C++ String::AsInteger方法代码示例

//.........这里部分代码省略.........
                  << "but was not specified" << std::endl;
        return(-1);
    }

    if((storeOrig.Length() != 0) && (storeOrig.Length() != 2))
    {
        printUsage(std::cerr);
        inputParameters.Status();
        std::cerr << "--storeOrig tag name must be 2 characters.\n";
        return(-1);
    }

    myOverlapHandler = new OverlapClipLowerBaseQual();
    if(myOverlapHandler == NULL)
    {
        printUsage(std::cerr);
        inputParameters.Status();
        std::cerr << "Failed to allocate the overlap handler\n";
        return(-1);
    }

    if(unmapped)
    {
        myOverlapHandler->markAsUnmapped();
    }

    // Setup the overlap handler.
    myOverlapHandler->keepStats(stats);
    if(storeOrig.Length() != 0)
    {
        myOverlapHandler->storeOrigCigar(storeOrig);
    }

    myIntExcludeFlags = excludeFlags.AsInteger();

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

    // For each step process the file.
    // Open the files & read/write the sam header.
    SamStatus::Status runStatus = SamStatus::SUCCESS;
    for(int i = 1; i <= myOverlapHandler->numSteps(); i++)
    {
        // Open the file for reading.
        mySamHeader.resetHeader();
        SamFile samIn(inFile, SamFile::READ, &mySamHeader);
        SamFile* samOutPtr = NULL;
        // Check if writing, if so, open the output file.
        if(i == myOverlapHandler->numSteps())
        {
            samOutPtr = new SamFile(outFile, SamFile::WRITE, &mySamHeader);
        }

        if(readName)
        {
            if(!noRNValidate)
            {
                samIn.setSortedValidation(SamFile::QUERY_NAME);
            }
            runStatus = handleSortedByReadName(samIn, samOutPtr);
        }
        else
        {
            // Coordinate sorted, so work with the pools.

int Dedup_LowMem::execute(int argc, char** argv)
{
    /* --------------------------------
     * process the arguments
     * -------------------------------*/
    String inFile, outFile, logFile;
    myDoRecab = false;
    bool removeFlag = false;
    bool verboseFlag = false;
    myForceFlag = false;
    myNumMissingMate = 0;
    myMinQual = DEFAULT_MIN_QUAL;
    String excludeFlags = "0xB04";
    uint16_t intExcludeFlags = 0;
    bool noeof = false;
    bool params = false;

    LongParamContainer parameters;
    parameters.addGroup("Required Parameters");
    parameters.addString("in", &inFile);
    parameters.addString("out", &outFile);
    parameters.addGroup("Optional Parameters");
    parameters.addInt("minQual", & myMinQual);
    parameters.addString("log", &logFile);
    parameters.addBool("oneChrom", &myOneChrom);
    parameters.addBool("recab", &myDoRecab);
    parameters.addBool("rmDups", &removeFlag);
    parameters.addBool("force", &myForceFlag);
    parameters.addString("excludeFlags", &excludeFlags);
    parameters.addBool("verbose", &verboseFlag);
    parameters.addBool("noeof", &noeof);
    parameters.addBool("params", &params);
    parameters.addPhoneHome(VERSION);
    myRecab.addRecabSpecificParameters(parameters);

    ParameterList inputParameters;
    inputParameters.Add(new LongParameters ("Input Parameters",
                                            parameters.getLongParameterList()));

    // 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);
    }

    if(inFile.IsEmpty())
    {
        printUsage(std::cerr);
        inputParameters.Status();
        std::cerr << "Specify an input file" << std::endl;
        return EXIT_FAILURE;
    }

    if(outFile.IsEmpty())
    {
        printUsage(std::cerr);
        inputParameters.Status();
        std::cerr << "Specify an output file" << std::endl;
        return EXIT_FAILURE;
    }

    intExcludeFlags = excludeFlags.AsInteger();

    if(myForceFlag && SamFlag::isDuplicate(intExcludeFlags))
    {
        printUsage(std::cerr);
        inputParameters.Status();
        std::cerr << "Cannot specify --force and Duplicate in the excludeFlags.  Since --force indicates to override"
                  << " previous duplicate setting and the excludeFlags says to skip those, you can't do both.\n";
        return EXIT_FAILURE;
    }

    if(!SamFlag::isSecondary(intExcludeFlags))
    {
        printUsage(std::cerr);
        inputParameters.Status();
        std::cerr << "ERROR: Secondary reads must be excluded, edit --excludeFlags to include 0x0100\n";
        return EXIT_FAILURE;
    }

    if(!(intExcludeFlags & SamFlag::SUPPLEMENTARY_ALIGNMENT))
    {
        printUsage(std::cerr);
        inputParameters.Status();
        std::cerr << "ERROR: Supplementary reads must be excluded, edit --excludeFlags to include 0x0800\n";
        return EXIT_FAILURE;
    }

    if(logFile.IsEmpty())
    {
        logFile = outFile + ".log";
    }

    if(myDoRecab)
    {
//.........这里部分代码省略.........

void testAsInteger()
{
    // Test AsInteger with ints & negative ints.
    String intString = "123";
    String negIntString = "-123";
    assert(intString.AsInteger() == 123);
    assert(negIntString.AsInteger() == -123);

    // Run the same tests with AsInteger that returns a bool and takes
    // in a long to set.
    long retValue;
    assert(intString.AsInteger(retValue));
    assert(retValue == 123);
    assert(negIntString.AsInteger(retValue));
    assert(retValue == -123);


    // Strings that are not integers
    // For AsInteger, it returns just the starting integer portion.
    // For AsInteger that returns a bool and a long set, it returns false
    // and sets the long to the starting int.
    String nonIntString = "abd";
    assert(nonIntString.AsInteger() == 0);
    assert(!nonIntString.AsInteger(retValue));

    nonIntString = "12ab33";
    assert(nonIntString.AsInteger() == 12);
    assert(!nonIntString.AsInteger(retValue));
    assert(retValue == 12);
    nonIntString = "as12ab3a4sd";
    assert(nonIntString.AsInteger() == 0);
    assert(!nonIntString.AsInteger(retValue));
    assert(retValue == 0);
    // Negatives are only recognized as the first characer.
    nonIntString = "-12ab3a4sd";
    assert(nonIntString.AsInteger() == -12);
    assert(!nonIntString.AsInteger(retValue));
    assert(retValue == -12);
    nonIntString = "-as12ab3a4sd";
    assert(nonIntString.AsInteger() == 0);
    assert(!nonIntString.AsInteger(retValue));
    assert(retValue == 0);
    nonIntString = "as-12ab3a4sd";
    assert(nonIntString.AsInteger() == 0);
    assert(!nonIntString.AsInteger(retValue));
    assert(retValue == 0);
    nonIntString = "as12-ab3a4sd";
    assert(nonIntString.AsInteger() == 0);
    assert(!nonIntString.AsInteger(retValue));
    assert(retValue == 0);
}