// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: region_phase(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(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; 
        // prt_overlap_region_stat(z, ulid);
        // if(/**ulid == 35437 &&**/ z->y_id == 15199 || z->y_id == 31315) {
        //     fprintf(stderr, "+0+[M::%s::utg%.6dl::%c] ulid::%ld, all::%u, non-best::%ld, best::%u\n", __func__, 
        //     (int32_t)z->y_id+1, "+-"[z->y_pos_strand], ulid, z->overlapLen, zwn, z->align_length);
        //     prt_overlap_region_stat(&(ol->list[k]), ulid);
        //     // prt_overlap_region_phase_stat(&(ol->list[k]), ulid);
        // }
        // z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s; 
        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
                    ovlp_bd(*cp) = 0;
                }

                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
            ovlp_bd(*cp) = 0;
        }
        // if(ulid == 35437 && z->y_id == 109111) {
        //     fprintf(stderr, "+1+[M::%s::utg%.6dl::%c] ulid::%ld, all::%u, non-best::%ld, best::%u\n", __func__, 
        //     (int32_t)z->y_id+1, "+-"[z->y_pos_strand], ulid, z->overlapLen, zwn, z->align_length);
        //     prt_overlap_region_stat(&(ol->list[k]));
        //     prt_overlap_region_phase_stat(&(ol->list[k]));
        // }
    }
    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]));
    // }
    

    int64_t srt_n = idx->n, 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;
    }
    ///hap->length

    for (k = 0; k < on; k++) {
        z = &(ol->list[k]); 
        // if(ulid == 35437 && z->y_id == 109111) {
        //     fprintf(stderr, "+2+[M::%s::utg%.6dl::%c] ulid::%ld, all::%u, non-best::%ld, best::%u\n", __func__, 
        //     (int32_t)z->y_id+1, "+-"[z->y_pos_strand], ulid, z->overlapLen, zwn, z->align_length);
        //     prt_overlap_region_stat(&(ol->list[k]));
        //     prt_overlap_region_phase_stat(&(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; 
        // if(ulid == 35437 && z->y_id == 109111/**zwn > z->overlapLen**/) {
        //     fprintf(stderr, "+3+[M::%s::utg%.6dl::%c] ulid::%ld, all::%u, non-best::%ld, best::%u\n", __func__, 
        //     (int32_t)z->y_id+1, "+-"[z->y_pos_strand], ulid, z->overlapLen, zwn, z->align_length);
        //     prt_overlap_region_stat(&(ol->list[k]));
        //     prt_overlap_region_phase_stat(&(ol->list[k]));
        // }
        assert(zwn <= z->overlapLen);
        z->align_length = z->overlapLen - zwn;
        // /**if(ulid == 35437 && z->y_id == 15199 || z->y_id == 31315)**/ {
        //     prt_overlap_region_phase_stat(z, ulid);
        //     fprintf(stderr, "[M::%s::utg%.6dl::%c] all::%u, non-best::%ld, best::%u\n\n", __func__, 
        //     (int32_t)z->y_id+1, "+-"[z->y_pos_strand], z->overlapLen, zwn, z->align_length);
        // }
        // prt_overlap_region_phase_stat(&(ol->list[k]));
        // z = &(ol->list[k]); 
        // if(z->align_length == z->overlapLen) {///prefer alignments without any trans hit
        //     z->align_length = z->overlapLen = z->x_pos_e+1-z->x_pos_s;
        // }
    }
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x48, %rsp
movq %r9, 0x40(%rsp)
movq %r8, %rbx
movq %rcx, %r8
movq %rdi, %r12
movq 0x10(%rdi), %r13
leaq (,%r13,2), %rcx
movq %r13, %rax
cmpq %rcx, 0x8(%rbx)
movq %r8, (%rsp)
jae 0x6f56a
decq %rcx
movq %rcx, %rax
shrq %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x2, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x4, %rax
orq %rcx, %rax
movq %rax, %rcx
shrq $0x8, %rcx
orq %rax, %rcx
movq %rcx, %rax
shrq $0x10, %rax
orq %rcx, %rax
leaq 0x1(%rax), %rcx
movq %rcx, 0x8(%rbx)
movq 0x10(%rbx), %rdi
leaq 0x8(,%rax,8), %rsi
callq 0x2370
movq (%rsp), %r8
movq %rax, 0x10(%rbx)
movq 0x10(%r12), %rax
cmpq %rax, 0x10(%r8)
jae 0x6f5ca
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(%r8)
movq (%r8), %rdi
leaq (%rax,%rax,8), %rax
leaq (%rax,%rax,2), %rax
leaq (%rcx,%rax), %rsi
incq %rsi
callq 0x2370
movq (%rsp), %r8
movq %rax, (%r8)
xorl %ecx, %ecx
movq %rcx, 0x8(%r8)
movq %rcx, (%rbx)
testq %r13, %r13
movq %r12, 0x20(%rsp)
movq %r13, 0x28(%rsp)
movq %rbx, 0x10(%rsp)
jle 0x6f963
xorl %edi, %edi
movq (%r12), %rsi
imulq $0xa8, %rdi, %rax
movq 0x48(%rsi,%rax), %r10
movl %ecx, 0x28(%rsi,%rax)
movl $0xffffffff, 0x20(%rsi,%rax) # imm = 0xFFFFFFFF
movl %ecx, 0x30(%rsi,%rax)
testq %r10, %r10
jle 0x6f94f
movq %rsi, %rdx
addq %rax, %rdx
movq %rdx, 0x38(%rsp)
movq 0x58(%rdx), %rax
movq $-0x80000000, %r9       # imm = 0x80000000
xorl %ebp, %ebp
movq $-0x80000000, %r13      # imm = 0x80000000
movq $-0x80000000, %rcx      # imm = 0x80000000
movq $-0x80000000, %r15      # imm = 0x80000000
movq $-0x80000000, %r14      # imm = 0x80000000
xorl %r12d, %r12d
movq %rdi, 0x18(%rsp)
movq %r10, 0x30(%rsp)
movslq (%rax,%rbp), %rdx
leaq 0x1(%r14), %rsi
cmpq %rdx, %rsi
jne 0x6f675
movslq 0x8(%rax,%rbp), %rdx
incq %rcx
cmpq %rdx, %rcx
je 0x6f7ce
cmpq $-0x80000000, %r15      # imm = 0x80000000
je 0x6f7c7
shlq $0x21, %r15
addq 0x8(%r8), %r15
movq 0x10(%rsp), %rbx
movq (%rbx), %rcx
movq 0x10(%rbx), %rax
cmpq 0x8(%rbx), %rcx
movq %r9, 0x8(%rsp)
jne 0x6f6cc
leaq (%rcx,%rcx), %rsi
testq %rcx, %rcx
movl $0x2, %ecx
cmoveq %rcx, %rsi
movq %rsi, 0x8(%rbx)
shlq $0x3, %rsi
movq %rax, %rdi
callq 0x2370
movq (%rsp), %r8
movq %rax, 0x10(%rbx)
movq (%rbx), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, (%rbx)
movq %r15, (%rax,%rcx,8)
shlq $0x21, %r14
movabsq $0x100000000, %rcx      # imm = 0x100000000
orq %rcx, %r14
addq 0x8(%r8), %r14
movq (%rbx), %rcx
cmpq 0x8(%rbx), %rcx
jne 0x6f720
leaq (%rcx,%rcx), %rsi
testq %rcx, %rcx
movl $0x2, %ecx
cmoveq %rcx, %rsi
movq %rsi, 0x8(%rbx)
shlq $0x3, %rsi
movq %rax, %rdi
callq 0x2370
movq (%rsp), %r8
movq %rax, 0x10(%rbx)
movq (%rbx), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, (%rbx)
movq %r14, (%rax,%rcx,8)
movq (%r8), %rax
movq 0x8(%r8), %rcx
cmpq 0x10(%r8), %rcx
jne 0x6f76a
leaq (%rcx,%rcx), %rdx
testq %rcx, %rcx
movl $0x2, %ecx
cmoveq %rcx, %rdx
movq %rdx, 0x10(%r8)
leaq (%rdx,%rdx,8), %rcx
leaq (%rcx,%rcx,2), %rsi
addq %rdx, %rsi
movq %rax, %rdi
callq 0x2370
movq (%rsp), %r8
movq %rax, (%r8)
movq 0x8(%r8), %rcx
movq 0x18(%rsp), %rdi
movq 0x8(%rsp), %r9
movq 0x30(%rsp), %r10
leaq 0x1(%rcx), %rdx
movq %rdx, 0x8(%r8)
leaq (%rcx,%rcx,8), %rdx
leaq (%rdx,%rdx,2), %rdx
addq %rcx, %rdx
movl %edi, 0xc(%rax,%rdx)
movl %r9d, 0x10(%rax,%rdx)
movl %r13d, 0x14(%rax,%rdx)
movl %r9d, (%rax,%rdx)
movq 0x38(%rsp), %rsi
movq 0x58(%rsi), %rcx
shlq $0x5, %r9
movl (%rcx,%r9), %ecx
movl %ecx, 0x4(%rax,%rdx)
movl $0x0, 0x8(%rax,%rdx)
andl $0xc0000000, 0x18(%rax,%rdx) # imm = 0xC0000000
movq 0x58(%rsi), %rax
movslq (%rax,%rbp), %r15
movq %r12, %r9
movslq 0xc(%rax,%rbp), %rcx
movslq 0x4(%rax,%rbp), %r14
leaq 0x1(%r12), %rbx
addq $0x20, %rbp
movq %r12, %r13
movq %rbx, %r12
cmpq %rbx, %r10
jne 0x6f657
cmpq $-0x80000000, %r15      # imm = 0x80000000
movq 0x20(%rsp), %r12
movq 0x28(%rsp), %r13
movl $0x0, %ecx
je 0x6f94f
shlq $0x21, %r15
addq 0x8(%r8), %r15
movq 0x10(%rsp), %rbp
movq (%rbp), %rcx
movq 0x10(%rbp), %rax
cmpq 0x8(%rbp), %rcx
movq %r9, 0x8(%rsp)
jne 0x6f858
leaq (%rcx,%rcx), %rsi
testq %rcx, %rcx
movl $0x2, %ecx
cmoveq %rcx, %rsi
movq %rsi, 0x8(%rbp)
shlq $0x3, %rsi
movq %rax, %rdi
callq 0x2370
movq (%rsp), %r8
movq %rax, 0x10(%rbp)
movq (%rbp), %rcx
shlq $0x21, %r14
movabsq $0x100000000, %rdx      # imm = 0x100000000
orq %rdx, %r14
leaq 0x1(%rcx), %rdx
movq %rdx, (%rbp)
movq %r15, (%rax,%rcx,8)
addq 0x8(%r8), %r14
movq (%rbp), %rcx
cmpq 0x8(%rbp), %rcx
jne 0x6f8af
leaq (%rcx,%rcx), %rsi
testq %rcx, %rcx
movl $0x2, %ecx
cmoveq %rcx, %rsi
movq %rsi, 0x8(%rbp)
shlq $0x3, %rsi
movq %rax, %rdi
callq 0x2370
movq (%rsp), %r8
movq %rax, 0x10(%rbp)
movq (%rbp), %rcx
leaq 0x1(%rcx), %rdx
movq %rdx, (%rbp)
movq %r14, (%rax,%rcx,8)
movq (%r8), %rax
movq 0x8(%r8), %rcx
cmpq 0x10(%r8), %rcx
jne 0x6f8fa
leaq (%rcx,%rcx), %rdx
testq %rcx, %rcx
movl $0x2, %ecx
cmoveq %rcx, %rdx
movq %rdx, 0x10(%r8)
leaq (%rdx,%rdx,8), %rcx
leaq (%rcx,%rcx,2), %rsi
addq %rdx, %rsi
movq %rax, %rdi
callq 0x2370
movq (%rsp), %r8
movq %rax, (%r8)
movq 0x8(%r8), %rcx
movq 0x18(%rsp), %rdi
movq 0x8(%rsp), %rsi
decq %rbx
leaq 0x1(%rcx), %rdx
movq %rdx, 0x8(%r8)
leaq (%rcx,%rcx,8), %rdx
leaq (%rdx,%rdx,2), %rdx
addq %rcx, %rdx
movl %edi, 0xc(%rax,%rdx)
movl %esi, 0x10(%rax,%rdx)
movl %ebx, 0x14(%rax,%rdx)
movl %esi, (%rax,%rdx)
movq 0x38(%rsp), %rcx
movq 0x58(%rcx), %rcx
shlq $0x5, %rsi
movl (%rcx,%rsi), %ecx
movl %ecx, 0x4(%rax,%rdx)
movl $0x0, 0x8(%rax,%rdx)
andl $0xc0000000, 0x18(%rax,%rdx) # imm = 0xC0000000
xorl %ecx, %ecx
incq %rdi
cmpq %r13, %rdi
jne 0x6f5ed
movq 0x10(%rsp), %rbx
movq (%rbx), %rcx
movq 0x10(%rbx), %rdi
leaq (%rdi,%rcx,8), %rsi
callq 0x45373
movq (%rbx), %r8
testq %r8, %r8
jle 0x6fa65
xorl %r13d, %r13d
xorl %r14d, %r14d
xorl %r12d, %r12d
movq %r8, 0x8(%rsp)
movq 0x10(%rsp), %rbx
movq 0x10(%rbx), %rax
movq (%rax,%r12,8), %rcx
movq %rcx, %rbp
shrq $0x21, %rbp
movabsq $0x100000000, %rdx      # imm = 0x100000000
testq %rdx, %rcx
jne 0x6f9f9
movq (%rbx), %rdx
cmpq 0x8(%rbx), %rdx
jne 0x6f9e6
leaq (%rdx,%rdx), %rsi
testq %rdx, %rdx
movl $0x2, %ecx
cmoveq %rcx, %rsi
movq %rsi, 0x8(%rbx)
shlq $0x3, %rsi
movq %rax, %rdi
callq 0x2370
movq 0x8(%rsp), %r8
movq %rax, 0x10(%rbx)
movl (%rax,%r12,8), %ecx
movq (%rbx), %rdx
leaq 0x1(%r14), %r15
movl %ecx, %ecx
leaq 0x1(%rdx), %rsi
movq %rsi, (%rbx)
movq %rcx, (%rax,%rdx,8)
jmp 0x6fa00
leaq -0x1(%r14), %r15
incq %rbp
cmpq %r13, %rbp
seta %cl
cmpq $0x2, %r14
setge %dl
andb %cl, %dl
cmpb $0x1, %dl
jne 0x6fa53
movq 0x20(%rsp), %rcx
movq (%rcx), %rdi
leaq (%rax,%r8,8), %rsi
movq 0x10(%rsp), %rbx
movq (%rbx), %rdx
subq %r8, %rdx
movq %r13, %rcx
movq %rbp, %r8
movq %r14, %r9
pushq 0x40(%rsp)
movq 0x8(%rsp), %rax
pushq (%rax)
callq 0x6c379
movq 0x18(%rsp), %r8
addq $0x10, %rsp
addq %r8, %rax
movq %rax, (%rbx)
incq %r12
movq %rbp, %r13
movq %r15, %r14
cmpq %r12, %r8
jne 0x6f98a
movq 0x28(%rsp), %rbx
testq %rbx, %rbx
movq 0x20(%rsp), %r11
jle 0x6fb2c
xorl %eax, %eax
movq (%r11), %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 0x6fb11
movq 0x58(%rcx), %rdi
xorl %r8d, %r8d
xorl %esi, %esi
xorl %edx, %edx
movq 0x48(%rcx), %r9
shlq $0x5, %r9
leaq (%rdi,%r8), %r10
movups (%r9,%r10), %xmm0
movups 0x10(%r9,%r10), %xmm1
movups %xmm1, 0x10(%rdi,%r8)
movups %xmm0, (%rdi,%r8)
movq 0x58(%rcx), %rdi
movl 0x1c(%rdi,%r8), %r9d
testl %r9d, %r9d
je 0x6faf3
addl %r9d, 0x30(%rcx)
movslq 0x4(%rdi,%r8), %r9
movslq (%rdi,%r8), %r10
subq %r10, %r9
addq %r9, %rdx
incq %rsi
movl 0x28(%rcx), %r9d
addq $0x20, %r8
cmpq %r9, %rsi
jb 0x6fab0
movl 0x20(%rcx), %edi
movq %rsi, 0x48(%rcx)
cmpq %rdi, %rdx
jle 0x6fb1b
jmp 0x6fb3b
movq $0x0, 0x48(%rcx)
xorl %edx, %edx
subl %edx, %edi
movl %edi, 0x28(%rcx)
incq %rax
cmpq %rbx, %rax
jne 0x6fa7a
addq $0x48, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x1c4620(%rip), %rdi    # 0x234162
leaq 0x1c1c0a(%rip), %rsi    # 0x231753
leaq 0x1c4627(%rip), %rcx    # 0x234177
movl $0x4bf1, %edx           # imm = 0x4BF1
callq 0x2110