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
  15 SffInfoCommand::SffInfoCommand(string option)  {
  16         try {
  17                 abort = false;
  18                 hasAccnos = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"sff","qfile","fasta","flow","trim","accnos","sfftxt","outputdir","inputdir", "outputdir"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         OptionParser parser(option);
  29                         map<string, string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32                         //check to make sure all parameters are valid for command
  33                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  34                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  35                         }
  36
  37                         //if the user changes the output directory command factory will send this info to us in the output parameter
  38                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = "";         }
  39
  40                         //if the user changes the input directory command factory will send this info to us in the output parameter
  41                         string inputDir = validParameter.validFile(parameters, "inputdir", false);        if (inputDir == "not found"){ inputDir = "";          }
  42
  43                         sffFilename = validParameter.validFile(parameters, "sff", false);
  44                         if (sffFilename == "not found") { m->mothurOut("sff is a required parameter for the sffinfo command."); m->mothurOutEndLine(); abort = true;  }
  45                         else {
  46                                 splitAtDash(sffFilename, filenames);
  47
  48                                 //go through files and make sure they are good, if not, then disregard them
  49                                 for (int i = 0; i < filenames.size(); i++) {
  50                                         if (inputDir != "") {
  51                                                 string path = hasPath(filenames[i]);
  52                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  53                                                 if (path == "") {       filenames[i] = inputDir + filenames[i];         }
  54                                         }
  55
  56                                         ifstream in;
  57                                         int ableToOpen = openInputFile(filenames[i], in, "noerror");
  58
  59                                         //if you can't open it, try default location
  60                                         if (ableToOpen == 1) {
  61                                                 if (m->getDefaultPath() != "") { //default path is set
  62                                                         string tryPath = m->getDefaultPath() + getSimpleName(filenames[i]);
  63                                                         m->mothurOut("Unable to open " + filenames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
  64                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
  65                                                         filenames[i] = tryPath;
  66                                                 }
  67                                         }
  68                                         in.close();
  69
  70                                         if (ableToOpen == 1) {
  71                                                 m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded."); m->mothurOutEndLine();
  72                                                 //erase from file list
  73                                                 filenames.erase(filenames.begin()+i);
  74                                                 i--;
  75                                         }
  76                                 }
  77
  78                                 //make sure there is at least one valid file left
  79                                 if (filenames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
  80                         }
  81
  82                         accnosName = validParameter.validFile(parameters, "accnos", false);
  83                         if (accnosName == "not found") { accnosName = "";  }
  84                         else {
  85                                 hasAccnos = true;
  86                                 splitAtDash(accnosName, accnosFileNames);
  87
  88                                 //go through files and make sure they are good, if not, then disregard them
  89                                 for (int i = 0; i < accnosFileNames.size(); i++) {
  90                                         if (inputDir != "") {
  91                                                 string path = hasPath(accnosFileNames[i]);
  92                                                 //if the user has not given a path then, add inputdir. else leave path alone.
  93                                                 if (path == "") {       accnosFileNames[i] = inputDir + accnosFileNames[i];             }
  94                                         }
  95
  96                                         ifstream in;
  97                                         int ableToOpen = openInputFile(accnosFileNames[i], in, "noerror");
  98
  99                                         //if you can't open it, try default location
 100                                         if (ableToOpen == 1) {
 101                                                 if (m->getDefaultPath() != "") { //default path is set
 102                                                         string tryPath = m->getDefaultPath() + getSimpleName(accnosFileNames[i]);
 103                                                         m->mothurOut("Unable to open " + accnosFileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine();
 104                                                         ableToOpen = openInputFile(tryPath, in, "noerror");
 105                                                         accnosFileNames[i] = tryPath;
 106                                                 }
 107                                         }
 108                                         in.close();
 109
 110                                         if (ableToOpen == 1) {
 111                                                 m->mothurOut("Unable to open " + accnosFileNames[i] + ". It will be disregarded."); m->mothurOutEndLine();
 112                                                 //erase from file list
 113                                                 accnosFileNames.erase(accnosFileNames.begin()+i);
 114                                                 i--;
 115                                         }
 116                                 }
 117
 118                                 //make sure there is at least one valid file left
 119                                 if (accnosFileNames.size() == 0) { m->mothurOut("no valid files."); m->mothurOutEndLine(); abort = true; }
 120                         }
 121
 122                         if (hasAccnos) {
 123                                 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(); }
 124                         }
 125
 126                         string temp = validParameter.validFile(parameters, "qfile", false);                     if (temp == "not found"){       temp = "T";                             }
 127                         qual = isTrue(temp);
 128
 129                         temp = validParameter.validFile(parameters, "fasta", false);                            if (temp == "not found"){       temp = "T";                             }
 130                         fasta = isTrue(temp);
 131
 132                         temp = validParameter.validFile(parameters, "flow", false);                                     if (temp == "not found"){       temp = "F";                             }
 133                         flow = isTrue(temp);
 134
 135                         temp = validParameter.validFile(parameters, "trim", false);                                     if (temp == "not found"){       temp = "T";                             }
 136                         trim = isTrue(temp);
 137
 138                         temp = validParameter.validFile(parameters, "sfftxt", false);                           if (temp == "not found"){       temp = "F";                             }
 139                         sfftxt = isTrue(temp);
 140                 }
 141         }
 142         catch(exception& e) {
 143                 m->errorOut(e, "SffInfoCommand", "SffInfoCommand");
 144                 exit(1);
 145         }
 146 }
 147 //**********************************************************************************************************************
 148
 149 void SffInfoCommand::help(){
 150         try {
 151                 m->mothurOut("The sffinfo command reads a sff file and extracts the sequence data.\n");
 152                 m->mothurOut("The sffinfo command parameters are sff, fasta, qfile, accnos, flow, sfftxt, and trim. sff is required. \n");
 153                 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");
 154                 m->mothurOut("The fasta parameter allows you to indicate if you would like a fasta formatted file generated.  Default=True. \n");
 155                 m->mothurOut("The qfile parameter allows you to indicate if you would like a quality file generated.  Default=True. \n");
 156                 m->mothurOut("The flow parameter allows you to indicate if you would like a flowgram file generated.  Default=False. \n");
 157                 m->mothurOut("The sfftxt parameter allows you to indicate if you would like a sff.txt file generated.  Default=False. \n");
 158                 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");
 159                 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");
 160                 m->mothurOut("Example sffinfo(sff=mySffFile.sff, trim=F).\n");
 161                 m->mothurOut("Note: No spaces between parameter labels (i.e. sff), '=' and parameters (i.e.yourSffFileName).\n\n");
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "SffInfoCommand", "help");
 165                 exit(1);
 166         }
 167 }
 168 //**********************************************************************************************************************
 169
 170 SffInfoCommand::~SffInfoCommand(){}
 171
 172 //**********************************************************************************************************************
 173 int SffInfoCommand::execute(){
 174         try {
 175
 176                 if (abort == true) { return 0; }
 177
 178                 for (int s = 0; s < filenames.size(); s++) {
 179
 180                         if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 181
 182                         int start = time(NULL);
 183
 184                         m->mothurOut("Extracting info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
 185
 186                         string accnos = "";
 187                         if (hasAccnos) { accnos = accnosFileNames[s]; }
 188
 189                         int numReads = extractSffInfo(filenames[s], accnos);
 190
 191                         m->mothurOut("It took " + toString(time(NULL) - start) + " secs to extract " + toString(numReads) + ".");
 192                 }
 193
 194                 if (m->control_pressed) {  for (int i = 0; i < outputNames.size(); i++) {       remove(outputNames[i].c_str());         } return 0; }
 195
 196                 //report output filenames
 197                 m->mothurOutEndLine();
 198                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 199                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 200                 m->mothurOutEndLine();
 201
 202                 return 0;
 203         }
 204         catch(exception& e) {
 205                 m->errorOut(e, "SffInfoCommand", "execute");
 206                 exit(1);
 207         }
 208 }
 209 //**********************************************************************************************************************
 210 int SffInfoCommand::extractSffInfo(string input, string accnos){
 211         try {
 212
 213                 if (outputDir == "") {  outputDir += hasPath(input); }
 214
 215                 if (accnos != "")       {  readAccnosFile(accnos);  }
 216                 else                            {       seqNames.clear();               }
 217
 218                 ofstream outSfftxt, outFasta, outQual, outFlow;
 219                 string outFastaFileName, outQualFileName;
 220                 string sfftxtFileName = outputDir + getRootName(getSimpleName(input)) + "sff.txt";
 221                 string outFlowFileName = outputDir + getRootName(getSimpleName(input)) + "flow";
 222                 if (trim) {
 223                         outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "fasta";
 224                         outQualFileName = outputDir + getRootName(getSimpleName(input)) + "qual";
 225                 }else{
 226                         outFastaFileName = outputDir + getRootName(getSimpleName(input)) + "raw.fasta";
 227                         outQualFileName = outputDir + getRootName(getSimpleName(input)) + "raw.qual";
 228                 }
 229
 230                 if (sfftxt) { openOutputFile(sfftxtFileName, outSfftxt); outSfftxt.setf(ios::fixed, ios::floatfield); outSfftxt.setf(ios::showpoint);  outputNames.push_back(sfftxtFileName); }
 231                 if (fasta)      { openOutputFile(outFastaFileName, outFasta);   outputNames.push_back(outFastaFileName); }
 232                 if (qual)       { openOutputFile(outQualFileName, outQual);             outputNames.push_back(outQualFileName);  }
 233                 if (flow)       { openOutputFile(outFlowFileName, outFlow);             outputNames.push_back(outFlowFileName);  }
 234
 235                 ifstream in;
 236                 in.open(input.c_str(), ios::binary);
 237
 238                 CommonHeader header;
 239                 readCommonHeader(in, header);
 240
 241                 int count = 0;
 242
 243                 //check magic number and version
 244                 if (header.magicNumber != 779314790) { m->mothurOut("Magic Number is not correct, not a valid .sff file"); m->mothurOutEndLine(); return count; }
 245                 if (header.version != "0001") { m->mothurOut("Version is not supported, only support version 0001."); m->mothurOutEndLine(); return count; }
 246
 247                 //print common header
 248                 if (sfftxt) { printCommonHeader(outSfftxt, header); }
 249
 250                 //read through the sff file
 251                 while (!in.eof()) {
 252
 253                         bool print = true;
 254
 255                         //read header
 256                         Header readheader;
 257                         readHeader(in, readheader);
 258
 259                         //read data
 260                         seqRead read;
 261                         readSeqData(in, read, header.numFlowsPerRead, readheader.numBases);
 262
 263                         //if you have provided an accosfile and this seq is not in it, then dont print
 264                         if (seqNames.size() != 0) {   if (seqNames.count(readheader.name) == 0) { print = false; }  }
 265
 266                         //print
 267                         if (print) {
 268                                 if (sfftxt) { printHeader(outSfftxt, readheader); printSffTxtSeqData(outSfftxt, read, readheader); }
 269                                 if (fasta)      {       printFastaSeqData(outFasta, read, readheader);  }
 270                                 if (qual)       {       printQualSeqData(outQual, read, readheader);    }
 271                                 if (flow)       {       printFlowSeqData(outFlow, read, readheader);    }
 272                         }
 273
 274                         count++;
 275
 276                         //report progress
 277                         if((count+1) % 10000 == 0){     m->mothurOut(toString(count+1)); m->mothurOutEndLine();         }
 278
 279                         if (m->control_pressed) { count = 0; break;   }
 280
 281                         if (count >= header.numReads) { break; }
 282                 }
 283
 284                 //report progress
 285                 if (!m->control_pressed) {   if((count) % 10000 != 0){  m->mothurOut(toString(count)); m->mothurOutEndLine();           }  }
 286
 287                 in.close();
 288
 289                 if (sfftxt) {  outSfftxt.close();       }
 290                 if (fasta)      {  outFasta.close();    }
 291                 if (qual)       {  outQual.close();             }
 292                 if (flow)       {  outFlow.close();             }
 293
 294                 return count;
 295         }
 296         catch(exception& e) {
 297                 m->errorOut(e, "SffInfoCommand", "extractSffInfo");
 298                 exit(1);
 299         }
 300 }
 301 //**********************************************************************************************************************
 302 int SffInfoCommand::readCommonHeader(ifstream& in, CommonHeader& header){
 303         try {
 304
 305                 if (!in.eof()) {
 306
 307                         //read magic number
 308                         char buffer[4];
 309                         in.read(buffer, 4);
 310                         header.magicNumber = be_int4(*(unsigned int *)(&buffer));
 311
 312                         //read version
 313                         char buffer9[4];
 314                         in.read(buffer9, 4);
 315                         header.version = "";
 316                         for (int i = 0; i < 4; i++) {  header.version += toString((int)(buffer9[i])); }
 317
 318                         //read offset
 319                         char buffer2 [8];
 320                         in.read(buffer2, 8);
 321                         header.indexOffset =  be_int8(*(unsigned long int *)(&buffer2));
 322
 323                         //read index length
 324                         char buffer3 [4];
 325                         in.read(buffer3, 4);
 326                         header.indexLength =  be_int4(*(unsigned int *)(&buffer3));
 327
 328                         //read num reads
 329                         char buffer4 [4];
 330                         in.read(buffer4, 4);
 331                         header.numReads =  be_int4(*(unsigned int *)(&buffer4));
 332
 333                         //read header length
 334                         char buffer5 [2];
 335                         in.read(buffer5, 2);
 336                         header.headerLength =  be_int2(*(unsigned short *)(&buffer5));
 337
 338                         //read key length
 339                         char buffer6 [2];
 340                         in.read(buffer6, 2);
 341                         header.keyLength = be_int2(*(unsigned short *)(&buffer6));
 342
 343                         //read number of flow reads
 344                         char buffer7 [2];
 345                         in.read(buffer7, 2);
 346                         header.numFlowsPerRead =  be_int2(*(unsigned short *)(&buffer7));
 347
 348                         //read format code
 349                         char buffer8 [1];
 350                         in.read(buffer8, 1);
 351                         header.flogramFormatCode = (int)(buffer8[0]);
 352
 353                         //read flow chars
 354                         char* tempBuffer = new char[header.numFlowsPerRead];
 355                         in.read(&(*tempBuffer), header.numFlowsPerRead);
 356                         header.flowChars = tempBuffer;
 357                         if (header.flowChars.length() > header.numFlowsPerRead) { header.flowChars = header.flowChars.substr(0, header.numFlowsPerRead);  }
 358                         delete[] tempBuffer;
 359
 360                         //read key
 361                         char* tempBuffer2 = new char[header.keyLength];
 362                         in.read(&(*tempBuffer2), header.keyLength);
 363                         header.keySequence = tempBuffer2;
 364                         if (header.keySequence.length() > header.keyLength) { header.keySequence = header.keySequence.substr(0, header.keyLength);  }
 365                         delete[] tempBuffer2;
 366
 367                         /* Pad to 8 chars */
 368                         unsigned long int spotInFile = in.tellg();
 369                         unsigned long int spot = (spotInFile + 7)& ~7;  // ~ inverts
 370                         in.seekg(spot);
 371
 372                 }else{
 373                         m->mothurOut("Error reading sff common header."); m->mothurOutEndLine();
 374                 }
 375
 376                 return 0;
 377         }
 378         catch(exception& e) {
 379                 m->errorOut(e, "SffInfoCommand", "readCommonHeader");
 380                 exit(1);
 381         }
 382 }
 383 //**********************************************************************************************************************
 384 int SffInfoCommand::readHeader(ifstream& in, Header& header){
 385         try {
 386
 387                 if (!in.eof()) {
 388
 389                         //read header length
 390                         char buffer [2];
 391                         in.read(buffer, 2);
 392                         header.headerLength = be_int2(*(unsigned short *)(&buffer));
 393
 394                         //read name length
 395                         char buffer2 [2];
 396                         in.read(buffer2, 2);
 397                         header.nameLength = be_int2(*(unsigned short *)(&buffer2));
 398
 399                         //read num bases
 400                         char buffer3 [4];
 401                         in.read(buffer3, 4);
 402                         header.numBases =  be_int4(*(unsigned int *)(&buffer3));
 403
 404                         //read clip qual left
 405                         char buffer4 [2];
 406                         in.read(buffer4, 2);
 407                         header.clipQualLeft =  be_int2(*(unsigned short *)(&buffer4));
 408                         header.clipQualLeft = 5;
 409
 410                         //read clip qual right
 411                         char buffer5 [2];
 412                         in.read(buffer5, 2);
 413                         header.clipQualRight =  be_int2(*(unsigned short *)(&buffer5));
 414
 415                         //read clipAdapterLeft
 416                         char buffer6 [2];
 417                         in.read(buffer6, 2);
 418                         header.clipAdapterLeft = be_int2(*(unsigned short *)(&buffer6));
 419
 420                         //read clipAdapterRight
 421                         char buffer7 [2];
 422                         in.read(buffer7, 2);
 423                         header.clipAdapterRight = be_int2(*(unsigned short *)(&buffer7));
 424
 425                         //read name
 426                         char* tempBuffer = new char[header.nameLength];
 427                         in.read(&(*tempBuffer), header.nameLength);
 428                         header.name = tempBuffer;
 429                         if (header.name.length() > header.nameLength) { header.name = header.name.substr(0, header.nameLength);  }
 430                         delete[] tempBuffer;
 431
 432                         /* Pad to 8 chars */
 433                         unsigned long int spotInFile = in.tellg();
 434                         unsigned long int spot = (spotInFile + 7)& ~7;
 435                         in.seekg(spot);
 436
 437                 }else{
 438                         m->mothurOut("Error reading sff header info."); m->mothurOutEndLine();
 439                 }
 440
 441                 return 0;
 442         }
 443         catch(exception& e) {
 444                 m->errorOut(e, "SffInfoCommand", "readHeader");
 445                 exit(1);
 446         }
 447 }
 448 //**********************************************************************************************************************
 449 int SffInfoCommand::readSeqData(ifstream& in, seqRead& read, int numFlowReads, int numBases){
 450         try {
 451
 452                 if (!in.eof()) {
 453
 454                         //read flowgram
 455                         read.flowgram.resize(numFlowReads);
 456                         for (int i = 0; i < numFlowReads; i++) {
 457                                 char buffer [2];
 458                                 in.read(buffer, 2);
 459                                 read.flowgram[i] = be_int2(*(unsigned short *)(&buffer));
 460                         }
 461
 462                         //read flowIndex
 463                         read.flowIndex.resize(numBases);
 464                         for (int i = 0; i < numBases; i++) {
 465                                 char temp[1];
 466                                 in.read(temp, 1);
 467                                 read.flowIndex[i] = be_int1(*(unsigned char *)(&temp));
 468                         }
 469
 470                         //read bases
 471                         char* tempBuffer = new char[numBases];
 472                         in.read(&(*tempBuffer), numBases);
 473                         read.bases = tempBuffer;
 474                         if (read.bases.length() > numBases) { read.bases = read.bases.substr(0, numBases);  }
 475                         delete[] tempBuffer;
 476
 477                         //read qual scores
 478                         read.qualScores.resize(numBases);
 479                         for (int i = 0; i < numBases; i++) {
 480                                 char temp[1];
 481                                 in.read(temp, 1);
 482                                 read.qualScores[i] = be_int1(*(unsigned char *)(&temp));
 483                         }
 484
 485                         /* Pad to 8 chars */
 486                         unsigned long int spotInFile = in.tellg();
 487                         unsigned long int spot = (spotInFile + 7)& ~7;
 488                         in.seekg(spot);
 489
 490                 }else{
 491                         m->mothurOut("Error reading."); m->mothurOutEndLine();
 492                 }
 493
 494                 return 0;
 495         }
 496         catch(exception& e) {
 497                 m->errorOut(e, "SffInfoCommand", "readSeqData");
 498                 exit(1);
 499         }
 500 }
 501 //**********************************************************************************************************************
 502 int SffInfoCommand::printCommonHeader(ofstream& out, CommonHeader& header) {
 503         try {
 504
 505                 out << "Common Header:\nMagic Number: " << header.magicNumber << endl;
 506                 out << "Version: " << header.version << endl;
 507                 out << "Index Offset: " << header.indexOffset << endl;
 508                 out << "Index Length: " << header.indexLength << endl;
 509                 out << "Number of Reads: " << header.numReads << endl;
 510                 out << "Header Length: " << header.headerLength << endl;
 511                 out << "Key Length: " << header.keyLength << endl;
 512                 out << "Number of Flows: " << header.numFlowsPerRead << endl;
 513                 out << "Format Code: " << header.flogramFormatCode << endl;
 514                 out << "Flow Chars: " << header.flowChars << endl;
 515                 out << "Key Sequence: " << header.keySequence << endl << endl;
 516
 517                 return 0;
 518         }
 519         catch(exception& e) {
 520                 m->errorOut(e, "SffInfoCommand", "printCommonHeader");
 521                 exit(1);
 522         }
 523 }
 524 //**********************************************************************************************************************
 525 int SffInfoCommand::printHeader(ofstream& out, Header& header) {
 526         try {
 527
 528                 out << ">" << header.name << endl;
 529                 out << "Run Prefix: " << endl;
 530                 out << "Region #:  " << endl;
 531                 out << "XY Location: " << endl << endl;
 532
 533                 out << "Run Name:  " << endl;
 534                 out << "Analysis Name:  " << endl;
 535                 out << "Full Path: " << endl << endl;
 536
 537                 out << "Read Header Len: " << header.headerLength << endl;
 538                 out << "Name Length: " << header.nameLength << endl;
 539                 out << "# of Bases: " << header.numBases << endl;
 540                 out << "Clip Qual Left: " << header.clipQualLeft << endl;
 541                 out << "Clip Qual Right: " << header.clipQualRight << endl;
 542                 out << "Clip Adap Left: " << header.clipAdapterLeft << endl;
 543                 out << "Clip Adap Right: " << header.clipAdapterRight << endl << endl;
 544
 545                 return 0;
 546         }
 547         catch(exception& e) {
 548                 m->errorOut(e, "SffInfoCommand", "printHeader");
 549                 exit(1);
 550         }
 551 }
 552
 553 //**********************************************************************************************************************
 554 int SffInfoCommand::printSffTxtSeqData(ofstream& out, seqRead& read, Header& header) {
 555         try {
 556
 557                 out << "Flowgram: ";
 558                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 559
 560                 out << endl <<  "Flow Indexes: ";
 561                 int sum = 0;
 562                 for (int i = 0; i < read.flowIndex.size(); i++) {  sum +=  read.flowIndex[i];  out << sum << '\t'; }
 563
 564                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 565                 for (int i = 0; i < (header.clipQualLeft-1); i++) { read.bases[i] = tolower(read.bases[i]); }
 566                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   read.bases[i] = toupper(read.bases[i]);  }
 567                 for (int i = (header.clipQualRight-1); i < read.bases.length(); i++) {   read.bases[i] = tolower(read.bases[i]);  }
 568
 569                 out << endl <<  "Bases: " << read.bases << endl << "Quality Scores: ";
 570                 for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 571
 572
 573                 out << endl << endl;
 574
 575                 return 0;
 576         }
 577         catch(exception& e) {
 578                 m->errorOut(e, "SffInfoCommand", "printSffTxtSeqData");
 579                 exit(1);
 580         }
 581 }
 582 //**********************************************************************************************************************
 583 int SffInfoCommand::printFastaSeqData(ofstream& out, seqRead& read, Header& header) {
 584         try {
 585
 586                 string seq = read.bases;
 587
 588                 if (trim) {
 589                         if(header.clipQualRight != 0){
 590                                 seq = seq.substr((header.clipQualLeft-1), (header.clipQualRight-header.clipQualLeft));
 591                         }
 592                         else {
 593                                 seq = seq.substr(header.clipQualLeft-1);
 594                         }
 595                 }else{
 596                         //if you wanted the sfftxt then you already converted the bases to the right case
 597                         if (!sfftxt) {
 598                                 //make the bases you want to clip lowercase and the bases you want to keep upper case
 599                                 if(header.clipQualRight == 0){  header.clipQualRight = seq.length();    }
 600                                 for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]);  }
 601                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++)  {   seq[i] = toupper(seq[i]);  }
 602                                 for (int i = (header.clipQualRight-1); i < seq.length(); i++) {   seq[i] = tolower(seq[i]);  }
 603                         }
 604                 }
 605
 606                 out << ">" << header.name << endl;
 607                 out << seq << endl;
 608
 609                 return 0;
 610         }
 611         catch(exception& e) {
 612                 m->errorOut(e, "SffInfoCommand", "printFastaSeqData");
 613                 exit(1);
 614         }
 615 }
 616
 617 //**********************************************************************************************************************
 618 int SffInfoCommand::printQualSeqData(ofstream& out, seqRead& read, Header& header) {
 619         try {
 620
 621                 if (trim) {
 622                         if(header.clipQualRight != 0){
 623                                 out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 624                                 for (int i = (header.clipQualLeft-1); i < (header.clipQualRight-1); i++) {   out << read.qualScores[i] << '\t'; }
 625                         }
 626                         else{
 627                                 out << ">" << header.name << " length=" << (header.clipQualRight-header.clipQualLeft) << endl;
 628                                 for (int i = (header.clipQualLeft-1); i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';   }
 629                         }
 630                 }else{
 631                         out << ">" << header.name << " length=" << read.qualScores.size() << endl;
 632                         for (int i = 0; i < read.qualScores.size(); i++) {   out << read.qualScores[i] << '\t';  }
 633                 }
 634
 635                 out << endl;
 636
 637                 return 0;
 638         }
 639         catch(exception& e) {
 640                 m->errorOut(e, "SffInfoCommand", "printQualSeqData");
 641                 exit(1);
 642         }
 643 }
 644
 645 //**********************************************************************************************************************
 646 int SffInfoCommand::printFlowSeqData(ofstream& out, seqRead& read, Header& header) {
 647         try {
 648
 649                 out << ">" << header.name << endl;
 650                 for (int i = 0; i < read.flowgram.size(); i++) { out << setprecision(2) << (read.flowgram[i]/(float)100) << '\t';  }
 651                 out << endl;
 652
 653                 return 0;
 654         }
 655         catch(exception& e) {
 656                 m->errorOut(e, "SffInfoCommand", "printFlowSeqData");
 657                 exit(1);
 658         }
 659 }
 660 //**********************************************************************************************************************
 661 int SffInfoCommand::readAccnosFile(string filename) {
 662         try {
 663                 //remove old names
 664                 seqNames.clear();
 665
 666                 ifstream in;
 667                 openInputFile(filename, in);
 668                 string name;
 669
 670                 while(!in.eof()){
 671                         in >> name; gobble(in);
 672
 673                         seqNames.insert(name);
 674
 675                         if (m->control_pressed) { seqNames.clear(); break; }
 676                 }
 677                 in.close();
 678
 679                 return 0;
 680         }
 681         catch(exception& e) {
 682                 m->errorOut(e, "SffInfoCommand", "readAccnosFile");
 683                 exit(1);
 684         }
 685 }
 686 //**********************************************************************************************************************/