exit(1);
 890         }
 891 }
 892 //**********************************************************************************************************************
 893 int SffInfoCommand::parseSffTxt() {
 894         try {
 895
 896                 ifstream inSFF;
 897                 m->openInputFile(sfftxtFilename, inSFF);
 898
 899                 if (outputDir == "") {  outputDir += m->hasPath(sfftxtFilename); }
 900
 901                 //output file names
 902                 ofstream outFasta, outQual, outFlow;
 903                 string outFastaFileName, outQualFileName;
 904                 string fileRoot = m->getRootName(m->getSimpleName(sfftxtFilename));
 905                 if (fileRoot.length() > 0) {
 906                         //rip off last .
 907                         fileRoot = fileRoot.substr(0, fileRoot.length()-1);
 908                         fileRoot = m->getRootName(fileRoot);
 909                 }
 910
 911                 string outFlowFileName = outputDir + fileRoot + "flow";
 912                 if (trim) {
 913                         outFastaFileName = outputDir + fileRoot + "fasta";
 914                         outQualFileName = outputDir + fileRoot + "qual";
 915                 }else{
 916                         outFastaFileName = outputDir + fileRoot + "raw.fasta";
 917                         outQualFileName = outputDir + fileRoot + "raw.qual";
 918                 }
 919
 920                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 921                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
 922                 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);  }
 923
 924                 //read common header
 925                 string commonHeader = m->getline(inSFF);
 926                 string magicNumber = m->getline(inSFF);
 927                 string version = m->getline(inSFF);
 928                 string indexOffset = m->getline(inSFF);
 929                 string indexLength = m->getline(inSFF);
 930                 int numReads = parseHeaderLineToInt(inSFF);
 931                 string headerLength = m->getline(inSFF);
 932                 string keyLength = m->getline(inSFF);
 933                 int numFlows = parseHeaderLineToInt(inSFF);
 934                 string flowgramCode = m->getline(inSFF);
 935                 string flowChars = m->getline(inSFF);
 936                 string keySequence = m->getline(inSFF);
 937                 m->gobble(inSFF);
 938
 939                 string seqName;
 940
 941                 if (flow)       {       outFlow << numFlows << endl;    }
 942
 943                 for(int i=0;i<numReads;i++){
 944
 945                         //sanity check
 946                         if (inSFF.eof()) { m->mothurOut("[ERROR]: Expected " + toString(numReads) + " but reached end of file at " + toString(i+1) + "."); m->mothurOutEndLine(); break; }
 947
 948                         Header header;
 949
 950                         //parse read header
 951                         inSFF >> seqName;
 952                         seqName = seqName.substr(1);
 953                         m->gobble(inSFF);
 954                         header.name = seqName;
 955
 956                         string runPrefix = parseHeaderLineToString(inSFF);              header.timestamp = runPrefix;
 957                         string regionNumber = parseHeaderLineToString(inSFF);   header.region = regionNumber;
 958                         string xyLocation = parseHeaderLineToString(inSFF);             header.xy = xyLocation;
 959                         m->gobble(inSFF);
 960
 961                         string runName = parseHeaderLineToString(inSFF);
 962                         string analysisName = parseHeaderLineToString(inSFF);
 963                         string fullPath = parseHeaderLineToString(inSFF);
 964                         m->gobble(inSFF);
 965
 966                         string readHeaderLen = parseHeaderLineToString(inSFF);  convert(readHeaderLen, header.headerLength);
 967                         string nameLength = parseHeaderLineToString(inSFF);             convert(nameLength, header.nameLength);
 968                         int numBases = parseHeaderLineToInt(inSFF);                             header.numBases = numBases;
 969                         string clipQualLeft = parseHeaderLineToString(inSFF);   convert(clipQualLeft, header.clipQualLeft);
 970                         int clipQualRight = parseHeaderLineToInt(inSFF);                header.clipQualRight = clipQualRight;
 971                         string clipAdapLeft = parseHeaderLineToString(inSFF);   convert(clipAdapLeft, header.clipAdapterLeft);
 972                         string clipAdapRight = parseHeaderLineToString(inSFF);  convert(clipAdapRight, header.clipAdapterRight);
 973                         m->gobble(inSFF);
 974
 975                         seqRead read;
 976
 977                         //parse read
 978                         vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows);      read.flowgram = flowVector;
 979                         vector<unsigned int> flowIndices = parseHeaderLineToIntVector(inSFF, numBases);
 980
 981                         //adjust for print
 982                         vector<unsigned int> flowIndicesAdjusted; flowIndicesAdjusted.push_back(flowIndices[0]);
 983                         for (int j = 1; j < flowIndices.size(); j++) {   flowIndicesAdjusted.push_back(flowIndices[j] - flowIndices[j-1]);   }
 984                         read.flowIndex = flowIndicesAdjusted;
 985
 986                         string bases = parseHeaderLineToString(inSFF);                                                                          read.bases = bases;
 987                         vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases);       read.qualScores = qualityScores;
 988                         m->gobble(inSFF);
 989
 990                         //if you have provided an accosfile and this seq is not in it, then dont print
 991                         bool print = true;
 992                         if (seqNames.size() != 0) {   if (seqNames.count(header.name) == 0) { print = false; }  }
 993
 994                         //print
 995                         if (print) {
 996                                 if (fasta)      {       printFastaSeqData(outFasta, read, header);      }
 997                                 if (qual)       {       printQualSeqData(outQual, read, header);        }
 998                                 if (flow)       {       printFlowSeqData(outFlow, read, header);        }
 999                         }
1000
1001                         //report progress
1002                         if((i+1) % 10000 == 0){ m->mothurOut(toString(i+1)); m->mothurOutEndLine();             }
1003
1004                         if (m->control_pressed) {  break;  }
1005                 }
1006
1007                 //report progress
1008                 if (!m->control_pressed) {   if((numReads) % 10000 != 0){       m->mothurOut(toString(numReads)); m->mothurOutEndLine();                }  }
1009
1010                 inSFF.close();
1011
1012                 if (fasta)      {  outFasta.close();    }
1013                 if (qual)       {  outQual.close();             }
1014                 if (flow)       {  outFlow.close();             }
1015
1016                 return 0;
1017         }
1018         catch(exception& e) {
1019                 m->errorOut(e, "SffInfoCommand", "parseSffTxt");
1020                 exit(1);
1021         }
1022 }
1023 //**********************************************************************************************************************
1024
1025 int SffInfoCommand::parseHeaderLineToInt(ifstream& file){
1026         try {
1027                 int number;
1028
1029                 while (!file.eof())     {
1030
1031                         char c = file.get();
1032                         if (c == ':'){
1033                                 file >> number;
1034                                 break;
1035                         }
1036
1037                 }
1038                 m->gobble(file);
1039                 return number;
1040         }
1041         catch(exception& e) {
1042                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToInt");
1043                 exit(1);
1044         }
1045
1046 }
1047
1048 //**********************************************************************************************************************
1049
1050 string SffInfoCommand::parseHeaderLineToString(ifstream& file){
1051         try {
1052                 string text;
1053
1054                 while (!file.eof())     {
1055                         char c = file.get();
1056
1057                         if (c == ':'){
1058                                 //m->gobble(file);
1059                                 //text = m->getline(file);
1060                                 file >> text;
1061                                 break;
1062                         }
1063                 }
1064                 m->gobble(file);
1065
1066                 return text;
1067         }
1068         catch(exception& e) {
1069                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToString");
1070                 exit(1);
1071         }
1072 }
1073
1074 //**********************************************************************************************************************
1075
1076 vector<unsigned short> SffInfoCommand::parseHeaderLineToFloatVector(ifstream& file, int length){
1077         try {
1078                 vector<unsigned short> floatVector(length);
1079
1080                 while (!file.eof())     {
1081                         char c = file.get();
1082                         if (c == ':'){
1083                                 float temp;
1084                                 for(int i=0;i<length;i++){
1085                                         file >> temp;
1086                                         floatVector[i] = temp * 100;
1087                                 }
1088                                 break;
1089                         }
1090                 }
1091                 m->gobble(file);
1092                 return floatVector;
1093         }
1094         catch(exception& e) {
1095                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToFloatVector");
1096                 exit(1);
1097         }
1098 }
1099
1100 //**********************************************************************************************************************
1101
1102 vector<unsigned int> SffInfoCommand::parseHeaderLineToIntVector(ifstream& file, int length){
1103         try {
1104                 vector<unsigned int> intVector(length);
1105
1106                 while (!file.eof())     {
1107                         char c = file.get();
1108                         if (c == ':'){
1109                                 for(int i=0;i<length;i++){
1110                                         file >> intVector[i];
1111                                 }
1112                                 break;
1113                         }
1114                 }
1115                 m->gobble(file);
1116                 return intVector;
1117         }
1118         catch(exception& e) {
1119                 m->errorOut(e, "SffInfoCommand", "parseHeaderLineToIntVector");
1120                 exit(1);
1121         }
1122 }
1123
1124 //**********************************************************************************************************************
1125
1126
1127
1128