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                 //initialize outputTypes
  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"};
  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;
  68                 hasAccnos = false;
  69
  70                 //allow user to run help
  71                 if(option == "help") { help(); abort = 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") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true;  }
 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);                           if (temp == "not found"){       temp = "F";                             }
 224                         sfftxt = m->isTrue(temp);
 225                 }
 226         }
 227         catch(exception& e) {
 228                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 229                 exit(1);
 230         }
 231 }
 232 //**********************************************************************************************************************
 233
 234 void SffInfoCommand::help(){
 235         try {
 236                 m->mothurOut("The sffinfo command reads a sff file and extracts the sequence data.\n");
 237                 m->mothurOut("The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n");
 238                 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");
 239                 m->mothurOut("The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n");
 240                 m->mothurOut("The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n");
 241                 m->mothurOut("The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=False. \n");
 242                 m->mothurOut("The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n");
 243                 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");
 244                 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");
 245                 m->mothurOut("Example sffinfo(sff=mySffFile.sff, trim=F).\n");
 246                 m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
 247         }
 248         catch(exception& e) {
 249                 m->errorOut(e, "SffInfoCommand", "help");
 250                 exit(1);
 251         }
 252 }
 253 //**********************************************************************************************************************
 254
 255 SffInfoCommand::~SffInfoCommand(){}
 256
 257 //**********************************************************************************************************************
 258 int SffInfoCommand::execute(){
 259         try {
 260
 261                 if (abort == true) { return 0; }
 262
 263                 for (int s = 0; s < filenames.size(); s++) {
 264
 265                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 266
 267                         int start = time(NULL);
 268
 269                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 270
 271                         string accnos = "";
 272                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 273
 274                         int numReads = extractSffInfo(filenames[s], accnos);
 275
 276                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 277                 }
 278
 279                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 280
 281                 //report output filenames
 282                 m->mothurOutEndLine();
 283                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 284                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 285                 m->mothurOutEndLine();
 286
 287                 return 0;
 288         }
 289         catch(exception& e) {
 290                 m->errorOut(e, "SffInfoCommand", "execute");
 291                 exit(1);
 292         }
 293 }
 294 //**********************************************************************************************************************
 295 int SffInfoCommand::extractSffInfo(string input, string accnos){
 296         try {
 297
 298                 if (outputDir == "") {  outputDir += m->hasPath(input); }
 299
 300                 if (accnos != "")       {  readAccnosFile(accnos);  }
 301                 else                            {       seqNames.clear();               }
 302
 303                 ofstream outSfftxt, outFasta, outQual, outFlow;
 304                 string outFastaFileName, outQualFileName;
 305                 string sfftxtFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "sff.txt";
 306                 string outFlowFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "flow";
 307                 if (trim) {
 308                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "fasta";
 309                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "qual";
 310                 }else{
 311                         outFastaFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.fasta";
 312                         outQualFileName = outputDir + m->getRootName(m->getSimpleName(input)) + "raw.qual";
 313                 }
 314
 315                 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); }
 316                 if (fasta)      { m->openOutputFile(outFastaFileName, outFasta);        outputNames.push_back(outFastaFileName); outputTypes["fasta"].push_back(outFastaFileName); }
 317                 if (qual)       { m->openOutputFile(outQualFileName, outQual);          outputNames.push_back(outQualFileName); outputTypes["qual"].push_back(outQualFileName);  }
 318                 if (flow)       { m->openOutputFile(outFlowFileName, outFlow);          outputNames.push_back(outFlowFileName);  outputTypes["flow"].push_back(outFlowFileName);  }
 319
 320                 ifstream in;
 321                 in.open(input.c_str(), ios::binary);
 322
 323                 CommonHeader header;
 324                 readCommonHeader(in, header);
 325
 326                 int count = 0;
 327
 328                 //check magic number and version
 329                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 330                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 331
 332                 //print common header
 333                 if (sfftxt) { printCommonHeader(outSfftxt, header); }
 334
 335                 //read through the sff file
 336                 while (!in.eof()) {
 337
 338                         bool print = true;
 339
 340                         //read header
 341                         Header readheader;
 342                         readHeader(in, readheader);
 343
 344                         //read data
 345                         seqRead read;
 346                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 347
 348                         //if you have provided an accosfile and this seq is not in it, then dont print
 349                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 350
 351                         //print
 352                         if (print) {
 353                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 354                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 355                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 356                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 357                         }
 358
 359                         count++;
 360
 361                         //report progress
 362                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 363
 364                         if (m->control_pressed) { count = 0; break;   }
 365
 366                         if (count >= header.numReads) { break; }
 367                 }
 368
 369                 //report progress
 370                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 371
 372                 in.close();
 373
 374                 if (sfftxt) {  outSfftxt.close();       }
 375                 if (fasta)      {  outFasta.close();    }
 376                 if (qual)       {  outQual.close();             }
 377                 if (flow)       {  outFlow.close();             }
 378
 379                 return count;
 380         }
 381         catch(exception& e) {
 382                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 383                 exit(1);
 384         }
 385 }
 386 //**********************************************************************************************************************
 387 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 388         try {
 389
 390                 if (!in.eof()) {
 391
 392                         //read magic number
 393                         char buffer[4];
 394                         in.read(buffer, 4);
 395                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 396
 397                         //read version
 398                         char buffer9[4];
 399                         in.read(buffer9, 4);
 400                         header.version = "";
 401                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 402
 403                         //read offset
 404                         char buffer2 [8];
 405                         in.read(buffer2, 8);
 406                         header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
 407
 408                         //read index length
 409                         char buffer3 [4];
 410                         in.read(buffer3, 4);
 411                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 412
 413                         //read num reads
 414                         char buffer4 [4];
 415                         in.read(buffer4, 4);
 416                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 417
 418                         //read header length
 419                         char buffer5 [2];
 420                         in.read(buffer5, 2);
 421                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 422
 423                         //read key length
 424                         char buffer6 [2];
 425                         in.read(buffer6, 2);
 426                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 427
 428                         //read number of flow reads
 429                         char buffer7 [2];
 430                         in.read(buffer7, 2);
 431                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 432
 433                         //read format code
 434                         char buffer8 [1];
 435                         in.read(buffer8, 1);
 436                         header.flogramFormatCode = (int)(buffer8[0]);
 437
 438                         //read flow chars
 439                         char* tempBuffer = new char[header.numFlowsPerRead];
 440                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 441                         header.flowChars = tempBuffer;
 442                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 443                         delete[] tempBuffer;
 444
 445                         //read key
 446                         char* tempBuffer2 = new char[header.keyLength];
 447                         in.read(&(*tempBuffer2), header.keyLength);
 448                         header.keySequence = tempBuffer2;
 449                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 450                         delete[] tempBuffer2;
 451
 452                         /* Pad to 8 chars */
 453                         unsigned long int spotInFile = in.tellg();
 454                         unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
 455                         in.seekg(spot);
 456
 457                 }else{
 458                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 459                 }
 460
 461                 return 0;
 462         }
 463         catch(exception& e) {
 464                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 465                 exit(1);
 466         }
 467 }
 468 //**********************************************************************************************************************
 469 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 470         try {
 471
 472                 if (!in.eof()) {
 473
 474                         //read header length
 475                         char buffer [2];
 476                         in.read(buffer, 2);
 477                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 478
 479                         //read name length
 480                         char buffer2 [2];
 481                         in.read(buffer2, 2);
 482                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 483
 484                         //read num bases
 485                         char buffer3 [4];
 486                         in.read(buffer3, 4);
 487                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 488
 489                         //read clip qual left
 490                         char buffer4 [2];
 491                         in.read(buffer4, 2);
 492                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 493                         header.clipQualLeft = 5;
 494
 495                         //read clip qual right
 496                         char buffer5 [2];
 497                         in.read(buffer5, 2);
 498                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 499
 500                         //read clipAdapterLeft
 501                         char buffer6 [2];
 502                         in.read(buffer6, 2);
 503                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 504
 505                         //read clipAdapterRight
 506                         char buffer7 [2];
 507                         in.read(buffer7, 2);
 508                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 509
 510                         //read name
 511                         char* tempBuffer = new char[header.nameLength];
 512                         in.read(&(*tempBuffer), header.nameLength);
 513                         header.name = tempBuffer;
 514                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 515                         delete[] tempBuffer;
 516
 517                         /* Pad to 8 chars */
 518                         unsigned long int spotInFile = in.tellg();
 519                         unsigned long int spot = (spotInFile + 7)& ~7;
 520                         in.seekg(spot);
 521
 522                 }else{
 523                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 524                 }
 525
 526                 return 0;
 527         }
 528         catch(exception& e) {
 529                 m->errorOut(e, "SffInfoCommand", "readHeader");
 530                 exit(1);
 531         }
 532 }
 533 //**********************************************************************************************************************
 534 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 535         try {
 536
 537                 if (!in.eof()) {
 538
 539                         //read flowgram
 540                         read.flowgram.resize(numFlowReads);
 541                         for (int i = 0; i < numFlowReads; i++) {
 542                                 char buffer [2];
 543                                 in.read(buffer, 2);
 544                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 545                         }
 546
 547                         //read flowIndex
 548                         read.flowIndex.resize(numBases);
 549                         for (int i = 0; i < numBases; i++) {
 550                                 char temp[1];
 551                                 in.read(temp, 1);
 552                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 553                         }
 554
 555                         //read bases
 556                         char* tempBuffer = new char[numBases];
 557                         in.read(&(*tempBuffer), numBases);
 558                         read.bases = tempBuffer;
 559                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 560                         delete[] tempBuffer;
 561
 562                         //read qual scores
 563                         read.qualScores.resize(numBases);
 564                         for (int i = 0; i < numBases; i++) {
 565                                 char temp[1];
 566                                 in.read(temp, 1);
 567                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 568                         }
 569
 570                         /* Pad to 8 chars */
 571                         unsigned long int spotInFile = in.tellg();
 572                         unsigned long int spot = (spotInFile + 7)& ~7;
 573                         in.seekg(spot);
 574
 575                 }else{
 576                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 577                 }
 578
 579                 return 0;
 580         }
 581         catch(exception& e) {
 582                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 583                 exit(1);
 584         }
 585 }
 586 //**********************************************************************************************************************
 587 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 588         try {
 589
 590                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 591                 out << "Version: " << header.version << endl;
 592                 out << "Index Offset: " << header.indexOffset << endl;
 593                 out << "Index Length: " << header.indexLength << endl;
 594                 out << "Number of Reads: " << header.numReads << endl;
 595                 out << "Header Length: " << header.headerLength << endl;
 596                 out << "Key Length: " << header.keyLength << endl;
 597                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 598                 out << "Format Code: " << header.flogramFormatCode << endl;
 599                 out << "Flow Chars: " << header.flowChars << endl;
 600                 out << "Key Sequence: " << header.keySequence << endl << endl;
 601
 602                 return 0;
 603         }
 604         catch(exception& e) {
 605                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 606                 exit(1);
 607         }
 608 }
 609 //**********************************************************************************************************************
 610 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 611         try {
 612
 613                 out << ">" << header.name << endl;
 614                 out << "Run Prefix: " << endl;
 615                 out << "Region #:  " << endl;
 616                 out << "XY Location: " << endl << endl;
 617
 618                 out << "Run Name:  " << endl;
 619                 out << "Analysis Name:  " << endl;
 620                 out << "Full Path: " << endl << endl;
 621
 622                 out << "Read Header Len: " << header.headerLength << endl;
 623                 out << "Name Length: " << header.nameLength << endl;
 624                 out << "# of Bases: " << header.numBases << endl;
 625                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 626                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 627                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 628                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 629
 630                 return 0;
 631         }
 632         catch(exception& e) {
 633                 m->errorOut(e, "SffInfoCommand", "printHeader");
 634                 exit(1);
 635         }
 636 }
 637
 638 //**********************************************************************************************************************
 639 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
 640         try {
 641
 642                 out << "Flowgram: ";
 643                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 644
 645                 out << endl <<  "Flow Indexes: ";
 646                 int sum = 0;
 647                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 648
 649                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 650                 if(header.clipQualRight == 0){  header.clipQualRight = read.bases.length();     }
 651                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 652                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 653                 for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
 654
 655                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 656                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 657
 658
 659                 out << endl << endl;
 660
 661                 return 0;
 662         }
 663         catch(exception& e) {
 664                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 665                 exit(1);
 666         }
 667 }
 668 //**********************************************************************************************************************
 669 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 670         try {
 671
 672                 string seq = read.bases;
 673
 674                 if (trim) {
 675                         if(header.clipQualRight < header.clipQualLeft){
 676                                 seq = "NNNN";
 677                         }
 678                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 679                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 680                         }
 681                         else {
 682                                 seq = seq.substr(header.clipQualLeft-1);
 683                         }
 684                 }else{
 685                         //if you wanted the sfftxt then you already converted the bases to the right case
 686                         if (!sfftxt) {
 687                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 688                                 if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
 689                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 690                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
 691                                 for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 692                         }
 693                 }
 694
 695                 out << ">" << header.name << endl;
 696                 out << seq << endl;
 697
 698                 return 0;
 699         }
 700         catch(exception& e) {
 701                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 702                 exit(1);
 703         }
 704 }
 705
 706 //**********************************************************************************************************************
 707 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 708         try {
 709
 710                 if (trim) {
 711                         if(header.clipQualRight < header.clipQualLeft){
 712                                 out << "0\t0\t0\t0";
 713                         }
 714                         else if((header.clipQualRight != 0) && ((header.clipQualRight-header.clipQualLeft) >= 0)){
 715                                 out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 716                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
 717                         }
 718                         else{
 719                                 out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 720                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
 721                         }
 722                 }else{
 723                         out << ">" << header.name << " length=" << read.qualScores.size() << endl;
 724                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 725                 }
 726
 727                 out << endl;
 728
 729                 return 0;
 730         }
 731         catch(exception& e) {
 732                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 733                 exit(1);
 734         }
 735 }
 736
 737 //**********************************************************************************************************************
 738 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 739         try {
 740
 741                 out << ">" << header.name << endl;
 742                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 743                 out << endl;
 744
 745                 return 0;
 746         }
 747         catch(exception& e) {
 748                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 749                 exit(1);
 750         }
 751 }
 752 //**********************************************************************************************************************
 753 int SffInfoCommand::readAccnosFile(string filename) {
 754         try {
 755                 //remove old names
 756                 seqNames.clear();
 757
 758                 ifstream in;
 759                 m->openInputFile(filename, in);
 760                 string name;
 761
 762                 while(!in.eof()){
 763                         in >> name; m->gobble(in);
 764
 765                         seqNames.insert(name);
 766
 767                         if (m->control_pressed) { seqNames.clear(); break; }
 768                 }
 769                 in.close();
 770
 771                 return 0;
 772         }
 773         catch(exception& e) {
 774                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 775                 exit(1);
 776         }
 777 }
 778 //**********************************************************************************************************************/