// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Overlaps.cpp
// Function: output_hic_graph_mmhap(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, long long, bub_label_t*, ug_opt_t*)
void output_hic_graph_mmhap(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, long long gap_fuzz, bub_label_t* b_mask_t, ug_opt_t *opt)
{ 
    hic_clean(sg);
    mmhap_t *rh = NULL;

    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 = 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
    
    hap_cov_t *cov = NULL;
    trans_chain* t_ch = NULL;
    t_ch = load_trans_ovlp(output_file_name, ug);
    // 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);
        print_utg(&copy_ug, copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, 
        min_ovlp, &new_rtg_edges);

        if(asm_opt.is_alt) {
            output_contig_graph_alternative(copy_sg, coverage_cut, output_file_name, sources, ruIndex, max_hang, 
            min_ovlp);
        }
        ma_ug_destroy(copy_ug);
        asg_destroy(copy_sg);
        // clean_u_trans_t_idx(&(cov->t_ch->k_trans), ug, sg);


        new_rtg_edges.a.n = 0;
        ma_ug_print_bed(ug, sg, &R_INF, coverage_cut, sources, &new_rtg_edges, 
                max_hang, min_ovlp, asm_opt.hic_inconsist_rate, NULL, NULL, cov->t_ch);

        refine_hic_trans_mmhap(opt, &(cov->t_ch->k_trans), sg, ug);
        dump_trans_ovlp(cov->t_ch, output_file_name, ug);
        // if((asm_opt.flag & HA_F_VERBOSE_GFA)) write_trans_chain(cov->t_ch, output_file_name);
    }

    // dbg_prt_utg_trans(&(cov?cov->t_ch->k_trans:t_ch->k_trans), ug, "pre");
    clean_u_trans_t_idx_filter_mmhap_adv(&(cov?cov->t_ch->k_trans:t_ch->k_trans), ug, sg, opt->sources, NULL);
    // dbg_prt_utg_trans(&(cov?cov->t_ch->k_trans:t_ch->k_trans), ug, "after");

    // refine_hic_trans_mmhap(opt, &(cov?cov->t_ch->k_trans:t_ch->k_trans), sg, ug);
    ///for debug
    // dbg_prt_utg_trans(&(cov?cov->t_ch->k_trans:t_ch->k_trans), ug, "dd");
    // char* gfa_name = (char*)malloc(strlen(output_file_name)+50); FILE* output_file = NULL;

    // sprintf(gfa_name, "%s.pre.clean_d_utg.noseq.gfa", output_file_name);
    // output_file = fopen(gfa_name, "w");
    // ma_ug_print_simple(ug, sg, coverage_cut, sources, ruIndex, "utg", output_file);
    // fclose(output_file);

    // sprintf(gfa_name, "%s.pre.clean_d_utg.gfa", output_file_name);
    // 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


    hic_analysis(ug, sg, cov?cov->t_ch:t_ch, opt, &rh, NULL);


    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); 


    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);

    // dbg_prt_trio_mmhap_label(ug, rh, output_file_name);

    output_trio_mmhap(sg, coverage_cut, output_file_name, sources, reverse_sources, tipsLen, tip_drop_ratio, 
    stops_threshold, ruIndex, chimeric_rate, drop_ratio, max_hang, min_ovlp, gap_fuzz, b_mask_t, opt, ug, rh, asm_opt.polyploidy);

    ma_ug_destroy(ug);
    free(rh->a.a); free(rh->h.a); free(rh);
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xb8, %rsp
movss %xmm2, 0x24(%rsp)
movss %xmm1, 0x20(%rsp)
movss %xmm0, 0x1c(%rsp)
movq %r9, 0x50(%rsp)
movq %r8, 0x48(%rsp)
movq %rcx, %r13
movq %rdx, %r12
movq %rsi, %rbx
movq %rdi, %rbp
callq 0xbfa5a
xorl %r15d, %r15d
movq %r15, 0x10(%rsp)
xorps %xmm0, %xmm0
leaq 0x98(%rsp), %r14
movups %xmm0, 0x8(%r14)
leaq 0x70(%rsp), %rax
movaps %xmm0, (%rax)
movq %r15, 0x10(%rax)
movq %rbp, %rdi
xorl %esi, %esi
callq 0xb2a6d
movq %r15, (%r14)
subq $0x8, %rsp
movq %rax, %rdi
movq %rbp, %rsi
movq %rbx, 0x48(%rsp)
movq %rbx, %rdx
movq %r13, 0x38(%rsp)
movq %r13, %rcx
movq %r12, %r13
movq %rax, %r12
movq %r14, %rbx
movq %r14, %r8
movl 0x108(%rsp), %r9d
pushq $0x1
leaq 0x80(%rsp), %rax
pushq %rax
movl 0x120(%rsp), %eax
pushq %rax
callq 0xb67c4
addq $0x20, %rsp
movq %r15, 0x8(%rsp)
movq %r13, 0x28(%rsp)
movq %r13, %rdi
movq %r12, %rsi
callq 0xc9cd4
movq %rax, %r14
movq %rax, 0x60(%rsp)
testq %rax, %rax
movq %r12, 0x38(%rsp)
je 0xca2b3
movq %r12, %r13
movl $0xa8, %r12d
leaq (%r15,%r12), %rax
testq %r15, %r15
leaq 0x60(%rsp), %r15
cmoveq %r15, %rax
movl $0x138, %edi            # imm = 0x138
addq (%rax), %rdi
movq 0x120(%rsp), %rbx
movq 0x8(%rbx), %rcx
movq %r13, %rsi
movq %rbp, %rdx
xorl %r8d, %r8d
callq 0xc80ab
movq 0x8(%rsp), %rax
addq %rax, %r12
testq %rax, %rax
cmoveq %r15, %r12
movq (%r12), %rdx
leaq 0x10(%rsp), %r8
movq %r13, %rdi
movq %rbp, %rsi
movq %rbx, %rcx
xorl %r9d, %r9d
callq 0x16364b
cmpq $0x0, 0x8(%rsp)
je 0xca102
leaq 0x8(%rsp), %rdi
callq 0xc9bdb
testq %r14, %r14
movq 0x30(%rsp), %r15
movq 0x40(%rsp), %r12
je 0xca11b
leaq 0x60(%rsp), %rdi
callq 0xbf611
movq 0x110(%rsp), %r14
movq 0xa8(%rsp), %rdi
callq 0x2220
movq 0x70(%rsp), %rcx
testq %rcx, %rcx
je 0xca1b8
xorl %eax, %eax
movq 0x80(%rsp), %rdx
leaq (%rax,%rax,2), %rsi
movl 0x4(%rdx,%rsi,8), %edi
movq 0x28(%rbp), %r8
movq (%r8,%rdi,8), %rdi
testl %edi, %edi
je 0xca1b1
movl 0x8(%rdx,%rsi,8), %esi
movq 0x8(%rbp), %rdx
movq %rdi, %r8
shrq $0x20, %r8
movl %edi, %r9d
leaq (%r8,%r8,2), %rdi
leaq (%rdx,%rdi,8), %r8
addq $0xc, %r8
shlq $0x3, %r9
leaq (%r9,%r9,2), %r10
xorl %r9d, %r9d
movl (%r8,%r9), %r11d
testl %r11d, %r11d
js 0xca191
cmpl %esi, -0x4(%r8,%r9)
je 0xca19c
addq $0x18, %r9
cmpq %r9, %r10
jne 0xca181
jmp 0xca1b1
leaq (%rdx,%rdi,8), %rcx
orl $0x80000000, %r11d      # imm = 0x80000000
movl %r11d, 0xc(%r9,%rcx)
movq 0x70(%rsp), %rcx
incl %eax
cmpq %rax, %rcx
ja 0xca13c
movq 0x80(%rsp), %rdi
callq 0x2220
movq %rbp, %rdi
callq 0xa0a7d
movq 0x10(%rsp), %rax
leaq 0x1cb57f(%rip), %rcx    # 0x295758
movl 0x1bc(%rcx), %ecx
subq $0x50, %rsp
movl %ecx, 0x48(%rsp)
movq %rax, 0x40(%rsp)
movq 0x88(%rsp), %r13
movq %r13, 0x38(%rsp)
movq 0x168(%rsp), %rax
movq %rax, 0x28(%rsp)
movq %r14, 0x20(%rsp)
movl 0x158(%rsp), %eax
movl %eax, 0x18(%rsp)
movl 0x150(%rsp), %eax
movl %eax, 0x10(%rsp)
movq 0x148(%rsp), %rax
movq %rax, 0x8(%rsp)
movq 0x140(%rsp), %rax
movq %rax, (%rsp)
movq %rbp, %rdi
movq %r12, %rsi
movq 0x78(%rsp), %rdx
movq %r15, %rcx
movq 0x98(%rsp), %r8
movq 0xa0(%rsp), %r9
movss 0x6c(%rsp), %xmm0
movss 0x70(%rsp), %xmm1
movss 0x74(%rsp), %xmm2
callq 0xc9dc2
addq $0x50, %rsp
movq %r13, %rdi
callq 0xa0761
movq 0x10(%rsp), %rax
movq 0x28(%rax), %rdi
callq 0x2220
movq 0x10(%rsp), %rax
movq 0x10(%rax), %rdi
callq 0x2220
movq 0x10(%rsp), %rdi
callq 0x2220
addq $0xb8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq $0x0, 0x98(%rsp)
movq %rbp, %rdi
callq 0xc8dad
movq %rax, %r15
movq %rax, 0x68(%rsp)
movq %r12, %rdi
callq 0xc8eab
leaq 0x58(%rsp), %rdi
movq %rax, (%rdi)
subq $0x8, %rsp
leaq 0x10(%rsp), %rax
movq %r15, %rsi
movq 0x38(%rsp), %r15
movq %r15, %rdx
movq 0x50(%rsp), %rcx
movq 0x48(%rsp), %r13
movq %r13, %r8
movq 0x58(%rsp), %r9
movss 0x24(%rsp), %xmm1
movss 0x28(%rsp), %xmm2
movss 0x2c(%rsp), %xmm3
pushq $0x0
pushq $0x1
pushq 0x130(%rsp)
pushq %rax
pushq %rbx
movl 0x138(%rsp), %r12d
pushq %r12
movl 0x138(%rsp), %eax
pushq %rax
movq 0x138(%rsp), %rbx
pushq %rbx
pushq 0x138(%rsp)
callq 0xc906a
addq $0x48, %rsp
leaq 0x60(%rsp), %rdi
movq 0x70(%rsp), %rsi
movq %r13, %rdx
movq 0x30(%rsp), %rcx
movq %r15, %r8
movq %rbx, %r9
movl 0x108(%rsp), %ebx
leaq 0xa0(%rsp), %rax
pushq %rax
pushq %r12
pushq %rbx
movq %r13, %rbx
movq %rsi, %r13
callq 0x7f44
addq $0x20, %rsp
leaq 0x1cb3c8(%rip), %r15    # 0x295758
cmpl $0x0, 0x1e4(%r15)
jne 0xca466
movq 0x58(%rsp), %rdi
callq 0xa0761
movq %r13, %rdi
callq 0xa0494
leaq 0x98(%rsp), %r9
movq $0x0, (%r9)
movl 0x154(%r15), %eax
movq 0x8(%rsp), %rcx
movq 0xa8(%rcx), %rcx
subq $0x30, %rsp
movq %rcx, 0x28(%rsp)
xorps %xmm0, %xmm0
movups %xmm0, 0x18(%rsp)
movl %eax, 0x10(%rsp)
movl 0x138(%rsp), %eax
movl %eax, 0x8(%rsp)
movl 0x130(%rsp), %eax
movl %eax, (%rsp)
leaq 0x1cbe2d(%rip), %rdx    # 0x296230
movq 0x68(%rsp), %r12
movq %r12, %rdi
movq %rbp, %rsi
movq %rbx, %rcx
movq 0x60(%rsp), %r8
callq 0xb8f0d
addq $0x30, %rsp
movq 0x8(%rsp), %rax
movl $0x138, %esi            # imm = 0x138
addq 0xa8(%rax), %rsi
movq 0x120(%rsp), %rdi
movq %rbp, %rdx
movq %r12, %rcx
callq 0xc87e0
movq 0x8(%rsp), %rax
movq 0xa8(%rax), %rdi
movq 0x28(%rsp), %rsi
movq %r12, %rdx
callq 0xc9c55
movq 0x8(%rsp), %r15
jmp 0xca08c
subq $0x8, %rsp
movq %r13, %rdi
movq %rbx, %rsi
movq 0x30(%rsp), %rdx
movq 0x38(%rsp), %rcx
movq 0x100(%rsp), %r8
movl 0x108(%rsp), %r9d
movl 0x110(%rsp), %eax
pushq %rax
callq 0x8832
addq $0x10, %rsp
jmp 0xca39e