#ifndef FMT_INDEX_H_
#define FMT_INDEX_H_

#define FMT_OCC_INTV_SHIFT 8
#define FMT_OCC_INTERVAL (1LL << FMT_OCC_INTV_SHIFT)
#define FMT_OCC_INTV_MASK (FMT_OCC_INTERVAL - 1)

#define FMT_MID_INTV_SHIFT 6
#define FMT_MID_INTERVAL (1LL << FMT_MID_INTV_SHIFT)
#define FMT_MID_INTV_MASK (FMT_MID_INTERVAL - 1)

// #undef FMT_MID_INTERVAL

// 获取碱基c（待查找序列的首个碱基）和对应的互补碱基对应的行，以及间隔
#define fmt_set_intv(fmt, c, ik) ((ik).x[0] = (fmt)->L2[(int)(c)] + 1, (ik).x[2] = (fmt)->L2[(int)(c) + 1] - (fmt)->L2[(int)(c)], (ik).x[1] = (fmt)->L2[3 - (c)] + 1, (ik).info = 0)
// k行（bwt str行（不包含$））对应的check point occ数据起始地址（小于k且是OCC_INTERVAL的整数倍）

#if FMT_MID_INTERVAL == 8
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 144))
#elif FMT_MID_INTERVAL == 16
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 80))
#elif FMT_MID_INTERVAL == 32
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 48))
#elif FMT_MID_INTERVAL == 64
//#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 32))
#define fmt_occ_intv(b, k) ((b)->bwt + ((k) >> 8 << 6))
#elif FMT_MID_INTERVAL == 128
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 24))
#else
#define fmt_occ_intv(b, k) ((b)->bwt + (k) / FMT_OCC_INTERVAL * (FMT_OCC_INTERVAL / 8 + 20))
#endif
// 字节val中包含bwt base为b的pre-bwt中T G C A（按顺序保存在32位整数里（每个占8bit））的数量
#define __fmt_occ_e2_aux4(fmt, b, val) \
    ((fmt)->cnt_table[(b)][(val) & 0xff] + (fmt)->cnt_table[b][(val) >> 8 & 0xff] + (fmt)->cnt_table[b][(val) >> 16 & 0xff] + (fmt)->cnt_table[b][(val) >> 24])

#define __fmt_occ_e2_aux2(fmt, b, val) \
    ((fmt)->cnt_occ[(b)][(val) & 0xff] + (fmt)->cnt_occ[b][(val) >> 8 & 0xff] + (fmt)->cnt_occ[b][(val) >> 16 & 0xff] + (fmt)->cnt_occ[b][(val) >> 24])

#define __fmt_mid_sum(x) \
    ((x) >> 24 & 0xff) + ((x) >> 16 & 0xff) + ((x) >> 8 & 0xff) + ((x) & 0xff)


#define XMER_LEN 14

// sa存储的行间隔
#define SA_INTV 4
#define SA_BYTES(n_sa) ((((33 * (n_sa) + 7) / 8) & (~7L)) + 8)

// x-mer entry, 1 - 14个碱基组成的hash key
struct XmerEntry
{
    uint8_t intv_arr[14];
};

struct XmerEntryArr
{
    uint8_t intv_arr[140];
};

struct XmerHash
{
    XmerEntryArr *xe10;
    XmerEntry *xe11;
    XmerEntry *xe12;
    XmerEntry *xe13;
    XmerEntry *xe14;
};

// fm-index, extend twice in one search step (one memory access)
struct FMTIndex
{
    bwtint_t primary;     // S^{-1}(0), or the primary index of BWT
    bwtint_t sec_primary; // second primary line
    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
    // occurance array, separated to two parts
    uint32_t cnt_occ[16][256]; // 前16-24位表示b（碱基）的occ，8-16位表示大于b的occ，0-8表示大于a的occ，ba格式
    uint8_t sec_bcp;                // base couple for sec primary line, AA=>0, AC=>1 ... TT=>15
    uint8_t first_base;             // 序列的第一个碱基2bit的int类型，0,1,2,3
    uint8_t last_base;              // dollar转换成的base
    // ref pac相关
    bwtint_t l_pac; // 参考序列长度
    uint8_t *pac;   // 保存2bit编码的参考序列
    // 保存kmer对应的fmt位置信息
    XmerHash xmer_hash;
    // suffix array
    int sa_intv;
    bwtint_t n_sa;
    uint8_t *sa;
};

#endif