// File: /workspace/github_cpp_makefile_star2_O2/chhylp123[P]hifiasm/Overlaps.cpp
// Function: topo_ovlp_collect(ma_ug_t*, asg_t*, ma_hit_t_alloc*, ma_hit_t_alloc*, ma_sub_t*, long long, float, long long, R_to_U*, float, float, int, int, hap_cov_t*)
utg_trans_t *topo_ovlp_collect(ma_ug_t *ug, asg_t *read_g, ma_hit_t_alloc* sources, 
ma_hit_t_alloc* reverse_sources, ma_sub_t* coverage_cut, 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, hap_cov_t *cov)
{
    utg_trans_t *o = init_utg_trans_t(ug, reverse_sources, coverage_cut, ruIndex, read_g, max_hang, min_ovlp);
    #define T_ROUND 2
    asg_t *g = ug->g;
    int round = T_ROUND;

    // print_debug_gfa(read_g, ug, coverage_cut, "debug_init", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);

    redo:
    asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, o, 1, NULL);
    cut_trio_tip_primary(g, ug, tipsLen, (uint32_t)-1, 0, read_g, reverse_sources, ruIndex, cov->is_r_het, 2);

    long long pre_cons = get_graph_statistic(g);
    long long cur_cons = 0;
    while(pre_cons != cur_cons)
    {
        while(pre_cons != cur_cons)
        {
            while(pre_cons != cur_cons)
            {    
                pre_cons = get_graph_statistic(g);
                asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, o, 1, NULL);
                
                ///need consider tangles  
                asg_arc_cut_trio_long_tip_primary(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, (uint32_t)-1, cov, o);              
                asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, cov, o);   
                asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov, o, (uint32_t)-1);   
                asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov, o, (uint32_t)-1);
                detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate, ruIndex, o, cov->is_r_het);    
                
                cur_cons = get_graph_statistic(g);
            }    

            // if(asm_opt.polyploidy > 2) asg_arc_decompress(g, ug, read_g, reverse_sources, ruIndex, o);
            if(asm_opt.polyploidy > 2)
            {
                asg_arc_decompress_mul(g, ug, read_g, (uint32_t)-1, DROP, reverse_sources, ruIndex, o);
            }
            
            cur_cons = get_graph_statistic(g);
        }
        if(round != T_ROUND)
        {
            unitig_arc_del_short_diploid_by_length_topo(g, ug, drop_ratio, asm_opt.max_short_tip, 
            reverse_sources, 0, 1);
        }
        cur_cons = get_graph_statistic(g);
    }

    
    cut_trio_tip_primary(g, ug, tipsLen, (uint32_t)-1, 0, read_g, reverse_sources, ruIndex, cov->is_r_het, 2);
    
    resolve_tangles(ug, read_g, reverse_sources, 20, 100, 0.05, 0.2, ruIndex, cov->is_r_het, (uint32_t)-1, drop_ratio); 
    drop_semi_circle(ug, g, read_g, reverse_sources, ruIndex, cov->is_r_het); 
    // print_debug_gfa(read_g, ug, coverage_cut, "debug_clean_end", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
    unitig_arc_del_short_diploid_by_length_topo(g, ug, drop_ratio, asm_opt.max_short_tip, reverse_sources, 0, 1);    
    
    if(round > 0)
    {
        if(round != T_ROUND)
        {
            unitig_arc_del_short_diploid_by_length(ug->g, drop_ratio);        
        }
        round--;
        goto redo;
    }
    return o;    
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movss %xmm2, 0xc(%rsp)
movss %xmm1, 0x44(%rsp)
movss %xmm0, 0x24(%rsp)
movq %r9, 0x48(%rsp)
movq %r8, %rdx
movq %rcx, %r8
movq %rsi, %r10
movq %rdi, %rbx
movq 0x98(%rsp), %rcx
movl 0xa0(%rsp), %r9d
movl 0xa8(%rsp), %eax
subq $0x8, %rsp
movq %r8, 0x40(%rsp)
movq %r8, %rsi
movq %r10, 0x38(%rsp)
movq %r10, %r8
pushq %rax
callq 0x14fe46
popq %rcx
popq %rdx
movq %rax, 0x28(%rsp)
movq 0x18(%rbx), %rax
movq %rax, 0x10(%rsp)
pushq $0x2
popq %rax
movq %rbx, 0x18(%rsp)
movl %eax, 0x20(%rsp)
movq %rbx, %rdi
xorl %esi, %esi
pushq $-0x1
popq %rbp
movl %ebp, %edx
pushq $0x5
popq %rcx
movq 0xb0(%rsp), %r13
movq %r13, %r8
movq 0x28(%rsp), %r9
pushq $0x0
pushq $0x1
callq 0x9716c
popq %rcx
popq %rdx
movq 0x10(%rsp), %r14
movq %r14, %rdi
movq %rbx, %rsi
movq 0x48(%rsp), %rdx
movl %ebp, %ecx
xorl %r8d, %r8d
movq 0x30(%rsp), %r9
pushq $0x2
pushq 0xa0(%r13)
pushq 0xa8(%rsp)
pushq 0x50(%rsp)
callq 0x93005
addq $0x20, %rsp
movq %r14, %rdi
callq 0x92d8d
movq %rax, %rbx
xorl %eax, %eax
cmpq %rax, %rbx
je 0x987b3
cmpq %rax, %rbx
jne 0x9871f
jmp 0x98774
movq 0x10(%rsp), %r14
movq %r14, %rdi
callq 0x92d8d
movq %rax, 0x50(%rsp)
movq 0x18(%rsp), %rbx
movq %rbx, %rdi
xorl %esi, %esi
pushq $-0x1
popq %rdx
pushq $0x5
popq %rcx
movq 0xb0(%rsp), %r8
movq 0x28(%rsp), %r13
movq %r13, %r9
pushq $0x0
pushq $0x1
callq 0x9716c
popq %rcx
popq %rdx
subq $0x8, %rsp
movq %r14, %rdi
movq %rbx, %rsi
movq 0x38(%rsp), %r12
movq %r12, %rdx
movq 0x40(%rsp), %r15
movq %r15, %rcx
movq 0xa0(%rsp), %r8
pushq $0x2
popq %r9
movss 0x2c(%rsp), %xmm0
pushq %r13
movq 0xc0(%rsp), %rax
pushq %rax
pushq $-0x1
callq 0x9342f
addq $0x18, %rsp
movq 0x18(%rsp), %r14
movq %r14, %rdi
movq %rbx, %rsi
movq %r12, %rdx
movq %r15, %rcx
pushq $0x2
popq %r8
movq 0xa0(%rsp), %rbp
movq %rbp, %r9
pushq %r13
pushq 0xc0(%rsp)
pushq $-0x1
callq 0x94044
addq $0x20, %rsp
movq %r14, %rdi
movq %rbx, %rsi
movq %r12, %rdx
movq %r15, %rcx
movq %rbp, %r8
pushq $0x2
popq %r9
movss 0x24(%rsp), %xmm0
pushq $-0x1
pushq %r13
movq 0xc0(%rsp), %rax
pushq %rax
movl 0xa8(%rsp), %ebp
pushq %rbp
callq 0x938d7
addq $0x20, %rsp
movq %r14, %rdi
movq %rbx, %rsi
movq %r12, %rdx
movq %r15, %rcx
pushq $0x2
popq %r8
movq 0x98(%rsp), %r9
pushq $-0x1
pushq %r13
movq 0xc0(%rsp), %rax
pushq %rax
pushq %rbp
callq 0x94b2d
addq $0x18, %rsp
movq %r14, %rdi
movq %rbx, %rsi
movq 0x58(%rsp), %rbx
movq %r12, %rdx
movq %r15, %rcx
pushq $0x2
popq %r8
movl %ebp, %r9d
movss 0x4c(%rsp), %xmm0
movq 0xb8(%rsp), %rax
pushq 0xa0(%rax)
pushq %r13
pushq 0xb0(%rsp)
callq 0x95038
addq $0x20, %rsp
movq %r14, %rdi
callq 0x92d8d
cmpq %rax, %rbx
jne 0x985c0
leaq 0x1bb029(%rip), %rax    # 0x253758
cmpl $0x3, 0x1bc(%rax)
jl 0x98765
movq 0x10(%rsp), %rdi
movq 0x18(%rsp), %rsi
movq 0x30(%rsp), %rdx
pushq $-0x1
popq %rcx
pushq $0x5
popq %r8
movq 0x38(%rsp), %r9
pushq 0x28(%rsp)
pushq 0xa0(%rsp)
callq 0x152cb1
popq %rcx
popq %rdx
movq 0x10(%rsp), %rdi
callq 0x92d8d
jmp 0x985b2
cmpl $0x2, 0x20(%rsp)
je 0x987a4
leaq 0x1bafd6(%rip), %rax    # 0x253758
movl 0x11c(%rax), %edx
movq 0x10(%rsp), %rdi
movq 0x18(%rsp), %rsi
movss 0xc(%rsp), %xmm0
xorl %r8d, %r8d
pushq $0x1
popq %r9
callq 0x7216e
movq 0x10(%rsp), %rdi
callq 0x92d8d
jmp 0x985a9
movq 0x10(%rsp), %rbp
movq %rbp, %rdi
movq 0x18(%rsp), %rbx
movq %rbx, %rsi
movq 0x48(%rsp), %rdx
pushq $-0x1
popq %rcx
xorl %r8d, %r8d
movq 0x30(%rsp), %r12
movq %r12, %r9
pushq $0x2
movq 0xb8(%rsp), %r13
pushq 0xa0(%r13)
movq 0xa8(%rsp), %r14
pushq %r14
movq 0x50(%rsp), %r15
pushq %r15
callq 0x93005
addq $0x20, %rsp
movq %rbx, %rdi
movq %r12, %rsi
movq %r15, %rdx
pushq $0x14
popq %rcx
pushq $0x64
popq %r8
movss 0x14f4a3(%rip), %xmm0   # 0x1e7cbc
movss 0x14f49f(%rip), %xmm1   # 0x1e7cc0
movq %r14, %r9
movss 0xc(%rsp), %xmm2
pushq $-0x1
pushq 0xa0(%r13)
callq 0x974ef
popq %rax
popq %rcx
movq 0xa0(%r13), %r9
movq %rbx, %rdi
movq %rbp, %rsi
movq %r12, %rdx
movq %r15, %rcx
movq %r14, %r8
callq 0x97ac1
leaq 0x1baefc(%rip), %rax    # 0x253758
movl 0x11c(%rax), %edx
movq %rbp, %rdi
movq %rbx, %rsi
movss 0xc(%rsp), %xmm0
xorl %r8d, %r8d
pushq $0x1
popq %r9
callq 0x7216e
movl 0x20(%rsp), %eax
movl %eax, %r13d
subl $0x1, %r13d
jb 0x988b9
cmpl $0x2, %eax
movl %r13d, %eax
movq 0x18(%rsp), %rbx
je 0x98539
movq 0x18(%rsp), %rax
movq 0x18(%rax), %rdi
movss 0xc(%rsp), %xmm0
callq 0x7264d
movq 0x18(%rsp), %rbx
movl %r13d, %eax
jmp 0x98539
movq 0x28(%rsp), %rax
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq