// File: /workspace/github_cpp_makefile_star2_O2/chhylp123[P]hifiasm/Overlaps.cpp
// Function: asg_arc_simple_large_bubbles(asg_t*, ma_hit_t_alloc*, long long, R_to_U*)
int asg_arc_simple_large_bubbles(asg_t *g, ma_hit_t_alloc* reverse_sources, long long miniedgeLen, 
R_to_U* ruIndex)
{
    double startTime = Get_T();
    ///the reason is that each read has two direction (query->target, target->query)
    uint32_t v, n_vtx = g->n_seq * 2, n_reduced = 0, convex, flag, is_hap;
    long long ll, base_maxLen, base_maxLen_i, all_covex;

    buf_t b;
    memset(&b, 0, sizeof(buf_t));

    for (v = 0; v < n_vtx; ++v) 
    {
        uint32_t i, n_arc = 0, nv = asg_arc_n(g, v);
        asg_arc_t *av = asg_arc_a(g, v);
        ///some node could be deleted
        if (nv < 2 || g->seq[v>>1].del || g->seq[v>>1].c == ALTER_LABLE) continue;
        n_arc = get_real_length(g, v, NULL);
        if (n_arc < 2) continue;

        base_maxLen = -1;
        base_maxLen_i = -1;
        all_covex = -1;
        is_hap = 0;

        for (i = 0; i < nv; i++)
        {
            if (!av[i].del)
            {
                flag = detect_single_path_with_dels_contigLen(g, av[i].v, &convex, &ll, NULL);
                if(flag != TWO_INPUT && flag != MUL_INPUT)
                {
                    break;
                }

                if(all_covex != -1 && (uint32_t)all_covex != convex)
                {
                    break;
                }

                if(all_covex == -1)
                {
                    all_covex = convex;
                }
                
                if(base_maxLen < ll)
                {
                    base_maxLen = ll;
                    base_maxLen_i = i;
                }

            }
        }


        if(i == nv)
        {
            for (i = 0; i < nv; i++)
            {
                if(i == base_maxLen_i) continue;
                if (!av[i].del)
                {
                    b.b.n = 0;
                    detect_single_path_with_dels_contigLen(g, av[i].v, &convex, &ll, &b);
                    if(b.b.n < 2) continue;
                    b.b.n--;

                    //we can only cut tips
                    /****************************may have bugs********************************/
                    if(check_if_diploid(av[base_maxLen_i].v, av[i].v, g, 
                    reverse_sources, miniedgeLen, ruIndex)==1)
                    {/****************************may have bugs********************************/
                        n_reduced++;
                        uint64_t k;

                        for (k = 0; k < b.b.n; k++)
                        {
                            g->seq[b.b.a[k]].c = ALTER_LABLE;
                        }
                        for (k = 0; k < b.b.n; k++)
                        {
                            asg_seq_drop(g, b.b.a[k]);
                        }

                        is_hap++;
                    }
                }
            }

            if(is_hap > 0)
            {
                i = base_maxLen_i;
                b.b.n = 0;
                detect_single_path_with_dels_contigLen(g, av[i].v, &convex, &ll, &b);
                uint64_t k;
                for (k = 0; k < b.b.n; k++)
                {
                    g->seq[b.b.a[k]].c = HAP_LABLE;
                }
            }
        }

    }


    asg_cleanup(g);
    asg_symm(g);
    free(b.b.a);
    
    if(VERBOSE >= 1)
    {
        fprintf(stderr, "[M::%s] removed %d long tips\n", 
        __func__, n_reduced);
        fprintf(stderr, "[M::%s] takes %0.2f s\n\n", __func__, Get_T()-startTime);
    }
    

    return n_reduced;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xc8, %rsp
movq %rcx, %r15
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %rbx
callq 0x251c
movl 0x14(%rbx), %r14d
addl %r14d, %r14d
xorps %xmm0, %xmm0
leaq 0x60(%rsp), %rax
movaps %xmm0, 0x50(%rax)
movaps %xmm0, 0x40(%rax)
movaps %xmm0, 0x30(%rax)
movaps %xmm0, 0x20(%rax)
movaps %xmm0, 0x10(%rax)
movaps %xmm0, (%rax)
andq $0x0, 0x60(%rax)
xorl %esi, %esi
movl $0x0, 0x20(%rsp)
movq %r15, 0x50(%rsp)
movq %r12, 0x48(%rsp)
movq %r13, 0x40(%rsp)
movq %r14, 0x30(%rsp)
cmpq %r14, %rsi
je 0x80f64
movq 0x28(%rbx), %rax
movq (%rax,%rsi,8), %rbp
cmpl $0x2, %ebp
jb 0x80cf8
movq 0x20(%rbx), %rax
movl %esi, %ecx
shrl %ecx
cmpl $0x0, (%rax,%rcx,8)
js 0x80cf8
cmpb $0x1, 0x4(%rax,%rcx,8)
je 0x80cf8
movq 0x8(%rbx), %r14
movq %rbx, %rdi
movq %rsi, (%rsp)
xorl %edx, %edx
callq 0xc2e7a
cmpl $0x2, %eax
jae 0x80cfd
movq 0x30(%rsp), %r14
movq (%rsp), %rsi
incq %rsi
jmp 0x80cad
movq %rbp, %rax
shrq $0x20, %rax
imulq $0x18, %rax, %rax
leaq (%r14,%rax), %rcx
movq %rcx, 0x28(%rsp)
movl %ebp, %edx
leaq (%r14,%rax), %r15
addq $0xc, %r15
xorl %r13d, %r13d
pushq $-0x1
popq %r14
movq %r14, %r12
movq %r14, 0x18(%rsp)
movq (%rsp), %rsi
movq %rdx, 0x10(%rsp)
cmpq %r13, %rdx
je 0x80dc3
cmpl $0x0, (%r15)
js 0x80da8
movl -0x4(%r15), %esi
movq %rbx, %rdi
leaq 0xc(%rsp), %rdx
leaq 0x38(%rsp), %rcx
xorl %r8d, %r8d
callq 0x70b8f
andl $0x5, %eax
cmpl $0x1, %eax
jne 0x80db1
cmpq $-0x1, %r14
sete %cl
movl 0xc(%rsp), %eax
cmpl %r14d, %eax
sete %dl
orb %cl, %dl
cmpb $0x1, %dl
jne 0x80db1
movl %eax, %eax
cmpq $-0x1, %r14
cmoveq %rax, %r14
movq 0x38(%rsp), %rax
cmpq %rax, %r12
cmovleq %rax, %r12
movq 0x18(%rsp), %rax
cmovlq %r13, %rax
movq %rax, 0x18(%rsp)
movq (%rsp), %rsi
movq 0x10(%rsp), %rdx
incq %r13
addq $0x18, %r15
jmp 0x80d33
cmpl %r13d, %ebp
movq (%rsp), %rsi
movq 0x10(%rsp), %rdx
jne 0x80f5a
imulq $0x18, 0x18(%rsp), %rax
movq 0x28(%rsp), %rcx
addq %rcx, %rax
addq $0x8, %rax
movq %rax, 0x58(%rsp)
movq %rcx, %rax
xorl %ebp, %ebp
movl $0x0, 0x24(%rsp)
movq 0x50(%rsp), %r15
movq 0x48(%rsp), %r12
movq 0x40(%rsp), %r13
cmpq %rdx, %rbp
je 0x80eef
cmpq %rbp, 0x18(%rsp)
je 0x80ee7
imulq $0x18, %rbp, %r14
cmpl $0x0, 0xc(%rax,%r14)
js 0x80ee7
addq %rax, %r14
andq $0x0, 0x98(%rsp)
movl 0x8(%r14), %esi
movq %rbx, %rdi
leaq 0xc(%rsp), %rdx
leaq 0x38(%rsp), %rcx
leaq 0x60(%rsp), %r8
callq 0x70b8f
movq 0x98(%rsp), %rax
cmpq $0x2, %rax
jb 0x80ed9
decq %rax
movq %rax, 0x98(%rsp)
movq 0x58(%rsp), %rax
movl (%rax), %edi
movl 0x8(%r14), %esi
movq %rbx, %rdx
movq %r13, %rcx
movq %r12, %r8
movq %r15, %r9
callq 0x70fd8
cmpq $0x1, %rax
jne 0x80ed9
movq 0x98(%rsp), %rax
movq 0xa8(%rsp), %rcx
xorl %edx, %edx
cmpq %rdx, %rax
je 0x80ea8
movq 0x20(%rbx), %rsi
movl (%rcx,%rdx,4), %edi
movb $0x1, 0x4(%rsi,%rdi,8)
incq %rdx
jmp 0x80e92
xorl %r14d, %r14d
cmpq %rax, %r14
jae 0x80ed1
movq 0xa8(%rsp), %rax
movl (%rax,%r14,4), %esi
movq %rbx, %rdi
callq 0x80870
incq %r14
movq 0x98(%rsp), %rax
jmp 0x80eab
incl 0x20(%rsp)
incl 0x24(%rsp)
movq (%rsp), %rsi
movq 0x28(%rsp), %rax
movq 0x10(%rsp), %rdx
incq %rbp
jmp 0x80df6
cmpl $0x0, 0x24(%rsp)
movq 0x30(%rsp), %r14
je 0x80cf8
andq $0x0, 0x98(%rsp)
movq %rax, %rcx
movl 0x18(%rsp), %eax
imulq $0x18, %rax, %rax
movl 0x8(%rcx,%rax), %esi
movq %rbx, %rdi
leaq 0xc(%rsp), %rdx
leaq 0x38(%rsp), %rcx
leaq 0x60(%rsp), %r8
callq 0x70b8f
movq 0x98(%rsp), %rax
movq 0xa8(%rsp), %rcx
xorl %edx, %edx
cmpq %rdx, %rax
je 0x80cf4
movq 0x20(%rbx), %rsi
movl (%rcx,%rdx,4), %edi
movb $0x2, 0x4(%rsi,%rdi,8)
incq %rdx
jmp 0x80f40
movq 0x30(%rsp), %r14
jmp 0x80cf8
movq %rbx, %rdi
callq 0x694eb
movq %rbx, %rdi
callq 0x69638
movq 0xa8(%rsp), %rdi
callq 0x2220
movl 0x20(%rsp), %eax
addq $0xc8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq