// File: chhylp123[P]hifiasm/Correct.cpp
// Function: cigar_gen_by_chain_adv(overlap_region*, Candidates_list*, long, long, ul_ov_t*, long, unsigned long, ul_idx_t const*, hpc_t*, All_reads*, char*, UC_Read*, bit_extz_t*, overlap_region*, double, long, unsigned long, long)
void cigar_gen_by_chain_adv(overlap_region *z, Candidates_list *cl, int64_t ch_idx, int64_t ch_n,
ul_ov_t *ov, int64_t on, uint64_t wl, const ul_idx_t *uref, hpc_t *hpc_g, All_reads *rref, char* qstr, 
UC_Read *tu, bit_extz_t *exz, overlap_region *aux_o, double e_rate, int64_t ql, uint64_t rid, int64_t h_khit)
{
    if(on <= 0) return;
    int64_t i, tl, id = z->y_id, m; 
    k_mer_hit *ch_a = cl->list + ch_idx;
    if(hpc_g) tl = hpc_len(*hpc_g, id);
    else if(uref) tl = uref->ug->u.a[id].len;
    else tl = Get_READ_LENGTH((*rref), id);
    // fprintf(stderr, "\n[M::%s::rid->%ld] utg%.6dl(%c), z::[%u, %u)\n", 
    // __func__, rid, (int32_t)z->y_id+1, "+-"[z->y_pos_strand],  z->x_pos_s, z->x_pos_e+1);
    on = fusion_chain_ovlp(z, ch_a, ch_n, ov, on, wl, ql, tl);
    aux_o->w_list.n = aux_o->w_list.c.n = 0; 
    aux_o->y_id = z->y_id; aux_o->y_pos_strand = z->y_pos_strand;
    aux_o->x_pos_s = z->x_pos_s; aux_o->x_pos_e = z->x_pos_e;
    aux_o->y_pos_s = z->y_pos_s; aux_o->y_pos_e = z->y_pos_e;

    
    for (i = 0; i < on; i++) {
        // if(aux_o->y_id == 109111) {
        //     fprintf(stderr, "[M::%s::i->%ld] ovq::[%u, %u), ovt::[%u, %u), hits::[%d, %d)\n", __func__, i, 
        //                                 ov->qs, ov->qe, ov->ts, ov->te,
        //                                 (ov->qn!=((uint32_t)-1))?(int32_t)ov->qn:-1, (int32_t)ov->tn);
        // }
        assert((i<=0)||(ov[i].qs>ov[i-1].qe));
        ovlp_base_aln(z, ch_a, ch_n, &(ov[i]), wl, uref, hpc_g, rref, qstr, tu, exz, aux_o, e_rate, ql, tl, rid);
    }

    int64_t aux_n = aux_o->w_list.n;
    ///for debug
    // if(aux_o->y_id == 109111) {
    //     for (i = 0; i < ((int64_t)aux_o->w_list.n); i++) {
    //         fprintf(stderr, "-0-[aln::i->%ld::ql->%d] q::[%d, %d), t::[%d, %d), err::%d, clen::%u, extra_end::%d, mode::%d\n", i, 
    //                     aux_o->w_list.a[i].x_end+1-aux_o->w_list.a[i].x_start,
    //                     aux_o->w_list.a[i].x_start, aux_o->w_list.a[i].x_end+1, 
    //                     aux_o->w_list.a[i].y_start, aux_o->w_list.a[i].y_end+1, 
    //                     aux_o->w_list.a[i].error, aux_o->w_list.a[i].clen, 
    //                     aux_o->w_list.a[i].extra_end, aux_o->w_list.a[i].error_threshold);
    //     }
    // }

    for (i = 0; i < aux_n; i++) {
        if(!(is_ualn_win(aux_o->w_list.a[i]))) continue;
        //will overwrite ch_a; does not matter
        rechain_aln(z, cl, aux_o, i, wl, uref, hpc_g, rref, qstr, tu, exz, e_rate, ql, tl, h_khit, rid);
    }

    ///for debug
    // if(aux_o->y_id == 109111) {
    //     for (i = 0; i < ((int64_t)aux_o->w_list.n); i++) {
    //         fprintf(stderr, "-2-[aln::i->%ld::ql->%d] q::[%d, %d), t::[%d, %d), err::%d, clen::%u, mode::%d\n", i, 
    //                     aux_o->w_list.a[i].x_end+1-aux_o->w_list.a[i].x_start,
    //                     aux_o->w_list.a[i].x_start, aux_o->w_list.a[i].x_end+1, 
    //                     aux_o->w_list.a[i].y_start, aux_o->w_list.a[i].y_end+1, 
    //                     aux_o->w_list.a[i].error, aux_o->w_list.a[i].clen, aux_o->w_list.a[i].error_threshold);
    //     }
    // }

    if(((int64_t)aux_o->w_list.n) > aux_n) {
        for (i = m = 0; i < ((int64_t)aux_o->w_list.n); i++) {
            if((i < aux_n) && (is_ualn_win(aux_o->w_list.a[i]))) continue;
            aux_o->w_list.a[m++] = aux_o->w_list.a[i];
        }
        aux_o->w_list.n = m;
        radix_sort_window_list_xs_srt(aux_o->w_list.a, aux_o->w_list.a+aux_o->w_list.n);
    }

    ///update z by aux_o
    update_overlap_region(z, aux_o, ql, tl);

    // debug_overlap_region(aux_o, qstr, tu, uref, hpc_g, rref);


    // ch_a = cl->list + ch_idx; //update
    // for (i = 0; i < wn; i++) z->w_list.a[i].clen = 0;///clean cigar
    // if(on > 1) {
    //     fprintf(stderr, "[M::%s::] rid::%lu, on::%ld\n", __func__, rid, on);
    // }
    // if(z->y_id == 126) prt_k_mer_hit(ch_a, ch_n);
    // for (i = ch_i = 0; i < on; i++) {
    //     assert((i<=0)||(ov[i].qs > ov[i-1].qe));
    //     ov[i].sec = 16;///do not know the aln type
    //     ch_i = sub_base_aln(z, dp, ch_a, ch_n, pe, ov[i].qs, ov[i].qe, wl, uref, hpc_g, rref, qstr, tu, exz, e_rate, ql, tl, ch_i, rid);
    //     pe = ov[i].qe;
    // }
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xd8, %rsp
movq 0x60(%rbp), %rax
movq 0x58(%rbp), %rax
movq 0x50(%rbp), %rax
movq 0x48(%rbp), %rax
movq 0x40(%rbp), %rax
movq 0x38(%rbp), %rax
movq 0x30(%rbp), %rax
movq 0x28(%rbp), %rax
movq 0x20(%rbp), %rax
movq 0x18(%rbp), %rax
movq 0x10(%rbp), %rax
movq %rdi, -0x30(%rbp)
movq %rsi, -0x38(%rbp)
movq %rdx, -0x40(%rbp)
movq %rcx, -0x48(%rbp)
movq %r8, -0x50(%rbp)
movq %r9, -0x58(%rbp)
movsd %xmm0, -0x60(%rbp)
cmpq $0x0, -0x58(%rbp)
jg 0x677e9
jmp 0x67c9f
movq -0x30(%rbp), %rax
movl 0x10(%rax), %eax
movq %rax, -0x78(%rbp)
movq -0x38(%rbp), %rax
movq (%rax), %rax
movq -0x40(%rbp), %rcx
shlq $0x4, %rcx
addq %rcx, %rax
movq %rax, -0x88(%rbp)
cmpq $0x0, 0x20(%rbp)
je 0x67838
movq 0x20(%rbp), %rax
movq (%rax), %rax
movq 0x10(%rax), %rax
imulq $0x28, -0x78(%rbp), %rcx
addq %rcx, %rax
movl (%rax), %eax
andl $0x7fffffff, %eax       # imm = 0x7FFFFFFF
sarl %eax
cltq
movq %rax, -0x70(%rbp)
jmp 0x67877
cmpq $0x0, 0x18(%rbp)
je 0x67861
movq 0x18(%rbp), %rax
movq (%rax), %rax
movq 0x10(%rax), %rax
imulq $0x28, -0x78(%rbp), %rcx
addq %rcx, %rax
movl (%rax), %eax
andl $0x7fffffff, %eax       # imm = 0x7FFFFFFF
movl %eax, %eax
movq %rax, -0x70(%rbp)
jmp 0x67875
movq 0x28(%rbp), %rax
movq 0x18(%rax), %rax
movq -0x78(%rbp), %rcx
movq (%rax,%rcx,8), %rax
movq %rax, -0x70(%rbp)
jmp 0x67877
movq -0x30(%rbp), %rdi
movq -0x88(%rbp), %rsi
movq -0x48(%rbp), %rdx
movq -0x50(%rbp), %rcx
movq -0x58(%rbp), %r8
movq 0x10(%rbp), %r9
movq 0x50(%rbp), %r10
movq -0x70(%rbp), %rax
movq %r10, (%rsp)
movq %rax, 0x8(%rsp)
callq 0x63b10
movq %rax, -0x58(%rbp)
movq 0x48(%rbp), %rax
movq $0x0, 0x60(%rax)
movq 0x48(%rbp), %rax
movq $0x0, 0x48(%rax)
movq -0x30(%rbp), %rax
movl 0x10(%rax), %ecx
movq 0x48(%rbp), %rax
movl %ecx, 0x10(%rax)
movq -0x30(%rbp), %rax
movl 0x1c(%rax), %ecx
movq 0x48(%rbp), %rax
movl %ecx, 0x1c(%rax)
movq -0x30(%rbp), %rax
movl 0x4(%rax), %ecx
movq 0x48(%rbp), %rax
movl %ecx, 0x4(%rax)
movq -0x30(%rbp), %rax
movl 0x8(%rax), %ecx
movq 0x48(%rbp), %rax
movl %ecx, 0x8(%rax)
movq -0x30(%rbp), %rax
movl 0x14(%rax), %ecx
movq 0x48(%rbp), %rax
movl %ecx, 0x14(%rax)
movq -0x30(%rbp), %rax
movl 0x18(%rax), %ecx
movq 0x48(%rbp), %rax
movl %ecx, 0x18(%rax)
movq $0x0, -0x68(%rbp)
movq -0x68(%rbp), %rax
cmpq -0x58(%rbp), %rax
jge 0x67a42
movb $0x1, %al
cmpq $0x0, -0x68(%rbp)
movb %al, -0x91(%rbp)
jle 0x6796b
movq -0x50(%rbp), %rax
imulq $0x1c, -0x68(%rbp), %rcx
addq %rcx, %rax
movl 0x4(%rax), %eax
movq -0x50(%rbp), %rcx
movq -0x68(%rbp), %rdx
subq $0x1, %rdx
imulq $0x1c, %rdx, %rdx
addq %rdx, %rcx
cmpl 0x8(%rcx), %eax
seta %al
movb %al, -0x91(%rbp)
movb -0x91(%rbp), %al
testb $0x1, %al
jne 0x67977
jmp 0x67979
jmp 0x67998
leaq 0x31c8f5(%rip), %rdi    # 0x384275
leaq 0x31a994(%rip), %rsi    # 0x38231b
movl $0x4398, %edx           # imm = 0x4398
leaq 0x31c900(%rip), %rcx    # 0x384293
callq 0x2130
movq -0x30(%rbp), %rdi
movq -0x88(%rbp), %rsi
movq -0x48(%rbp), %rdx
movq -0x50(%rbp), %rcx
imulq $0x1c, -0x68(%rbp), %rax
addq %rax, %rcx
movq 0x10(%rbp), %r8
movq 0x18(%rbp), %r9
movq 0x20(%rbp), %rax
movq %rax, -0xa8(%rbp)
movq 0x28(%rbp), %r13
movq 0x30(%rbp), %r12
movq 0x38(%rbp), %r15
movq 0x40(%rbp), %r14
movq 0x48(%rbp), %rbx
movsd -0x60(%rbp), %xmm0
movq 0x50(%rbp), %r11
movq -0x70(%rbp), %r10
movq 0x58(%rbp), %rax
movq %rax, -0xa0(%rbp)
movq -0xa8(%rbp), %rax
movq %rax, (%rsp)
movq -0xa0(%rbp), %rax
movq %r13, 0x8(%rsp)
movq %r12, 0x10(%rsp)
movq %r15, 0x18(%rsp)
movq %r14, 0x20(%rsp)
movq %rbx, 0x28(%rsp)
movq %r11, 0x30(%rsp)
movq %r10, 0x38(%rsp)
movq %rax, 0x40(%rsp)
callq 0x64220
movq -0x68(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x68(%rbp)
jmp 0x67920
movq 0x48(%rbp), %rax
movq 0x48(%rax), %rax
movq %rax, -0x90(%rbp)
movq $0x0, -0x68(%rbp)
movq -0x68(%rbp), %rax
cmpq -0x90(%rbp), %rax
jge 0x67b61
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x68(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
movswl 0x14(%rax), %eax
cmpl $0x7fff, %eax           # imm = 0x7FFF
jne 0x67abd
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x68(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
cmpl $0x0, 0x1c(%rax)
jne 0x67abd
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x68(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
movswl 0x12(%rax), %eax
cmpl $0x0, %eax
jl 0x67ac2
jmp 0x67b50
movq -0x30(%rbp), %rdi
movq -0x38(%rbp), %rsi
movq 0x48(%rbp), %rdx
movq -0x68(%rbp), %rcx
movq 0x10(%rbp), %r8
movq 0x18(%rbp), %r9
movq 0x20(%rbp), %rax
movq %rax, -0xb8(%rbp)
movq 0x28(%rbp), %r13
movq 0x30(%rbp), %r12
movq 0x38(%rbp), %r15
movq 0x40(%rbp), %r14
movsd -0x60(%rbp), %xmm0
movq 0x50(%rbp), %rbx
movq -0x70(%rbp), %r11
movq 0x60(%rbp), %r10
movq 0x58(%rbp), %rax
movq %rax, -0xb0(%rbp)
movq -0xb8(%rbp), %rax
movq %rax, (%rsp)
movq -0xb0(%rbp), %rax
movq %r13, 0x8(%rsp)
movq %r12, 0x10(%rsp)
movq %r15, 0x18(%rsp)
movq %r14, 0x20(%rsp)
movq %rbx, 0x28(%rsp)
movq %r11, 0x30(%rsp)
movq %r10, 0x38(%rsp)
movq %rax, 0x40(%rsp)
callq 0x66760
movq -0x68(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x68(%rbp)
jmp 0x67a59
movq 0x48(%rbp), %rax
movq 0x48(%rax), %rax
cmpq -0x90(%rbp), %rax
jle 0x67c8a
movq $0x0, -0x80(%rbp)
movq $0x0, -0x68(%rbp)
movq -0x68(%rbp), %rax
movq 0x48(%rbp), %rcx
cmpq 0x48(%rcx), %rax
jge 0x67c5a
movq -0x68(%rbp), %rax
cmpq -0x90(%rbp), %rax
jge 0x67bfa
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x68(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
movswl 0x14(%rax), %eax
cmpl $0x7fff, %eax           # imm = 0x7FFF
jne 0x67bfa
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x68(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
cmpl $0x0, 0x1c(%rax)
jne 0x67bfa
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x68(%rbp), %rcx
shlq $0x5, %rcx
addq %rcx, %rax
movswl 0x12(%rax), %eax
cmpl $0x0, %eax
jge 0x67bfa
jmp 0x67c49
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rcx
movq -0x68(%rbp), %rax
shlq $0x5, %rax
addq %rax, %rcx
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x80(%rbp), %rdx
movq %rdx, %rsi
addq $0x1, %rsi
movq %rsi, -0x80(%rbp)
shlq $0x5, %rdx
addq %rdx, %rax
movq (%rcx), %rdx
movq %rdx, (%rax)
movq 0x8(%rcx), %rdx
movq %rdx, 0x8(%rax)
movq 0x10(%rcx), %rdx
movq %rdx, 0x10(%rax)
movq 0x18(%rcx), %rcx
movq %rcx, 0x18(%rax)
movq -0x68(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x68(%rbp)
jmp 0x67b86
movq -0x80(%rbp), %rcx
movq 0x48(%rbp), %rax
movq %rcx, 0x48(%rax)
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rdi
movq 0x48(%rbp), %rax
movq 0x58(%rax), %rsi
movq 0x48(%rbp), %rax
movq 0x48(%rax), %rax
shlq $0x5, %rax
addq %rax, %rsi
callq 0x2f3b0
movq -0x30(%rbp), %rdi
movq 0x48(%rbp), %rsi
movq 0x50(%rbp), %rdx
movq -0x70(%rbp), %rcx
callq 0x673f0
addq $0xd8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nopw %cs:(%rax,%rax)