/*
Description: read ends结构体主要用来标记冗余，包含一些序列的测序过程中的物理信息等

Copyright : All right reserved by ICT

Author : Zhang Zhonghai
Date : 2023/11/3
*/

#ifndef READ_ENDS_H_
#define READ_ENDS_H_

#include <stdint.h>

/* 包含了所有read ends信息，如picard里边的 ReadEndsForMarkDuplicates*/
struct ReadEnds 
{
    /* PhysicalLocationInt中的成员变量 */
    /**
     * Small class that provides access to the physical location information about a cluster.
     * All values should be defaulted to -1 if unavailable.  Tile should only allow
     * non-zero positive integers, x and y coordinates must be non-negative.
     * This is different from PhysicalLocationShort in that the x and y positions are ints, not shorts
     * thus, they do not overflow within a HiSeqX tile.
     */
    int16_t tile = -1;
    int32_t x = -1;
    int32_t y = -1;

    /* ReadEnds中的成员变量 */
    /** Little struct-like class to hold read pair (and fragment) end data for duplicate marking. */
    static const int8_t F = 0, R = 1, FF = 2, FR = 3, RR = 4, RF = 5;
    int16_t libraryId;
    int8_t orientation;
    int32_t read1ReferenceIndex = -1;
    int32_t read1Coordinate = -1;
    int32_t read2ReferenceIndex = -1;
    int32_t read2Coordinate = -1; // This field is overloaded for flow based processing as the end coordinate of read 1. (paired reads not supported)
    /* Additional information used to detect optical dupes */
    int16_t readGroup = -1;
    /** For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate */
    int8_t orientationForOpticalDuplicates = -1;
    /** A *transient* flag marking this read end as being an optical duplicate. */
    bool isOpticalDuplicate = false;

    /* ReadEndsForMarkDuplicates中的成员变量 */
    /** Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar **/
    int16_t score = 0;
    int64_t read1IndexInFile = -1;
    int64_t read2IndexInFile = -1;
    int64_t duplicateSetSize = -1;

    /* ReadEndsForMarkDuplicatesWithBarcodes中的成员变量 (好像用不到) */
    int32_t barcode = 0; // primary barcode for this read (and pair)
    int32_t readOneBarcode = 0; // read one barcode, 0 if not present
    int32_t readTwoBarcode = 0; // read two barcode, 0 if not present or not paired
};

#endif