// File: /workspace/github_cpp_makefile_star2_O1/chhylp123[P]hifiasm/Overlaps.cpp
// Function: asg_arc_cut_long_equal_tips_assembly(asg_t*, ma_hit_t_alloc*, long long, R_to_U*)
int asg_arc_cut_long_equal_tips_assembly(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;

    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), n_tips;
        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;
        n_tips = 0;
        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(base_maxLen < ll)
                {
                    base_maxLen = ll;
                    base_maxLen_i = i;
                }

                if(flag == END_TIPS)
                {
                    n_tips++;
                }
            }
        }

        ///at least one tip
        if(n_tips > 0)
        {
            for (i = 0; i < nv; i++)
            {
                if(i == base_maxLen_i) continue;
                if (!av[i].del)
                {
                    b.b.n = 0;
                    if(detect_single_path_with_dels_contigLen(g, av[i].v, &convex, &ll, &b) 
                    != END_TIPS)
                    {
                        continue;
                    }
                    //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, 0x58(%rsp)
movq %rdx, 0x50(%rsp)
movq %rsi, 0x48(%rsp)
movq %rdi, %rbx
callq 0x300fc
movl 0x14(%rbx), %eax
xorps %xmm0, %xmm0
movaps %xmm0, 0xb0(%rsp)
movaps %xmm0, 0xa0(%rsp)
movaps %xmm0, 0x90(%rsp)
movaps %xmm0, 0x80(%rsp)
movaps %xmm0, 0x70(%rsp)
movaps %xmm0, 0x60(%rsp)
movq $0x0, 0xc0(%rsp)
addl %eax, %eax
je 0xbb1ce
movl %eax, %r14d
xorl %r15d, %r15d
movl $0xffffffff, %ebp       # imm = 0xFFFFFFFF
xorl %r12d, %r12d
movq %r14, 0x38(%rsp)
movq 0x28(%rbx), %rax
movq (%rax,%r15,8), %rdi
cmpl $0x2, %edi
jb 0xbb1c0
movq 0x20(%rbx), %rax
movl %r15d, %ecx
shrl %ecx
cmpl $0x0, (%rax,%rcx,8)
js 0xbb1c0
cmpb $0x1, 0x4(%rax,%rcx,8)
je 0xbb1c0
movq %rdi, %rax
andq %rbp, %rax
je 0xbb1c0
movq 0x8(%rbx), %rcx
movq %rdi, %rdx
shrq $0x20, %rdx
leaq (%rdx,%rdx,2), %rdx
leaq (%rcx,%rdx,8), %rsi
movq %rsi, 0x28(%rsp)
leaq (%rcx,%rdx,8), %r14
addq $0xc, %r14
shlq $0x3, %rax
leaq (%rax,%rax,2), %rax
xorl %ecx, %ecx
xorl %edx, %edx
movl (%r14,%rcx), %esi
notl %esi
shrl $0x1f, %esi
addl %esi, %edx
addq $0x18, %rcx
cmpq %rcx, %rax
jne 0xbae8e
cmpl $0x2, %edx
jae 0xbaeb1
movq 0x38(%rsp), %r14
jmp 0xbb1c0
movq %r15, 0x8(%rsp)
movl %r12d, 0x4(%rsp)
cmpl $0x1, %edi
adcl $0x0, %edi
movq $-0x1, %r13
xorl %r15d, %r15d
xorl %eax, %eax
movq $-0x1, %r12
movq %rdi, 0x20(%rsp)
cmpl $0x0, (%r14)
js 0xbaf1f
movl -0x4(%r14), %esi
movq %rbx, %rdi
leaq 0x1c(%rsp), %rdx
leaq 0x30(%rsp), %rcx
xorl %r8d, %r8d
movl %eax, 0x10(%rsp)
callq 0xa96f6
movq 0x20(%rsp), %rdi
movq 0x30(%rsp), %rcx
cmpq %rcx, %r12
cmovleq %rcx, %r12
cmovlq %r15, %r13
xorl %ecx, %ecx
cmpl $0x5, %eax
movl 0x10(%rsp), %eax
sete %cl
addl %ecx, %eax
incq %r15
addq $0x18, %r14
cmpq %r15, %rdi
jne 0xbaed9
testl %eax, %eax
movl 0x4(%rsp), %r12d
je 0xbb152
leaq (,%r13,2), %rax
addq %r13, %rax
movq 0x28(%rsp), %rcx
leaq (%rcx,%rax,8), %rax
addq $0x8, %rax
movq %rax, 0x40(%rsp)
xorl %r14d, %r14d
movl $0x0, 0x18(%rsp)
movq 0x8(%rsp), %r15
movq %r13, 0x10(%rsp)
cmpq %r14, %r13
je 0xbb13c
leaq (%r14,%r14,2), %rax
movq 0x28(%rsp), %rcx
cmpl $0x0, 0xc(%rcx,%rax,8)
js 0xbb13c
leaq (%rcx,%rax,8), %r15
movq $0x0, 0x98(%rsp)
movl 0x8(%r15), %esi
movq %rbx, %rdi
leaq 0x1c(%rsp), %rdx
leaq 0x30(%rsp), %rcx
leaq 0x60(%rsp), %r8
callq 0xa96f6
cmpl $0x5, %eax
jne 0xbb12d
movq 0x40(%rsp), %rax
movl (%rax), %edi
movl 0x8(%r15), %esi
movq %rbx, %rdx
movq 0x48(%rsp), %rcx
movq 0x50(%rsp), %r8
movq 0x58(%rsp), %r9
callq 0xa9c9f
cmpq $0x1, %rax
jne 0xbb12d
movl %r12d, 0x4(%rsp)
movq 0x98(%rsp), %rax
testq %rax, %rax
je 0xbb017
movq 0x20(%rbx), %rcx
movq 0xa8(%rsp), %rdx
xorl %esi, %esi
movl (%rdx,%rsi,4), %edi
movb $0x1, 0x4(%rcx,%rdi,8)
incq %rsi
cmpq %rsi, %rax
jne 0xbb007
cmpq $0x0, 0x98(%rsp)
je 0xbb121
xorl %eax, %eax
movq 0xa8(%rsp), %rcx
movl (%rcx,%rax,4), %ecx
movq 0x20(%rbx), %rdx
cmpb $0x1, 0x4(%rdx,%rcx,8)
jne 0xbb110
addl %ecx, %ecx
xorl %edx, %edx
leaq (%rdx,%rcx), %rsi
movq 0x28(%rbx), %rdi
movq (%rdi,%rsi,8), %r8
movq %r8, %rdi
andq %rbp, %rdi
je 0xbb100
shrq $0x20, %r8
leaq (%r8,%r8,2), %r8
shlq $0x3, %r8
addq 0x8(%rbx), %r8
xorl %r9d, %r9d
leaq (%r9,%r9,2), %r11
movl 0xc(%r8,%r11,8), %r10d
testl %r10d, %r10d
js 0xbb0f4
leaq (%r8,%r11,8), %r15
movq 0x20(%rbx), %r12
movl 0x8(%r15), %r11d
movl %r11d, %r13d
shrl %r13d
cmpb $0x1, 0x4(%r12,%r13,8)
je 0xbb0f4
orl $0x80000000, %r10d      # imm = 0x80000000
movl %r10d, 0xc(%r15)
xorq $0x1, %r11
movq 0x28(%rbx), %r10
movq (%r10,%r11,8), %r11
movq %r11, %r10
andq %rbp, %r10
je 0xbb0f4
movq 0x8(%rbx), %r15
shrq $0x20, %r11
shlq $0x3, %r10
leaq (%r10,%r10,2), %r10
leaq (%r11,%r11,2), %r11
leaq (%r15,%r11,8), %r11
addq $0xc, %r11
xorl %r15d, %r15d
movl -0x4(%r11,%r15), %r12d
xorl %esi, %r12d
cmpl $0x1, %r12d
jne 0xbb0eb
orb $-0x80, 0x3(%r11,%r15)
addq $0x18, %r15
cmpq %r15, %r10
jne 0xbb0d7
incq %r9
cmpq %rdi, %r9
jne 0xbb071
leaq 0x1(%rdx), %rsi
testq %rdx, %rdx
movq %rsi, %rdx
je 0xbb046
incq %rax
cmpq 0x98(%rsp), %rax
jb 0xbb028
movl 0x4(%rsp), %r12d
incl %r12d
incl 0x18(%rsp)
movq 0x8(%rsp), %r15
movq 0x20(%rsp), %rdi
movq 0x10(%rsp), %r13
incq %r14
cmpq %rdi, %r14
jne 0xbaf6a
cmpl $0x0, 0x18(%rsp)
sete %al
jmp 0xbb159
movb $0x1, %al
movq 0x8(%rsp), %r15
testb %al, %al
movq 0x38(%rsp), %r14
movq 0x28(%rsp), %rcx
jne 0xbb1c0
movq $0x0, 0x98(%rsp)
movl %r13d, %eax
leaq (%rax,%rax,2), %rax
movl 0x8(%rcx,%rax,8), %esi
movq %rbx, %rdi
leaq 0x1c(%rsp), %rdx
leaq 0x30(%rsp), %rcx
leaq 0x60(%rsp), %r8
callq 0xa96f6
movq 0x98(%rsp), %rax
testq %rax, %rax
je 0xbb1c0
movq 0x20(%rbx), %rcx
movq 0xa8(%rsp), %rdx
xorl %esi, %esi
movl (%rdx,%rsi,4), %edi
movb $0x2, 0x4(%rcx,%rdi,8)
incq %rsi
cmpq %rsi, %rax
jne 0xbb1b0
incq %r15
cmpq %r14, %r15
jne 0xbae27
jmp 0xbb1d1
xorl %r12d, %r12d
movq %rbx, %rdi
callq 0xa02fa
movq %rbx, %rdi
callq 0xa0333
movq %rbx, %rdi
callq 0xa03e9
orb $-0x80, 0x17(%rbx)
movq 0xa8(%rsp), %rdi
callq 0x2220
movl %r12d, %eax
addq $0xc8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq