#include <stdlib.h>
#include <stdint.h>
#include <assert.h>
#include <stdio.h>
#include <immintrin.h>
#include <emmintrin.h>
#include "thread_mem.h"

#ifdef __GNUC__
#define LIKELY(x) __builtin_expect((x), 1)
#define UNLIKELY(x) __builtin_expect((x), 0)
#else
#define LIKELY(x) (x)
#define UNLIKELY(x) (x)
#endif

#undef MAX
#undef MIN
#define MAX(x, y) ((x) > (y) ? (x) : (y))
#define MIN(x, y) ((x) < (y) ? (x) : (y))
#define SIMD_WIDTH 16
#define BASE_BYTES 2
#define SCORE_BYTES 2
#define BOUNDARY_SCORE_NUM 2
#define TMP_SCORE_ARRAY_NUM 9
#define MEM_ALIGN_BYTES 32
#define ALIGN_SHIFT_BITS 5
#define SIMD_BYTES 32

#define AMBIGUOUS_BASE_CODE 4
#define AMBIGUOUS_BASE_SCORE -1

// 32字节对齐（256位）
#define align_mem(x) (((x) + 31) >> 5 << 5)
#define align_number(x) align_mem(x)

/* 去掉多余计算的值 */
static const uint16_t h_vec_int_mask[SIMD_WIDTH][SIMD_WIDTH] = {
    {0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0},
    {0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff, 0xffff}};

// #define permute_mask _MM_SHUFFLE(0, 1, 2, 3)
#define permute_mask 27
// 初始化变量
#define SIMD_INIT                                                  \
    int oe_del = o_del + e_del, oe_ins = o_ins + e_ins;            \
    __m256i zero_vec;                                              \
    __m256i max_vec, last_max_vec = _mm256_set1_epi16(init_score); \
    __m256i oe_del_vec;                                            \
    __m256i oe_ins_vec;                                            \
    __m256i e_del_vec;                                             \
    __m256i e_ins_vec;                                             \
    __m256i h_vec_mask[SIMD_WIDTH];                                \
    zero_vec = _mm256_setzero_si256();                             \
    oe_del_vec = _mm256_set1_epi16(-oe_del);                       \
    oe_ins_vec = _mm256_set1_epi16(-oe_ins);                       \
    e_del_vec = _mm256_set1_epi16(-e_del);                         \
    e_ins_vec = _mm256_set1_epi16(-e_ins);                         \
    __m256i match_sc_vec = _mm256_set1_epi16(base_match_score);    \
    __m256i mis_sc_vec = _mm256_set1_epi16(-base_mis_score);       \
    __m256i amb_sc_vec = _mm256_set1_epi16(AMBIGUOUS_BASE_SCORE);  \
    __m256i amb_vec = _mm256_set1_epi16(AMBIGUOUS_BASE_CODE);      \
    for (i = 0; i < SIMD_WIDTH; ++i)                               \
        h_vec_mask[i] = _mm256_loadu_si256((__m256i *)(&h_vec_int_mask[i]));

/*
 * e 表示当前ref的碱基被删除
 * f 表示当前seq的碱基插入
 * m 表示当前碱基匹配（可以相等，也可以不想等）
 * h 表示最大值
 */
// load向量化数据
#define SIMD_LOAD                                                          \
    __m256i m1 = _mm256_loadu_si256((__m256i *)(&cur_match_arr[j]));       \
    __m256i e1 = _mm256_loadu_si256((__m256i *)(&cur_del_arr[j]));         \
    __m256i m1j1 = _mm256_loadu_si256((__m256i *)(&cur_match_arr[j - 1])); \
    __m256i f1j1 = _mm256_loadu_si256((__m256i *)(&cur_ins_arr[j - 1]));   \
    __m256i h0j1 = _mm256_loadu_si256((__m256i *)(&last_max_arr[j - 1]));  \
    __m256i qs_vec = _mm256_loadu_si256((__m256i *)(&read_seq[j]));        \
    __m256i ts_vec = _mm256_loadu_si256((__m256i *)(&ref_seq[i]));

// 比对ref和seq的序列，计算罚分
#define SIMD_CMP_SEQ                                                                                                         \
    /* 将待比对的target序列逆序排列 */                                                                            \
    ts_vec = _mm256_permute4x64_epi64(ts_vec, permute_mask);                                                                 \
    ts_vec = _mm256_shufflelo_epi16(ts_vec, permute_mask);                                                                   \
    ts_vec = _mm256_shufflehi_epi16(ts_vec, permute_mask);                                                                   \
    __m256i match_mask_vec = _mm256_cmpeq_epi16(qs_vec, ts_vec);             /* 比对query和target字符序列 */          \
    __m256i mis_score_vec = _mm256_andnot_si256(match_mask_vec, mis_sc_vec); /* 未匹配上的位置赋值mismatch分数 */ \
    __m256i score_vec = _mm256_and_si256(match_sc_vec, match_mask_vec);      /* 匹配上的位置赋值match分数 */       \
    score_vec = _mm256_or_si256(score_vec, mis_score_vec);                                                                   \
    /* 计算模棱两可的字符（N)的位置的分数 */                                                                 \
    __m256i q_amb_mask_vec = _mm256_cmpeq_epi16(qs_vec, amb_vec);                                                            \
    __m256i t_amb_mask_vec = _mm256_cmpeq_epi16(ts_vec, amb_vec);                                                            \
    __m256i amb_mask_vec = _mm256_or_si256(q_amb_mask_vec, t_amb_mask_vec);                                                  \
    score_vec = _mm256_andnot_si256(amb_mask_vec, score_vec);                                                                \
    __m256i amb_score_vec = _mm256_and_si256(amb_mask_vec, amb_sc_vec);                                                      \
    score_vec = _mm256_or_si256(score_vec, amb_score_vec);

// 向量化计算h, e, f, m
#define SIMD_COMPUTE                                      \
    __m256i en_vec0 = _mm256_add_epi16(m1, oe_del_vec);   \
    __m256i en_vec1 = _mm256_add_epi16(e1, e_del_vec);    \
    __m256i en_vec = _mm256_max_epi16(en_vec0, en_vec1);  \
    __m256i fn_vec0 = _mm256_add_epi16(m1j1, oe_ins_vec); \
    __m256i fn_vec1 = _mm256_add_epi16(f1j1, e_ins_vec);  \
    __m256i fn_vec = _mm256_max_epi16(fn_vec0, fn_vec1);  \
    __m256i mn_vec0 = _mm256_add_epi16(h0j1, score_vec);  \
    __m256i mn_mask = _mm256_cmpgt_epi16(h0j1, zero_vec); \
    __m256i mn_vec = _mm256_and_si256(mn_vec0, mn_mask);  \
    __m256i hn_vec0 = _mm256_max_epi16(en_vec, fn_vec);   \
    __m256i hn_vec = _mm256_max_epi16(hn_vec0, mn_vec);   \
    en_vec = _mm256_max_epi16(en_vec, zero_vec);          \
    fn_vec = _mm256_max_epi16(fn_vec, zero_vec);          \
    mn_vec = _mm256_max_epi16(mn_vec, zero_vec);          \
    hn_vec = _mm256_max_epi16(hn_vec, zero_vec);

#define SIMD_STORE                                              \
    max_vec = _mm256_max_epu8(max_vec, hn_vec);                 \
    _mm256_storeu_si256((__m256i *)&next_del_arr[j], en_vec);   \
    _mm256_storeu_si256((__m256i *)&next_ins_arr[j], fn_vec);   \
    _mm256_storeu_si256((__m256i *)&next_match_arr[j], mn_vec); \
    _mm256_storeu_si256((__m256i *)&next_max_arr[j], hn_vec);

// 去除多余的部分
#define SIMD_REMOVE_EXTRA                                            \
    en_vec = _mm256_and_si256(en_vec, h_vec_mask[read_end_pos - j]); \
    fn_vec = _mm256_and_si256(fn_vec, h_vec_mask[read_end_pos - j]); \
    mn_vec = _mm256_and_si256(mn_vec, h_vec_mask[read_end_pos - j]); \
    hn_vec = _mm256_and_si256(hn_vec, h_vec_mask[read_end_pos - j]);

// 找最大值和位置
#define SIMD_FIND_MAX                                                                                                  \
    __m256i cmp_max = _mm256_cmpgt_epi16(max_vec, last_max_vec);                                                       \
    uint32_t cmp_result = _mm256_movemask_epi8(cmp_max);                                                               \
    if (cmp_result > 0)                                                                                                \
    {                                                                                                                  \
        max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 2));                                  \
        max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 4));                                  \
        max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 6));                                  \
        max_vec = _mm256_max_epu16(max_vec, _mm256_alignr_epi8(max_vec, max_vec, 8));                                  \
        max_vec = _mm256_max_epu16(max_vec, _mm256_permute2x128_si256(max_vec, max_vec, 0x01));                        \
        int16_t *maxVal = (int16_t *)&max_vec;                                                                         \
        m = maxVal[0];                                                                                                 \
        for (j = aligned_read_start_pos, i = aligned_ref_end_pos; j <= read_end_pos; j += SIMD_WIDTH, i -= SIMD_WIDTH) \
        {                                                                                                              \
            __m256i h2_vec = _mm256_loadu_si256((__m256i *)(&next_max_arr[j]));                                        \
            __m256i vcmp = _mm256_cmpeq_epi16(h2_vec, max_vec);                                                        \
            uint32_t mask = _mm256_movemask_epi8(vcmp);                                                                \
            if (mask > 0)                                                                                              \
            {                                                                                                          \
                int pos = SIMD_WIDTH - 1 - ((__builtin_clz(mask)) >> 1);                                               \
                mj = j - 1 + pos;                                                                                      \
                mi = i - 1 - pos;                                                                                      \
                for (; mj + 1 < qlen && mi + 1 < tlen; mj++, mi++)                                                     \
                {                                                                                                      \
                    if (read_seq[mj + 2] == ref_seq[mi + 1 + SIMD_WIDTH])                                              \
                    {                                                                                                  \
                        m += base_match_score;                                                                         \
                    }                                                                                                  \
                    else                                                                                               \
                    {                                                                                                  \
                        break;                                                                                         \
                    }                                                                                                  \
                }                                                                                                      \
            }                                                                                                          \
        }                                                                                                              \
        last_max_vec = _mm256_set1_epi16(m);                                                                           \
    }

// 每轮迭代后，交换数组
#define SWAP_DATA_POINTER           \
    int16_t *tmp = last_max_arr;    \
    last_max_arr = cur_max_arr;     \
    cur_max_arr = next_max_arr;     \
    next_max_arr = tmp;             \
    tmp = cur_del_arr;              \
    cur_del_arr = next_del_arr;     \
    next_del_arr = tmp;             \
    tmp = cur_ins_arr;              \
    cur_ins_arr = next_ins_arr;     \
    next_ins_arr = tmp;             \
    tmp = cur_match_arr;            \
    cur_match_arr = next_match_arr; \
    next_match_arr = tmp;

int ksw_extend_avx2_aligned(thread_mem_t *tmem,
                            int qlen,              // query length  待匹配段碱基的query长度
                            const uint8_t *query,  // read碱基序列
                            int tlen,              // target length reference的长度
                            const uint8_t *target, // reference序列
                            int extend_left,       // 是不是向左扩展
                            int o_del,             // deletion 错配开始的惩罚系数
                            int e_del,             // deletion extension的惩罚系数
                            int o_ins,             // insertion 错配开始的惩罚系数
                            int e_ins,             // insertion extension的惩罚系数SIMD_BTYES
                            int base_match_score,  // 碱基match时的分数
                            int base_mis_score,    // 碱基mismatch时的惩罚分数（正数）
                            int window_size,       // 提前剪枝系数，w =100   匹配位置和beg的最大距离
                            int end_bonus,         // 如果query比对到了最后一个字符，额外奖励分值
                            int init_score,        // 该seed的初始得分（完全匹配query的碱基数）
                            int *_qle,             // 匹配得到全局最大得分的碱基在query的位置
                            int *_tle,             // 匹配得到全局最大得分的碱基在reference的位置
                            int *_gtle,            // query全部匹配上的target的长度
                            int *_gscore,          // query的端到端匹配得分
                            int *_max_off)         // 取得最大得分时在query和reference上位置差的 最大值
{
    int16_t *cur_match_arr, *next_match_arr,
        *last_max_arr, *cur_max_arr, *next_max_arr,
        *cur_del_arr, *next_del_arr,
        *cur_ins_arr, *next_ins_arr; // hA0保存上上个col的H，其他的保存上个H E F M
    int16_t *read_seq, *ref_seq;
    uint8_t *mem_addr;

    int read_size = align_number(qlen * BASE_BYTES + MEM_ALIGN_BYTES);
    int ref_size = align_number((tlen + SIMD_WIDTH) * BASE_BYTES);
    int back_diagnal_num = tlen + qlen; // 循环跳出条件 D从1开始遍历
    int score_array_size = align_number((qlen + BOUNDARY_SCORE_NUM) * SCORE_BYTES);
    int score_element_num = score_array_size / SCORE_BYTES;
    int score_mem_size = score_array_size * TMP_SCORE_ARRAY_NUM;
    int request_mem_size = read_size + ref_size + score_mem_size + MEM_ALIGN_BYTES * 3; // 左侧内存地址对齐 + 数据向左偏移一个元素 + 末尾SIMD补齐

    int i, ref_start_pos, di, j, read_start_pos, read_end_pos, max, max_i, max_j, max_ins, max_del, max_ie, gscore, max_off;
    int span, beg1, end1; // 边界条件计算
    int aligned_read_start_pos, aligned_ref_end_pos;
    int ref_end_pos;

    SIMD_INIT; // 初始化simd用的数据

    assert(init_score > 0);

    // allocate memory
    mem_addr = thread_mem_request(tmem, request_mem_size);
    mem_addr = (void *)align_mem((uint64_t)mem_addr);
    ref_seq = (int16_t *)&mem_addr[0];
    read_seq = (int16_t *)(mem_addr + ref_size + SIMD_BYTES - BASE_BYTES);
    if (extend_left)
    {
        for (i = 0; i < qlen; ++i)
            read_seq[i + 1] = query[qlen - 1 - i];
        for (i = 0; i < tlen; ++i)
            ref_seq[i + SIMD_WIDTH] = target[tlen - 1 - i];
    }
    else
    {
        for (i = 0; i < qlen; ++i)
            read_seq[i + 1] = query[i];
        for (i = 0; i < tlen; ++i)
            ref_seq[i + SIMD_WIDTH] = target[i];
    }

    mem_addr += read_size + ref_size + (SIMD_BYTES - SCORE_BYTES);
    for (i = 0; i < score_mem_size; i += SIMD_BYTES)
    {
        _mm256_storeu_si256((__m256i *)&mem_addr[i], zero_vec);
    }

    last_max_arr = (int16_t *)&mem_addr[0];
    cur_max_arr = &last_max_arr[score_element_num];
    next_max_arr = &cur_max_arr[score_element_num];
    cur_match_arr = &next_max_arr[score_element_num];
    next_match_arr = &cur_match_arr[score_element_num];
    cur_del_arr = &next_match_arr[score_element_num];
    next_del_arr = &cur_del_arr[score_element_num];
    cur_ins_arr = &next_del_arr[score_element_num];
    next_ins_arr = &cur_ins_arr[score_element_num];

    // adjust $window_size if it is too large
    // get the max score
    max = base_match_score;
    max_ins = (int)((double)(qlen * max + end_bonus - o_ins) / e_ins + 1.);
    max_ins = max_ins > 1 ? max_ins : 1;
    window_size = window_size < max_ins ? window_size : max_ins;
    max_del = (int)((double)(qlen * max + end_bonus - o_del) / e_del + 1.);
    max_del = max_del > 1 ? max_del : 1;
    window_size = window_size < max_del ? window_size : max_del; // TODO: is this necessary?
    if (tlen < qlen)
        window_size = MIN(tlen - 1, window_size);

    // DP loop
    max = init_score, max_i = max_j = -1;
    max_ie = -1, gscore = -1;
    ;
    max_off = 0;
    read_start_pos = 1;
    read_end_pos = qlen;
    // init init_score
    last_max_arr[0] = init_score; // 左上角

    if (qlen == 0 || tlen == 0)
        back_diagnal_num = 0; // 防止意外情况
    if (window_size >= qlen)
    {
        max_ie = 0;
        gscore = 0;
    }

    for (di = 1; LIKELY(di < back_diagnal_num); ++di)
    {
        // 边界条件一定要注意！ tlen 大于，等于，小于 qlen时的情况
        if (di > tlen)
        {
            span = MIN(back_diagnal_num - di, window_size); // 计算的窗口，或者说范围
            beg1 = MAX(di - tlen + 1, ((di - window_size) / 2) + 1);
        }
        else
        {
            span = MIN(di - 1, window_size);
            beg1 = MAX(1, ((di - window_size) / 2) + 1);
        }
        end1 = MIN(qlen, beg1 + span);

        if (read_start_pos < beg1)
            read_start_pos = beg1;
        if (read_end_pos > end1)
            read_end_pos = end1;
        if (read_start_pos > read_end_pos)
            break; // 不用计算了，直接跳出，否则hA2没有被赋值，里边是上一轮hA0的值，会出bug

        read_start_pos = 1;
        read_end_pos = qlen;
        ref_end_pos = di - (read_start_pos - 1); // ref开始计算的位置，倒序
        span = read_end_pos - read_start_pos;
        ref_start_pos = ref_end_pos - span - 1; // 0开始的ref索引位置

        // 每一轮需要记录的数据
        int m = 0, mj = -1, mi = -1;
        max_vec = zero_vec;

        // 要处理边界
        // 左边界 处理f (insert)
        if (ref_start_pos == 0)
        {
            cur_max_arr[read_end_pos] = MAX(0, init_score - (o_ins + e_ins * read_end_pos));
        }
        // 上边界 delete
        if (read_start_pos == 1)
        {
            cur_max_arr[0] = MAX(0, init_score - (o_del + e_del * ref_end_pos));
        }
        else
        {
            cur_max_arr[read_start_pos - 1] = 0;
            cur_del_arr[read_start_pos - 1] = 0;
        }

        // aligned_read_start_pos = (read_start_pos >> ALIGN_SHIFT_BITS << ALIGN_SHIFT_BITS) + 1;
        // aligned_ref_end_pos = ref_end_pos + (read_start_pos - aligned_read_start_pos);

        aligned_read_start_pos = read_start_pos;
        aligned_ref_end_pos = ref_end_pos;

        // fprintf(stderr, "%d\t%d\n", read_start_pos, aligned_read_start_pos);

        for (j = aligned_read_start_pos, i = aligned_ref_end_pos; j <= read_end_pos + 1 - SIMD_WIDTH; j += SIMD_WIDTH, i -= SIMD_WIDTH)
        {
            // 取数据
            SIMD_LOAD;
            // 比对seq，计算罚分
            SIMD_CMP_SEQ;
            // 计算
            SIMD_COMPUTE;
            // 存储结果
            SIMD_STORE;
        }
        // 剩下的计算单元
        if (j <= read_end_pos)
        {
            // 取数据
            SIMD_LOAD;
            // 比对seq，计算罚分
            SIMD_CMP_SEQ;
            // 计算
            SIMD_COMPUTE;
            // 去除多余计算的部分
            SIMD_REMOVE_EXTRA;
            // 存储结果
            SIMD_STORE;
        }

        SIMD_FIND_MAX;

        // 注意最后跳出循环j的值
        j = read_end_pos + 1;

        if (j == qlen + 1) // 遍历到了query最后一个碱基，此时next_max_arr[qlen]为全局匹配的最大分值
        {
            max_ie = gscore > next_max_arr[qlen] ? max_ie : ref_start_pos;
            gscore = gscore > next_max_arr[qlen] ? gscore : next_max_arr[qlen];
        }
        if (m > max)
        {
            max = m, max_i = mi, max_j = mj;
            max_off = max_off > abs(mj - mi) ? max_off : abs(mj - mi);
        }

        // 调整计算的边界
        // for (j = read_start_pos; LIKELY(j <= read_end_pos); ++j)
        //{
        //    int has_val = cur_max_arr[j - 1] | next_max_arr[j];
        //    if (has_val)
        //    {
        //        break;
        //    }
        //}
        // read_start_pos = j;
        //
        // next_max_arr[read_end_pos + 1] = 0;
        // for (j = read_end_pos + 1; LIKELY(j >= read_start_pos); --j)
        //{
        //    int has_val = cur_max_arr[j - 1] | next_max_arr[j];
        //    if (has_val)
        //    {
        //        break;
        //    }
        //}
        // read_end_pos = j + 1 <= qlen ? j + 1 : qlen;
        // swap m, h, e, f
        SWAP_DATA_POINTER;
    }

    thread_mem_release(tmem, request_mem_size);
    if (_qle)
        *_qle = max_j + 1;
    if (_tle)
        *_tle = max_i + 1;
    if (_gtle)
        *_gtle = max_ie + 1;
    if (_gscore)
        *_gscore = gscore;
    if (_max_off)
        *_max_off = max_off;
    return max;
}