#pragma once

#include <string>
#include <stdint.h>

using std::string;

/*
 * 标记冗余过程中的一些数据统计
 */
struct DuplicationMetrics {
    /**
     * The library on which the duplicate marking was performed.
     */
    string LIBRARY = "";
    /**
     * The number of mapped reads examined which did not have a mapped mate pair,
     * either because the read is unpaired, or the read is paired to an unmapped mate.
     */
    uint64_t UNPAIRED_READS_EXAMINED = 0;
    /**
     * The number of mapped read pairs examined. (Primary, non-supplemental)
     */
    uint64_t READ_PAIRS_EXAMINED = 0;
    /**
     * The number of reads that were either secondary or supplementary
     */
    uint64_t SECONDARY_OR_SUPPLEMENTARY_RDS = 0;
    /**
     * The total number of unmapped reads examined. (Primary, non-supplemental)
     */
    uint64_t UNMAPPED_READS = 0;
    /**
     * The number of fragments that were marked as duplicates.
     */
    uint64_t UNPAIRED_READ_DUPLICATES = 0;
    /**
     * The number of read pairs that were marked as duplicates.
     */
    uint64_t READ_PAIR_DUPLICATES = 0;
    /**
     * The number of read pairs duplicates that were caused by optical duplication.
     * Value is always < READ_PAIR_DUPLICATES, which counts all duplicates regardless of source.
     */
    uint64_t READ_PAIR_OPTICAL_DUPLICATES = 0;
    /**
     * The fraction of mapped sequence that is marked as duplicate.
     */
    double PERCENT_DUPLICATION = 0.0;
    /**
     * The estimated number of unique molecules in the library based on PE duplication.
     */
    uint64_t ESTIMATED_LIBRARY_SIZE = 0;

    // 其他的统计数据

    // addSingletonToCount需要记录的数据
    uint64_t DuplicateCountHist = 0;
    uint64_t NonOpticalDuplicateCountHist = 0;

    // track optical duplicates 需要记录的数据
    uint64_t OpticalDuplicatesCountHist = 0;
    uint64_t OpticalDuplicatesByLibraryId = 0;
    
    // 统计相关的函数
    void AddSingletonToCount() { 
        ++this->DuplicateCountHist;
        ++this->NonOpticalDuplicateCountHist;
    }
};