#ifndef FMT_INDEX_H_
#define FMT_INDEX_H_

#include "bwt.h"

// 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_table[5][256]; // 4对应原来的cnt_table，0,1,2,3,分别对应该碱基的扩展
    int sec_bcp;                // base couple for sec primary line, AA=>0, AC=>1 ... TT=>15
    int first_base;             // 序列的第一个碱基2bit的int类型，0,1,2,3
    int last_base;              // dollar转换成的base
    // suffix array
    int sa_intv;
    bwtint_t n_sa;
    uint8_t *sa;
};

#endif