// File: chhylp123[P]hifiasm/Correct.cpp
// Function: aln_wlst_adv(overlap_region*, All_reads*, hpc_t*, ul_idx_t const*, char*, char*, char*, Correct_dumy*, unsigned int, unsigned int, long, long, long, long, double, unsigned int)
inline uint32_t aln_wlst_adv(overlap_region *z, All_reads *rref, hpc_t *hpc_g, 
const ul_idx_t *uref, char *qstr, char *tstr, char *tstr1, Correct_dumy* dumy,
uint32_t rev, uint32_t id, int64_t qs, int64_t qe, int64_t t_s, int64_t block_s, 
double e_rate, uint32_t is_cigar)
{
    int64_t ql, aln_l, t_tot_l; window_list *p = NULL; int r_ts = 0, t_end;
    int64_t aux_beg, aux_end, t_pri_l;
    int64_t thres; char *q_string, *t_string; unsigned int error;
    ql = qe + 1 - qs;
    ///there are two potiential reasons for unmatched window:
    ///1. this window has a large number of differences
    ///2. DP does not start from the right offset
    if(rref) {
        thres = double_error_threshold(get_init_err_thres(ql, e_rate, block_s, THRESHOLD), ql);
    } else {
        thres = double_ul_error_threshold(get_init_err_thres(ql, e_rate, block_s, THRESHOLD_MAX_SIZE), ql);
    }
    aln_l = ql + (thres << 1);
    if(hpc_g) t_tot_l = hpc_len(*hpc_g, id);
    else if(uref) t_tot_l = uref->ug->u.a[id].len;
    else t_tot_l = Get_READ_LENGTH((*rref), id);

    if(!init_waln(thres, t_s, t_tot_l, aln_l, &aux_beg, &aux_end, &t_s, &t_pri_l)) return 0;
    if(t_pri_l + thres < ql) return 0;

    q_string = qstr + qs; 
    if(rref) {
        fill_subregion(tstr, t_s, t_pri_l, rev, rref, id, aux_beg, aux_end); t_string = tstr;
    } else {
        t_string = return_str_seq(tstr, t_s, t_pri_l, rev, hpc_g, uref, id, aux_beg, aux_end);
    }

    if(is_cigar) {
        ///note!!! need notification
        t_end = Reserve_Banded_BPM_PATH(t_string, aln_l, q_string, ql, thres, &error, &r_ts,
        &(dumy->path_length), dumy->matrix_bit, dumy->path, -1, -1);
    } else {
        ///note!!! need notification
        t_end = Reserve_Banded_BPM(t_string, aln_l, q_string, ql, thres, &error);    
    }
    if(error!=(unsigned int)-1) {
        if(is_cigar) {
            ///this condition is always wrong
            ///in best case, r_ts = threshold, t_end = aln_l - thres - 1
            if (((t_end+1) == aln_l) || (r_ts == 0)) {
                if(recal_boundary(q_string, tstr1, ql, thres, t_s, r_ts, t_end,
                aux_beg, aux_end, error, id, aln_l, rev, dumy, rref, hpc_g, uref, 
                &t_s, &r_ts, &t_end, &aux_beg, &aux_end, &error)) {
                    t_string = update_des_str(tstr, t_s, aln_l-aux_beg-aux_end, rev, rref, hpc_g, uref,
                                                    id, aux_beg, aux_end, hpc_g?NULL:tstr1);
                }
            }
        }

        kv_pushp(window_list, z->w_list, &p);
        p->x_start = qs; p->x_end = qe; ///must set x_start/x_end here
        if(is_cigar) {
            generate_cigar(dumy->path, dumy->path_length, p, &(z->w_list), &r_ts, &t_end, &error, q_string, ql, t_string);  
        } else {
            p->cidx = p->clen = 0;
        }
        p->y_start = t_s + r_ts;///difference
        p->y_end = t_s + t_end;
        p->error = error;
        p->extra_begin = aux_beg;
        p->extra_end = aux_end;
        p->error_threshold = thres;
        z->align_length += ql; 
        
        return 1;
    }
    return 0;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x1d8, %rsp            # imm = 0x1D8
movl 0x50(%rbp), %eax
movq 0x48(%rbp), %rax
movq 0x40(%rbp), %rax
movq 0x38(%rbp), %rax
movq 0x30(%rbp), %rax
movl 0x28(%rbp), %eax
movl 0x20(%rbp), %eax
movq 0x18(%rbp), %rax
movq 0x10(%rbp), %rax
movq %rdi, -0x38(%rbp)
movq %rsi, -0x40(%rbp)
movq %rdx, -0x48(%rbp)
movq %rcx, -0x50(%rbp)
movq %r8, -0x58(%rbp)
movq %r9, -0x60(%rbp)
movsd %xmm0, -0x68(%rbp)
movq $0x0, -0x88(%rbp)
movl $0x0, -0x8c(%rbp)
movq 0x38(%rbp), %rax
addq $0x1, %rax
subq 0x30(%rbp), %rax
movq %rax, -0x70(%rbp)
cmpq $0x0, -0x40(%rbp)
je 0xa63bd
movq -0x70(%rbp), %rdi
movsd -0x68(%rbp), %xmm0
movq 0x48(%rbp), %rsi
movl $0xf, %edx
callq 0x9e1c0
movl %eax, %edi
movq -0x70(%rbp), %rax
movl %eax, %esi
callq 0x9e370
cltq
movq %rax, -0xb0(%rbp)
jmp 0xa63ea
movq -0x70(%rbp), %rdi
movsd -0x68(%rbp), %xmm0
movq 0x48(%rbp), %rsi
movl $0x1f, %edx
callq 0x9e1c0
movl %eax, %edi
movq -0x70(%rbp), %rax
movl %eax, %esi
callq 0x9f400
cltq
movq %rax, -0xb0(%rbp)
movq -0x70(%rbp), %rax
movq -0xb0(%rbp), %rcx
shlq %rcx
addq %rcx, %rax
movq %rax, -0x78(%rbp)
cmpq $0x0, -0x48(%rbp)
je 0xa642c
movq -0x48(%rbp), %rax
movq (%rax), %rax
movq 0x10(%rax), %rax
movl 0x28(%rbp), %ecx
imulq $0x28, %rcx, %rcx
addq %rcx, %rax
movl (%rax), %eax
andl $0x7fffffff, %eax       # imm = 0x7FFFFFFF
sarl %eax
cltq
movq %rax, -0x80(%rbp)
jmp 0xa646c
cmpq $0x0, -0x50(%rbp)
je 0xa6457
movq -0x50(%rbp), %rax
movq (%rax), %rax
movq 0x10(%rax), %rax
movl 0x28(%rbp), %ecx
imulq $0x28, %rcx, %rcx
addq %rcx, %rax
movl (%rax), %eax
andl $0x7fffffff, %eax       # imm = 0x7FFFFFFF
movl %eax, %eax
movq %rax, -0x80(%rbp)
jmp 0xa646a
movq -0x40(%rbp), %rax
movq 0x18(%rax), %rax
movl 0x28(%rbp), %ecx
movq (%rax,%rcx,8), %rax
movq %rax, -0x80(%rbp)
jmp 0xa646c
movq -0xb0(%rbp), %rdi
movq 0x40(%rbp), %rsi
movq -0x80(%rbp), %rdx
movq -0x78(%rbp), %rcx
leaq -0x98(%rbp), %r8
leaq -0xa0(%rbp), %r9
leaq 0x40(%rbp), %r10
leaq -0xa8(%rbp), %rax
movq %r10, (%rsp)
movq %rax, 0x8(%rsp)
callq 0x33f90
cmpl $0x0, %eax
jne 0xa64b7
movl $0x0, -0x2c(%rbp)
jmp 0xa6aec
movq -0xa8(%rbp), %rax
addq -0xb0(%rbp), %rax
cmpq -0x70(%rbp), %rax
jge 0xa64d7
movl $0x0, -0x2c(%rbp)
jmp 0xa6aec
movq -0x58(%rbp), %rax
addq 0x30(%rbp), %rax
movq %rax, -0xb8(%rbp)
cmpq $0x0, -0x40(%rbp)
je 0xa6539
movq -0x60(%rbp), %rdi
movq 0x40(%rbp), %rsi
movq -0xa8(%rbp), %rdx
movl 0x20(%rbp), %eax
movb %al, %cl
movq -0x40(%rbp), %r8
movl 0x28(%rbp), %eax
movl %eax, %r9d
movq -0x98(%rbp), %rax
movl %eax, %r10d
movq -0xa0(%rbp), %rax
movzbl %cl, %ecx
movl %r10d, (%rsp)
movl %eax, 0x8(%rsp)
callq 0x32160
movq -0x60(%rbp), %rax
movq %rax, -0xc0(%rbp)
jmp 0xa6586
movq -0x60(%rbp), %rdi
movq 0x40(%rbp), %rsi
movq -0xa8(%rbp), %rdx
movl 0x20(%rbp), %eax
movb %al, %cl
movq -0x48(%rbp), %r8
movq -0x50(%rbp), %r9
movl 0x28(%rbp), %eax
movl %eax, %r11d
movq -0x98(%rbp), %r10
movq -0xa0(%rbp), %rax
movzbl %cl, %ecx
movq %r11, (%rsp)
movq %r10, 0x8(%rsp)
movq %rax, 0x10(%rsp)
callq 0xa71f0
movq %rax, -0xc0(%rbp)
cmpl $0x0, 0x50(%rbp)
je 0xa6617
movq -0xc0(%rbp), %rdi
movq -0x78(%rbp), %rax
movl %eax, %esi
movq -0xb8(%rbp), %rdx
movq -0x70(%rbp), %rax
movl %eax, %ecx
movq -0xb0(%rbp), %rax
movw %ax, %r8w
movq 0x18(%rbp), %r11
addq $0x7d70, %r11           # imm = 0x7D70
movq 0x18(%rbp), %r10
addq $0xff0, %r10            # imm = 0xFF0
movq 0x18(%rbp), %rax
addq $0xa14, %rax            # imm = 0xA14
leaq -0xc4(%rbp), %r9
leaq -0x8c(%rbp), %rbx
movzwl %r8w, %r8d
movq %rbx, (%rsp)
movq %r11, 0x8(%rsp)
movq %r10, 0x10(%rsp)
movq %rax, 0x18(%rsp)
movl $0xffffffff, 0x20(%rsp) # imm = 0xFFFFFFFF
movl $0xffffffff, 0x28(%rsp) # imm = 0xFFFFFFFF
callq 0x9e3d0
movl %eax, -0x90(%rbp)
jmp 0xa664e
movq -0xc0(%rbp), %rdi
movq -0x78(%rbp), %rax
movl %eax, %esi
movq -0xb8(%rbp), %rdx
movq -0x70(%rbp), %rax
movl %eax, %ecx
movq -0xb0(%rbp), %rax
leaq -0xc4(%rbp), %r9
movzwl %ax, %r8d
callq 0x9c2b0
movl %eax, -0x90(%rbp)
cmpl $-0x1, -0xc4(%rbp)
je 0xa6ae5
cmpl $0x0, 0x50(%rbp)
je 0xa68fe
movl -0x90(%rbp), %eax
addl $0x1, %eax
cltq
cmpq -0x78(%rbp), %rax
je 0xa6683
cmpl $0x0, -0x8c(%rbp)
jne 0xa68fc
movq -0xb8(%rbp), %rdi
movq 0x10(%rbp), %rsi
movq -0x70(%rbp), %rdx
movq -0xb0(%rbp), %rcx
movq 0x40(%rbp), %r8
movslq -0x8c(%rbp), %r9
movslq -0x90(%rbp), %rax
movq %rax, -0x118(%rbp)
movq -0x98(%rbp), %rax
movq %rax, -0x110(%rbp)
movq -0xa0(%rbp), %rax
movq %rax, -0x108(%rbp)
movl -0xc4(%rbp), %eax
movl %eax, -0xfc(%rbp)
movl 0x28(%rbp), %eax
movq %rax, -0xf8(%rbp)
movq -0x78(%rbp), %rax
movq %rax, -0xf0(%rbp)
movl 0x20(%rbp), %eax
movl %eax, -0xe4(%rbp)
movq 0x18(%rbp), %rax
movq %rax, -0xe0(%rbp)
movq -0x40(%rbp), %rax
movq %rax, -0xd8(%rbp)
movq -0x48(%rbp), %r13
movq -0x50(%rbp), %r12
leaq 0x40(%rbp), %r15
leaq -0x8c(%rbp), %r14
leaq -0x90(%rbp), %rbx
leaq -0x98(%rbp), %r11
leaq -0xa0(%rbp), %r10
leaq -0xc4(%rbp), %rax
movq %rax, -0xd0(%rbp)
movq -0x118(%rbp), %rax
movq %rax, (%rsp)
movq -0x110(%rbp), %rax
movq %rax, 0x8(%rsp)
movq -0x108(%rbp), %rax
movq %rax, 0x10(%rsp)
movl -0xfc(%rbp), %eax
movl %eax, 0x18(%rsp)
movq -0xf8(%rbp), %rax
movq %rax, 0x20(%rsp)
movq -0xf0(%rbp), %rax
movq %rax, 0x28(%rsp)
movl -0xe4(%rbp), %eax
movl %eax, 0x30(%rsp)
movq -0xe0(%rbp), %rax
movq %rax, 0x38(%rsp)
movq -0xd8(%rbp), %rax
movq %rax, 0x40(%rsp)
movq -0xd0(%rbp), %rax
movq %r13, 0x48(%rsp)
movq %r12, 0x50(%rsp)
movq %r15, 0x58(%rsp)
movq %r14, 0x60(%rsp)
movq %rbx, 0x68(%rsp)
movq %r11, 0x70(%rsp)
movq %r10, 0x78(%rsp)
movq %rax, 0x80(%rsp)
callq 0xc6a20
cmpl $0x0, %eax
je 0xa68fa
movq -0x60(%rbp), %rax
movq %rax, -0x168(%rbp)
movq 0x40(%rbp), %rax
movq %rax, -0x160(%rbp)
movq -0x78(%rbp), %rax
subq -0x98(%rbp), %rax
subq -0xa0(%rbp), %rax
movq %rax, -0x158(%rbp)
movl 0x20(%rbp), %eax
movb %al, -0x149(%rbp)
movq -0x40(%rbp), %rax
movq %rax, -0x148(%rbp)
movq -0x48(%rbp), %rax
movq %rax, -0x140(%rbp)
movq -0x50(%rbp), %rax
movq %rax, -0x138(%rbp)
movl 0x28(%rbp), %eax
movq %rax, -0x130(%rbp)
movq -0x98(%rbp), %rax
movq %rax, -0x128(%rbp)
movq -0xa0(%rbp), %rax
movq %rax, -0x120(%rbp)
cmpq $0x0, -0x48(%rbp)
je 0xa687c
xorl %eax, %eax
movq %rax, -0x170(%rbp)
jmp 0xa6887
movq 0x10(%rbp), %rax
movq %rax, -0x170(%rbp)
movq -0x120(%rbp), %r10
movq -0x128(%rbp), %r11
movq -0x130(%rbp), %rbx
movq -0x138(%rbp), %r14
movq -0x140(%rbp), %r9
movq -0x148(%rbp), %r8
movb -0x149(%rbp), %cl
movq -0x158(%rbp), %rdx
movq -0x160(%rbp), %rsi
movq -0x168(%rbp), %rdi
movq -0x170(%rbp), %rax
movzbl %cl, %ecx
movq %r14, (%rsp)
movq %rbx, 0x8(%rsp)
movq %r11, 0x10(%rsp)
movq %r10, 0x18(%rsp)
movq %rax, 0x20(%rsp)
callq 0xc6da0
movq %rax, -0xc0(%rbp)
jmp 0xa68fc
jmp 0xa68fe
jmp 0xa6900
movq -0x38(%rbp), %rax
movq 0x48(%rax), %rax
movq -0x38(%rbp), %rcx
cmpq 0x50(%rcx), %rax
jne 0xa6972
movq -0x38(%rbp), %rax
cmpq $0x0, 0x50(%rax)
je 0xa6931
movq -0x38(%rbp), %rax
movq 0x50(%rax), %rax
shlq %rax
movq %rax, -0x178(%rbp)
jmp 0xa693f
movl $0x2, %eax
movq %rax, -0x178(%rbp)
jmp 0xa693f
movq -0x178(%rbp), %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x50(%rax)
movq -0x38(%rbp), %rax
movq 0x58(%rax), %rdi
movq -0x38(%rbp), %rax
movq 0x50(%rax), %rsi
shlq $0x5, %rsi
callq 0x2360
movq %rax, %rcx
movq -0x38(%rbp), %rax
movq %rcx, 0x58(%rax)
movq -0x38(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x38(%rbp), %rdx
movq 0x48(%rdx), %rcx
movq %rcx, %rsi
addq $0x1, %rsi
movq %rsi, 0x48(%rdx)
shlq $0x5, %rcx
addq %rcx, %rax
movq %rax, -0x88(%rbp)
movq 0x30(%rbp), %rax
movl %eax, %ecx
movq -0x88(%rbp), %rax
movl %ecx, (%rax)
movq 0x38(%rbp), %rax
movl %eax, %ecx
movq -0x88(%rbp), %rax
movl %ecx, 0x4(%rax)
cmpl $0x0, 0x50(%rbp)
je 0xa6a28
movq 0x18(%rbp), %rdi
addq $0xa14, %rdi            # imm = 0xA14
movq 0x18(%rbp), %rax
movl 0x7d70(%rax), %esi
movq -0x88(%rbp), %rdx
movq -0x38(%rbp), %rcx
addq $0x48, %rcx
movq -0xb8(%rbp), %r11
movq -0x70(%rbp), %rax
movl %eax, %r10d
movq -0xc0(%rbp), %rax
leaq -0x8c(%rbp), %r8
leaq -0x90(%rbp), %r9
leaq -0xc4(%rbp), %rbx
movq %rbx, (%rsp)
movq %r11, 0x8(%rsp)
movl %r10d, 0x10(%rsp)
movq %rax, 0x18(%rsp)
callq 0x9f0f0
jmp 0xa6a44
movq -0x88(%rbp), %rax
movl $0x0, 0x1c(%rax)
movq -0x88(%rbp), %rax
movl $0x0, 0x18(%rax)
movq 0x40(%rbp), %rax
movslq -0x8c(%rbp), %rcx
addq %rcx, %rax
movl %eax, %ecx
movq -0x88(%rbp), %rax
movl %ecx, 0x8(%rax)
movq 0x40(%rbp), %rax
movslq -0x90(%rbp), %rcx
addq %rcx, %rax
movl %eax, %ecx
movq -0x88(%rbp), %rax
movl %ecx, 0xc(%rax)
movl -0xc4(%rbp), %eax
movw %ax, %cx
movq -0x88(%rbp), %rax
movw %cx, 0x14(%rax)
movq -0x98(%rbp), %rax
movw %ax, %cx
movq -0x88(%rbp), %rax
movw %cx, 0x10(%rax)
movq -0xa0(%rbp), %rax
movw %ax, %cx
movq -0x88(%rbp), %rax
movw %cx, 0x12(%rax)
movq -0xb0(%rbp), %rax
movw %ax, %cx
movq -0x88(%rbp), %rax
movw %cx, 0x16(%rax)
movq -0x70(%rbp), %rdx
movq -0x38(%rbp), %rax
movl 0x28(%rax), %ecx
addq %rdx, %rcx
movl %ecx, 0x28(%rax)
movl $0x1, -0x2c(%rbp)
jmp 0xa6aec
movl $0x0, -0x2c(%rbp)
movl -0x2c(%rbp), %eax
addq $0x1d8, %rsp            # imm = 0x1D8
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nopw %cs:(%rax,%rax)
nopl (%rax,%rax)