C++ SamRecord::rmTags方法代码示例

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.........