// File: chhylp123[P]hifiasm/Overlaps.cpp
// Function: get_ug_coverage_aggressive(ma_ug_t*, unsigned int, asg_t*, ma_sub_t const*, ma_hit_t_alloc*, R_to_U*, unsigned char*, unsigned long*)
uint32_t get_ug_coverage_aggressive(ma_ug_t *ug, uint32_t uID, asg_t* read_g, 
const ma_sub_t* coverage_cut, ma_hit_t_alloc* sources, R_to_U* ruIndex, uint8_t* r_flag,
uint64_t *n_utg)
{
    ma_utg_t* u = &(ug->u.a[uID]);
    uint32_t k, j, rId, tn, is_Unitig;
    long long R_bases = 0, C_bases = 0;
    ma_hit_t *h;
    if(u->m == 0) return 0;

    for (k = 0; k < u->n; k++)
    {
        rId = u->a[k]>>33;
        r_flag[rId] = 1;
    }

    (*n_utg) = u->n;
    uint32_t nv, i;
    asg_arc_t *av = NULL;
    for (i = 0; i < 2; i++)
    {
        nv = asg_arc_n(ug->g, (uID<<1)+i);
        av = asg_arc_a(ug->g, (uID<<1)+i);
        for (j = 0; j < nv; j++)
        {
            u = &(ug->u.a[av[j].v>>1]);
            for (k = 0; k < u->n; k++)
            {
                rId = u->a[k]>>33;
                r_flag[rId] = 2;
            }
        }
    }
    

    u = &(ug->u.a[uID]);
    for (k = 0; k < u->n; k++)
    {
        rId = u->a[k]>>33;
        R_bases += (coverage_cut[rId].e - coverage_cut[rId].s);
        for (j = 0; j < (uint64_t)(sources[rId].length); j++)
        {
            h = &(sources[rId].buffer[j]);
            if(h->el != 1) continue;
            tn = Get_tn((*h));
            if(read_g->seq[tn].del == 1)
            {
                ///get the id of read that contains it 
                get_R_to_U(ruIndex, tn, &tn, &is_Unitig);
                if(tn == (uint32_t)-1 || is_Unitig == 1 || read_g->seq[tn].del == 1) continue;
            }
            if(read_g->seq[tn].del == 1) continue;
            if(r_flag[tn] == 0) continue;
            if(r_flag[tn] == 2)
            {
                (*n_utg)++;
                r_flag[tn] = 3;
            } 
            C_bases += (Get_qe((*h)) - Get_qs((*h)));
            ///if(uID == 35701) fprintf(stderr, "flag: %u, coverage: %d\n", r_flag[tn], (int)(Get_qe((*h)) - Get_qs((*h))));
        }
    }





    for (k = 0; k < u->n; k++)
    {
        rId = u->a[k]>>33;
        r_flag[rId] = 0;
    }

    for (i = 0; i < 2; i++)
    {
        nv = asg_arc_n(ug->g, (uID<<1)+i);
        av = asg_arc_a(ug->g, (uID<<1)+i);
        for (j = 0; j < nv; j++)
        {
            u = &(ug->u.a[av[j].v>>1]);
            for (k = 0; k < u->n; k++)
            {
                rId = u->a[k]>>33;
                r_flag[rId] = 0;
            }
        }
    }

    ///if(uID == 35701) fprintf(stderr, "C_bases: %lld, R_bases: %lld, (*n_utg): %lu\n", C_bases, R_bases, (*n_utg));
    return C_bases/R_bases;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x80, %rsp
movq 0x18(%rbp), %rax
movq 0x10(%rbp), %rax
movq %rdi, -0x10(%rbp)
movl %esi, -0x14(%rbp)
movq %rdx, -0x20(%rbp)
movq %rcx, -0x28(%rbp)
movq %r8, -0x30(%rbp)
movq %r9, -0x38(%rbp)
movq -0x10(%rbp), %rax
movq 0x10(%rax), %rax
movl -0x14(%rbp), %ecx
imulq $0x28, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0x40(%rbp)
movq $0x0, -0x60(%rbp)
movq $0x0, -0x68(%rbp)
movq -0x40(%rbp), %rax
cmpl $0x0, 0xc(%rax)
jne 0xee746
movl $0x0, -0x4(%rbp)
jmp 0xeeb85
movl $0x0, -0x44(%rbp)
movl -0x44(%rbp), %eax
movq -0x40(%rbp), %rcx
cmpl 0x10(%rcx), %eax
jae 0xee785
movq -0x40(%rbp), %rax
movq 0x18(%rax), %rax
movl -0x44(%rbp), %ecx
movq (%rax,%rcx,8), %rax
shrq $0x21, %rax
movl %eax, -0x4c(%rbp)
movq 0x10(%rbp), %rax
movl -0x4c(%rbp), %ecx
movb $0x1, (%rax,%rcx)
movl -0x44(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x44(%rbp)
jmp 0xee74d
movq -0x40(%rbp), %rax
movl 0x10(%rax), %eax
movl %eax, %ecx
movq 0x18(%rbp), %rax
movq %rcx, (%rax)
movq $0x0, -0x80(%rbp)
movl $0x0, -0x78(%rbp)
cmpl $0x2, -0x78(%rbp)
jae 0xee893
movq -0x10(%rbp), %rax
movq 0x18(%rax), %rax
movq 0x28(%rax), %rax
movl -0x14(%rbp), %ecx
shll %ecx
addl -0x78(%rbp), %ecx
movl %ecx, %ecx
movq (%rax,%rcx,8), %rax
movl %eax, -0x74(%rbp)
movq -0x10(%rbp), %rax
movq 0x18(%rax), %rax
movq 0x8(%rax), %rax
movq -0x10(%rbp), %rcx
movq 0x18(%rcx), %rcx
movq 0x28(%rcx), %rcx
movl -0x14(%rbp), %edx
shll %edx
addl -0x78(%rbp), %edx
movl %edx, %edx
movq (%rcx,%rdx,8), %rcx
shrq $0x20, %rcx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0x80(%rbp)
movl $0x0, -0x48(%rbp)
movl -0x48(%rbp), %eax
cmpl -0x74(%rbp), %eax
jae 0xee883
movq -0x10(%rbp), %rax
movq 0x10(%rax), %rax
movq -0x80(%rbp), %rcx
movl -0x48(%rbp), %edx
imulq $0x18, %rdx, %rdx
addq %rdx, %rcx
movl 0x8(%rcx), %ecx
shrl %ecx
movl %ecx, %ecx
imulq $0x28, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0x40(%rbp)
movl $0x0, -0x44(%rbp)
movl -0x44(%rbp), %eax
movq -0x40(%rbp), %rcx
cmpl 0x10(%rcx), %eax
jae 0xee876
movq -0x40(%rbp), %rax
movq 0x18(%rax), %rax
movl -0x44(%rbp), %ecx
movq (%rax,%rcx,8), %rax
shrq $0x21, %rax
movl %eax, -0x4c(%rbp)
movq 0x10(%rbp), %rax
movl -0x4c(%rbp), %ecx
movb $0x2, (%rax,%rcx)
movl -0x44(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x44(%rbp)
jmp 0xee83e
jmp 0xee878
movl -0x48(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x48(%rbp)
jmp 0xee807
jmp 0xee885
movl -0x78(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x78(%rbp)
jmp 0xee7a4
movq -0x10(%rbp), %rax
movq 0x10(%rax), %rax
movl -0x14(%rbp), %ecx
imulq $0x28, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0x40(%rbp)
movl $0x0, -0x44(%rbp)
movl -0x44(%rbp), %eax
movq -0x40(%rbp), %rcx
cmpl 0x10(%rcx), %eax
jae 0xeea43
movq -0x40(%rbp), %rax
movq 0x18(%rax), %rax
movl -0x44(%rbp), %ecx
movq (%rax,%rcx,8), %rax
shrq $0x21, %rax
movl %eax, -0x4c(%rbp)
movq -0x28(%rbp), %rax
movl -0x4c(%rbp), %ecx
imulq $0xc, %rcx, %rcx
addq %rcx, %rax
movl 0x4(%rax), %eax
movq -0x28(%rbp), %rcx
movl -0x4c(%rbp), %edx
imulq $0xc, %rdx, %rdx
addq %rdx, %rcx
movl (%rcx), %ecx
andl $0x7fffffff, %ecx       # imm = 0x7FFFFFFF
subl %ecx, %eax
movl %eax, %eax
addq -0x60(%rbp), %rax
movq %rax, -0x60(%rbp)
movl $0x0, -0x48(%rbp)
movl -0x48(%rbp), %eax
movq -0x30(%rbp), %rcx
movl -0x4c(%rbp), %edx
imulq $0x18, %rdx, %rdx
addq %rdx, %rcx
movl 0xc(%rcx), %ecx
cmpq %rcx, %rax
jae 0xeea33
movq -0x30(%rbp), %rax
movl -0x4c(%rbp), %ecx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movq (%rax), %rax
movl -0x48(%rbp), %ecx
imulq $0x28, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0x70(%rbp)
movq -0x70(%rbp), %rax
movzbl 0x20(%rax), %eax
cmpl $0x1, %eax
je 0xee95e
jmp 0xeea25
movq -0x70(%rbp), %rax
movl 0xc(%rax), %eax
movl %eax, -0x50(%rbp)
movq -0x20(%rbp), %rax
movq 0x20(%rax), %rax
movl -0x50(%rbp), %ecx
movl (%rax,%rcx,8), %eax
shrl $0x1f, %eax
cmpl $0x1, %eax
jne 0xee9b8
movq -0x38(%rbp), %rdi
movl -0x50(%rbp), %esi
leaq -0x50(%rbp), %rdx
leaq -0x54(%rbp), %rcx
callq 0xd3d50
cmpl $-0x1, -0x50(%rbp)
je 0xee9b4
cmpl $0x1, -0x54(%rbp)
je 0xee9b4
movq -0x20(%rbp), %rax
movq 0x20(%rax), %rax
movl -0x50(%rbp), %ecx
movl (%rax,%rcx,8), %eax
shrl $0x1f, %eax
cmpl $0x1, %eax
jne 0xee9b6
jmp 0xeea25
jmp 0xee9b8
movq -0x20(%rbp), %rax
movq 0x20(%rax), %rax
movl -0x50(%rbp), %ecx
movl (%rax,%rcx,8), %eax
shrl $0x1f, %eax
cmpl $0x1, %eax
jne 0xee9d0
jmp 0xeea25
movq 0x10(%rbp), %rax
movl -0x50(%rbp), %ecx
movzbl (%rax,%rcx), %eax
cmpl $0x0, %eax
jne 0xee9e2
jmp 0xeea25
movq 0x10(%rbp), %rax
movl -0x50(%rbp), %ecx
movzbl (%rax,%rcx), %eax
cmpl $0x2, %eax
jne 0xeea0b
movq 0x18(%rbp), %rax
movq (%rax), %rcx
addq $0x1, %rcx
movq %rcx, (%rax)
movq 0x10(%rbp), %rax
movl -0x50(%rbp), %ecx
movb $0x3, (%rax,%rcx)
movq -0x70(%rbp), %rax
movl 0x8(%rax), %eax
movq -0x70(%rbp), %rcx
movq (%rcx), %rcx
subl %ecx, %eax
movl %eax, %eax
addq -0x68(%rbp), %rax
movq %rax, -0x68(%rbp)
movl -0x48(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x48(%rbp)
jmp 0xee910
jmp 0xeea35
movl -0x44(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x44(%rbp)
jmp 0xee8b0
movl $0x0, -0x44(%rbp)
movl -0x44(%rbp), %eax
movq -0x40(%rbp), %rcx
cmpl 0x10(%rcx), %eax
jae 0xeea82
movq -0x40(%rbp), %rax
movq 0x18(%rax), %rax
movl -0x44(%rbp), %ecx
movq (%rax,%rcx,8), %rax
shrq $0x21, %rax
movl %eax, -0x4c(%rbp)
movq 0x10(%rbp), %rax
movl -0x4c(%rbp), %ecx
movb $0x0, (%rax,%rcx)
movl -0x44(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x44(%rbp)
jmp 0xeea4a
movl $0x0, -0x78(%rbp)
cmpl $0x2, -0x78(%rbp)
jae 0xeeb78
movq -0x10(%rbp), %rax
movq 0x18(%rax), %rax
movq 0x28(%rax), %rax
movl -0x14(%rbp), %ecx
shll %ecx
addl -0x78(%rbp), %ecx
movl %ecx, %ecx
movq (%rax,%rcx,8), %rax
movl %eax, -0x74(%rbp)
movq -0x10(%rbp), %rax
movq 0x18(%rax), %rax
movq 0x8(%rax), %rax
movq -0x10(%rbp), %rcx
movq 0x18(%rcx), %rcx
movq 0x28(%rcx), %rcx
movl -0x14(%rbp), %edx
shll %edx
addl -0x78(%rbp), %edx
movl %edx, %edx
movq (%rcx,%rdx,8), %rcx
shrq $0x20, %rcx
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0x80(%rbp)
movl $0x0, -0x48(%rbp)
movl -0x48(%rbp), %eax
cmpl -0x74(%rbp), %eax
jae 0xeeb68
movq -0x10(%rbp), %rax
movq 0x10(%rax), %rax
movq -0x80(%rbp), %rcx
movl -0x48(%rbp), %edx
imulq $0x18, %rdx, %rdx
addq %rdx, %rcx
movl 0x8(%rcx), %ecx
shrl %ecx
movl %ecx, %ecx
imulq $0x28, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0x40(%rbp)
movl $0x0, -0x44(%rbp)
movl -0x44(%rbp), %eax
movq -0x40(%rbp), %rcx
cmpl 0x10(%rcx), %eax
jae 0xeeb5b
movq -0x40(%rbp), %rax
movq 0x18(%rax), %rax
movl -0x44(%rbp), %ecx
movq (%rax,%rcx,8), %rax
shrq $0x21, %rax
movl %eax, -0x4c(%rbp)
movq 0x10(%rbp), %rax
movl -0x4c(%rbp), %ecx
movb $0x0, (%rax,%rcx)
movl -0x44(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x44(%rbp)
jmp 0xeeb23
jmp 0xeeb5d
movl -0x48(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x48(%rbp)
jmp 0xeeaec
jmp 0xeeb6a
movl -0x78(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x78(%rbp)
jmp 0xeea89
movq -0x68(%rbp), %rax
cqto
idivq -0x60(%rbp)
movl %eax, -0x4(%rbp)
movl -0x4(%rbp), %eax
addq $0x80, %rsp
popq %rbp
retq
nopw %cs:(%rax,%rax)