C++ SamFile::OpenForWrite方法代码示例

void modify::modifyTags()
{
    assert(samIn.OpenForRead(myFilename.c_str()));
    // Read the sam header.
    assert(samIn.ReadHeader(samHeader));
   
    SamFile samOut;
    SamFile bamOut;

    std::string inputType = myFilename.substr(myFilename.find_last_of('.'));
    std::string outFileBase = "results/updateTagFrom";
    if(inputType == ".bam")
    {
        outFileBase += "Bam";
    }
    else
    {
        outFileBase += "Sam";
    }

    std::string outFile = outFileBase + ".sam";
    assert(samOut.OpenForWrite(outFile.c_str()));
    outFile = outFileBase + ".bam";
    assert(bamOut.OpenForWrite(outFile.c_str()));
    assert(samOut.WriteHeader(samHeader));
    assert(bamOut.WriteHeader(samHeader));

    int count = 0;
    // Read the records.
    while(samIn.ReadRecord(samHeader, samRecord))
    {
        if(count == 0)
        {
            assert(samRecord.rmTag("MD", 'Z'));
        }
        else if(count == 2)
        {
            assert(samRecord.rmTags("XT:A;MD:Z;AB:c;NM:i"));
        }
        else if(count == 4)
        {
            assert(samRecord.rmTags("MD:Z,AB:c,NM:i"));
        }

        assert(bamOut.WriteRecord(samHeader, samRecord));
        assert(samOut.WriteRecord(samHeader, samRecord));
        ++count;
    }
}

//.........这里部分代码省略.........
                              properPairCount);
    Logger::gLogger->writeLog("Total number of unmapped reads: %u",
                              unmappedCount);
    Logger::gLogger->writeLog("Total number of reverse strand mapped reads: %u",
                              reverseCount);
    Logger::gLogger->writeLog("Total number of QC-failed reads: %u",
                              qualCheckFailCount);
    Logger::gLogger->writeLog("Total number of secondary reads: %u",
                              secondaryCount);
    Logger::gLogger->writeLog("Total number of supplementary reads: %u",
                              supplementaryCount);
    Logger::gLogger->writeLog("Size of singleKeyMap (must be zero): %u",
                              myFragmentMap.size());
    Logger::gLogger->writeLog("Size of pairedKeyMap (must be zero): %u",
                              myPairedMap.size());
    Logger::gLogger->writeLog("Total number of missing mates: %u",
                              myNumMissingMate);
    Logger::gLogger->writeLog("Total number of reads excluded from duplicate checking: %u",
                              excludedCount);
    Logger::gLogger->writeLog("--------------------------------------------------------------------------");
    Logger::gLogger->writeLog("Sorting the indices of %d duplicated records",
                              myDupList.size());

    // sort the indices of duplicate records
    std::sort(myDupList.begin(), myDupList.end(),
              std::less<uint32_t> ());

    // get ready to write the output file by making a second pass
    // through the input file
    samIn.OpenForRead(inFile.c_str());
    samIn.ReadHeader(header);

    SamFile samOut;
    samOut.OpenForWrite(outFile.c_str());
    samOut.WriteHeader(header);

    // If we are recalibrating, output the model information.
    if(myDoRecab)
    {
        myRecab.modelFitPrediction(outFile);
    }

    // an iterator to run through the duplicate indices
    int currentDupIndex = 0;
    bool moreDups = !myDupList.empty();

    // let the user know what we're doing
    Logger::gLogger->writeLog("\nWriting %s", outFile.c_str());

    // count the duplicate records as a check
    uint32_t singleDuplicates(0), pairedDuplicates(0);

    // start reading records and writing them out
    SamRecord record;
    while(samIn.ReadRecord(header, record))
    {
        uint32_t currentIndex = samIn.GetCurrentRecordCount();

        bool foundDup = moreDups &&
                        (currentIndex == myDupList[currentDupIndex]);

        // modify the duplicate flag and write out the record,
        // if it's appropriate
        int flag = record.getFlag();
        if (foundDup)
        {

int Revert::execute(int argc, char **argv)
{
    // Extract command line arguments.
    String inFile = "";
    String outFile = "";
    bool cigar = false;
    bool qual = false;
    bool noeof = false;
    bool params = false;
    bool rmBQ = false;
    String rmTags = "";
    myKeepTags = false;

    ParameterList inputParameters;
    BEGIN_LONG_PARAMETERS(longParameterList)
        LONG_STRINGPARAMETER("in", &inFile)
        LONG_STRINGPARAMETER("out", &outFile)
        LONG_PARAMETER("cigar", &cigar)
        LONG_PARAMETER("qual", &qual)
        LONG_PARAMETER("keepTags", &myKeepTags)
        LONG_PARAMETER("rmBQ", &rmBQ)
        LONG_STRINGPARAMETER("rmTags", &rmTags)
        LONG_PARAMETER("noeof", &noeof)
        LONG_PARAMETER("params", &params)
        LONG_PHONEHOME(VERSION)
        END_LONG_PARAMETERS();
   
    inputParameters.Add(new LongParameters ("Input Parameters", 
                                            longParameterList));
    
    // parameters start at index 2 rather than 1.
    inputParameters.Read(argc, argv, 2);

    // If no eof block is required for a bgzf file, set the bgzf file type to 
    // not look for it.
    if(noeof)
    {
        // Set that the eof block is not required.
        BgzfFileType::setRequireEofBlock(false);
    }
    
    // Check to see if the in file was specified, if not, report an error.
    if(inFile == "")
    {
        usage();
        inputParameters.Status();
        // In file was not specified but it is mandatory.
        std::cerr << "--in is a mandatory argument, "
                  << "but was not specified" << std::endl;
        return(-1);
    }

    if(outFile == "")
    {
        usage();
        inputParameters.Status();
        // In file was not specified but it is mandatory.
        std::cerr << "--out is a mandatory argument, "
                  << "but was not specified" << std::endl;
        return(-1);
    }

    if(params)
    {
        inputParameters.Status();
    }

    // Open the input file for reading.
    SamFile samIn;
    samIn.OpenForRead(inFile);

    // Open the output file for writing.
    SamFile samOut;
    samOut.OpenForWrite(outFile);

    // Read the sam header.
    SamFileHeader samHeader;
    samIn.ReadHeader(samHeader);

    // Write the sam header.
    samOut.WriteHeader(samHeader);

    SamRecord samRecord;

    // Set returnStatus to success.  It will be changed to the
    // failure reason if any of the writes or updates fail.
    SamStatus::Status returnStatus = SamStatus::SUCCESS;

    // Keep reading records until ReadRecord returns false.
    while(samIn.ReadRecord(samHeader, samRecord))
    {
        // Update the cigar & position.
        if(cigar)
        {
            if(!updateCigar(samRecord))
            {
                // Failed to update the cigar & position.
                fprintf(stderr, "%s\n", samIn.GetStatusMessage());
                returnStatus = samIn.GetStatus();
            }
//.........这里部分代码省略.........

//.........这里部分代码省略.........
    GenomeSequence* refPtr = NULL;
    if(refFile != "")
    {
        refPtr = new GenomeSequence(refFile);
    }

    SamRecord::SequenceTranslation translation;
    if((useBases) && (refPtr != NULL))
    {
        translation = SamRecord::BASES;
    }
    else if((useEquals) && (refPtr != NULL))
    {
        translation = SamRecord::EQUAL;
    }
    else
    {
        useOrigSeq = true;
        translation = SamRecord::NONE;
    }
    
    if(params)
    {
        inputParameters.Status();
    }

    // Open the input file for reading.
    SamFile samIn;
    if(recover) samIn.setAttemptRecovery(true);
    samIn.OpenForRead(inFile);

    // Open the output file for writing.
    SamFile samOut;
    samOut.OpenForWrite(outFile);
    samOut.SetWriteSequenceTranslation(translation);
    samOut.SetReference(refPtr);

    // Read the sam header.
    SamFileHeader samHeader;
    samIn.ReadHeader(samHeader);

    // Write the sam header.
    samOut.WriteHeader(samHeader);

    SamRecord samRecord;

    // Set returnStatus to success.  It will be changed
    // to the failure reason if any of the writes fail.
    SamStatus::Status returnStatus = SamStatus::SUCCESS;

    while(1) {
        try {
            // Keep reading records until ReadRecord returns false.
            while(samIn.ReadRecord(samHeader, samRecord))
            {
                // left shift if necessary.
                if(lshift)
                {
                    samRecord.shiftIndelsLeft();
                }

                // Successfully read a record from the file, so write it.
                if(!samOut.WriteRecord(samHeader, samRecord))
                {
                    // Failed to write a record.
                    fprintf(stderr, "%s\n", samOut.GetStatusMessage());

//.........这里部分代码省略.........
  else {
    for(uint32_t i=0; i < vsPGHeaders.size(); ++i) {
      gpLogger->write_log("\t--PG [%s]",vsPGHeaders[i].c_str());
    }
  }

  if ( (vsHDHeaders.empty() ) && ( vsRGHeaders.empty() ) && ( vsPGHeaders.empty() ) && ( !bClear ) && ( sFasta.empty() ) ) {
    gpLogger->warning("No option is in effect for modifying BAM files. The input and output files will be identical");
  }

  if ( ( vsHDHeaders.size() > 1 ) || ( vsRGHeaders.size() > 1 ) ) {
    gpLogger->error("HD and RG headers cannot be multiple");
  }

  FastaFile fastaFile;
  if ( ! sFasta.empty() ) {
    if ( fastaFile.open(sFasta.c_str()) ) {
      gpLogger->write_log("Reading the reference file %s",sFasta.c_str());
      fastaFile.readThru();
      fastaFile.close();
      gpLogger->write_log("Finished reading the reference file %s",sFasta.c_str());      
    }
    else {
      gpLogger->error("Failed to open reference file %s",sFasta.c_str());
    }
  }

  SamFile samIn;
  SamFile samOut;

  if ( ! samIn.OpenForRead(sInFile.c_str()) ) {
    gpLogger->error("Cannot open BAM file %s for reading - %s",sInFile.c_str(), SamStatus::getStatusString(samIn.GetStatus()) );
  }
  if ( ! samOut.OpenForWrite(sOutFile.c_str()) ) {
    gpLogger->error("Cannot open BAM file %s for writing - %s",sOutFile.c_str(), SamStatus::getStatusString(samOut.GetStatus()) );
  }

  SamFileHeader samHeader;
  SamHeaderRecord* pSamHeaderRecord;
  samIn.ReadHeader(samHeader);

  // check the sanity of SQ file
  // make sure the SN and LN matches, with the same order
  if ( bCheckSQ ) {
    unsigned int numSQ = 0;
    while( (pSamHeaderRecord = samHeader.getNextHeaderRecord()) != NULL ) {
      if ( pSamHeaderRecord->getType() == SamHeaderRecord::SQ ) {
	++numSQ;
      }
    }

    if ( numSQ != fastaFile.vsSequenceNames.size() ) {
      gpLogger->error("# of @SQ tags are different from the original BAM and the reference file");
    }

    // iterator over all @SQ objects
    for(unsigned int i=0; i < numSQ; ++i) {
      pSamHeaderRecord = samHeader.getSQ(fastaFile.vsSequenceNames[i].c_str());
      if ( fastaFile.vsSequenceNames[i].compare(pSamHeaderRecord->getTagValue("SN")) != 0 ) {
	gpLogger->error("SequenceName is not identical between fasta and input BAM file");
      }
      else if ( static_cast<int>(fastaFile.vnSequenceLengths[i]) != atoi(pSamHeaderRecord->getTagValue("LN")) ) {
	gpLogger->error("SequenceLength is not identical between fasta and input BAM file");
      }
      else {
	if ( !sAS.empty() ) 

bool BamProcessor::init (const ContalignParams& p)
{
    read_cnt_ = proc_cnt_ = toolongs_ = unaligned_cnt_ = fail_cnt_ = nomd_cnt_ = realigned_cnt_ = modified_cnt_ = pos_adjusted_cnt_ = 0;
    log_diff_ = log_matr_ = log_base_ = false;

    p_ = &p;

    if (!*p.inbam ())
        ers << "Input file name not specified" << Throw;

    limit_ = p.limit ();
    skip_ = p.skip ();

    infile_.OpenForRead (p.inbam ());
    if (!infile_.IsOpen ())
        ers << p.inbam () << ThrowEx (FileNotFoundRerror);

    bool index_ok = false;
    if (*p.bamidx ())
    {
        index_ok = infile_.ReadBamIndex (p.bamidx ());
        if (!index_ok)
            warn << "Unable to open specified BAM index: " << p.bamidx () << ". Default index will be attempted" <<  std::endl;
    }
    if (!index_ok)
    {
        try
        {
            index_ok = infile_.ReadBamIndex ();
        }
        catch (std::exception& e)
        {
            // for some reason not converted into return status by libStatGen
        }
        if (!index_ok)
            warn << "Unable to open default BAM index for " << p.inbam () << std::endl;
    }
    if (*p.refname () || p.refno () != -1)
    {
        if (!index_ok)
            ers << "Reference section specified, but the BAM index could not be open." << Throw;
        if (*p.refname ())
        {
            if (p.endpos () != 0)
            {
                infile_.SetReadSection (p.refname (), p.begpos (), p.endpos ());
                info << "Read section set : " << p.refname () << ": " << p.begpos () << "-" << p.endpos () << std::endl;
            }
            else
            {
                infile_.SetReadSection (p.refname ());
                info << "Read section set : " << p.refname () << std::endl;
            }
        }
        else
        {
            if (p.endpos () != 0)
            {
                info << "Read section set : ref# " << p.refno () << ": " << p.begpos () << "-" << p.endpos () << std::endl;
                infile_.SetReadSection (p.refno (), p.begpos (), p.endpos ());
            }
            else
            {
                info << "Read section set : ref# " << p.refno () << std::endl;
                infile_.SetReadSection (p.refno ());
            }
        }
    }
    if (*p.outbam ())
    {
        if (!p.overwrite () && file_exists (p.outbam ()))
            ers << "Output file " << p.outbam () << " exists. Use --ov key to allow overwriting" << Throw;
        outfile_.OpenForWrite (p.outbam ());
        if (!outfile_.IsOpen ())
            ers << "Unable to open output file " << p.outbam () << std::endl;
    }
    if (*p.logfname ())
    {
        if (!p.overwrite () && file_exists (p.logfname ()))
            ers << "Log file " << p.logfname () << " exists. Use --ov key to allow overwriting" << Throw;
        logfile_.open (p.logfname (), std::fstream::out);
        if (!logfile_.is_open ())
            ers << "Unable to open log file " << p.logfname () << std::endl;

        time_t t = time (NULL);
        logfile_ << "Context-aware realigner log\nStarted at " << asctime (localtime (&t)) << "\nParameters:\n";
        logfile_ << *(p.parameters_);
        logfile_ << std::endl;
        log_base_ = p.logging ("base");
        log_diff_ = p.logging ("diff");
        log_matr_ = p.logging ("matr");
    }
    band_width_ = p.bwid ();

    switch (p.algo ())
    {
        case ContalignParams::TEMPL:
        {
            matrix_.configure (genstr::nucleotides.symbols (), genstr::nucleotides.size (), genstr::NegUnitaryMatrix <int, 4>().values ());
            gap_cost_.configure (p.gip (), p.gep ());
//.........这里部分代码省略.........

// main function
int TrimBam::execute(int argc, char ** argv)
{
  SamFile samIn;
  SamFile samOut;
  int numTrimBaseL = 0;
  int numTrimBaseR = 0;
  bool noeof = false;
  bool ignoreStrand = false;
  bool noPhoneHome = false;
  std::string inName = "";
  std::string outName = "";

  if ( argc < 5 ) {
    usage();
    std::cerr << "ERROR: Incorrect number of parameters specified\n";
    return(-1);
  }
  inName = argv[2];
  outName = argv[3];

  static struct option getopt_long_options[] = {
      // Input options
      { "left", required_argument, NULL, 'L'},
      { "right", required_argument, NULL, 'R'},
      { "ignoreStrand", no_argument, NULL, 'i'},
      { "noeof", no_argument, NULL, 'n'},
      { "noPhoneHome", no_argument, NULL, 'p'},
      { "nophonehome", no_argument, NULL, 'P'},
      { "phoneHomeThinning", required_argument, NULL, 't'},
      { "phonehomethinning", required_argument, NULL, 'T'},
      { NULL, 0, NULL, 0 },
  };
  
  int argIndex = 4;
  if(argv[argIndex][0] != '-')
  {
      // This is the number of bases to trim off both sides
      // so convert to a number.
      numTrimBaseL = atoi(argv[argIndex]);
      numTrimBaseR = numTrimBaseL;
      ++argIndex;
  }

  int c = 0;
  int n_option_index = 0;
  // Process any additional parameters
  while ( ( c = getopt_long(argc, argv,
                            "L:R:in", getopt_long_options, &n_option_index) )
          != -1 )
  {
      switch(c) 
      {
          case 'L':
              numTrimBaseL = atoi(optarg);
              break;
          case 'R':
              numTrimBaseR = atoi(optarg);
              break;
          case 'i':
              ignoreStrand = true;
              break;
          case 'n':
              noeof = true;
              break;
          case 'p':
          case 'P':
              noPhoneHome = true;
              break;
          case 't':
          case 'T':
              PhoneHome::allThinning = atoi(optarg);
              break;
          default:
              fprintf(stderr,"ERROR: Unrecognized option %s\n",
                      getopt_long_options[n_option_index].name);
              return(-1);
      }
  }

  if(!noPhoneHome)
  {
      PhoneHome::checkVersion(getProgramName(), VERSION);
  }
  
  if(noeof)
  {
      // Set that the eof block is not required.
      BgzfFileType::setRequireEofBlock(false);
  }

  if ( ! samIn.OpenForRead(inName.c_str()) ) {
      fprintf(stderr, "***Problem opening %s\n",inName.c_str());
    return(-1);
  }

  if(!samOut.OpenForWrite(outName.c_str())) {
    fprintf(stderr, "%s\n", samOut.GetStatusMessage());
    return(samOut.GetStatus());
  }
//.........这里部分代码省略.........

//.........这里部分代码省略.........
    {
        std::cerr << "Can't specify both refID and refName" << std::endl;
        inputParameters.Status();
        return(-1);
    }
    if(myRefID != UNSET_REF && bed.Length() != 0)
    {
        std::cerr << "Can't specify both refID and bed" << std::endl;
        inputParameters.Status();
        return(-1);
    }
    if(myRefName.Length() != 0 && bed.Length() != 0)
    {
        std::cerr << "Can't specify both refName and bed" << std::endl;
        inputParameters.Status();
        return(-1);
    }

    if(!bed.IsEmpty())
    {
        myBedFile = ifopen(bed, "r");
    }

    if(params)
    {
        inputParameters.Status();
    }

    // Open the file for reading.   
    mySamIn.OpenForRead(inFile);

    // Open the output file for writing.
    SamFile samOut;
    samOut.OpenForWrite(outFile);

    // Open the bam index file for reading if a region was specified.
    if((myRefName.Length() != 0) || (myRefID != UNSET_REF) || (myBedFile != NULL))
    {
        mySamIn.ReadBamIndex(indexFile);
    }

    // Read & write the sam header.
    mySamIn.ReadHeader(mySamHeader);
    samOut.WriteHeader(mySamHeader);

    // Read the sam records.
    SamRecord samRecord;
    // Track the status.
    int numSectionRecords = 0;

    // Set returnStatus to success.  It will be changed
    // to the failure reason if any of the writes fail.
    SamStatus::Status returnStatus = SamStatus::SUCCESS;
        
    while(getNextSection())
    {
        // Keep reading records until they aren't anymore.
        while(mySamIn.ReadRecord(mySamHeader, samRecord))
        {
            if(!readName.IsEmpty())
            {
                // Check for readname.
                if(strcmp(samRecord.getReadName(), readName.c_str()) != 0)
                {
                    // not a matching read name, so continue to the next record.
                    continue;