/*
Description: 通过fmt-idx数据结构对seed过程进行加速（fm-index twice search in one time）

Copyright : All right reserved by ICT

Author : Zhang Zhonghai
Date : 2023/12/24
*/
#ifndef BWA_FMT_IDX_H
#define BWA_FMT_IDX_H
#include <stdint.h>
#include <stddef.h>
#include "bwt.h"

typedef uint64_t bwtint_t;

/*
    ignore the first 12 bases, and give the entrence directly
*/
typedef struct {
    uint8_t range[9]; // 前36位表示起始行，后36位表示结束行（fm-index索引行）
} kmer_range_t;

typedef struct
{
    bwtint_t primary;  // S^{-1}(0), or the primary index of BWT
    bwtint_t L2[5];    // C(), cumulative count
    bwtint_t seq_len;  // sequence length
    bwtint_t bwt_size; // size of bwt, about seq_len/4
    uint32_t *bwt;     // BWT
    // kmer entry
    kmer_range_t *kmer_range;
    // occurance array, separated to two parts
    uint32_t cnt_table[256];
    // suffix array
    int sa_intv;
    bwtint_t n_sa;
    bwtint_t *sa;
} bwtd_t;

// 创建fmt-index索引数据
void BuildBwtdFromBwt(bwt_t *bwt, bwtd_t **bwtd_p);

#endif