// File: chhylp123[P]hifiasm/Overlaps.cpp
// Function: output_bp_trio_graph(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, bub_label_t*, long long, ug_opt_t*)
void output_bp_trio_graph(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, bub_label_t* b_mask_t,
long long gap_fuzz, ug_opt_t *opt)
{
    hic_clean(sg);

    kvec_asg_arc_t_warp new_rtg_edges;
    kv_init(new_rtg_edges.a); 
    ma_ug_t *ug = NULL;
    ug = ma_ug_gen_primary(sg, PRIMARY_LABLE);
    
    hap_cov_t *cov = NULL;
    trans_chain* t_ch = NULL;
    if((asm_opt.flag & HA_F_VERBOSE_GFA)) t_ch = load_hc_trans(output_file_name);
    
    if(!t_ch) {
        new_rtg_edges.a.n = 0;
        asg_t *copy_sg = copy_read_graph(sg);
        ma_ug_t *copy_ug = copy_untig_graph(ug);    
        ///asm_opt.purge_overlap_len = asm_opt.purge_overlap_len_hic;
        ///asm_opt.purge_simi_thres = asm_opt.purge_simi_rate_hic;
        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);
        
        ma_ug_destroy(copy_ug);
        asg_destroy(copy_sg);

        if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_trans_chain(cov->t_ch, output_file_name);
    }

    // clean_u_trans_t_idx_filter_adv(&(cov?cov->t_ch->k_trans:t_ch->k_trans), ug, sg);
    trio_phasing_refine(ug, sg, cov?&(cov->t_ch->k_trans):&(t_ch->k_trans), opt);
    
    if(cov) destory_hap_cov_t(&cov);
    if(t_ch) destory_trans_chain(&t_ch);


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



    ma_ug_destroy(ug);
    kv_destroy(new_rtg_edges.a); 


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

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xe8, %rsp
movq 0x40(%rbp), %rax
movq 0x38(%rbp), %rax
movq 0x30(%rbp), %rax
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, -0x90(%rbp)
movq -0x30(%rbp), %rdi
xorl %esi, %esi
callq 0xe7ae0
movq %rax, -0x90(%rbp)
movq $0x0, -0x98(%rbp)
movq $0x0, -0xa0(%rbp)
leaq 0x2b0105(%rip), %rax    # 0x3c47f8
movl (%rax), %eax
andl $0x4, %eax
cmpl $0x0, %eax
je 0x11470d
movq -0x40(%rbp), %rdi
callq 0xfd250
movq %rax, -0xa0(%rbp)
cmpq $0x0, -0xa0(%rbp)
jne 0x11481a
movq $0x0, -0x88(%rbp)
movq -0x30(%rbp), %rdi
callq 0x10b830
movq %rax, -0xa8(%rbp)
movq -0x90(%rbp), %rdi
callq 0x10ba70
movq %rax, -0xb0(%rbp)
movq -0xa8(%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 0x30(%rbp), %rax
leaq -0xb0(%rbp), %rdi
movss 0x27210b(%rip), %xmm0   # 0x38689c
leaq -0x88(%rbp), %r11
leaq -0x98(%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 -0xb0(%rbp), %rdi
callq 0xcd6f0
movq -0xa8(%rbp), %rdi
callq 0xcd170
leaq 0x2b0001(%rip), %rax    # 0x3c47f8
movl (%rax), %eax
andl $0x4, %eax
cmpl $0x0, %eax
je 0x114818
movq -0x98(%rbp), %rax
movq 0xa8(%rax), %rdi
movq -0x40(%rbp), %rsi
callq 0xfd080
jmp 0x11481a
movq -0x90(%rbp), %rax
movq %rax, -0xc0(%rbp)
movq -0x30(%rbp), %rax
movq %rax, -0xb8(%rbp)
cmpq $0x0, -0x98(%rbp)
je 0x11485a
movq -0x98(%rbp), %rax
movq 0xa8(%rax), %rax
addq $0x138, %rax            # imm = 0x138
movq %rax, -0xc8(%rbp)
jmp 0x11486e
movq -0xa0(%rbp), %rax
addq $0x138, %rax            # imm = 0x138
movq %rax, -0xc8(%rbp)
movq -0xb8(%rbp), %rsi
movq -0xc0(%rbp), %rdi
movq -0xc8(%rbp), %rdx
movq 0x40(%rbp), %rcx
callq 0x20d940
cmpq $0x0, -0x98(%rbp)
je 0x1148a2
leaq -0x98(%rbp), %rdi
callq 0x10c960
cmpq $0x0, -0xa0(%rbp)
je 0x1148b8
leaq -0xa0(%rbp), %rdi
callq 0xfc940
movq -0x90(%rbp), %rdi
callq 0xcd6f0
movq -0x78(%rbp), %rdi
callq 0x2210
movq -0x30(%rbp), %rdi
movq -0x38(%rbp), %rsi
movq -0x40(%rbp), %rdx
movq -0x48(%rbp), %rcx
movq -0x50(%rbp), %r8
leaq 0x2aff10(%rip), %rax    # 0x3c47f8
movl 0x11c(%rax), %eax
shll %eax
movslq %eax, %r9
movq 0x18(%rbp), %r15
movl 0x20(%rbp), %r14d
movl 0x28(%rbp), %ebx
movq 0x38(%rbp), %r11
movq 0x30(%rbp), %r10
movq 0x40(%rbp), %rax
movss 0x271f8e(%rip), %xmm0   # 0x3868a0
movss 0x271f8a(%rip), %xmm1   # 0x3868a4
movss 0x271f7a(%rip), %xmm2   # 0x38689c
xorl %r12d, %r12d
movq $0x3, (%rsp)
movq %r15, 0x8(%rsp)
movl %r14d, 0x10(%rsp)
movl %ebx, 0x18(%rsp)
movq %r11, 0x20(%rsp)
movq %r10, 0x28(%rsp)
movq $0x0, 0x30(%rsp)
movq $0x0, 0x38(%rsp)
movq %rax, 0x40(%rsp)
callq 0x10ca20
addq $0xe8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nopw %cs:(%rax,%rax)