#include "paired_sam.h"

#include <stdint.h>
#include <stdio.h>

#include "ksw_align_avx.h"
#include "kvec.h"

// 原版生成sam函数
static void worker_sam(void* data, int i, int tid) {
    mem_worker_t* w = (mem_worker_t*)data;
    if (bwa_verbose >= 4)
        printf("=====> Finalizing read pair '%s' <=====\n", w->seqs[i << 1 | 0].name);
    mem_sam_pe(w->opt, w->bns, w->pac, w->pes, (w->n_processed >> 1) + i, &w->seqs[i << 1], &w->regs[i << 1], &w->sams[i << 1], tid);
    free(w->regs[i << 1 | 0].a);
    free(w->regs[i << 1 | 1].a);
}

// 应该是推测read的方向，正链还是反向互补等等
static inline int mem_infer_dir(int64_t l_pac, int64_t b1, int64_t b2, int64_t* dist) {
    int64_t p2;
    int r1 = (b1 >= l_pac), r2 = (b2 >= l_pac);
    p2 = r1 == r2 ? b2 : (l_pac << 1) - 1 - b2;  // p2 is the coordinate of read 2 on the read 1 strand
    *dist = p2 > b1 ? p2 - b1 : b1 - p2;
    return (r1 == r2 ? 0 : 1) ^ (p2 > b1 ? 0 : 3);
}

// 根据ref的begin和end计算对应的rid和修正之后的end
static int get_rid_range(const bntseq_t* bns, const uint8_t* pac, int64_t* beg, int64_t mid, int64_t* end) {
    int64_t far_beg, far_end;
    int is_rev;
    int rid;

    if (*end < *beg)
        *end ^= *beg, *beg ^= *end, *end ^= *beg;  // if end is smaller, swap
    assert(*beg <= mid && mid < *end);
    rid = bns_pos2rid(bns, bns_depos(bns, mid, &is_rev));
    far_beg = bns->anns[rid].offset;
    far_end = far_beg + bns->anns[rid].len;
    if (is_rev) {  // flip to the reverse strand
        int64_t tmp = far_beg;
        far_beg = (bns->l_pac << 1) - far_end;
        far_end = (bns->l_pac << 1) - tmp;
    }
    *beg = *beg > far_beg ? *beg : far_beg;
    *end = *end < far_end ? *end : far_end;
    return rid;
}

// 获取ref序列
static inline uint8_t* get_ref_seq(const bntseq_t* bns, const uint8_t* pac, int64_t beg, int64_t end) {
    int64_t len;
    return bns_get_seq(bns->l_pac, pac, beg, end, &len);
}

// 计算当前seq是否需要做matesw，需要的话保存必要的数据
static void get_matesw_data(const mem_opt_t* opt, const bntseq_t* bns, const uint8_t* pac, const mem_pestat_t pes[4], const mem_alnreg_t* a,
                           bseq1_t* seq, mem_alnreg_v* ma, int64_t sid, mem_stats_t *stats, matesw_data_v* msw8, matesw_data_v* msw16) {
    int64_t l_pac = bns->l_pac;
    int l_ms = seq->l_seq;
    int i, r, skip[4], rid;
    stats->max_seq_len = max_(stats->max_seq_len, l_ms);
    for (r = 0; r < 4; ++r) skip[r] = pes[r].failed ? 1 : 0;
    for (i = 0; i < ma->n; ++i) {  // check which orinentation has been found
        int64_t dist;
        r = mem_infer_dir(l_pac, a->rb, ma->a[i].rb, &dist);
        if (dist >= pes[r].low && dist <= pes[r].high)
            skip[r] = 1;
    }
    if (skip[0] + skip[1] + skip[2] + skip[3] == 4)
        return;  // consistent pair exist; no need to perform SW
    for (r = 0; r < 4; ++r) {
        int is_rev, is_larger;
        int64_t rb, re;  // 左闭右开
        if (skip[r])
            continue;
        is_rev = (r >> 1 != (r & 1));  // whether to reverse complement the mate
        is_larger = !(r >> 1);         // whether the mate has larger coordinate
        if (!is_rev) {
            rb = is_larger ? a->rb + pes[r].low : a->rb - pes[r].high;
            // if on the same strand, end position should be larger to make room for the seq length
            re = (is_larger ? a->rb + pes[r].high : a->rb - pes[r].low) + l_ms;
        } else {
            rb = (is_larger ? a->rb + pes[r].low : a->rb - pes[r].high) - l_ms;  // similarly on opposite strands
            re = is_larger ? a->rb + pes[r].high : a->rb - pes[r].low;
        }
        if (rb < 0)
            rb = 0;
        if (re > l_pac << 1)
            re = l_pac << 1;
        rid = get_rid_range(bns, pac, &rb, (rb + re) >> 1, &re); // 计算ref对应的染色体id和区间起始终止位置
        if (a->rid == rid && re - rb >= opt->min_seed_len) {  // no funny things happening
            stats->max_msw_ref_len = max_(stats->max_msw_ref_len, re - rb);
            // fprintf(stderr, "zzh here\n");
            int xtra = KSW_XSUBO | KSW_XSTART | (l_ms * opt->a < 250 ? KSW_XBYTE : 0) | (opt->min_seed_len * opt->a);
            matesw_data_t* p;
            if ((xtra & KSW_XBYTE))
                p = kv_pushp(matesw_data_t, *msw8);
            else
                p = kv_pushp(matesw_data_t, *msw16);
            p->is_rev = is_rev;
            p->xtra = xtra;
            p->rb = rb;
            p->re = re;
            p->seq_id = sid;
            kv_push(matesw_data_t*, seq->msw, p);  // 将matesw任务和对应的seq关联起来
        }
    }
}
// 先计算哪些read需要做matesw
static void worker_matesw_data(void* data, int idx, int tid) {
    mem_worker_t* w = (mem_worker_t*)data;
    const mem_opt_t* opt = w->opt;
    int64_t i_s = idx << 1;
    bseq1_t* s = &w->seqs[i_s];
    mem_alnreg_v* a = &w->regs[i_s];
    s->msw.n = 0; // 清空之前的matesw数据
    int i, j;
    mem_alnreg_v b[2];
    kv_init(b[0]);
    kv_init(b[1]);
    // fprintf(stderr, "zzh test\n");
    for (i = 0; i < 2; ++i)
        for (j = 0; j < a[i].n; ++j)
            if (a[i].a[j].score >= a[i].a[0].score - opt->pen_unpaired)
                kv_push(mem_alnreg_t, b[i], a[i].a[j]);
    for (i = 0; i < 2; ++i)
        for (j = 0; j < b[i].n && j < opt->max_matesw; ++j)
            get_matesw_data(opt, w->bns, w->pac, w->pes, &b[i].a[j], &s[!i], &a[!i], i_s + !i, &w->mem_stats[tid], w->matesw_arr8[tid], w->matesw_arr16[tid]);
    free(b[0].a);
    free(b[1].a);
}

// 再多线程计算matesw，利用inter-query的simd并行
static void worker_calc_matesw_avx512_u8(void* data, int idx, int tid) {
    mem_worker_t* w = (mem_worker_t*)data;
    int startIdx = idx * SIMD512_WIDTH8;
    int endIdx = (idx + 1) * SIMD512_WIDTH8;
    if (endIdx > w->msw_tasks8.n)
        endIdx = w->msw_tasks8.n;
    int i = 0, j = 0, k = 0;
    int maxSeqLen = 0, maxRefLen = 0;
    uint8_t* refArr[SIMD512_WIDTH8] = {0};
    uint8_t* seqArr[SIMD512_WIDTH8] = {0};
    int refLen[SIMD512_WIDTH8] = {0};
    int seqLen[SIMD512_WIDTH8] = {0};
    int seqQuantaLen[SIMD512_WIDTH8] = {0};
    int xtraA[SIMD512_WIDTH8] = {0};
    kswr_avx_t alns[SIMD512_WIDTH8] = {0};

    matesw_buf_t* msw_buf = &w->msw_buf[tid];  // 缓冲区

    for (i = startIdx, j = 0; i < endIdx; ++i, ++j) {
        matesw_data_t* task = kv_A(w->msw_tasks8, i);
        // 1. 获取对应的ref
        refArr[j] = get_ref_seq(w->bns, w->pac, task->rb, task->re);
        refLen[j] = task->re - task->rb;
        maxRefLen = max_(maxRefLen, refLen[j]);
        // 2. 获取对应的seq
        seqArr[j] = (uint8_t*)w->seqs[task->seq_id].seq;
        seqLen[j] = w->seqs[task->seq_id].l_seq;
        int quanta = (seqLen[j] + 16 - 1) / 16;  // based on SSE-8 bit lane
        quanta *= 16;
        seqQuantaLen[j] = quanta;
        maxSeqLen = max_(maxSeqLen, quanta);
        // 3. 其他数据
        xtraA[j] = task->xtra;
    }
    // 如果不到64个，补全剩下的
    for (; j < SIMD512_WIDTH8; ++j) {
        refArr[j] = refArr[0];
        refLen[j] = refLen[0];
        seqArr[j] = seqArr[0];
        seqLen[j] = seqLen[0];
        xtraA[j] = xtraA[0];
    }
    // 将ref和seq赋值给对应的用来计算的缓存
    uint8_t* mySeq1SoA = msw_buf->refArr;
    uint8_t* mySeq2SoA = msw_buf->seqArr;

    for (j = 0; j < SIMD512_WIDTH8; ++j) {
        uint8_t* seq1 = refArr[j];
        uint8_t* seq2 = seqArr[j];
        // 处理ref
        for (k = 0; k < refLen[j]; ++k) {
            mySeq1SoA[k * SIMD512_WIDTH8 + j] = (seq1[k] == AMBIG_ ? AMBR : seq1[k]);
        }
        for (; k < maxRefLen; ++k) {
            mySeq1SoA[k * SIMD512_WIDTH8 + j] = 0xFF;
        }
        // 处理seq
        for (k = 0; k < seqLen[j]; ++k) {
            mySeq2SoA[k * SIMD512_WIDTH8 + j] = (seq2[k] == AMBIG_ ? AMBR : seq2[k]);
        }
        for (; k < seqQuantaLen[j]; ++k) {
            mySeq2SoA[k * SIMD512_WIDTH8 + j] = DUMMY5;
        }
        for (; k < maxSeqLen; ++k) {
            mySeq2SoA[k * SIMD512_WIDTH8 + j] = 0xFF;
        }
    }

    const mem_opt_t* opt = w->opt;
    // 利用smid指令计算
    ksw_align_avx512_u8(opt->a, -1 * opt->b, opt->o_ins, opt->e_ins, opt->o_del, opt->e_del, msw_buf, mySeq1SoA, mySeq2SoA, maxRefLen, maxSeqLen,
                        xtraA, refLen, alns, 0);
    // 保存结果
    for (i = startIdx, j = 0; i < endIdx; ++i, ++j) {
        matesw_data_t* task = kv_A(w->msw_tasks8, i);
        task->aln = alns[j];
        free(refArr[j]);
    }
}

static void worker_calc_matesw16(void* data, int i, int tid) {}

// 最后再计算并生成sam数据
static void workder_gen_sam(void* data, int i, int tid) {
    mem_worker_t* w = (mem_worker_t*)data;
    free(w->regs[i << 1 | 0].a);
    free(w->regs[i << 1 | 1].a);
}

// 划分matesw任务
static void gather_matesw_task(mem_worker_t* w, matesw_data_v** msw_arr, matesw_ptr_v* tasks) {
    tasks->n = 0;
    int i = 0, j = 0;
    for (i = 0; i < w->opt->n_threads; ++i) {
        for (j = 0; j < msw_arr[i]->n; ++j)
            kv_push(matesw_data_t*, *tasks, &kv_A(*msw_arr[i], j));
    }
}

// 更新stats
static void update_mem_stats(mem_worker_t* w) {
    int i = 0, max_seq_len = 0, max_ref_len = 0;
    for (i = 0; i < w->opt->n_threads; ++i) {
        max_seq_len = max_(max_seq_len, w->mem_stats[i].max_seq_len);
        max_ref_len = max_(max_ref_len, w->mem_stats[i].max_msw_ref_len);
    }
    int quanta = (max_seq_len + 16 - 1) / 16;  // based on SSE-8 bit lane
    quanta *= 16;
    max_seq_len = quanta + 1;
    for (i = 0; i < w->opt->n_threads; ++i) {
        w->mem_stats[i].max_seq_len = max_seq_len;
        w->mem_stats[i].max_msw_ref_len = max_ref_len;
    }
}

// 开辟缓冲区
static void alloc_update_cache_avx512(mem_worker_t* w) {
    int i = 0;
    for (i = 0; i < w->opt->n_threads; ++i) {
        matesw_buf_t* b = &w->msw_buf[i];
        // 更新跟ref len有关的缓冲区
        if (b->ref_len < w->mem_stats[i].max_msw_ref_len) {
            b->ref_len = w->mem_stats[i].max_msw_ref_len;
            if (b->refArr) _mm_free(b->refArr);
            if (b->rowMax) _mm_free(b->rowMax);
            b->refArr = (uint8_t*)_mm_malloc(b->ref_len * SIMD512_WIDTH8 * sizeof(uint8_t), 64);
            b->rowMax = (uint8_t*)_mm_malloc(b->ref_len * SIMD512_WIDTH8 * sizeof(uint8_t), 64);
        }
        // 更新跟seq len有关的缓冲区
        if (b->seq_len < w->mem_stats[i].max_seq_len) {
            b->seq_len = w->mem_stats[i].max_seq_len;
            if (b->seqArr) _mm_free(b->seqArr);
            if (b->H0) _mm_free(b->H0);
            if (b->H1) _mm_free(b->H1);
            if (b->Hmax) _mm_free(b->Hmax);
            if (b->F) _mm_free(b->F);
            b->seqArr = (uint8_t*)_mm_malloc(b->seq_len * SIMD512_WIDTH8 * sizeof(uint8_t), 64);
            b->H0 = (uint8_t*)_mm_malloc(b->seq_len * SIMD512_WIDTH8 * sizeof(uint8_t), 64);
            b->H1 = (uint8_t*)_mm_malloc(b->seq_len * SIMD512_WIDTH8 * sizeof(uint8_t), 64);
            b->Hmax = (uint8_t*)_mm_malloc(b->seq_len * SIMD512_WIDTH8 * sizeof(uint8_t), 64);
            b->F = (uint8_t*)_mm_malloc(b->seq_len * SIMD512_WIDTH8 * sizeof(uint8_t), 64);
        }
    }
}

// 针对pair end数据，生成sam的过程
void gen_paired_sam(mem_worker_t* w) {
    int i = 0;
    for (i = 0; i < w->opt->n_threads; ++i) {
        w->matesw_arr8[i]->n = 0; // 清空之前的数据
        w->matesw_arr16[i]->n = 0;
    }
    if (w->opt->flag & MEM_F_NO_RESCUE) {
        kt_for(w->opt->n_threads, worker_sam, w, w->n_reads >> 1);  // generate alignment
    } else {
        // 1. 计算哪些read需要matesw
        PROF_START(get_matesw_data);
        kt_for(w->opt->n_threads, worker_matesw_data, w, w->n_reads >> 1);
        PROF_END(gprof[G_get_matesw_data], get_matesw_data);
        // 更新stats
        PROF_START(update_stats_cache);
        update_mem_stats(w);
        // 开辟缓冲区
        alloc_update_cache_avx512(w);
        PROF_END(gprof[G_update_stats_cache], update_stats_cache);
        // 2. matesw计算过程
        PROF_START(gather_matesw_task);
        gather_matesw_task(w, w->matesw_arr8, &w->msw_tasks8);
        gather_matesw_task(w, w->matesw_arr16, &w->msw_tasks16);
        PROF_END(gprof[G_gather_matesw_task], gather_matesw_task);
        PROF_START(calc_matesw);
        if (w->msw_tasks8.n > 0)
            kt_for(w->opt->n_threads, worker_calc_matesw_avx512_u8, w, (w->msw_tasks8.n + SIMD512_WIDTH8 - 1) / SIMD512_WIDTH8);
        if (w->msw_tasks16.n > 0)
            kt_for(w->opt->n_threads, worker_calc_matesw16, w, (w->msw_tasks16.n + SIMD512_WIDTH16 - 1) / SIMD512_WIDTH16);
        PROF_END(gprof[G_calc_matesw], calc_matesw);
        // 3. 
        kt_for(w->opt->n_threads, workder_gen_sam, w, w->n_reads >> 1);
    }
    fprintf(stderr, "zzh %d : 8: %ld 16: %ld\n", i, w->msw_tasks8.n, w->msw_tasks16.n);
}