// File: /workspace/github_cpp_makefile_star2_O1/chhylp123[P]hifiasm/Correct.cpp
// Function: region_phase_adv(overlap_region_alloc*, ul_idx_t const*, ug_opt_t const*, kv_ul_ov_t*, asg64_v*, asg64_v*, asg64_v*, long)
void region_phase_adv(overlap_region_alloc* ol, const ul_idx_t *uref, const ug_opt_t *uopt, kv_ul_ov_t *c_idx, asg64_v* idx, asg64_v* buf, asg64_v* buf1, int64_t ulid)
{
    int64_t on = ol->length, k, i, zwn, q[2], t[2], w[2]; 
    uint64_t m; overlap_region *z; ul_ov_t *cp;
    kv_resize(uint64_t, *idx, (ol->length<<1)); 
    kv_resize(ul_ov_t, *c_idx, ol->length);
    for (k = idx->n = c_idx->n = 0; k < on; k++) {
        z = &(ol->list[k]); zwn = z->w_list.n; 
        z->align_length = 0; z->overlapLen = (uint32_t)-1;
        z->non_homopolymer_errors = 0;
        if(!zwn) continue;
        q[0] = q[1] = t[0] = t[1] = w[0] = w[1] = INT32_MIN;
        for (i = 0; i < zwn; i++) {
            if((z->w_list.a[i].x_start==(q[1]+1)) && ((z->w_list.a[i].y_start==(t[1]+1)))) {
                q[1] = z->w_list.a[i].x_end;
                t[1] = z->w_list.a[i].y_end;
                w[1] = i;
            } else {
                if(q[0] != INT32_MIN) {
                    m = ((uint64_t)q[0])<<1; m <<= 32; 
                    m += c_idx->n; kv_push(uint64_t, *idx, m);
                    m = (((uint64_t)q[1])<<1)+1; m <<= 32; 
                    m += c_idx->n; kv_push(uint64_t, *idx, m);

                    kv_pushp(ul_ov_t, *c_idx, &cp);
                    ovlp_id(*cp) = k; ///ovlp id
                    ovlp_min_wid(*cp) = w[0]; ///beg id of windows
                    ovlp_max_wid(*cp) = w[1]; ///end id of windows
                    ovlp_cur_wid(*cp) = w[0]; ///cur id of windows
                    ovlp_cur_xoff(*cp) = z->w_list.a[w[0]].x_start; ///cur xpos
                    ovlp_cur_coff(*cp) = 0; ///cur cigar off in cur window
                }

                q[0] = z->w_list.a[i].x_start; q[1] = z->w_list.a[i].x_end;
                t[0] = z->w_list.a[i].y_start; t[1] = z->w_list.a[i].y_end;
                w[0] = i; w[1] = i;
            }
        }
        if(q[0] != INT32_MIN) {
            m = ((uint64_t)q[0])<<1; m <<= 32; 
            m += c_idx->n; kv_push(uint64_t, *idx, m);
            m = (((uint64_t)q[1])<<1)+1; m <<= 32; 
            m += c_idx->n; kv_push(uint64_t, *idx, m);

            kv_pushp(ul_ov_t, *c_idx, &cp);
            ovlp_id(*cp) = k; ///ovlp id
            ovlp_min_wid(*cp) = w[0]; ///beg id of windows
            ovlp_max_wid(*cp) = w[1]; ///end id of windows
            ovlp_cur_wid(*cp) = w[0]; ///cur id of windows
            ovlp_cur_xoff(*cp) = z->w_list.a[w[0]].x_start; ///cur xpos
            ovlp_cur_coff(*cp) = 0; ///cur cigar off in cur window
        }
    }
    radix_sort_bc64(idx->a, idx->a+idx->n);
    //this is used with gen_region_phase, now give up
    //gen_gov_idx(ol, uref, uopt, G_CHAIN_BW, N_GCHAIN_RATE, buf1);
    // for (m = 0; m < c_idx->n; m++) {
    //     fprintf(stderr, "+++[M::%s::utg%.6dl] q[%d, %d), t[%d, %d), wn::%d\n", __func__, 
    //     (int32_t)ol->list[ovlp_id(c_idx->a[m])].y_id+1,
    //     ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_min_wid(c_idx->a[m])].x_start,
    //     ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_max_wid(c_idx->a[m])].x_end+1,
    //     ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_min_wid(c_idx->a[m])].y_start,
    //     ol->list[ovlp_id(c_idx->a[m])].w_list.a[ovlp_max_wid(c_idx->a[m])].y_end+1,
    //     ovlp_max_wid(c_idx->a[m])+1-ovlp_min_wid(c_idx->a[m]));
    // }
    
    if(rphase_detect0(ol, c_idx, idx, buf, buf1)) {//refine phasing
        reacal_phase(ol, c_idx, idx, buf, buf1);
    }

    for (k = 0; k < on; k++) {
        z = &(ol->list[k]); 
        z->overlapLen = z->x_pos_e+1-z->x_pos_s; 
        z->non_homopolymer_errors = 0; zwn = 0;
        for (i = m = 0; i < z->align_length; i++) {
            z->w_list.a[m] = z->w_list.a[z->w_list.n+i];
            if(z->w_list.a[m].clen > 0) {
                z->non_homopolymer_errors += z->w_list.a[m].clen;
                zwn += z->w_list.a[m].x_end-z->w_list.a[m].x_start;
            } 
            m++;
        }
        z->w_list.n = m; 
        assert(zwn <= z->overlapLen);
        z->align_length = z->overlapLen - zwn;
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x48, %rsp
movq %r9, %r14
movq %rcx, %r9
movq %rdi, %rbx
movq 0x10(%rdi), %r15
leaq (%r15,%r15), %rax
movq %r8, 0x10(%rsp)
cmpq %rax, 0x8(%r8)
movq %rcx, (%rsp)
jae 0x799ab
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq 0x10(%rsp), %r12
movq %rax, 0x8(%r12)
movq 0x10(%r12), %rdi
leaq 0x8(,%rcx,8), %rsi
callq 0x2370
movq (%rsp), %r9
movq %rax, 0x10(%r12)
movq %r14, 0x28(%rsp)
movq 0x10(%rbx), %rax
cmpq %rax, 0x10(%r9)
jae 0x79a14
decq %rax
movq %rax, %rcx
shrq %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x2, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x4, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x8, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x10, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x10(%r9)
movq (%r9), %rdi
leaq (%rax,%rax,8), %rax
leaq (%rax,%rax,2), %rax
leaq (%rcx,%rax), %rsi
incq %rsi
callq 0x2370
movq (%rsp), %r9
movq %rax, (%r9)
movq 0x80(%rsp), %rbp
xorl %ecx, %ecx
movq %rcx, 0x8(%r9)
movq 0x10(%rsp), %rax
movq %rcx, (%rax)
testq %r15, %r15
jle 0x79dd8
xorl %edi, %edi
movq %rbx, 0x38(%rsp)
movq %r15, 0x30(%rsp)
movq (%rbx), %rax
imulq $0xa8, %rdi, %rcx
leaq (%rax,%rcx), %r8
movq 0x48(%rax,%rcx), %rsi
xorl %edx, %edx
movl %edx, 0x28(%rax,%rcx)
movl $0xffffffff, 0x20(%rax,%rcx) # imm = 0xFFFFFFFF
movl %edx, 0x30(%rax,%rcx)
movq %rsi, 0x40(%rsp)
testq %rsi, %rsi
je 0x79dcc
movq %rdi, 0x20(%rsp)
movq %r8, 0x8(%rsp)
jle 0x79c6a
movq $-0x80000000, 0x18(%rsp) # imm = 0x80000000
xorl %ebp, %ebp
movq $-0x80000000, %r15      # imm = 0x80000000
movq $-0x80000000, %rax      # imm = 0x80000000
movq $-0x80000000, %r12      # imm = 0x80000000
movq $-0x80000000, %r13      # imm = 0x80000000
xorl %ebx, %ebx
movq 0x58(%r8), %rcx
movslq (%rcx,%rbp), %rdx
leaq 0x1(%r13), %rsi
cmpq %rdx, %rsi
jne 0x79acd
movslq 0x8(%rcx,%rbp), %rdx
incq %rax
cmpq %rdx, %rax
je 0x79c1f
cmpq $-0x80000000, %r12      # imm = 0x80000000
je 0x79c12
shlq $0x21, %r12
addq 0x8(%r9), %r12
movq 0x10(%rsp), %r14
movq 0x8(%r14), %rax
cmpq %rax, (%r14)
jne 0x79b1e
leaq (%rax,%rax), %rsi
testq %rax, %rax
movl $0x2, %eax
cmoveq %rax, %rsi
movq %rsi, 0x8(%r14)
movq 0x10(%r14), %rdi
shlq $0x3, %rsi
callq 0x2370
movq 0x8(%rsp), %r8
movq (%rsp), %r9
movq %rax, 0x10(%r14)
movq (%r14), %rax
movq 0x10(%r14), %rdi
leaq 0x1(%rax), %rcx
movq %rcx, (%r14)
movq %r12, (%rdi,%rax,8)
shlq $0x21, %r13
movabsq $0x100000000, %rax      # imm = 0x100000000
orq %rax, %r13
addq 0x8(%r9), %r13
movq 0x8(%r14), %rax
cmpq %rax, (%r14)
jne 0x79b78
leaq (%rax,%rax), %rsi
testq %rax, %rax
movl $0x2, %eax
cmoveq %rax, %rsi
movq %rsi, 0x8(%r14)
shlq $0x3, %rsi
callq 0x2370
movq 0x8(%rsp), %r8
movq (%rsp), %r9
movq %rax, 0x10(%r14)
movq (%r14), %rax
movq 0x10(%r14), %rcx
leaq 0x1(%rax), %rdx
movq %rdx, (%r14)
movq %r13, (%rcx,%rax,8)
movq 0x10(%r9), %rax
cmpq %rax, 0x8(%r9)
jne 0x79bc7
leaq (%rax,%rax), %rcx
testq %rax, %rax
movl $0x2, %eax
cmoveq %rax, %rcx
movq %rcx, 0x10(%r9)
movq (%r9), %rdi
leaq (%rcx,%rcx,8), %rax
leaq (%rax,%rax,2), %rsi
addq %rcx, %rsi
callq 0x2370
movq 0x8(%rsp), %r8
movq (%rsp), %r9
movq %rax, (%r9)
movq (%r9), %rax
movq 0x8(%r9), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, 0x8(%r9)
leaq (%rcx,%rcx,8), %rdx
leaq (%rdx,%rdx,2), %rdx
addq %rcx, %rdx
movq 0x20(%rsp), %rdi
movl %edi, 0xc(%rax,%rdx)
movq 0x18(%rsp), %rsi
movl %esi, 0x10(%rax,%rdx)
movl %r15d, 0x14(%rax,%rdx)
movl %esi, (%rax,%rdx)
movq 0x58(%r8), %rcx
shlq $0x5, %rsi
movl (%rcx,%rsi), %ecx
movl %ecx, 0x4(%rax,%rdx)
movl $0x0, 0x8(%rax,%rdx)
movq 0x58(%r8), %rcx
movslq (%rcx,%rbp), %r12
movq %rbx, 0x18(%rsp)
movslq 0xc(%rcx,%rbp), %rax
movslq 0x4(%rcx,%rbp), %r13
leaq 0x1(%rbx), %r14
addq $0x20, %rbp
movq %rbx, %r15
movq %r14, %rbx
cmpq %r14, 0x40(%rsp)
jne 0x79aab
shlq $0x21, %r13
movabsq $0x100000000, %rax      # imm = 0x100000000
orq %rax, %r13
decl %r14d
movq 0x38(%rsp), %rbx
movq 0x30(%rsp), %r15
movq 0x80(%rsp), %rbp
jmp 0x79c8a
movl $0x80000000, %r14d      # imm = 0x80000000
movq $-0x80000000, %r12      # imm = 0x80000000
movabsq $0x100000000, %r13      # imm = 0x100000000
movq $-0x80000000, 0x18(%rsp) # imm = 0x80000000
cmpq $-0x80000000, %r12      # imm = 0x80000000
je 0x79dcc
shlq $0x21, %r12
addq 0x8(%r9), %r12
movq 0x10(%rsp), %rbp
movq 0x8(%rbp), %rax
cmpq %rax, (%rbp)
jne 0x79cdc
leaq (%rax,%rax), %rsi
testq %rax, %rax
movl $0x2, %eax
cmoveq %rax, %rsi
movq %rsi, 0x8(%rbp)
movq 0x10(%rbp), %rdi
shlq $0x3, %rsi
callq 0x2370
movq 0x8(%rsp), %r8
movq (%rsp), %r9
movq %rax, 0x10(%rbp)
movq (%rbp), %rax
movq 0x10(%rbp), %rdi
leaq 0x1(%rax), %rcx
movq %rcx, (%rbp)
movq %r12, (%rdi,%rax,8)
addq 0x8(%r9), %r13
movq 0x8(%rbp), %rax
cmpq %rax, (%rbp)
jne 0x79d28
leaq (%rax,%rax), %rsi
testq %rax, %rax
movl $0x2, %eax
cmoveq %rax, %rsi
movq %rsi, 0x8(%rbp)
shlq $0x3, %rsi
callq 0x2370
movq 0x8(%rsp), %r8
movq (%rsp), %r9
movq %rax, 0x10(%rbp)
movq (%rbp), %rax
movq 0x10(%rbp), %rcx
leaq 0x1(%rax), %rdx
movq %rdx, (%rbp)
movq %r13, (%rcx,%rax,8)
movq 0x10(%r9), %rax
cmpq %rax, 0x8(%r9)
jne 0x79d79
leaq (%rax,%rax), %rcx
testq %rax, %rax
movl $0x2, %eax
cmoveq %rax, %rcx
movq %rcx, 0x10(%r9)
movq (%r9), %rdi
leaq (%rcx,%rcx,8), %rax
leaq (%rax,%rax,2), %rsi
addq %rcx, %rsi
callq 0x2370
movq 0x8(%rsp), %r8
movq (%rsp), %r9
movq %rax, (%r9)
movq (%r9), %rax
movq 0x8(%r9), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, 0x8(%r9)
leaq (%rcx,%rcx,8), %rdx
leaq (%rdx,%rdx,2), %rdx
addq %rcx, %rdx
movq 0x20(%rsp), %rdi
movl %edi, 0xc(%rax,%rdx)
movq 0x18(%rsp), %rsi
movl %esi, 0x10(%rax,%rdx)
movl %r14d, 0x14(%rax,%rdx)
movl %esi, (%rax,%rdx)
movq 0x58(%r8), %rcx
shlq $0x5, %rsi
movl (%rcx,%rsi), %ecx
movl %ecx, 0x4(%rax,%rdx)
movl $0x0, 0x8(%rax,%rdx)
movq 0x80(%rsp), %rbp
incq %rdi
cmpq %r15, %rdi
jne 0x79a3f
movq 0x10(%rsp), %r12
movq (%r12), %rax
movq 0x10(%r12), %rdi
leaq (%rdi,%rax,8), %rsi
movq %r9, %r13
callq 0x45d47
movq %rbx, %rdi
movq %r13, %rsi
movq %r12, %rdx
movq 0x28(%rsp), %r14
movq %r14, %rcx
movq %rbp, %r8
callq 0x79157
testq %rax, %rax
je 0x79e24
movq %rbx, %rdi
movq %r13, %rsi
movq %r12, %rdx
movq %r14, %rcx
movq %rbp, %r8
callq 0x79550
testq %r15, %r15
jle 0x79eda
xorl %eax, %eax
movq (%rbx), %rdx
imulq $0xa8, %rax, %rsi
leaq (%rdx,%rsi), %rcx
movl 0x8(%rdx,%rsi), %edi
subl 0x4(%rdx,%rsi), %edi
incl %edi
movl %edi, 0x20(%rdx,%rsi)
movl $0x0, 0x30(%rdx,%rsi)
cmpl $0x0, 0x28(%rdx,%rsi)
je 0x79eb9
xorl %edi, %edi
xorl %esi, %esi
xorl %edx, %edx
movq 0x48(%rcx), %r8
movq 0x58(%rcx), %r9
shlq $0x5, %r8
leaq (%r9,%rdi), %r10
movups (%r8,%r10), %xmm0
movups 0x10(%r8,%r10), %xmm1
movups %xmm1, 0x10(%r9,%rdi)
movups %xmm0, (%r9,%rdi)
movq 0x58(%rcx), %r8
movl 0x1c(%r8,%rdi), %r9d
testl %r9d, %r9d
je 0x79ea7
addl %r9d, 0x30(%rcx)
movslq 0x4(%r8,%rdi), %r9
movslq (%r8,%rdi), %r8
subq %r8, %r9
addq %r9, %rdx
incq %rsi
movl 0x28(%rcx), %r8d
addq $0x20, %rdi
cmpq %r8, %rsi
jb 0x79e60
jmp 0x79ebd
xorl %edx, %edx
xorl %esi, %esi
movq %rsi, 0x48(%rcx)
movl 0x20(%rcx), %esi
cmpq %rsi, %rdx
jg 0x79ee9
subl %edx, %esi
movl %esi, 0x28(%rcx)
incq %rax
cmpq %r15, %rax
jne 0x79e2f
addq $0x48, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x1ae162(%rip), %rdi    # 0x228052
leaq 0x1ab74c(%rip), %rsi    # 0x225643
leaq 0x1ae9f0(%rip), %rcx    # 0x2288ee
movl $0x5676, %edx           # imm = 0x5676
callq 0x2110