// File: chhylp123[P]hifiasm/Correct.cpp
// Function: correct_ul_overlap(overlap_region_alloc*, ul_idx_t const*, UC_Read*, Correct_dumy*, UC_Read*, Graph*, Graph*, Cigar_record*, haplotype_evdience_alloc*, Round2_alignment*, kvec_t_u64_warp*, window_list_alloc*, int, int, int*, int*, double, long long, void*)
void correct_ul_overlap(overlap_region_alloc* overlap_list, const ul_idx_t *uref, 
                        UC_Read* g_read, Correct_dumy* dumy, UC_Read* overlap_read, 
                        Graph* g, Graph* DAGCon, Cigar_record* current_cigar, 
                        haplotype_evdience_alloc* hap, Round2_alignment* second_round, 
                        kvec_t_u64_warp* v_idx, window_list_alloc* win_ciagr_buf, 
                        int force_repeat, int is_consensus, int* fully_cov, int* abnormal, 
                        double max_ov_diff_ec, long long winLen, void *km)
{
    
    clear_Correct_dumy(dumy, overlap_list, km);

    Window_Pool w_inf;
    init_Window_Pool(&w_inf, g_read->length, winLen, (int)(1.0/max_ov_diff_ec));
    /**
    uint64_t i;
    for (i = 0; i < overlap_list->length; i++) {
        verify_ul_window_s(&(overlap_list->list[i]), uref, g_read->seq, dumy->overlap_region, max_ov_diff_ec, w_inf.window_length, THRESHOLD_MAX_SIZE, km);
        // align_ul_ed(&(overlap_list->list[i]), uref, NULL, g_read->seq, dumy->overlap_region, max_ov_diff_ec, w_inf.window_length, km);
    }
    **/
   
    
    // recalcate_window(overlap_list, R_INF, g_read, dumy, overlap_read);
    // partition_overlaps(overlap_list, R_INF, g_read, dumy, hap, force_repeat);
    // recalcate_window_ul_advance(overlap_list, uref, g_read, dumy, overlap_read, max_ov_diff_ec, w_inf.window_length, km);
    // recalcate_window_advance(overlap_list, NULL, uref, g_read, dumy, overlap_read, v_idx, w_inf.window_length, max_ov_diff_ec, max_ov_diff_ec);
    /**
    refine_ed_aln(overlap_list, NULL, uref, g_read, dumy, overlap_read, v_idx, w_inf.window_length, max_ov_diff_ec, max_ov_diff_ec);
    **/
    refine_ed_aln_test(overlap_list, NULL, uref, g_read, dumy, overlap_read, v_idx, w_inf.window_length, max_ov_diff_ec, max_ov_diff_ec);
    // fprintf(stderr, "[M::%s-beg] occ[0]->%lu, occ[1]->%lu, occ[2]->%lu, occ[3]->%lu\n", __func__, 
    // ovlp_occ(overlap_list, 0), ovlp_occ(overlap_list, 1), ovlp_occ(overlap_list, 2), ovlp_occ(overlap_list, 3));
    ///after this function, overlap_list is sorted by x_pos_e; used for g_chain
    partition_ul_overlaps_advance(overlap_list, uref, g_read, overlap_read, dumy, hap, force_repeat, max_ov_diff_ec, w_inf.window_length, km);
    // print_ovlp_occ_stat(overlap_list, g_read->length, 1);
    // print_ovlp_occ_stat(overlap_list, g_read->length, 2);
    // fprintf(stderr, "[M::%s-end] occ[0]->%lu, occ[1]->%lu, occ[2]->%lu, occ[3]->%lu\n", __func__, 
    // ovlp_occ(overlap_list, 0), ovlp_occ(overlap_list, 1), ovlp_occ(overlap_list, 2), ovlp_occ(overlap_list, 3));
    // debug_phasing_status(overlap_list, uref->ug, 0, hap, g_read, 20, 1176);
    // debug_phasing_status(overlap_list, uref->ug, 0, hap, g_read, 20, 1167);
    // debug_phasing_status(overlap_list, uref->ug, 0, hap, g_read, 20, 1170);
    /**
    
    
    if(is_consensus)
    {
        generate_consensus(overlap_list, R_INF, g_read, dumy, g, DAGCon, current_cigar, second_round);
    }


    (*fully_cov) = check_if_fully_covered(overlap_list, R_INF, g_read, dumy, g, abnormal);
    **/
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x90, %rsp
movq 0x68(%rbp), %rax
movq 0x60(%rbp), %rax
movq 0x58(%rbp), %rax
movq 0x50(%rbp), %rax
movl 0x48(%rbp), %eax
movl 0x40(%rbp), %eax
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, -0x8(%rbp)
movq %rsi, -0x10(%rbp)
movq %rdx, -0x18(%rbp)
movq %rcx, -0x20(%rbp)
movq %r8, -0x28(%rbp)
movq %r9, -0x30(%rbp)
movsd %xmm0, -0x38(%rbp)
movq -0x20(%rbp), %rdi
movq -0x8(%rbp), %rsi
movq 0x68(%rbp), %rdx
callq 0x4c460
movq -0x18(%rbp), %rax
movq 0x8(%rax), %rsi
movq 0x60(%rbp), %rdx
movsd 0x335925(%rip), %xmm0   # 0x382000
divsd -0x38(%rbp), %xmm0
cvttsd2si %xmm0, %eax
movslq %eax, %rcx
leaq -0x70(%rbp), %rdi
callq 0x9f470
movq -0x8(%rbp), %rdi
movq -0x10(%rbp), %rdx
movq -0x18(%rbp), %rcx
movq -0x20(%rbp), %r8
movq -0x28(%rbp), %r9
movq 0x30(%rbp), %r10
movq -0x68(%rbp), %rax
movsd -0x38(%rbp), %xmm0
movsd -0x38(%rbp), %xmm1
xorl %esi, %esi
movq %r10, (%rsp)
movq %rax, 0x8(%rsp)
callq 0xa4e00
movq -0x8(%rbp), %rdi
movq -0x10(%rbp), %rsi
movq -0x18(%rbp), %rdx
movq -0x28(%rbp), %rcx
movq -0x20(%rbp), %r8
movq 0x20(%rbp), %r9
movl 0x40(%rbp), %r11d
movsd -0x38(%rbp), %xmm0
movq -0x68(%rbp), %r10
movq 0x68(%rbp), %rax
movl %r11d, (%rsp)
movq %r10, 0x8(%rsp)
movq %rax, 0x10(%rsp)
callq 0x4b540
addq $0x90, %rsp
popq %rbp
retq
nopl (%rax,%rax)