#ifndef __KMER__
#define __KMER__
#include "Process_Read.h"

#define ALL (0xffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff)

#define SAFE_SHIFT(k) k & ((k < 64)?ALL:0)


static unsigned char seq_nt6_table[256] = {
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 0, 5, 1,  5, 5, 5, 2,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  3, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 0, 5, 1,  5, 5, 5, 2,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  3, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,
    5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5,  5, 5, 5, 5
};



typedef struct
{
    ///最大64-mer
    ///x[0]低位
    ///x[1]高位
    uint64_t x[2];

} Hash_code;



typedef struct
{
	char* str;
	long long l;
    long long i;

} HPC_seq;


inline uint64_t get_HPC_code(HPC_seq* seq)
{

    if(seq->i < seq ->l)
    {
        char code = seq->str[seq->i];

        for (; seq->i < seq->l; seq->i++)
        {
            if (seq->str[seq->i] != code)
            {
                break;
            }
        }

        return (uint64_t)seq_nt6_table[(uint8_t)code];
    }
    else
    {
        ///end
        return 6;
    }
    
}

inline void k_mer_append(Hash_code* code, uint64_t c, int k)
{

    uint64_t mask = ALL >> (64 -k);

    code->x[0] = ((code->x[0]<<1) | (c&1))  & mask;
    code->x[1] = ((code->x[1]<<1) | (c>>1)) & mask;
}

void init_HPC_seq(HPC_seq* seq, char* str, long long l);
void init_Hash_code(Hash_code* code);


#endif