C++ (Cpp) VcfRecord::getInfo示例

int VcfCleaner::execute(int argc, char **argv)
{
    String refFile = "";
    String inputVcf = "";
    String outputVcf = "";
    bool uncompress = false;
    bool params = false;
    
    // Read in the parameters.    
    ParameterList inputParameters;
    BEGIN_LONG_PARAMETERS(longParameterList)
        LONG_PARAMETER_GROUP("Required Parameters")
        LONG_STRINGPARAMETER("in", &inputVcf)
        LONG_STRINGPARAMETER("out", &outputVcf)
        LONG_PARAMETER_GROUP("Optional Parameters")
        LONG_PARAMETER("uncompress", &uncompress)
        LONG_PARAMETER("params", &params)
        END_LONG_PARAMETERS();
   
    inputParameters.Add(new LongParameters ("Input Parameters", 
                                            longParameterList));
    
    inputParameters.Read(argc-1, &(argv[1]));
    
    // Check that all files were specified.
    if(inputVcf == "")
    {
        usage();
        inputParameters.Status();
        std::cerr << "Missing \"--in\", a required parameter.\n\n";
        return(-1);
    }
    if(outputVcf == "")
    {
        usage();
        inputParameters.Status();
        std::cerr << "Missing \"--out\", a required parameter.\n\n";
        return(-1);
    }

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

    VcfFileReader inFile;
    VcfFileWriter outFile;
    VcfHeader header;
    VcfRecord record;

    // Open the file.
    inFile.open(inputVcf, header);
    if(uncompress)
    {
        outFile.open(outputVcf, header, InputFile::DEFAULT);
    }
    else
    {
        outFile.open(outputVcf, header);
    }

    int numReadRecords = 0;
    int numWrittenRecords = 0;
    int returnVal = 0;

    // Set to only store/write the GT field.
    VcfRecordGenotype::addStoreField("GT");
    while(inFile.readRecord(record))
    {
        ++numReadRecords;
        // Check if any samples are missing GT or if any are not phased.
        if(!record.hasAllGenotypeAlleles() || !record.allPhased())
        {
            // Missing a GT or not phased, so continue without writing.
            continue;
        }
        
        // Clear the INFO field.
        record.getInfo().clear();
        // Write the record.
        if(!outFile.writeRecord(record))
        {
            // Write error.
            std::cerr << "Failed writing a vcf record.\n";
            returnVal = -1;
        }
        ++numWrittenRecords;
    }
 
    inFile.close();   
    outFile.close();   

    std::cerr << "NumReadRecords: " << numReadRecords
              << "; NumWrittenRecords: " << numWrittenRecords << "\n";
    return(returnVal);
}