// File: chhylp123[P]hifiasm/Overlaps.cpp
// Function: output_bp_graph_adv(asg_t*, ma_sub_t*, char*, ma_hit_t_alloc*, ma_hit_t_alloc*, long long, float, long long, R_to_U*, float, float, int, int, int, bub_label_t*, ug_opt_t*)
void output_bp_graph_adv(asg_t *sg, ma_sub_t* coverage_cut, char* output_file_name, 
ma_hit_t_alloc* sources, ma_hit_t_alloc* reverse_sources, 
long long tipsLen, float tip_drop_ratio, long long stops_threshold, 
R_to_U* ruIndex, float chimeric_rate, float drop_ratio, int max_hang, int min_ovlp, 
int gap_fuzz, bub_label_t* b_mask_t, ug_opt_t *opt)
{ 
    hic_clean(sg);

    kvec_asg_arc_t_warp new_rtg_edges, d_edges;
    kv_init(new_rtg_edges.a); kv_init(d_edges.a);
    ma_ug_t *ug = NULL;
    ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);

    new_rtg_edges.a.n = 0;
    ma_ug_seq(ug, sg, coverage_cut, sources, &new_rtg_edges, max_hang, min_ovlp, &d_edges, 1);///polish

    new_rtg_edges.a.n = 0;
    hap_cov_t *cov = NULL;
    asg_t *copy_sg = copy_read_graph(sg);
    ma_ug_t *copy_ug = copy_untig_graph(ug);
    /*******************************for debug************************************/
    adjust_utg_by_primary(&copy_ug, copy_sg, TRIO_THRES, sources, reverse_sources, coverage_cut, 
    tipsLen, tip_drop_ratio, stops_threshold, ruIndex, chimeric_rate, drop_ratio, 
    max_hang, min_ovlp, &new_rtg_edges, &cov, b_mask_t, 1, 0/**1**/);
    // adjust_utg_advance(copy_sg, copy_ug, reverse_sources, ruIndex, b_mask_t);
    // get_utg_ovlp(&copy_ug, copy_sg, sources, reverse_sources, coverage_cut, 
    // ruIndex, max_hang, min_ovlp, &new_rtg_edges, b_mask_t, NULL);
    // exit(1);
    /*******************************for debug************************************/
    print_utg(&copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, 
    min_ovlp, &new_rtg_edges);
    ma_ug_destroy(copy_ug);
    asg_destroy(copy_sg);

    // gen_bp_phasing(opt, &(cov->t_ch->k_trans), ug, sg);
    clean_u_trans_t_idx(&(cov->t_ch->k_trans), ug, sg);
    set_trio_flag_by_cov(ug, sg, cov);

    //for debug
    // char* gfa_name = (char*)malloc(strlen(output_file_name)+50);
    // sprintf(gfa_name, "%s.pre.clean_d_utg.noseq.gfa", output_file_name);
    // FILE* output_file = fopen(gfa_name, "w");
    // ma_ug_print(ug, sg, coverage_cut, sources, ruIndex, "utg", output_file);
    // fclose(output_file);
    // free(gfa_name);
    // exit(1);
    //for debug

    
    // print_untig_by_read(copy_ug, "m64011_190830_220126/88867583/ccs", 603738, NULL, NULL, "sb");
    
    ///debug_gfa_space(ug, cov);

    
    // print_r_het(cov, R_INF.trio_flag, "out-1");
    // print_debug_gfa(ug, sg, coverage_cut, output_file_name, sources, ruIndex);

    destory_hap_cov_t(&cov);
    ma_ug_destroy(ug);
    kv_destroy(new_rtg_edges.a);

    asg_arc_t* av = NULL;
    uint32_t v, w, k, i, nv;
    for (i = 0; i < d_edges.a.n; i++)
    {
        v = d_edges.a.a[i].ul>>32; 
        w = d_edges.a.a[i].v;
        av = asg_arc_a(sg, v);
        nv = asg_arc_n(sg, v);
        for (k = 0; k < nv; k++)
        {
            if(av[k].del) continue;
            if(av[k].v == w) 
            {
                av[k].del = 1;
                break;
            }
        }
    }    
    kv_destroy(d_edges.a);
    asg_cleanup(sg);


    output_trio_unitig_graph(sg, coverage_cut, output_file_name, FATHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 
    0.05, 0.9, max_hang, min_ovlp, gap_fuzz, 0, b_mask_t, NULL, NULL, NULL);
    output_trio_unitig_graph(sg, coverage_cut, output_file_name, MOTHER, sources, reverse_sources, (asm_opt.max_short_tip*2), 0.15, 3, ruIndex, 
    0.05, 0.9, max_hang, min_ovlp, gap_fuzz, 0, b_mask_t, NULL, NULL, NULL);
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x118, %rsp            # imm = 0x118
movq 0x40(%rbp), %rax
movq 0x38(%rbp), %rax
movl 0x30(%rbp), %eax
movl 0x28(%rbp), %eax
movl 0x20(%rbp), %eax
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)
movss %xmm0, -0x5c(%rbp)
movss %xmm1, -0x60(%rbp)
movss %xmm2, -0x64(%rbp)
movq -0x30(%rbp), %rdi
callq 0xfd5f0
movq $0x0, -0x80(%rbp)
movq $0x0, -0x88(%rbp)
movq $0x0, -0x78(%rbp)
movq $0x0, -0xa0(%rbp)
movq $0x0, -0xa8(%rbp)
movq $0x0, -0x98(%rbp)
movq $0x0, -0xb0(%rbp)
movq -0x30(%rbp), %rdi
xorl %esi, %esi
callq 0xe7ae0
movq %rax, -0xb0(%rbp)
movq $0x0, -0x88(%rbp)
movq -0xb0(%rbp), %rdi
movq -0x30(%rbp), %rsi
movq -0x38(%rbp), %rdx
movq -0x48(%rbp), %rcx
movl 0x20(%rbp), %r9d
movl 0x28(%rbp), %r10d
leaq -0x88(%rbp), %r8
leaq -0xa8(%rbp), %rax
movl %r10d, (%rsp)
movq %rax, 0x8(%rsp)
movl $0x1, 0x10(%rsp)
callq 0xed140
movq $0x0, -0x88(%rbp)
movq $0x0, -0xb8(%rbp)
movq -0x30(%rbp), %rdi
callq 0x10b830
movq %rax, -0xc0(%rbp)
movq -0xb0(%rbp), %rdi
callq 0x10ba70
movq %rax, -0xc8(%rbp)
movq -0xc0(%rbp), %rsi
movq -0x48(%rbp), %rdx
movq -0x50(%rbp), %rcx
movq -0x38(%rbp), %r8
movq -0x58(%rbp), %r9
movss -0x5c(%rbp), %xmm1
movq 0x10(%rbp), %r12
movq 0x18(%rbp), %r15
movss -0x60(%rbp), %xmm2
movss -0x64(%rbp), %xmm3
movl 0x20(%rbp), %r14d
movl 0x28(%rbp), %ebx
movq 0x38(%rbp), %rax
leaq -0xc8(%rbp), %rdi
movss 0x2728cb(%rip), %xmm0   # 0x38689c
leaq -0x88(%rbp), %r11
leaq -0xb8(%rbp), %r10
xorl %r13d, %r13d
movq %r12, (%rsp)
movq %r15, 0x8(%rsp)
movl %r14d, 0x10(%rsp)
movl %ebx, 0x18(%rsp)
movq %r11, 0x20(%rsp)
movq %r10, 0x28(%rsp)
movq %rax, 0x30(%rsp)
movl $0x1, 0x38(%rsp)
movl $0x0, 0x40(%rsp)
callq 0x10bde0
movq -0xc0(%rbp), %rsi
movq -0x38(%rbp), %rdx
movq -0x40(%rbp), %rcx
movq -0x48(%rbp), %r8
movq 0x18(%rbp), %r9
movl 0x20(%rbp), %r11d
movl 0x28(%rbp), %r10d
leaq -0xc8(%rbp), %rdi
leaq -0x88(%rbp), %rax
movl %r11d, (%rsp)
movl %r10d, 0x8(%rsp)
movq %rax, 0x10(%rsp)
callq 0xfcd70
movq -0xc8(%rbp), %rdi
callq 0xcd6f0
movq -0xc0(%rbp), %rdi
callq 0xcd170
movq -0xb8(%rbp), %rax
movq 0xa8(%rax), %rdi
addq $0x138, %rdi            # imm = 0x138
movq -0xb0(%rbp), %rsi
movq -0x30(%rbp), %rdx
callq 0x113cd0
movq -0xb0(%rbp), %rdi
movq -0x30(%rbp), %rsi
movq -0xb8(%rbp), %rdx
callq 0x10fe00
leaq -0xb8(%rbp), %rdi
callq 0x10c960
movq -0xb0(%rbp), %rdi
callq 0xcd6f0
movq -0x78(%rbp), %rdi
callq 0x2210
movq $0x0, -0xd0(%rbp)
movl $0x0, -0xe0(%rbp)
movl -0xe0(%rbp), %eax
cmpq -0xa8(%rbp), %rax
jae 0x114223
movq -0x98(%rbp), %rax
movl -0xe0(%rbp), %ecx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movq (%rax), %rax
shrq $0x20, %rax
movl %eax, -0xd4(%rbp)
movq -0x98(%rbp), %rax
movl -0xe0(%rbp), %ecx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movl 0x8(%rax), %eax
movl %eax, -0xd8(%rbp)
movq -0x30(%rbp), %rax
movq 0x8(%rax), %rax
movq -0x30(%rbp), %rcx
movq 0x28(%rcx), %rcx
movl -0xd4(%rbp), %edx
movq (%rcx,%rdx,8), %rcx
shrq $0x20, %rcx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0xd0(%rbp)
movq -0x30(%rbp), %rax
movq 0x28(%rax), %rax
movl -0xd4(%rbp), %ecx
movq (%rax,%rcx,8), %rax
movl %eax, -0xe4(%rbp)
movl $0x0, -0xdc(%rbp)
movl -0xdc(%rbp), %eax
cmpl -0xe4(%rbp), %eax
jae 0x11420d
movq -0xd0(%rbp), %rax
movl -0xdc(%rbp), %ecx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movl 0xc(%rax), %eax
shrl $0x1f, %eax
cmpl $0x0, %eax
je 0x1141b0
jmp 0x1141f9
movq -0xd0(%rbp), %rax
movl -0xdc(%rbp), %ecx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movl 0x8(%rax), %eax
cmpl -0xd8(%rbp), %eax
jne 0x1141f7
movq -0xd0(%rbp), %rax
movl -0xdc(%rbp), %ecx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movl 0xc(%rax), %ecx
andl $0x7fffffff, %ecx       # imm = 0x7FFFFFFF
orl $0x80000000, %ecx       # imm = 0x80000000
movl %ecx, 0xc(%rax)
jmp 0x11420d
jmp 0x1141f9
movl -0xdc(%rbp), %eax
addl $0x1, %eax
movl %eax, -0xdc(%rbp)
jmp 0x114181
jmp 0x11420f
movl -0xe0(%rbp), %eax
addl $0x1, %eax
movl %eax, -0xe0(%rbp)
jmp 0x1140e2
movq -0x98(%rbp), %rdi
callq 0x2210
movq -0x30(%rbp), %rdi
callq 0xcdd10
movq -0x30(%rbp), %rdi
movq -0x38(%rbp), %rsi
movq -0x40(%rbp), %rdx
movq -0x48(%rbp), %r8
movq -0x50(%rbp), %r9
leaq 0x2b05a5(%rip), %rax    # 0x3c47f8
movl 0x11c(%rax), %eax
shll %eax
movslq %eax, %r15
movq 0x18(%rbp), %r14
movl 0x20(%rbp), %ebx
movl 0x28(%rbp), %r11d
movl 0x30(%rbp), %r10d
movq 0x38(%rbp), %rax
movl $0x1, %ecx
movss 0x272622(%rip), %xmm0   # 0x3868a0
movss 0x27261e(%rip), %xmm1   # 0x3868a4
movss 0x27260e(%rip), %xmm2   # 0x38689c
xorl %r12d, %r12d
xorl %r12d, %r12d
movq %r15, (%rsp)
movq $0x3, 0x8(%rsp)
movq %r14, 0x10(%rsp)
movl %ebx, 0x18(%rsp)
movl %r11d, 0x20(%rsp)
movl %r10d, 0x28(%rsp)
movl $0x0, 0x30(%rsp)
movq %rax, 0x38(%rsp)
movq $0x0, 0x40(%rsp)
movq $0x0, 0x48(%rsp)
movq $0x0, 0x50(%rsp)
callq 0x100cf0
movq -0x30(%rbp), %rdi
movq -0x38(%rbp), %rsi
movq -0x40(%rbp), %rdx
movq -0x48(%rbp), %r8
movq -0x50(%rbp), %r9
leaq 0x2b04fc(%rip), %rax    # 0x3c47f8
movl 0x11c(%rax), %eax
shll %eax
movslq %eax, %r15
movq 0x18(%rbp), %r14
movl 0x20(%rbp), %ebx
movl 0x28(%rbp), %r11d
movl 0x30(%rbp), %r10d
movq 0x38(%rbp), %rax
movl $0x2, %ecx
movss 0x272579(%rip), %xmm0   # 0x3868a0
movss 0x272575(%rip), %xmm1   # 0x3868a4
movss 0x272565(%rip), %xmm2   # 0x38689c
xorl %r12d, %r12d
xorl %r12d, %r12d
movq %r15, (%rsp)
movq $0x3, 0x8(%rsp)
movq %r14, 0x10(%rsp)
movl %ebx, 0x18(%rsp)
movl %r11d, 0x20(%rsp)
movl %r10d, 0x28(%rsp)
movl $0x0, 0x30(%rsp)
movq %rax, 0x38(%rsp)
movq $0x0, 0x40(%rsp)
movq $0x0, 0x48(%rsp)
movq $0x0, 0x50(%rsp)
callq 0x100cf0
addq $0x118, %rsp            # imm = 0x118
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nopl (%rax)