// File: /workspace/github_cpp_makefile_star2_O1/chhylp123[P]hifiasm/Overlaps.cpp
// Function: get_contained_reads_chain(ma_hit_t*, ma_hit_t_alloc*, ma_sub_t*, R_to_U*, ma_ug_t*, asg_t*, int, int, unsigned int, unsigned int, kvec_t_u32_warp*, kvec_asg_arc_t_warp*, unsigned int*, unsigned int*, unsigned int*, unsigned int, unsigned int)
int get_contained_reads_chain(ma_hit_t *h, ma_hit_t_alloc* sources, ma_sub_t *coverage_cut, 
R_to_U* ruIndex, ma_ug_t *ug, asg_t *r_g, int max_hang, int min_ovlp, uint32_t endRid, uint32_t uId,
kvec_t_u32_warp* chain_buffer, kvec_asg_arc_t_warp* chain_edges, uint32_t* return_ava_cur,
uint32_t* return_ava_ol, uint32_t* return_chainLen, uint32_t thresLen, uint32_t ignore_trio_flag)
{
    (*return_chainLen) = (*return_ava_cur) = (*return_ava_ol) = (uint32_t)-1;
    uint32_t trio_flag, non_trio_flag = (uint32_t)-1, contain_rId, contain_uId, is_Unitig;
    uint32_t chainLen = 0, ava_cur, test_oLen;
    int ql, tl;
    int32_t r;
    ma_sub_t *sq = NULL;
    ma_sub_t *st = NULL;
    asg_arc_t t;
    asg_t* nsg = ug->g;
    chain_buffer->a.n = 0;
    kv_push(uint32_t, chain_buffer->a, uId);
    if(chain_edges) chain_edges->a.n = 0;
    

    ///continue
    ///need to update h, endRid, chainLen, chain_buffer and chain_edges
    while (h)
    {
        sq = &(coverage_cut[Get_qn(*h)]);
        st = &(coverage_cut[Get_tn(*h)]);
        trio_flag = R_INF.trio_flag[Get_qn(*h)];

        ///don't want to edges between different haps
        non_trio_flag = (uint32_t)-1;
        if(ignore_trio_flag == 0)
        {
            if(trio_flag == FATHER) non_trio_flag = MOTHER;
            if(trio_flag == MOTHER) non_trio_flag = FATHER;
            if(R_INF.trio_flag[Get_tn(*h)] == non_trio_flag) break;
        }

        ///just need deleted edges
        ///sq might be deleted or not
        if(!st->del) break;
        if(!h->del) break;

        ///tn must be contained in another existing read
        get_R_to_U(ruIndex, Get_tn(*h), &contain_rId, &is_Unitig);
        if(contain_rId == (uint32_t)-1 || is_Unitig == 1) break;
        if(r_g->seq[contain_rId].del) break;

        get_R_to_U(ruIndex, contain_rId, &contain_uId, &is_Unitig);
        if(contain_uId == (uint32_t)-1 || is_Unitig != 1) break;
        if(nsg->seq[contain_uId].del) break;
        ///contain_uId must be a unitig

        ql = sq->e - sq->s; tl = st->e - st->s;
        r = ma_hit2arc(h, ql, tl, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);

        ///if st is contained in sq, or vice verse, skip
        if(r < 0) break;

        ///if sq and v are not in the same direction, skip
        ///endRid is (t.ul>>32), and t.v is a contained read
        if((t.ul>>32) != endRid) break;

        if(chain_edges) kv_push(asg_arc_t, chain_edges->a, t);
        chainLen++;
        kv_push(uint32_t, chain_buffer->a, contain_uId);
        ///endRid is (t.ul>>32), and t.v is a contained read
        ///find edges from t.v to existing unitigs
        ava_cur = get_num_edges2existing_nodes_advance(ug, r_g, sources, coverage_cut, ruIndex, 
                    max_hang, min_ovlp, t.v, &test_oLen, chain_buffer->a.a, chain_buffer->a.n, 
                    ignore_trio_flag);
        //means find an aim
        if(ava_cur > 0)
        {
            /**
            //do nothing if the chainLen == 1
            if(chainLen > 1)
            {
                asg_arc_t t_max;
                ma_hit_t_alloc* x = &(sources[(endRid>>1)]);
                uint32_t ava_ol_max = 0, ava_max = 0, k;
                for (k = 0; k < x->length; k++)
                {
                    h = &(x->buffer[k]);
                    sq = &(coverage_cut[Get_qn(*h)]);
                    st = &(coverage_cut[Get_tn(*h)]);
                    trio_flag = R_INF.trio_flag[Get_qn(*h)];

                    ///don't want to edges between different haps
                    non_trio_flag = (uint32_t)-1;
                    if(trio_flag == FATHER) non_trio_flag = MOTHER;
                    if(trio_flag == MOTHER) non_trio_flag = FATHER;
                    if(R_INF.trio_flag[Get_tn(*h)] == non_trio_flag) continue;
                    
                    ///just need deleted edges
                    ///sq might be deleted or not
                    if(!st->del) continue;
                    if(!h->del) continue;

                    ///tn must be contained in another existing read
                    get_R_to_U(ruIndex, Get_tn(*h), &contain_rId, &is_Unitig);
                    if(contain_rId == (uint32_t)-1 || is_Unitig == 1) continue;
                    if(r_g->seq[contain_rId].del) continue;

                    get_R_to_U(ruIndex, contain_rId, &contain_uId, &is_Unitig);
                    if(contain_uId == (uint32_t)-1 || is_Unitig != 1) continue;
                    if(nsg->seq[contain_uId].del) continue;
                    ///contain_uId must be a unitig

                    ql = sq->e - sq->s; tl = st->e - st->s;
                    r = ma_hit2arc(h, ql, tl, max_hang, asm_opt.max_hang_rate, min_ovlp, &t);

                    ///if st is contained in sq, or vice verse, skip
                    if(r < 0) continue;

                    ///if sq and v are not in the same direction, skip
                    if((t.ul>>32) != endRid) continue;

                    ///pop the last contain_uId
                    chain_buffer->a.n--;
                    kv_push(uint32_t, chain_buffer->a, contain_uId);

                    ///note: t.v is a contained read
                    ///we need to find existing reads linked with w
                    ava_cur = get_num_edges2existing_nodes_advance(ug, r_g, sources, coverage_cut, ruIndex, 
                    max_hang, min_ovlp, t.v, &test_oLen, chain_buffer->a.a, chain_buffer->a.n, 1);

                    if((ava_cur > ava_max) || (ava_cur == ava_max && test_oLen > ava_ol_max))
                    {
                        ava_max = ava_cur;
                        ava_ol_max = test_oLen;
                        t_max = t;
                    }
                }

                if(ava_max > 0)
                {
                    ava_cur = ava_max;
                    test_oLen = ava_ol_max;
                    if(chain_edges)
                    {
                        //pop the last edge
                        chain_edges->a.n--;
                        kv_push(asg_arc_t, chain_edges->a, t_max);
                    } 
                }
                else
                {
                    break;
                }
            }
            **/

            (*return_ava_cur) = ava_cur;
            (*return_ava_ol) = test_oLen;
            (*return_chainLen) = chainLen;
            h = NULL;
            return 1;
        }

        if(chainLen >= thresLen) break;

        ///endRid is (t.ul>>32), and t.v is a contained read
        ///haven't found a existing unitig from t.v
        ///check if t.v can link to a new contained read
        endRid = t.v; 
        h = get_best_contained_read(ug, r_g, sources, coverage_cut, ruIndex, 
            max_hang, min_ovlp, endRid, ignore_trio_flag);
    }

    return 0;    
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %r9, %r12
movq %rcx, 0x10(%rsp)
movq %rdx, 0x8(%rsp)
movq %rsi, 0x20(%rsp)
movq %rdi, %r13
movq 0xd0(%rsp), %rcx
movq 0xc8(%rsp), %rdx
movq 0xc0(%rsp), %rsi
movq 0xb8(%rsp), %rdi
movq 0xb0(%rsp), %r14
movl 0xa8(%rsp), %ebx
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
movl %eax, (%rdx)
movl %eax, (%rsi)
movl %eax, (%rcx)
movq %r8, 0x28(%rsp)
movq 0x18(%r8), %rax
movq %rax, 0x38(%rsp)
movq $0x0, (%r14)
cmpq $0x0, 0x8(%r14)
jne 0xf2ab8
movq $0x2, 0x8(%r14)
movq 0x10(%r14), %rdi
movl $0x8, %esi
callq 0x2370
movq 0xb8(%rsp), %rdi
movq %rax, 0x10(%r14)
movq (%r14), %rax
movq 0x10(%r14), %rcx
leaq 0x1(%rax), %rdx
movq %rdx, (%r14)
movl %ebx, (%rcx,%rax,4)
testq %rdi, %rdi
je 0xf2ad5
movq $0x0, (%rdi)
testq %r13, %r13
je 0xf2dc6
movl 0xe0(%rsp), %ecx
movl 0xd8(%rsp), %eax
movl 0xa0(%rsp), %ebx
cmpl $0x1, %eax
adcl $0x0, %eax
movl %eax, 0x18(%rsp)
movl $0x1, %ebp
movq %r12, 0x30(%rsp)
movq (%r13), %rax
shrq $0x20, %rax
movl 0xc(%r13), %edi
movq %rcx, %r15
testl %ecx, %ecx
jne 0xf2b4d
leaq 0x19870f(%rip), %rcx    # 0x28b230
movq 0x28(%rcx), %rcx
movb (%rcx,%rax), %dl
xorl %esi, %esi
cmpb $0x1, %dl
sete %sil
leal (%rsi,%rsi,2), %esi
decl %esi
cmpb $0x2, %dl
movl $0x1, %edx
cmovel %edx, %esi
movzbl (%rcx,%rdi), %ecx
cmpl %ecx, %esi
je 0xf2dc6
leaq (%rdi,%rdi,2), %rcx
movq 0x8(%rsp), %rdx
leaq (%rdx,%rcx,4), %rdx
movl (%rdx), %ecx
testl %ecx, %ecx
jns 0xf2dc6
cmpq $0x0, 0x18(%r13)
jns 0xf2dc6
movq 0x10(%rsp), %r10
movq (%r10), %rsi
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
movl $0x0, 0x4(%rsp)
cmpq %rdi, %rsi
jbe 0xf2ba6
movq 0x8(%r10), %r9
movl (%r9,%rdi,4), %edi
cmpl $-0x1, %edi
je 0xf2ba6
movl %edi, %r8d
andl $0x7fffffff, %r8d       # imm = 0x7FFFFFFF
shrl $0x1f, %edi
jmp 0xf2ba8
xorl %edi, %edi
cmpl $-0x1, %r8d
je 0xf2dce
testb %dil, %dil
jne 0xf2dce
movq 0x20(%r12), %rdi
movl %r8d, %r8d
cmpl $0x0, (%rdi,%r8,8)
js 0xf2dce
movb $0x1, %dil
movl $0xffffffff, %r12d      # imm = 0xFFFFFFFF
cmpq %r8, %rsi
jbe 0xf2bf9
movq 0x8(%r10), %rsi
movl (%rsi,%r8,4), %esi
cmpl $-0x1, %esi
je 0xf2bf9
movl %esi, %r12d
andl $0x7fffffff, %r12d      # imm = 0x7FFFFFFF
testl %esi, %esi
setns %dil
cmpl $-0x1, %r12d
je 0xf2dce
testb %dil, %dil
jne 0xf2dce
movq 0x38(%rsp), %rsi
movq 0x20(%rsi), %rsi
movl %r12d, %edi
cmpl $0x0, (%rsi,%rdi,8)
js 0xf2dce
leaq (%rax,%rax,2), %rax
movq 0x8(%rsp), %rsi
leaq (%rsi,%rax,4), %rax
movl 0x4(%rax), %esi
movl (%rax), %eax
movl $0x7fffffff, %edi       # imm = 0x7FFFFFFF
andl %edi, %eax
subl %eax, %esi
movl 0x4(%rdx), %edx
andl %edi, %ecx
subl %ecx, %edx
leaq 0x197b0d(%rip), %rax    # 0x28a758
movss 0x158(%rax), %xmm0
movq %r13, %rdi
movl 0x90(%rsp), %ecx
movl 0x98(%rsp), %r13d
movl %r13d, %r8d
leaq 0x40(%rsp), %r9
callq 0xa159b
testl %eax, %eax
js 0xf2dce
cmpl %ebx, 0x44(%rsp)
jne 0xf2dce
movq 0xb8(%rsp), %rsi
testq %rsi, %rsi
je 0xf2cf8
movq 0x8(%rsi), %rax
cmpq %rax, (%rsi)
jne 0xf2cd3
leaq (%rax,%rax), %rcx
testq %rax, %rax
movl $0x2, %eax
cmoveq %rax, %rcx
movq %rcx, 0x8(%rsi)
movq 0xb8(%rsp), %rax
movq 0x10(%rax), %rdi
shlq $0x3, %rcx
leaq (%rcx,%rcx,2), %rsi
callq 0x2370
movq 0xb8(%rsp), %rsi
movq %rax, 0x10(%rsi)
movq (%rsi), %rax
movq 0x10(%rsi), %rcx
leaq 0x1(%rax), %rdx
movq %rdx, (%rsi)
leaq (%rax,%rax,2), %rax
movq 0x50(%rsp), %rdx
movq %rdx, 0x10(%rcx,%rax,8)
movups 0x40(%rsp), %xmm0
movups %xmm0, (%rcx,%rax,8)
movq 0x8(%r14), %rax
cmpq %rax, (%r14)
jne 0xf2d26
leaq (%rax,%rax), %rsi
testq %rax, %rax
movl $0x2, %eax
cmoveq %rax, %rsi
movq %rsi, 0x8(%r14)
movq 0x10(%r14), %rdi
shlq $0x2, %rsi
callq 0x2370
movq %rax, 0x10(%r14)
movq (%r14), %rax
movq 0x10(%r14), %r10
leaq 0x1(%rax), %r11
movq %r11, (%r14)
movl %r12d, (%r10,%rax,4)
movl 0x48(%rsp), %ebx
movq 0x28(%rsp), %rdi
movq 0x30(%rsp), %r12
movq %r12, %rsi
movq 0x20(%rsp), %rdx
movq 0x8(%rsp), %rcx
movq 0x10(%rsp), %r8
movl 0x90(%rsp), %r9d
pushq %r15
pushq %r11
pushq %r10
leaq 0x34(%rsp), %rax
pushq %rax
pushq %rbx
pushq %r13
callq 0x102777
addq $0x30, %rsp
testl %eax, %eax
jne 0xf2de1
cmpl %ebp, 0x18(%rsp)
je 0xf2dce
subq $0x8, %rsp
movq 0x30(%rsp), %rdi
movq %r12, %rsi
movq 0x28(%rsp), %rdx
movq 0x10(%rsp), %rcx
movq 0x18(%rsp), %r8
movl 0x98(%rsp), %r9d
pushq %r15
pushq %rbx
pushq %r13
callq 0xf2622
addq $0x20, %rsp
movq %r15, %rcx
movq %rax, %r13
incl %ebp
testq %rax, %rax
jne 0xf2b07
jmp 0xf2dce
movl $0x0, 0x4(%rsp)
movl 0x4(%rsp), %eax
addq $0x58, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0xc0(%rsp), %rcx
movl %eax, (%rcx)
movl 0x1c(%rsp), %eax
movq 0xc8(%rsp), %rcx
movl %eax, (%rcx)
movq 0xd0(%rsp), %rax
movl %ebp, (%rax)
movl $0x1, 0x4(%rsp)
jmp 0xf2dce