// File: /workspace/github_cpp_makefile_star2_O2/chhylp123[P]hifiasm/Overlaps.cpp
// Function: clean_primary_untig_graph(ma_ug_t*, asg_t*, ma_hit_t_alloc*, ma_hit_t_alloc*, ma_sub_t*, long long, float, long long, R_to_U*, buf_t*, unsigned char*, float, unsigned int, unsigned int, float, int, int, float, hap_cov_t*)
void clean_primary_untig_graph(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, buf_t* b_0, uint8_t* visit, float density, 
uint32_t miniHapLen, uint32_t miniBiGraph, float chimeric_rate, int is_final_clean, 
int just_bubble_pop, float drop_ratio, hap_cov_t *cov)
{
    #define T_ROUND 2
    asg_t *g = ug->g;
    int round = T_ROUND;

    redo:
    ///print_graph_statistic(g, "beg");
    ///print_debug_gfa(read_g, ug, coverage_cut, "debug_trans_ovlp_hg002", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
    asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, NULL, 1, NULL);
    if(just_bubble_pop == 0)
    {
        cut_trio_tip_primary(g, ug, tipsLen, (uint32_t)-1, 0, read_g, reverse_sources, ruIndex, cov->is_r_het, 2);
    }
    // print_debug_gfa(read_g, ug, coverage_cut, "debug_init", sources, ruIndex, asm_opt.max_hang_Len, asm_opt.min_overlap_Len);
    long long pre_cons = get_graph_statistic(g);
    long long cur_cons = 0;
    while(pre_cons != cur_cons)
    {   
        pre_cons = get_graph_statistic(g);
        asg_pop_bubble_primary_trio(ug, NULL, (uint32_t)-1, DROP, cov, NULL, 1, NULL);
        if(just_bubble_pop == 0)
        {
            ///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, NULL); 
            asg_arc_cut_trio_long_equal_tips_assembly(g, ug, read_g, reverse_sources, 2, ruIndex, (uint32_t)-1, cov, NULL);   
            asg_arc_cut_trio_long_tip_primary_complex(g, ug, read_g, reverse_sources, ruIndex, 2, tip_drop_ratio, stops_threshold, cov, NULL, (uint32_t)-1);   
            asg_arc_cut_trio_long_equal_tips_assembly_complex(g, ug, read_g, reverse_sources, 2, ruIndex, stops_threshold, cov, NULL, (uint32_t)-1);
            detect_chimeric_by_topo(g, ug, read_g, reverse_sources, 2, stops_threshold, chimeric_rate, ruIndex, NULL, cov->is_r_het);    
            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);
    }
    if(just_bubble_pop == 0)
    {   
        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);    
    ///print_graph_statistic(g, "end");
    if(round > 0)
    {
        if(round != T_ROUND)
        {
            unitig_arc_del_short_diploid_by_length(ug->g, drop_ratio);        
        }
        round--;
        goto redo;
    }    
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x48, %rsp
movss %xmm3, 0xc(%rsp)
movss %xmm2, 0x34(%rsp)
movss %xmm0, 0x1c(%rsp)
movq %r9, 0x38(%rsp)
movq %rcx, 0x28(%rsp)
movq %rsi, 0x20(%rsp)
movq %rdi, %r14
movq 0x18(%rdi), %rbx
pushq $0x2
popq %rax
pushq $-0x1
popq %r15
pushq $0x5
popq %r12
movq %rdi, 0x10(%rsp)
movl %eax, 0x18(%rsp)
movq %r14, %rdi
xorl %esi, %esi
movl %r15d, %edx
movl %r12d, %ecx
movq 0xc0(%rsp), %r8
xorl %r9d, %r9d
pushq $0x0
pushq $0x1
callq 0x9716c
popq %rcx
popq %rdx
cmpl $0x0, 0xb8(%rsp)
jne 0x981fa
movq %rbx, %rdi
movq %r14, %rsi
movq 0x38(%rsp), %rdx
movl %r15d, %ecx
xorl %r8d, %r8d
movq 0x20(%rsp), %r9
pushq $0x2
movq 0xc8(%rsp), %rax
pushq 0xa0(%rax)
pushq 0x98(%rsp)
pushq 0x40(%rsp)
callq 0x93005
addq $0x20, %rsp
movq %rbx, %rdi
callq 0x92d8d
movq %rax, %r13
xorl %eax, %eax
cmpq %rax, %r13
je 0x983a0
movq %rbx, %rdi
callq 0x92d8d
movq %rax, %r13
movq %r14, %rdi
xorl %esi, %esi
movl %r15d, %edx
movl %r12d, %ecx
movq 0xc0(%rsp), %r8
xorl %r9d, %r9d
pushq $0x0
pushq $0x1
callq 0x9716c
popq %rcx
popq %rdx
cmpl $0x0, 0xb8(%rsp)
jne 0x98393
subq $0x8, %rsp
movq %rbx, %rdi
movq %r14, %rsi
movq 0x28(%rsp), %r12
movq %r12, %rdx
movq 0x30(%rsp), %r15
movq %r15, %rcx
movq %r13, 0x48(%rsp)
movq 0x90(%rsp), %r8
pushq $0x2
popq %rbp
movl %ebp, %r9d
movss 0x24(%rsp), %xmm0
pushq $0x0
movq 0xd0(%rsp), %r14
pushq %r14
pushq $-0x1
callq 0x9342f
addq $0x18, %rsp
movq %rbx, %rdi
movq 0x18(%rsp), %rsi
movq %r12, %rdx
movq %r15, %rcx
pushq $0x2
popq %r8
movq 0x90(%rsp), %r13
movq %r13, %r9
pushq $0x0
pushq %r14
pushq $-0x1
callq 0x94044
addq $0x20, %rsp
movq %rbx, %rdi
movq 0x10(%rsp), %rsi
movq %r12, %rdx
movq %r15, %rcx
movq %r13, %r8
movl %ebp, %r9d
movss 0x1c(%rsp), %xmm0
pushq $-0x1
pushq $0x0
pushq %r14
movq %r14, %rbp
movl 0x98(%rsp), %r13d
pushq %r13
callq 0x938d7
addq $0x20, %rsp
movq %rbx, %rdi
movq 0x10(%rsp), %rsi
movq %r12, %rdx
movq %r15, %rcx
pushq $0x2
popq %r14
movq %r14, %r8
movq 0x88(%rsp), %r9
pushq $-0x1
pushq $0x0
pushq %rbp
pushq %r13
callq 0x94b2d
addq $0x18, %rsp
movq %rbx, %rdi
movq 0x18(%rsp), %rsi
movq %r12, %rdx
pushq $0x5
popq %r12
movq %r15, %rcx
pushq $-0x1
popq %r15
movq %r14, %r8
movl %r13d, %r9d
movq 0x48(%rsp), %r13
movss 0x3c(%rsp), %xmm0
pushq 0xa0(%rbp)
movq 0x20(%rsp), %r14
pushq $0x0
pushq 0xa0(%rsp)
callq 0x95038
addq $0x20, %rsp
cmpl $0x2, 0x18(%rsp)
je 0x98393
leaq 0x1bb3e3(%rip), %rax    # 0x253758
movl 0x11c(%rax), %edx
movq %rbx, %rdi
movq %r14, %rsi
movss 0xc(%rsp), %xmm0
xorl %r8d, %r8d
pushq $0x1
popq %r9
callq 0x7216e
movq %rbx, %rdi
callq 0x92d8d
jmp 0x98207
cmpl $0x0, 0xb8(%rsp)
jne 0x983e4
movq %rbx, %rdi
movq %r14, %rsi
movq 0x38(%rsp), %rdx
movl %r15d, %ecx
xorl %r8d, %r8d
movq 0x20(%rsp), %r9
pushq $0x2
movq 0xc8(%rsp), %rax
pushq 0xa0(%rax)
pushq 0x98(%rsp)
pushq 0x40(%rsp)
callq 0x93005
addq $0x20, %rsp
movq %r14, %rdi
movq 0x20(%rsp), %r12
movq %r12, %rsi
movq 0x28(%rsp), %r15
movq %r15, %rdx
pushq $0x14
popq %rcx
pushq $0x64
popq %r8
movss 0x14f8b6(%rip), %xmm0   # 0x1e7cbc
movss 0x14f8b2(%rip), %xmm1   # 0x1e7cc0
movq 0x88(%rsp), %r13
movq %r13, %r9
movss 0xc(%rsp), %xmm2
pushq $-0x1
movq 0xc8(%rsp), %r14
pushq 0xa0(%r14)
callq 0x974ef
popq %rax
popq %rcx
movq 0xa0(%r14), %r9
movq 0x10(%rsp), %r14
movq %r14, %rdi
movq %rbx, %rsi
movq %r12, %rdx
movq %r15, %rcx
movq %r13, %r8
callq 0x97ac1
leaq 0x1bb2fa(%rip), %rax    # 0x253758
movl 0x11c(%rax), %edx
movq %rbx, %rdi
movq %r14, %rsi
movss 0xc(%rsp), %xmm0
xorl %r8d, %r8d
pushq $0x1
popq %r9
callq 0x7216e
movl 0x18(%rsp), %eax
movl %eax, %ebp
subl $0x1, %ebp
jb 0x984b0
cmpl $0x2, %eax
movl %ebp, %eax
pushq $-0x1
popq %r15
pushq $0x5
popq %r12
je 0x98191
movq 0x18(%r14), %rdi
movss 0xc(%rsp), %xmm0
callq 0x7264d
movl %ebp, %eax
jmp 0x98191
addq $0x48, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq