// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: rphase_detect0(overlap_region_alloc*, kv_ul_ov_t*, asg64_v*, asg64_v*, asg64_v*)
uint64_t rphase_detect0(overlap_region_alloc* ol, kv_ul_ov_t *c_idx, asg64_v* idx, asg64_v* buf, asg64_v* suf)
{
    uint64_t srt_n = idx->n, i, k, h, qs, qe, ts, te, rr = 0, ovlp; overlap_region *z, *p;
    int64_t dp, old_dp, beg, end;
    for (i = k = 0, dp = old_dp = 0, beg = 0, end = -1; i < srt_n; ++i) {///[beg, end) but coordinates in idx is [, ]
        ///if idx->a.a[] is qe
        old_dp = dp;
        if ((idx->a[i]>>32)&1) {
            --dp; end = (idx->a[i]>>33)+1;
        }else {
            //meet a new overlap; the overlaps are pushed by the x_pos_s
            ++dp; end = (idx->a[i]>>33);
            kv_push(uint64_t, *idx, ((uint32_t)idx->a[i]));
        }
        // fprintf(stderr, "\n[M::%s::] beg::%ld, end::%ld, old_dp::%ld\n", __func__, beg, end, old_dp);
        if((end > beg) && (old_dp >= 2)) {
            // fprintf(stderr, "\n[M::%s::] beg::%ld, end::%ld, old_dp::%ld\n", __func__, beg, end, old_dp);
            // kv_resize(uint64_t, *buf, ((uint32_t)old_dp)<<1);
            // idx->n = srt_n + gen_region_phase(ol->list, idx->a+srt_n, idx->n-srt_n, beg, end, old_dp, c_idx->a, buf, buf1);   
            idx->n = srt_n + gen_region_phase_robust(ol->list, idx->a+srt_n, idx->n-srt_n, beg, end, old_dp, c_idx->a, buf);
        }
        beg = end;
    }
    idx->n = srt_n; 
    
    suf->n = 0; kv_resize(uint64_t, *suf, (ol->length<<1)); 
    uint64_t *sep = suf->a, *sid = suf->a + ol->length, sid_n; 
    for (k = h = sid_n = 0; k < ol->length; k++) {
        z = &(ol->list[k]); 
        z->overlapLen = (uint32_t)-1; z->non_homopolymer_errors = 0; 
        for (i = 0; i < z->align_length; i++) {
            z->non_homopolymer_errors += z->w_list.a[z->w_list.n+i].clen;
        }
        for (; h < c_idx->n && ovlp_id(c_idx->a[h]) < k; h++);
        if(h < c_idx->n && ovlp_id(c_idx->a[h]) == k) {
            qs = z->w_list.a[ovlp_min_wid(c_idx->a[h])].x_start;
            qe = z->w_list.a[ovlp_max_wid(c_idx->a[h])].x_end+1;
            for (; h < c_idx->n && ovlp_id(c_idx->a[h]) == k; h++) {
                qe = z->w_list.a[ovlp_max_wid(c_idx->a[h])].x_end+1;
            }
            sid[sid_n] = ((qs<<32)|sid_n);
            sep[sid_n] = ((k<<32)|qe);
            sid_n++;
            // kv_push(uint64_t, *suf, ((qs<<32)|h));
        }
    }
    radix_sort_bc64(sid, sid+sid_n);
    for (k = 0; k < sid_n; k++) {
        qs = sid[k]>>32; qe = ((uint32_t)sep[(uint32_t)sid[k]]); 
        z = &(ol->list[sep[(uint32_t)sid[k]]>>32]);
        if(z->non_homopolymer_errors == 0) continue;
        for (i = rr = 0; i < sid_n; i++) {
            ts = sid[i]>>32; te = ((uint32_t)sep[(uint32_t)sid[i]]); 
            p = &(ol->list[sep[(uint32_t)sid[i]]>>32]);
            if(ts >= qe) break;
            if(te <= qs) continue;
            ovlp = ((MIN(qe, te) > MAX(qs, ts))? (MIN(qe, te) - MAX(qs, ts)):0);
            if(ovlp < 512) continue;
            if(z->non_homopolymer_errors > p->non_homopolymer_errors + rphase_thres) continue;
            rr = 1; break;
        }
        if(rr) z->overlapLen = 1;
    }
    return rr;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %r8, 0x18(%rsp)
movq %rcx, 0x20(%rsp)
movq %rdx, %r15
movq %rsi, (%rsp)
movq %rdi, 0x8(%rsp)
movq (%rdx), %r8
testq %r8, %r8
je 0x78d99
xorl %r14d, %r14d
xorl %r12d, %r12d
xorl %ebx, %ebx
movq %r8, 0x10(%rsp)
movq 0x10(%r15), %rax
movq (%rax,%r14,8), %rcx
movq %rcx, %rbp
shrq $0x21, %rbp
btq $0x20, %rcx
jb 0x78d32
movq (%r15), %rdx
cmpq 0x8(%r15), %rdx
jne 0x78d1f
leaq (%rdx,%rdx), %rsi
testq %rdx, %rdx
movl $0x2, %ecx
cmoveq %rcx, %rsi
movq %rsi, 0x8(%r15)
shlq $0x3, %rsi
movq %rax, %rdi
callq 0x2370
movq 0x10(%rsp), %r8
movq %rax, 0x10(%r15)
movl (%rax,%r14,8), %ecx
movq (%r15), %rdx
leaq 0x1(%rbx), %r13
movl %ecx, %ecx
leaq 0x1(%rdx), %rsi
movq %rsi, (%r15)
movq %rcx, (%rax,%rdx,8)
jmp 0x78d39
leaq -0x1(%rbx), %r13
incq %rbp
cmpq %r12, %rbp
seta %cl
cmpq $0x2, %rbx
setge %dl
andb %cl, %dl
cmpb $0x1, %dl
jne 0x78d87
movq 0x8(%rsp), %rcx
movq (%rcx), %rdi
leaq (%rax,%r8,8), %rsi
movq (%r15), %rdx
subq %r8, %rdx
movq %r12, %rcx
movq %rbp, %r8
movq %rbx, %r9
pushq 0x20(%rsp)
movq 0x8(%rsp), %rax
pushq (%rax)
callq 0x6c379
movq 0x20(%rsp), %r8
addq $0x10, %rsp
addq %r8, %rax
movq %rax, (%r15)
incq %r14
movq %rbp, %r12
movq %r13, %rbx
cmpq %r14, %r8
jne 0x78cd0
movq %r8, (%r15)
movq 0x18(%rsp), %rbx
movq $0x0, (%rbx)
movq 0x8(%rsp), %r13
movq 0x10(%r13), %rsi
leaq (%rsi,%rsi), %rax
cmpq %rax, 0x8(%rbx)
jae 0x78e15
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, 0x8(%rbx)
movq 0x10(%rbx), %rdi
leaq 0x8(,%rcx,8), %rsi
callq 0x2370
movq %rax, %r15
movq %rax, 0x10(%rbx)
movq 0x10(%r13), %rsi
jmp 0x78e19
movq 0x10(%rbx), %r15
leaq (%r15,%rsi,8), %r12
testq %rsi, %rsi
je 0x79026
movq (%r13), %rax
xorl %ebx, %ebx
xorl %ecx, %ecx
xorl %edx, %edx
movq (%rsp), %rbp
imulq $0xa8, %rcx, %r8
leaq (%rax,%r8), %rdi
movl $0xffffffff, 0x20(%rax,%r8) # imm = 0xFFFFFFFF
movl $0x0, 0x30(%rax,%r8)
movl 0x28(%rax,%r8), %r8d
testq %r8, %r8
je 0x78e89
movq 0x48(%rdi), %r9
movq 0x58(%rdi), %r10
shlq $0x5, %r8
shlq $0x5, %r9
addq %r10, %r9
addq $0x1c, %r9
xorl %r10d, %r10d
xorl %r11d, %r11d
addl (%r9,%r10), %r11d
addq $0x20, %r10
cmpq %r10, %r8
jne 0x78e78
movl %r11d, 0x30(%rdi)
movq 0x8(%rbp), %r10
cmpq %r10, %rdx
jae 0x78f4d
movq (%rbp), %r8
leaq (%rdx,%rdx,8), %r9
leaq (%r9,%r9,2), %r11
addq %rdx, %r11
leaq (%r8,%r11), %r9
addq $0xc, %r9
addq %r8, %r11
addq $0x28, %r11
movl (%r9), %r14d
cmpq %r14, %rcx
jbe 0x78ed1
incq %rdx
addq $0x1c, %r9
addq $0x1c, %r11
cmpq %rdx, %r10
jne 0x78eb4
movq %r10, %rdx
jmp 0x78f4d
jne 0x78f4d
cmpq %r10, %rdx
jae 0x78efe
movl (%r9), %esi
cmpq %rsi, %rcx
jne 0x78efe
leaq -0x1(%r10), %rsi
incq %rdx
cmpq %r10, %rdx
jae 0x78f5b
movl (%r11), %r14d
addq $0x1c, %r11
cmpq %r14, %rcx
je 0x78ee4
leaq -0x1(%rdx), %rsi
jmp 0x78f01
movq %rdx, %rsi
movq 0x58(%rdi), %rdi
movl 0x4(%r9), %r9d
shlq $0x5, %r9
movslq (%rdi,%r9), %r9
leaq (%rsi,%rsi,8), %r10
leaq (%r10,%r10,2), %r10
addq %rsi, %r10
movl 0x14(%r8,%r10), %esi
shlq $0x5, %rsi
movslq 0x4(%rdi,%rsi), %rsi
incq %rsi
shlq $0x20, %r9
orq %rbx, %r9
movq %r9, (%r12,%rbx,8)
movq %rcx, %rdi
shlq $0x20, %rdi
orq %rsi, %rdi
movq %rdi, (%r15,%rbx,8)
incq %rbx
movq 0x10(%r13), %rsi
incq %rcx
cmpq %rsi, %rcx
jb 0x78e34
jmp 0x78f60
movq %r10, %rdx
jmp 0x78f01
leaq (%r12,%rbx,8), %rsi
movq %r12, %rdi
callq 0x45373
testq %rbx, %rbx
je 0x79031
movq (%r13), %rcx
xorl %edx, %edx
xorl %eax, %eax
movq (%r12,%rdx,8), %rsi
movl %esi, %edi
movq (%r15,%rdi,8), %r9
movq %r9, %rdi
shrq $0x20, %rdi
imulq $0xa8, %rdi, %rdi
movl 0x30(%rcx,%rdi), %r8d
testl %r8d, %r8d
je 0x7900a
shrq $0x20, %rsi
movl %r9d, %eax
addq %rcx, %rdi
xorl %r9d, %r9d
movq (%r12,%r9,8), %r10
movq %r10, %r11
shrq $0x20, %r11
cmpq %rax, %r11
jae 0x79008
movl %r10d, %r10d
movq (%r15,%r10,8), %r10
movl %r10d, %r14d
cmpl %esi, %r14d
jbe 0x79000
cmpq %r14, %rax
cmovbq %rax, %r14
cmpq %r11, %rsi
cmovaq %rsi, %r11
subq %r11, %r14
jbe 0x79000
cmpq $0x200, %r14            # imm = 0x200
jb 0x79000
shrq $0x20, %r10
imulq $0xa8, %r10, %r10
movl 0x30(%rcx,%r10), %r10d
addl $0x4, %r10d
cmpl %r10d, %r8d
jbe 0x79018
incq %r9
cmpq %r9, %rbx
jne 0x78fac
xorl %eax, %eax
incq %rdx
cmpq %rbx, %rdx
jne 0x78f7d
jmp 0x79033
movl $0x1, 0x20(%rdi)
movl $0x1, %eax
jmp 0x7900a
movq %r12, %rdi
movq %r12, %rsi
callq 0x45373
xorl %eax, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq