/* The MIT License

   Copyright (c) 2025-     Zhonghai Zhang (ICT)

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <time.h>
#include <unistd.h>
#include <zlib.h>

#include "bntseq.h"
#include "bwa.h"
#include "bwt.h"
#include "rle.h"
#include "rope.h"
#include "utils.h"
#include "kvec.h"
#include "hyb_idx.h"


#ifdef _DIVBWT
#include "divsufsort.h"
#endif

#ifdef USE_MALLOC_WRAPPERS
#include "malloc_wrap.h"
#endif

int bwa_bwt2fullbytesa(int argc, char* argv[])  // the "bwt2bytesa" command
{
    bwt_t* bwt;
    if (optind + 2 > argc) {
        fprintf(stderr, "Usage: %s bwt2bytesa <in.bwt> <out.bytesa>\n", PROG_NAME);
        return 1;
    }
    bwt = bwt_restore_bwt(argv[optind]);
    bwt_cal_byte_sa(bwt);
    _store_data_to_file(argv[optind + 1], bwt->byte_sa, sizeof(bwtint_t), SA_BYTES(bwt->n_sa) >> 3);
    return 0;
}

// extract suffix array from non-sampled suffix array
int bwa_extract_sa(int argc, char* argv[]) {
    bwt_t* bwt;
    int c, sa_intv = 32;
    while ((c = getopt(argc, argv, "i:")) >= 0) {
        switch (c) {
        case 'i':
            sa_intv = atoi(optarg);
            break;
        default:
            return 1;
        }
    }
    if (optind + 3 > argc) {
        fprintf(stderr, "Usage: bwa extractsa [-i %d] <in.bwt> <in.full_bytesa> <out.sa>\n", sa_intv);
        return 1;
    }
    bwt = bwt_restore_bwt(argv[optind]);

    fprintf(stderr, "bwt seq_len %ld, intv: %d\n", bwt->seq_len, sa_intv);
    //exit(0);

    _load_file_to_data(argv[optind + 1], bwt->byte_sa);

    if (bwt->sa) free(bwt->sa);
    bwt->sa_intv = sa_intv;
    bwt->n_sa = (bwt->seq_len + sa_intv) / sa_intv;
    bwt->sa = (bwtint_t*)calloc(bwt->n_sa, sizeof(bwtint_t));
    uint64_t i;
    for (i = 0; i < bwt->seq_len; ++i) {
        if (i % sa_intv == 0)
            bwt->sa[i / sa_intv] = bwt_get_sa(bwt->byte_sa, i);
    }
    if (i % sa_intv == 0)
        bwt->sa[i / sa_intv] = bwt_get_sa(bwt->byte_sa, i);
    bwt->sa[0] = (bwtint_t)-1;  // before this line, bwt->sa[0] = bwt->seq_len
    // bwt_cal_sa(bwt, sa_intv);
    bwt_dump_sa(argv[optind + 2], bwt);
    // bwt_destroy(bwt);
    return 0;
}

// extract byte suffix array from non-sampled suffix array
int bwa_extract_byte_sa(int argc, char* argv[]) {
    bwt_t* bwt;
    int c, sa_intv = 32;
    while ((c = getopt(argc, argv, "i:")) >= 0) {
        switch (c) {
        case 'i':
            sa_intv = atoi(optarg);
            break;
        default:
            return 1;
        }
    }
    if (optind + 3 > argc) {
        fprintf(stderr, "Usage: bwa extractbytesa [-i %d] <in.bwt> <in.full_bytesa> <out.bytesa>\n", sa_intv);
        return 1;
    }
    bwt = bwt_restore_bwt(argv[optind]);

    // fprintf(stderr, "bwt seq_len %ld, intv: %d\n", bwt->seq_len, sa_intv);
    // exit(0);

    uint8_t *full_byte_sa = NULL;
    _load_file_to_data(argv[optind + 1], full_byte_sa);

    bwt->sa_intv = sa_intv;
    bwt->n_sa = (bwt->seq_len + sa_intv) / sa_intv;
    bwt->byte_sa = (uint8_t*)calloc(SA_BYTES(bwt->n_sa), 1);
    uint64_t i;
    for (i = 0; i < bwt->seq_len; ++i) {
        if (i % sa_intv == 0)
            bwt_set_sa(bwt->byte_sa, i / sa_intv, bwt_get_sa(full_byte_sa, i));
    }
    if (i % sa_intv == 0)
        bwt_set_sa(bwt->byte_sa, i / sa_intv, bwt_get_sa(full_byte_sa, i));
    bwt_set_sa(bwt->byte_sa, 0, 8589934591);  // before this line, bwt->sa[0] = bwt->seq_len
    bwt_dump_byte_sa(argv[optind + 2], bwt);
    // bwt_destroy(bwt);
    return 0;
}

// 生成所有KMER_LEN长度的序列，字节表示(0A,1C,2G,3T)
void gen_kmer_bits(uint8_t** seq_arr, uint64_t* kmer_arr_size, int kmer_len) {
    uint64_t i;
    uint64_t seq_up_val = (1L << (kmer_len << 1));
    *kmer_arr_size = seq_up_val;
    *seq_arr = (uint8_t*)realloc(*seq_arr, seq_up_val * (uint64_t)kmer_len);
    for (i = 0; i < seq_up_val; ++i) {
        const uint64_t base_idx = i * kmer_len;
        for (int j = kmer_len - 1; j >= 0; --j) {
            (*seq_arr)[base_idx + kmer_len - 1 - j] = (i >> (j << 1)) & 3;
        }
    }
}

void bwt_create_kmer_idx(bwt_t* bwt) {
    uint64_t kmer_arr_size = 0;
    uint8_t* seq_arr = 0;
    bwtintv_t ik, ok[4];
    uint64_t j;
    int i, c1;
    int qlen = 10;
    KmerHash* kh = &bwt->kmer_hash;

    kh->ke10 = (KmerEntryArr*)malloc((1 << (10 << 1)) * sizeof(KmerEntryArr));
    kh->ke11 = (KmerEntry*)malloc((1 << (11 << 1)) * sizeof(KmerEntry));
    kh->ke12 = (KmerEntry*)malloc((1 << (12 << 1)) * sizeof(KmerEntry));
    kh->ke13 = (KmerEntry*)malloc((1 << (13 << 1)) * sizeof(KmerEntry));
    kh->ke14 = (KmerEntry*)malloc((1 << (14 << 1)) * sizeof(KmerEntry));

    // 长度为10的kmer
    gen_kmer_bits(&seq_arr, &kmer_arr_size, 10);
    for (j = 0; j < kmer_arr_size; ++j) {
        uint8_t* q = &seq_arr[j * 10];
        uint8_t* mem_addr = kh->ke10[j].intv_arr;
        bwt_set_intv(bwt, q[0], ik);
        kmer_setval_at(mem_addr, ik, 0);
        // 每次扩展一个碱基
        for (i = 1; i < qlen; ++i) {
            c1 = 3 - q[i];
            bwt_extend(bwt, &ik, ok, 0);
            ik = ok[c1];
            kmer_setval_at(mem_addr, ik, i);
        }
    }
    fprintf(stderr, "Kmer idx for length 10 done.\n");
#define GEN_KMER_FOR_LEN(len)                                                  \
    do {                                                                       \
        gen_kmer_bits(&seq_arr, &kmer_arr_size, (len));                        \
        for (j = 0; j < kmer_arr_size; ++j) {                                  \
            bwtintv_t p = bwt_forward_search(bwt, &seq_arr[j * (len)], (len)); \
            kmer_setval_at(bwt->kmer_hash.ke##len[j].intv_arr, p, 0);          \
        }                                                                      \
        fprintf(stderr, "Kmer idx for length %d done.\n", len);                     \
    } while (0)

    GEN_KMER_FOR_LEN(11);  // 长度11的kmer
    GEN_KMER_FOR_LEN(12);
    GEN_KMER_FOR_LEN(13);
    GEN_KMER_FOR_LEN(14);
    free(seq_arr);
}

int bwa_bwt2kmer(int argc, char* argv[]) {
    bwt_t* bwt;
    if (optind + 2 > argc) {
        fprintf(stderr, "Usage: bwa extractbytesa <in.bwt> <out.kmer>\n");
        return 1;
    }
    bwt = bwt_restore_bwt(argv[optind]);

    bwt_create_kmer_idx(bwt);

    bwt_dump_kmer_idx(argv[optind + 1], &bwt->kmer_hash);

    return 0;
}

int bwa_bwt2hyb(int argc, char* argv[]) {}

// 创建正向的kmer
inline uint64_t build_forward_kmer(const uint8_t* q, int qlen, int kmer_len, int* base_consumed) {
    uint64_t qbit = 0, i;
    qlen = qlen < kmer_len ? qlen : kmer_len;
    for (i = 0; i < qlen; ++i) {
        if (q[i] > 3)
            break;  // 要考虑碱基是N
        qbit |= (uint64_t)q[i] << ((kmer_len - 1 - i) << 1);
    }
    *base_consumed = i;
    return qbit;
}

int hyb_test(int argc, char* argv[]) {
    bwt_t* bwt;
    if (optind + 1 > argc) {
        fprintf(stderr, "Usage: bwa hybtest <idx_prefix>\n");
        return 1;
    }

    char fn[MAX_PATH];
    snprintf(fn, MAX_PATH, "%s.bwt", argv[optind]);

    bwt = bwt_restore_bwt(fn);
    snprintf(fn, MAX_PATH, "%s.hyb.kmer", argv[optind]);
    bwt->kmer_hash = bwt_restore_kmer_idx(fn);

    uint8_t test_seq[14] = {0, 1, 2, 3, 0, 1, 2, 3, 0, 1, 2, 3, 0, 1};  // ACGTACGTACGTAC
    bwtintv_t ok1, ok2;
    ok1 = bwt_forward_search(bwt, test_seq, 14);

    int base_consumed = 0;
    uint64_t qbit = build_forward_kmer(test_seq, 14, 14, &base_consumed);

    bwt_kmer_get(&bwt->kmer_hash, &ok2, qbit, 13);

    fprintf(stderr, "forward search: [%lu, %lu, %lu), kmer idx: [%lu, %lu, %lu)\n", ok1.x[0], ok1.x[1], ok1.x[2], ok2.x[0], ok2.x[1], ok2.x[2]);

    return 0;
}