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