C++ SamRecord::setFlag方法代码示例

void SamFilter::filterRead(SamRecord& record)
{
    // Filter the read by marking it as unmapped.
    uint16_t flag = record.getFlag(); 
    SamFlag::setUnmapped(flag);
    // Clear N/A flags.
    flag &= ~SamFlag::PROPER_PAIR;
    flag &= ~SamFlag::SECONDARY_ALIGNMENT;
    flag &= ~SamFlag::SUPPLEMENTARY_ALIGNMENT;
    record.setFlag(flag);
    // Clear Cigar
    record.setCigar("*");
    // Clear mapping quality
    record.setMapQuality(0);
}

//.........这里部分代码省略.........
    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)
        {
            // this record is a duplicate, so mark it.
            record.setFlag( flag | 0x400 );
            currentDupIndex++;
            // increment duplicate counters to verify we found them all
            if ( ( ( flag & 0x0001 ) == 0 ) || ( flag & 0x0008 ) )
            {   // unpaired or mate unmapped
                singleDuplicates++;
            }
            else
            {
                pairedDuplicates++;
            }
            // recalibrate if necessary.
            if(myDoRecab)
            {
                myRecab.processReadApplyTable(record);
            }

            // write the record if we are not removing duplicates
            if (!removeFlag ) samOut.WriteRecord(header, record);
        }
        else
        {
            if(myForceFlag)
            {
                // this is not a duplicate we've identified but we want to
                // remove any duplicate marking
                record.setFlag( flag & 0xfffffbff ); // unmark duplicate
            }
            // Not a duplicate, so recalibrate if necessary.
            if(myDoRecab)
            {
                myRecab.processReadApplyTable(record);
            }
            samOut.WriteRecord(header, record);
        }

        // Let the user know we're still here
        if (verboseFlag && (currentIndex % 100000 == 0)) {
            Logger::gLogger->writeLog("recordCount=%u", currentIndex);
        }
    }

    // We're done.  Close the files and print triumphant messages.
    samIn.Close();
    samOut.Close();

    Logger::gLogger->writeLog("Successfully %s %u unpaired and %u paired duplicate reads",
                              removeFlag ? "removed" : "marked" ,
                              singleDuplicates,
                              pairedDuplicates/2);
    Logger::gLogger->writeLog("\nDedup_LowMem complete!");
    return 0;
}