LLM4Binary/decompile-bench-makefile huggingface dataset:
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: append_overlap_region_alloc_debug(overlap_region_alloc*, overlap_region*)
void append_overlap_region_alloc_debug(overlap_region_alloc* list, overlap_region* tmp)
{
   
    if (list->length + 1 > list->size)
    {
        list->size = list->size * 2;
        list->list = (overlap_region*)realloc(list->list, sizeof(overlap_region)*list->size);
    }

    
    list->list[list->length].x_id = tmp->x_id;
    list->list[list->length].x_pos_e = tmp->x_pos_e;
    list->list[list->length].x_pos_s = tmp->x_pos_s;
    list->list[list->length].x_pos_strand = tmp->x_pos_strand;

    list->list[list->length].y_id = tmp->y_id;
    list->list[list->length].y_pos_e = tmp->y_pos_e;
    list->list[list->length].y_pos_s = tmp->y_pos_s;
    list->list[list->length].y_pos_strand = tmp->y_pos_strand;

    list->list[list->length].shared_seed = tmp->shared_seed;

    list->length++;
}

// Assembly:
pushq %r14
pushq %rbx
pushq %rax
movq %rsi, %r14
movq %rdi, %rbx
movq 0x10(%rdi), %rdx
leaq 0x1(%rdx), %rcx
movq (%rdi), %rax
movq 0x8(%rdi), %rsi
cmpq %rsi, %rcx
jbe 0x3e411
leaq (%rsi,%rsi), %rcx
movq %rcx, 0x8(%rbx)
imulq $0x150, %rsi, %rsi      # imm = 0x150
movq %rax, %rdi
callq 0x2370
movq %rax, (%rbx)
movq 0x10(%rbx), %rdx
leaq 0x1(%rdx), %rcx
imulq $0xa8, %rdx, %rdx
movups (%r14), %xmm0
movups %xmm0, (%rax,%rdx)
movups 0x10(%r14), %xmm0
movups %xmm0, 0x10(%rax,%rdx)
movl 0x24(%r14), %esi
movl %esi, 0x24(%rax,%rdx)
movq %rcx, 0x10(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: debug_chain(k_mer_hit*, long long, Chain_Data*)
void debug_chain(k_mer_hit* a, long long a_n, Chain_Data* dp)
{
    long long i, j, current_j;
    long long selfLen, indels;
    long long distance_self_pos, distance_pos, distance_gap;
    for (i = 0; i < a_n; ++i) 
    {
        selfLen = indels = 0;
        j = i;
        while (j >= 0)
        {
            current_j = j;

            j = dp->pre[j];

            if(j != -1)
            {
                distance_self_pos = a[current_j].self_offset - a[j].self_offset;
                distance_pos = a[current_j].offset - a[j].offset;
                distance_gap = distance_pos > distance_self_pos? distance_pos - distance_self_pos : distance_self_pos - distance_pos;

                indels += distance_gap; 
                selfLen += distance_self_pos;
            }
        }

        if(indels != dp->indels[i])
        {
            fprintf(stderr, "indels: %lld, dp->indels[i]: %ld\n", indels, (long)dp->indels[i]);
        }

        if(selfLen != dp->self_length[i])
        {
            fprintf(stderr, "selfLen: %lld, dp->self_length[i]: %ld\n", selfLen, (long)dp->self_length[i]);
        }

    }
}

// Assembly:
testq %rsi, %rsi
jle 0x3e516
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %rdx, %rbx
movq %rsi, %r14
movq %rdi, %r15
movq 0x256b7e(%rip), %r12    # 0x294fe0
xorl %r13d, %r13d
movq 0x8(%rbx), %rax
movq %r13, %rsi
xorl %ebp, %ebp
xorl %edx, %edx
movq (%rax,%rsi,8), %rcx
cmpq $-0x1, %rcx
je 0x3e4b9
shlq $0x4, %rsi
movl 0x4(%r15,%rsi), %edi
movl 0x8(%r15,%rsi), %esi
movq %rcx, %r8
shlq $0x4, %r8
subl 0x8(%r15,%r8), %esi
subl 0x4(%r15,%r8), %edi
movq %rsi, %r8
subq %rdi, %r8
movq %rdi, %r9
subq %rsi, %r9
cmpl %esi, %edi
cmovbeq %r8, %r9
addq %r9, %rdx
addq %rsi, %rbp
movq %rcx, %rsi
testq %rcx, %rcx
jns 0x3e470
movq 0x10(%rbx), %rax
movslq (%rax,%r13,4), %rcx
cmpq %rcx, %rdx
jne 0x3e4dd
movq 0x18(%rbx), %rax
movslq (%rax,%r13,4), %rcx
cmpq %rcx, %rbp
jne 0x3e4f1
incq %r13
cmpq %r14, %r13
jne 0x3e465
jmp 0x3e508
movq (%r12), %rdi
leaq 0x1f2e9e(%rip), %rsi    # 0x231386
xorl %eax, %eax
callq 0x22b0
jmp 0x3e4c6
movq (%r12), %rdi
leaq 0x1f2eac(%rip), %rsi    # 0x2313a8
movq %rbp, %rdx
xorl %eax, %eax
callq 0x22b0
jmp 0x3e4d3
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: resize_Chain_Data(Chain_Data*, long long, void*)
void resize_Chain_Data(Chain_Data* x, long long size, void *km)
{
	if (size + 1 > x->size) {
		x->size = size + 1;
		kroundup64(x->size);
        if(!km) {
            REALLOC(x->score, x->size);
            REALLOC(x->pre, x->size);
            REALLOC(x->indels, x->size);
            REALLOC(x->self_length, x->size);
            REALLOC(x->occ, x->size);
            REALLOC(x->tmp, x->size);
        } else {
            KREALLOC(km, x->score, x->size);
            KREALLOC(km, x->pre, x->size);
            KREALLOC(km, x->indels, x->size);
            KREALLOC(km, x->self_length, x->size);
            KREALLOC(km, x->occ, x->size);
            KREALLOC(km, x->tmp, x->size);
        }
	}
}

// Assembly:
cmpq %rsi, 0x38(%rdi)
jg 0x3ee1a
pushq %r14
pushq %rbx
pushq %rax
movq %rdx, %r14
movq %rdi, %rbx
movq %rsi, %rax
sarq %rax
orq %rsi, %rax
movq %rax, %rcx
sarq $0x2, %rcx
orq %rax, %rcx
movq %rcx, %rax
sarq $0x4, %rax
orq %rcx, %rax
movq %rax, %rcx
sarq $0x8, %rcx
orq %rax, %rcx
movq %rcx, %rax
sarq $0x10, %rax
orq %rcx, %rax
movq %rax, %rcx
sarq $0x20, %rcx
orq %rax, %rcx
leaq 0x1(%rcx), %rax
movq %rax, 0x38(%rdi)
movq (%rdi), %rsi
leaq 0x4(,%rcx,4), %rdx
testq %r14, %r14
je 0x3ed9c
movq %r14, %rdi
callq 0x1ee21d
movq %rax, (%rbx)
movq 0x8(%rbx), %rsi
movq 0x38(%rbx), %rdx
shlq $0x3, %rdx
movq %r14, %rdi
callq 0x1ee21d
movq %rax, 0x8(%rbx)
movq 0x10(%rbx), %rsi
movq 0x38(%rbx), %rdx
shlq $0x2, %rdx
movq %r14, %rdi
callq 0x1ee21d
movq %rax, 0x10(%rbx)
movq 0x18(%rbx), %rsi
movq 0x38(%rbx), %rdx
shlq $0x2, %rdx
movq %r14, %rdi
callq 0x1ee21d
movq %rax, 0x18(%rbx)
movq 0x20(%rbx), %rsi
movq 0x38(%rbx), %rdx
shlq $0x2, %rdx
movq %r14, %rdi
callq 0x1ee21d
movq %rax, 0x20(%rbx)
movq 0x28(%rbx), %rsi
movq 0x38(%rbx), %rdx
shlq $0x3, %rdx
movq %r14, %rdi
callq 0x1ee21d
jmp 0x3ee0f
movq %rsi, %rdi
movq %rdx, %rsi
callq 0x2370
movq %rax, (%rbx)
movq 0x8(%rbx), %rdi
movq 0x38(%rbx), %rsi
shlq $0x3, %rsi
callq 0x2370
movq %rax, 0x8(%rbx)
movq 0x10(%rbx), %rdi
movq 0x38(%rbx), %rsi
shlq $0x2, %rsi
callq 0x2370
movq %rax, 0x10(%rbx)
movq 0x18(%rbx), %rdi
movq 0x38(%rbx), %rsi
shlq $0x2, %rsi
callq 0x2370
movq %rax, 0x18(%rbx)
movq 0x20(%rbx), %rdi
movq 0x38(%rbx), %rsi
shlq $0x2, %rsi
callq 0x2370
movq %rax, 0x20(%rbx)
movq 0x28(%rbx), %rdi
movq 0x38(%rbx), %rsi
shlq $0x3, %rsi
callq 0x2370
movq %rax, 0x28(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: append_window_list(overlap_region*, unsigned long, unsigned long, int, int, int, int, int, int, int, void*)
void append_window_list(overlap_region* region, uint64_t x_start, uint64_t x_end, int y_start, int y_end, int error,
                        int extra_begin, int extra_end, int error_threshold, int blockLen, void *km)
{
    window_list *p = NULL;
    kv_pushp(window_list, region->w_list, &p);

    p->x_start = x_start;
    p->x_end = x_end;
    p->y_start = y_start;
    p->y_end = y_end;
    p->error = error;
    p->extra_begin = extra_begin;
    p->extra_end = extra_end;
    p->error_threshold = error_threshold;
    p->cidx = p->clen = 0;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movl %r9d, %ebx
movl %r8d, %ebp
movl %ecx, %r14d
movq %rdx, %r15
movq %rsi, %r12
movq %rdi, %r13
movl 0x50(%rsp), %esi
movl 0x48(%rsp), %edi
movl 0x40(%rsp), %r8d
movq 0x48(%r13), %rcx
cmpq 0x50(%r13), %rcx
jne 0x3f030
leaq (%rcx,%rcx), %rax
testq %rcx, %rcx
movl $0x2, %esi
cmovneq %rax, %rsi
movq %rsi, 0x50(%r13)
movq 0x58(%r13), %rdi
shlq $0x5, %rsi
callq 0x2370
movl 0x40(%rsp), %r8d
movl 0x48(%rsp), %edi
movl 0x50(%rsp), %esi
movq %rax, 0x58(%r13)
movq 0x48(%r13), %rcx
jmp 0x3f034
movq 0x58(%r13), %rax
leaq 0x1(%rcx), %rdx
movq %rdx, 0x48(%r13)
shlq $0x5, %rcx
movl %r12d, (%rax,%rcx)
movl %r15d, 0x4(%rax,%rcx)
movl %r14d, 0x8(%rax,%rcx)
movl %ebp, 0xc(%rax,%rcx)
movw %bx, 0x14(%rax,%rcx)
movw %r8w, 0x10(%rax,%rcx)
movw %di, 0x12(%rax,%rcx)
movw %si, 0x16(%rax,%rcx)
movq $0x0, 0x18(%rax,%rcx)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: test_single_list(Candidates_list*, k_mer_pos*, unsigned long, unsigned long, unsigned long)
void test_single_list(Candidates_list* candidates, k_mer_pos* n_list, uint64_t n_lengh, uint64_t end_pos, uint64_t strand)
{
    uint64_t i;
    long long j = 0;
    for (i = 0; i < n_lengh; i++)
    {
        
        for (; j < candidates->length; j++)
        {
            if (
                n_list[i].offset == (uint64_t)candidates->list[j].offset
                &&
                n_list[i].readID == candidates->list[j].readID
                &&
                end_pos == (uint64_t)candidates->list[j].self_offset
                &&
                strand == candidates->list[j].strand
            )
            {
                break;
            }   
        }

        if (j == candidates->length)
        {
            fprintf(stderr, "ERROR 4\n");
        }
    }
}

// Assembly:
testq %rdx, %rdx
je 0x3f147
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %rbx
movq %rcx, %r14
movq %rdx, %r8
movq %rsi, %r12
movq %rdi, %r13
xorl %ebp, %ebp
xorl %r15d, %r15d
movq %rdx, (%rsp)
movq 0x8(%r13), %rax
cmpq %rax, %rbp
jge 0x3f104
movl (%r12,%r15,8), %ecx
movq (%r13), %rdx
movq %rbp, %rsi
shlq $0x4, %rsi
addq %rsi, %rdx
addq $0x8, %rdx
cmpl -0x4(%rdx), %ecx
jne 0x3f0f3
movl -0x8(%rdx), %esi
movl 0x4(%r12,%r15,8), %edi
xorl %esi, %edi
testl $0x7fffffff, %edi       # imm = 0x7FFFFFFF
jne 0x3f0f3
movl (%rdx), %edi
xorq %r14, %rdi
shrl $0x1f, %esi
movl %esi, %esi
xorq %rbx, %rsi
orq %rdi, %rsi
je 0x3f104
incq %rbp
addq $0x10, %rdx
cmpq %rbp, %rax
jne 0x3f0ca
movq %rax, %rbp
jmp 0x3f113
cmpq %rax, %rbp
je 0x3f113
incq %r15
cmpq %r8, %r15
jne 0x3f0ab
jmp 0x3f139
movq 0x255ec6(%rip), %rax    # 0x294fe0
movq (%rax), %rcx
movl $0x8, %esi
movl $0x1, %edx
leaq 0x1f23aa(%rip), %rdi    # 0x2314d8
callq 0x2410
movq (%rsp), %r8
jmp 0x3f109
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: destory_Candidates_list_buf(void*, Candidates_list*, int)
void destory_Candidates_list_buf(void *km, Candidates_list* l, int is_z)
{
    kfree(km, l->list);
    kfree(km, l->chainDP.score);
    kfree(km, l->chainDP.pre);
    kfree(km, l->chainDP.indels);
    kfree(km, l->chainDP.self_length);
    kfree(km, l->chainDP.occ);
    kfree(km, l->chainDP.tmp);
    if(is_z) memset(l, 0, sizeof(*l));
}

// Assembly:
pushq %rbp
pushq %r14
pushq %rbx
movl %edx, %ebp
movq %rsi, %rbx
movq %rdi, %r14
movq (%rsi), %rsi
callq 0x1ee04f
movq 0x18(%rbx), %rsi
movq %r14, %rdi
callq 0x1ee04f
movq 0x20(%rbx), %rsi
movq %r14, %rdi
callq 0x1ee04f
movq 0x28(%rbx), %rsi
movq %r14, %rdi
callq 0x1ee04f
movq 0x30(%rbx), %rsi
movq %r14, %rdi
callq 0x1ee04f
movq 0x38(%rbx), %rsi
movq %r14, %rdi
callq 0x1ee04f
movq 0x40(%rbx), %rsi
movq %r14, %rdi
callq 0x1ee04f
testl %ebp, %ebp
je 0x3f25f
xorps %xmm0, %xmm0
movups %xmm0, 0x40(%rbx)
movups %xmm0, 0x30(%rbx)
movups %xmm0, 0x20(%rbx)
movups %xmm0, 0x10(%rbx)
movups %xmm0, (%rbx)
movq $0x0, 0x50(%rbx)
popq %rbx
popq %r14
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: push_ovlp_chain_qgen(overlap_region*, unsigned int, long, long, long, k_mer_hit*, k_mer_hit*)
void push_ovlp_chain_qgen(overlap_region* o, uint32_t xid, int64_t xl, int64_t yl, int64_t sc, 
k_mer_hit *beg, k_mer_hit *end)
{
    int64_t xr, yr; 
    o->x_id = xid; o->y_id = beg->readID;
    o->x_pos_strand = 0; o->y_pos_strand = beg->strand;
    o->x_pos_s = beg->self_offset; o->y_pos_s = beg->offset;
    o->x_pos_e = end->self_offset; o->y_pos_e = end->offset;

    if(o->x_pos_s <= o->y_pos_s) {
        o->y_pos_s -= o->x_pos_s; o->x_pos_s = 0;
    } else {
        o->x_pos_s -= o->y_pos_s; o->y_pos_s = 0;
    }

    xr = xl-o->x_pos_e-1; yr = yl-o->y_pos_e-1;
    if(xr <= yr) {
        o->x_pos_e = xl-1; o->y_pos_e += xr;        
    } else {
        o->y_pos_e = yl-1; o->x_pos_e += yr; 
    }

    o->shared_seed = sc;
    o->align_length = 0;
    o->is_match = 0;
    o->non_homopolymer_errors = 0;
    o->strong = 0;
    o->overlapLen = 0;
}

// Assembly:
pushq %rbx
movq 0x10(%rsp), %r10
movl %esi, (%rdi)
movl $0x7fffffff, %eax       # imm = 0x7FFFFFFF
andl (%r9), %eax
movl %eax, 0x10(%rdi)
xorl %eax, %eax
movl %eax, 0xc(%rdi)
movl (%r9), %esi
shrl $0x1f, %esi
movl %esi, 0x1c(%rdi)
movl 0x4(%r9), %r11d
movl 0x8(%r9), %r9d
movl 0x4(%r10), %esi
movl 0x8(%r10), %r10d
movl %r9d, %ebx
subl %r11d, %ebx
cmovbl %eax, %ebx
subl %r9d, %r11d
cmovbl %eax, %r11d
movl %ebx, 0x4(%rdi)
movl %r11d, 0x14(%rdi)
movq %rsi, %r9
notq %r9
addq %rcx, %r9
leal (%r9,%r10), %r11d
notq %r10
addq %rdx, %r10
decl %ecx
decl %edx
addl %r10d, %esi
cmpq %r9, %r10
cmovgl %ecx, %esi
cmovgl %r11d, %edx
movl %esi, 0x18(%rdi)
movl %edx, 0x8(%rdi)
movl %r8d, 0x24(%rdi)
movl %eax, 0x28(%rdi)
movb %al, 0x2c(%rdi)
movl %eax, 0x30(%rdi)
movb %al, 0x2e(%rdi)
movl %eax, 0x20(%rdi)
popq %rbx
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: filter_non_ovlp_xchains(overlap_region*, long, long*)
int64_t filter_non_ovlp_xchains(overlap_region *a, int64_t a_n, int64_t *n_v)
{
    int64_t k, i, n_mchain, omx, opx, ovx, os, oe; overlap_region *m, *p, t;
    for (k = n_mchain = (*n_v) = 0; k < a_n; k++) {
		m = &(a[k]); 
        omx = m->x_pos_e + 1 - m->x_pos_s;
		for (i = 0; i < n_mchain; i++) {
			p = &(a[i]);
            opx = p->x_pos_e + 1 - p->x_pos_s;

            os = ((m->x_pos_s>=p->x_pos_s)? m->x_pos_s:p->x_pos_s);
            oe = ((m->x_pos_e<=p->x_pos_e)? m->x_pos_e:p->x_pos_e) + 1;
			ovx = oe>os?oe-os:0;
            if((ovx > omx*0.1) || (ovx > opx*0.1)) break;
		}
		if(i < n_mchain) continue;

        if (n_mchain != k) {
            t = a[k]; a[k] = a[n_mchain]; a[n_mchain] = t;
        }
        (*n_v) += a[n_mchain].align_length;
		n_mchain++;
	}
	return n_mchain;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0xb8, %rsp
movq $0x0, (%rdx)
testq %rsi, %rsi
jle 0x40cd3
movq %rdx, %r13
movq %rsi, %r14
movq %rdi, %r15
leaq 0x8(%rdi), %rax
movq %rax, 0x8(%rsp)
xorl %eax, %eax
movsd 0x1f005c(%rip), %xmm3   # 0x230c10
xorl %ebx, %ebx
xorl %r12d, %r12d
movq %rsi, (%rsp)
imulq $0xa8, %rbx, %rbp
testq %r12, %r12
jle 0x40c53
movl 0x4(%r15,%rbp), %ecx
movl 0x8(%r15,%rbp), %edx
movl %edx, %esi
subl %ecx, %esi
incl %esi
xorps %xmm0, %xmm0
cvtsi2sd %rsi, %xmm0
mulsd %xmm3, %xmm0
movq 0x8(%rsp), %rsi
movq %r12, %rdi
movl -0x4(%rsi), %r8d
cmpl %r8d, %ecx
movl %r8d, %r10d
cmoval %ecx, %r10d
movl (%rsi), %r9d
cmpl %r9d, %edx
movl %r9d, %r11d
cmovbl %edx, %r11d
incl %r11d
cmpl %r10d, %r11d
ja 0x40c1a
xorpd %xmm1, %xmm1
jmp 0x40c25
subq %r10, %r11
xorps %xmm1, %xmm1
cvtsi2sd %r11, %xmm1
ucomisd %xmm0, %xmm1
ja 0x40cc5
subl %r8d, %r9d
incl %r9d
xorps %xmm2, %xmm2
cvtsi2sd %r9, %xmm2
mulsd %xmm3, %xmm2
ucomisd %xmm2, %xmm1
ja 0x40cc5
addq $0xa8, %rsi
decq %rdi
jne 0x40bf1
cmpq %rbx, %r12
je 0x40caf
addq %r15, %rbp
movl $0xa8, %edx
leaq 0x10(%rsp), %rdi
movq %rbp, %rsi
callq 0x2160
movq %r13, %r14
imulq $0xa8, %r12, %r13
addq %r15, %r13
movl $0xa8, %edx
movq %rbp, %rdi
movq %r13, %rsi
callq 0x2160
movl $0xa8, %edx
movq %r13, %rdi
movq %r14, %r13
movq (%rsp), %r14
leaq 0x10(%rsp), %rsi
callq 0x2160
movsd 0x1eff65(%rip), %xmm3   # 0x230c10
movq (%r13), %rax
imulq $0xa8, %r12, %rcx
movl 0x28(%r15,%rcx), %ecx
addq %rcx, %rax
movq %rax, (%r13)
incq %r12
incq %rbx
cmpq %r14, %rbx
jne 0x40bbd
jmp 0x40cd6
xorl %r12d, %r12d
movq %r12, %rax
addq $0xb8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Hash_Table.cpp
// Function: lchain_dp_trace(k_mer_hit*, long, long, double, long)
uint64_t lchain_dp_trace(k_mer_hit* a, int64_t a_n, int64_t max_lgap, double sgap_rate, int64_t sgap)
{
    // fprintf(stderr, "[M::%s::] a_n::%ld\n", __func__, a_n);
    if(a_n <= 0) return 0;
    int64_t i, st, occ = 0; 

    for (i = 1, st = 0; i <= a_n; ++i) {
        // fprintf(stderr, "[M::%s::i->%ld] q::%u, t::%u, cnt::%u, readID::%u\n", __func__, 
        // i-1, a[i-1].self_offset, a[i-1].offset, a[i-1].cnt, a[i-1].readID);
        if((i == a_n) || (is_alnw(a[i]))) {///[st, i)
            if(i > st) {
                occ += filter_bad_seed_dp((st>0)?&(a[st-1]):NULL, (i<a_n)?&(a[i]):NULL, a, a_n, max_lgap, sgap_rate, sgap);
            }
            st = i+1;
        }
    }

    if(occ) {
        for (i = occ = 0; i < a_n; ++i) {
            if(a[i].self_offset == ((uint32_t)-1)) continue;
            a[occ++] = a[i];
        }
        a_n = occ;
    }
    return a_n;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rcx, 0x10(%rsp)
movsd %xmm0, 0x8(%rsp)
testq %rsi, %rsi
jle 0x44288
movq %rdx, %r12
movq %rsi, %rbx
movq %rdi, %r14
leaq -0x10(%rdi), %rax
movq %rax, (%rsp)
leaq 0x1(%rsi), %rbp
movl $0x1, %r15d
xorl %r13d, %r13d
xorl %eax, %eax
cmpq %rbx, %r15
je 0x441fd
movq %r15, %rcx
shlq $0x4, %rcx
movl (%r14,%rcx), %ecx
notl %ecx
testl $0x7fffffff, %ecx       # imm = 0x7FFFFFFF
jne 0x4424e
cmpq %rax, %r15
jle 0x44246
movq %rax, %rdi
shlq $0x4, %rdi
addq (%rsp), %rdi
testq %rax, %rax
movl $0x0, %eax
cmovleq %rax, %rdi
movq %r15, %rsi
shlq $0x4, %rsi
addq %r14, %rsi
cmpq %rbx, %r15
cmovgeq %rax, %rsi
movq %r14, %rdx
movq %rbx, %rcx
movq %r12, %r8
movsd 0x8(%rsp), %xmm0
movq 0x10(%rsp), %r9
callq 0x43f11
addq %rax, %r13
incq %r15
movq %r15, %rax
jmp 0x44251
incq %r15
cmpq %rbp, %r15
jne 0x441e3
testq %r13, %r13
je 0x4428c
leaq 0x8(%r14), %rcx
xorl %eax, %eax
cmpl $-0x1, (%rcx)
je 0x4427d
leaq -0x8(%rcx), %rdx
leaq 0x1(%rax), %rsi
shlq $0x4, %rax
movups (%rdx), %xmm0
movups %xmm0, (%r14,%rax)
movq %rsi, %rax
addq $0x10, %rcx
decq %rbx
jne 0x44261
jmp 0x4428f
xorl %eax, %eax
jmp 0x4428f
movq %rbx, %rax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nop
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: append_Edge_alloc(Edge_alloc*, unsigned long, unsigned long, unsigned long, unsigned long)
void append_Edge_alloc(Edge_alloc* list,  uint64_t in_node, uint64_t out_node, uint64_t weight, uint64_t length)
{
	if (list->length + 1 > list->size) {
		uint64_t old_size = list->size;
		list->size = list->size + INCREASE_EDGE_SIZE;
		list->list = (Edge*)realloc(list->list, sizeof(Edge)*list->size);
		memset(&list->list[old_size], 0, (list->size - old_size) * sizeof(Edge));
	}

	list->list[list->length].in_node = in_node;
	list->list[list->length].out_node = out_node;
	list->list[list->length].weight = weight;
	list->list[list->length].length = length;
	list->list[list->length].num_insertions = 0;
	list->list[list->length].self_edge_ID = list->length;

	list->length++;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x18, %rsp
movq %rdx, %r12
movq %rsi, %r13
movq %rdi, %r14
movq 0x10(%rdi), %rax
leaq 0x1(%rax), %rsi
movq (%rdi), %rbp
movq 0x8(%rdi), %r15
cmpq %r15, %rsi
jbe 0x44362
leaq 0x5(%r15), %rax
movq %rax, 0x8(%r14)
imulq $0x38, %r15, %rbx
leaq 0x118(%rbx), %rsi
movq %rbp, %rdi
movq %r8, 0x10(%rsp)
movq %rcx, 0x8(%rsp)
callq 0x2370
movq %rax, %rbp
movq %rax, (%r14)
addq %rax, %rbx
movq 0x8(%r14), %rax
subq %r15, %rax
imulq $0x38, %rax, %rdx
movq %rbx, %rdi
xorl %esi, %esi
callq 0x20e0
movq 0x8(%rsp), %rcx
movq 0x10(%rsp), %r8
movq 0x10(%r14), %rax
leaq 0x1(%rax), %rsi
imulq $0x38, %rax, %rdx
movq %r13, (%rbp,%rdx)
movq %r12, 0x8(%rbp,%rdx)
movq %rcx, 0x10(%rbp,%rdx)
movq %r8, 0x20(%rbp,%rdx)
movq $0x0, 0x18(%rbp,%rdx)
movq %rax, 0x28(%rbp,%rdx)
movq %rsi, 0x10(%r14)
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: add_and_check_bi_direction_edge(Graph*, Node*, Node*, unsigned long, unsigned long)
int add_and_check_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t weight, uint64_t flag)
{
    Edge* e_forward;
    Edge* e_backward;

    //if there are no edge from in_node to out_node
    if(!get_bi_Edge(graph, in_node, out_node, &e_forward, &e_backward))
    {
        append_Edge_alloc(&(Output_Edges((*in_node))), (*in_node).ID, (*out_node).ID, weight, flag);
        append_Edge_alloc(&(Input_Edges((*out_node))), (*in_node).ID, (*out_node).ID, weight, flag);

        Output_Edges((*in_node)).list[Output_Edges((*in_node)).length - 1].reverse_edge_ID 
        = Input_Edges((*out_node)).length - 1;

        Input_Edges((*out_node)).list[Input_Edges((*out_node)).length - 1].reverse_edge_ID
        = Output_Edges((*in_node)).length - 1;

        return 1;
    }
    else//if there is an edge from in_node to out_node, do nothing
    {
        return 0;
    }
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r15
movq %rcx, %r12
movq %rdx, %rbx
movq %rsi, %r14
cmpb $0x44, 0x18(%rsi)
je 0x443bb
cmpb $0x44, 0x18(%rbx)
jne 0x4441f
leaq 0x40(%r14), %rdi
movq (%r14), %rsi
movq (%rbx), %rdx
movq %r12, %rcx
movq %r15, %r8
callq 0x442e2
leaq 0x60(%rbx), %rdi
movq (%r14), %rsi
movq (%rbx), %rdx
movq %r12, %rcx
movq %r15, %r8
callq 0x442e2
movq 0x70(%rbx), %rax
leaq -0x1(%rax), %rcx
movq 0x40(%r14), %rdx
movq 0x50(%r14), %rsi
imulq $0x38, %rsi, %rdi
movq %rcx, -0x8(%rdx,%rdi)
decq %rsi
movq 0x60(%rbx), %rcx
imulq $0x38, %rax, %rax
movq %rsi, -0x8(%rcx,%rax)
movl $0x1, %eax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
movq 0x70(%rbx), %rcx
movq %rcx, %rdx
negq %rdx
xorl %esi, %esi
cmpq %rcx, %rsi
jge 0x443bb
movq 0x60(%rbx), %rax
imulq $0x38, %rsi, %rdi
incq %rsi
addq %rdi, %rax
addq $0x8, %rax
cmpq $-0x1, (%rax)
jne 0x44461
addq $0x38, %rax
leaq (%rdx,%rsi), %rdi
incq %rdi
incq %rsi
cmpq $0x1, %rdi
jne 0x44442
jmp 0x443bb
movq -0x8(%rax), %rdi
xorl %eax, %eax
cmpq (%r14), %rdi
jne 0x4442b
jmp 0x44413
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: add_bi_direction_edge(Graph*, Node*, Node*, unsigned long, unsigned long)
void add_bi_direction_edge(Graph* graph, Node* in_node, Node* out_node, uint64_t weight, uint64_t flag)
{

    append_Edge_alloc(&(Output_Edges((*in_node))), (*in_node).ID, (*out_node).ID, weight, flag);
    append_Edge_alloc(&(Input_Edges((*out_node))), (*in_node).ID, (*out_node).ID, weight, flag);

    Output_Edges((*in_node)).list[Output_Edges((*in_node)).length - 1].reverse_edge_ID 
    = Input_Edges((*out_node)).length - 1;

    Input_Edges((*out_node)).list[Input_Edges((*out_node)).length - 1].reverse_edge_ID
    = Output_Edges((*in_node)).length - 1;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
movq %r8, %r14
movq %rcx, %r15
movq %rdx, %rbx
movq %rsi, %r12
leaq 0x40(%rsi), %rdi
movq (%rsi), %rsi
movq (%rdx), %rdx
callq 0x442e2
leaq 0x60(%rbx), %rdi
movq (%r12), %rsi
movq (%rbx), %rdx
movq %r15, %rcx
movq %r14, %r8
callq 0x442e2
movq 0x70(%rbx), %rax
leaq -0x1(%rax), %rcx
movq 0x40(%r12), %rdx
movq 0x50(%r12), %rsi
imulq $0x38, %rsi, %rdi
movq %rcx, -0x8(%rdx,%rdi)
decq %rsi
movq 0x60(%rbx), %rcx
imulq $0x38, %rax, %rax
movq %rsi, -0x8(%rcx,%rax)
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: remove_and_check_bi_direction_edge_from_nodes(Graph*, Node*, Node*)
int remove_and_check_bi_direction_edge_from_nodes(Graph* graph, Node* in_node, Node* out_node)
{
    Edge* e_forward;
    Edge* e_backward;

    //if there are no edge from in_node to out_node
    //1. remove these two edges
    //2. increase the edge_list.delete_length in both in_node and out_node
    if(get_bi_Edge(graph, in_node, out_node, &e_forward, &e_backward))
    {
        e_forward->in_node = (uint64_t)-1;
        e_forward->out_node = (uint64_t)-1;
        e_forward->weight = (uint64_t)-1;
        e_forward->length = (uint64_t)-1;
        e_forward->num_insertions = (uint64_t)-1;
        e_forward->self_edge_ID = (uint64_t)-1;
        e_forward->reverse_edge_ID = (uint64_t)-1;


        e_backward->in_node = (uint64_t)-1;
        e_backward->out_node = (uint64_t)-1;
        e_backward->weight = (uint64_t)-1;
        e_backward->length = (uint64_t)-1;
        e_backward->num_insertions = (uint64_t)-1;
        e_backward->self_edge_ID = (uint64_t)-1;
        e_backward->reverse_edge_ID = (uint64_t)-1;

        Output_Edges(*in_node).delete_length++;
        Input_Edges((*out_node)).delete_length++;

        return 1;
    }
    else//if there is an edge from in_node to out_node, do nothing
    {
        return 0;
    }
}

// Assembly:
xorl %eax, %eax
cmpb $0x44, 0x18(%rsi)
je 0x445dc
cmpb $0x44, 0x18(%rdx)
je 0x445dc
pushq %rbx
movq 0x70(%rdx), %r9
movq %r9, %r10
negq %r10
xorl %eax, %eax
xorl %r11d, %r11d
cmpq %r9, %r11
jge 0x445db
movq 0x60(%rdx), %rcx
imulq $0x38, %r11, %r8
incq %r11
addq %r8, %rcx
addq $0x30, %rcx
movq -0x28(%rcx), %r8
cmpq $-0x1, %r8
jne 0x44542
addq $0x38, %rcx
leaq (%r10,%r11), %r8
incq %r8
incq %r11
cmpq $0x1, %r8
jne 0x4451f
jmp 0x445db
movq -0x30(%rcx), %rbx
cmpq (%rsi), %rbx
jne 0x44504
movq -0x8(%rcx), %r9
movq 0x18(%rdi), %rax
movq %rbx, %rdi
shlq $0x7, %rdi
movq 0x40(%rax,%rdi), %r10
cmpq 0x50(%rax,%rdi), %r9
jae 0x44588
imulq $0x38, %r9, %rdi
cmpq %rbx, (%r10,%rdi)
jne 0x44588
addq %r10, %rdi
cmpq %r8, 0x8(%rdi)
jne 0x44588
shlq $0x7, %r8
imulq $0x38, (%rcx), %rcx
addq 0x60(%rax,%r8), %rcx
jmp 0x4459f
imulq $0x38, (%rcx), %rcx
addq %rcx, %r10
shlq $0x7, %r8
imulq $0x38, %r9, %rcx
addq 0x60(%rax,%r8), %rcx
movq %r10, %rdi
movq $-0x1, %rax
movq %rax, 0x30(%rdi)
pcmpeqd %xmm0, %xmm0
movdqu %xmm0, 0x20(%rdi)
movdqu %xmm0, 0x10(%rdi)
movdqu %xmm0, (%rdi)
movq %rax, 0x30(%rcx)
movdqu %xmm0, 0x20(%rcx)
movdqu %xmm0, 0x10(%rcx)
movdqu %xmm0, (%rcx)
incq 0x58(%rsi)
incq 0x78(%rdx)
movl $0x1, %eax
popq %rbx
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: remove_and_check_bi_direction_edge_from_edge(Graph*, Edge*)
int remove_and_check_bi_direction_edge_from_edge(Graph* graph, Edge* e)
{
    Edge* e_forward;
    Edge* e_backward;

    if(If_Edge_Exist(*e))
    {
        get_bi_direction_edges(graph, e, &e_forward, &e_backward);
        Output_Edges(G_Node(*graph, e_forward->in_node)).delete_length++;
        Input_Edges(G_Node(*graph, e_forward->out_node)).delete_length++;

        e_forward->in_node = (uint64_t)-1;
        e_forward->out_node = (uint64_t)-1;
        e_forward->weight = (uint64_t)-1;
        e_forward->length = (uint64_t)-1;
        e_forward->num_insertions = (uint64_t)-1;
        e_forward->self_edge_ID = (uint64_t)-1;
        e_forward->reverse_edge_ID = (uint64_t)-1;


        e_backward->in_node = (uint64_t)-1;
        e_backward->out_node = (uint64_t)-1;
        e_backward->weight = (uint64_t)-1;
        e_backward->length = (uint64_t)-1;
        e_backward->num_insertions = (uint64_t)-1;
        e_backward->self_edge_ID = (uint64_t)-1;
        e_backward->reverse_edge_ID = (uint64_t)-1;

        return 1;
    }
    else
    {
        return 0;
    }
}

// Assembly:
movq 0x8(%rsi), %rax
cmpq $-0x1, %rax
je 0x44695
movq (%rsi), %r8
movq 0x28(%rsi), %r9
movq 0x18(%rdi), %rcx
movq %r8, %rdx
shlq $0x7, %rdx
movq 0x40(%rcx,%rdx), %rdi
cmpq 0x50(%rcx,%rdx), %r9
jae 0x4462f
imulq $0x38, %r9, %rdx
cmpq %r8, (%rdi,%rdx)
jne 0x4462f
addq %rdi, %rdx
cmpq %rax, 0x8(%rdx)
jne 0x4462f
movq %rax, %rdi
shlq $0x7, %rdi
imulq $0x38, 0x30(%rsi), %rsi
addq 0x60(%rcx,%rdi), %rsi
jmp 0x4464e
imulq $0x38, 0x30(%rsi), %r10
leaq (%rdi,%r10), %rdx
shlq $0x7, %rax
imulq $0x38, %r9, %rsi
addq 0x60(%rcx,%rax), %rsi
movq (%rdi,%r10), %r8
movq 0x8(%rdi,%r10), %rax
shlq $0x7, %r8
incq 0x58(%rcx,%r8)
shlq $0x7, %rax
incq 0x78(%rcx,%rax)
movq $-0x1, %rax
movq %rax, 0x30(%rdx)
pcmpeqd %xmm0, %xmm0
movdqu %xmm0, 0x20(%rdx)
movdqu %xmm0, 0x10(%rdx)
movdqu %xmm0, (%rdx)
movq %rax, 0x30(%rsi)
movdqu %xmm0, 0x20(%rsi)
movdqu %xmm0, 0x10(%rsi)
movdqu %xmm0, (%rsi)
movl $0x1, %eax
retq
xorl %eax, %eax
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: destory_Node_alloc(Node_alloc*)
void destory_Node_alloc(Node_alloc* list)
{
	uint64_t i;
	for (i = 0; i < list->size; i++) {
		destory_Edge_alloc(&list->list[i].deletion_edges);
		destory_Edge_alloc(&list->list[i].insertion_edges);
		destory_Edge_alloc(&list->list[i].mismatch_edges);
	}
	free(list->list);
	free(list->sort.list);
	free(list->sort.visit);
	free(list->sort.iterative_buffer);
	free(list->sort.iterative_buffer_visit);
}

// Assembly:
pushq %r15
pushq %r14
pushq %rbx
movq %rdi, %rbx
cmpq $0x0, 0x40(%rdi)
je 0x44727
xorl %r14d, %r14d
xorl %r15d, %r15d
movq (%rbx), %rax
movq 0x40(%rax,%r14), %rdi
testq %rdi, %rdi
je 0x446f9
callq 0x2220
movq (%rbx), %rax
movq 0x60(%rax,%r14), %rdi
testq %rdi, %rdi
je 0x4470b
callq 0x2220
movq (%rbx), %rax
movq 0x20(%rax,%r14), %rdi
testq %rdi, %rdi
je 0x4471a
callq 0x2220
incq %r15
subq $-0x80, %r14
cmpq 0x40(%rbx), %r15
jb 0x446e4
movq (%rbx), %rdi
callq 0x2220
movq 0x8(%rbx), %rdi
callq 0x2220
movq 0x10(%rbx), %rdi
callq 0x2220
movq 0x28(%rbx), %rdi
callq 0x2220
movq 0x30(%rbx), %rdi
popq %rbx
popq %r14
popq %r15
jmp 0x2220
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: clear_Node_alloc(Node_alloc*)
void clear_Node_alloc(Node_alloc* list)
{
	uint64_t i =0;
	for (i = 0; i < list->length; i++) { // TODO: is this list->size or list->length? The original version is list->length.
		clear_Edge_alloc(&list->list[i].insertion_edges);
		clear_Edge_alloc(&list->list[i].mismatch_edges);
		clear_Edge_alloc(&list->list[i].deletion_edges);
	}
	list->length = 0;
	list->delete_length = 0;
}

// Assembly:
leaq 0x48(%rdi), %rax
cmpq $0x0, 0x48(%rdi)
je 0x4478f
xorl %ecx, %ecx
xorps %xmm0, %xmm0
xorl %edx, %edx
movq (%rdi), %rsi
movups %xmm0, 0x70(%rsi,%rcx)
movq (%rdi), %rsi
movups %xmm0, 0x30(%rsi,%rcx)
movq (%rdi), %rsi
movups %xmm0, 0x50(%rsi,%rcx)
incq %rdx
subq $-0x80, %rcx
cmpq 0x48(%rdi), %rdx
jb 0x4476a
xorps %xmm0, %xmm0
movups %xmm0, (%rax)
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: append_Node_alloc(Node_alloc*, char)
uint64_t append_Node_alloc(Node_alloc* list, char base)
{
	if (list->length + 1 > list->size) {
		uint64_t old_size = list->size;
		list->size = list->size * 2;
		list->list = (Node*)realloc(list->list, sizeof(Node) * list->size);
		memset(&list->list[old_size], 0, (list->size - old_size) * sizeof(Node));
	}

	list->list[list->length].ID = list->length;
	list->list[list->length].base = base;
	list->list[list->length].weight = 1;
	list->list[list->length].num_insertions = 0;
	init_Edge_alloc(&list->list[list->length].deletion_edges);
	init_Edge_alloc(&list->list[list->length].insertion_edges);
	init_Edge_alloc(&list->list[list->length].mismatch_edges);

	list->length++;

	return list->length - 1;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movl %esi, %ebp
movq %rdi, %rbx
movq 0x48(%rdi), %rax
leaq 0x1(%rax), %rcx
movq (%rdi), %r14
movq 0x40(%rdi), %r15
cmpq %r15, %rcx
jbe 0x447f3
leaq (%r15,%r15), %rax
movq %rax, 0x40(%rbx)
movq %r15, %rsi
shlq $0x8, %rsi
movq %r14, %rdi
callq 0x2370
movq %rax, %r14
movq %rax, (%rbx)
movq %r15, %rdi
shlq $0x7, %rdi
addq %rax, %rdi
movq 0x40(%rbx), %rdx
subq %r15, %rdx
shlq $0x7, %rdx
xorl %esi, %esi
callq 0x20e0
movq 0x48(%rbx), %rax
movq %rax, %rcx
shlq $0x7, %rcx
addq %rcx, %r14
addq $0x40, %r14
movq %rax, -0x40(%r14)
movb %bpl, -0x28(%r14)
movq $0x1, -0x38(%r14)
movq $0x0, -0x30(%r14)
cmpq $0x0, (%r14)
jne 0x44834
movq $0x32, 0x8(%r14)
movl $0xaf0, %edi            # imm = 0xAF0
callq 0x2280
movq %rax, (%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x10(%r14)
movq (%rbx), %rax
movq 0x48(%rbx), %rcx
shlq $0x7, %rcx
leaq (%rax,%rcx), %r14
addq $0x60, %r14
cmpq $0x0, (%r14)
jne 0x4486d
movq $0x32, 0x8(%r14)
movl $0xaf0, %edi            # imm = 0xAF0
callq 0x2280
xorps %xmm0, %xmm0
movq %rax, (%r14)
movups %xmm0, 0x10(%r14)
movq (%rbx), %rax
movq 0x48(%rbx), %rcx
shlq $0x7, %rcx
leaq (%rax,%rcx), %r14
addq $0x20, %r14
cmpq $0x0, (%r14)
jne 0x448a0
movq $0x32, 0x8(%r14)
movl $0xaf0, %edi            # imm = 0xAF0
callq 0x2280
movq %rax, (%r14)
xorps %xmm0, %xmm0
movups %xmm0, 0x10(%r14)
movq 0x48(%rbx), %rax
leaq 0x1(%rax), %rcx
movq %rcx, 0x48(%rbx)
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: init_Graph(Graph*)
void init_Graph(Graph* g)
{
    init_Node_alloc(&g->g_nodes);
    g->g_n_edges = 0;
    g->g_n_nodes = 0;
    g->g_next_nodeID = 0;
    g->s_end_nodeID = 0;
    g->s_start_nodeID = 0;
    g->seq = NULL;
    g->seqID = (uint64_t)-1;

    init_Queue(&(g->node_q));
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
xorps %xmm0, %xmm0
movups %xmm0, 0x50(%rdi)
movups %xmm0, 0x60(%rdi)
movups %xmm0, 0x40(%rdi)
movups %xmm0, 0x30(%rdi)
movups %xmm0, 0x20(%rdi)
movq $0x3e80, 0x58(%rdi)     # imm = 0x3E80
movl $0x3e80, %edi           # imm = 0x3E80
movl $0x80, %esi
callq 0x2120
movq %rax, 0x18(%rbx)
xorl %eax, %eax
movq %rax, 0x98(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, (%rbx)
movq %rax, 0x10(%rbx)
movups %xmm0, 0xa8(%rbx)
movq $-0x1, 0xa0(%rbx)
movups %xmm0, 0x70(%rbx)
movq %rax, 0x80(%rbx)
movq $0x14, 0x88(%rbx)
movl $0xa0, %edi
callq 0x2280
movq %rax, 0x90(%rbx)
popq %rbx
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: clear_Graph(Graph*)
void clear_Graph(Graph* g)
{
    clear_Node_alloc(&g->g_nodes);

    g->g_n_edges = 0;
    g->g_n_nodes = 0;
    g->g_next_nodeID = 0;
    g->s_end_nodeID = 0;
    g->s_start_nodeID = 0;
    g->seq = NULL;
    g->seqID = (uint64_t)-1;

    clear_Queue(&(g->node_q));
}

// Assembly:
pushq %rbx
movq %rdi, %rbx
addq $0x18, %rdi
callq 0x44758
xorl %eax, %eax
movq %rax, 0x98(%rbx)
xorps %xmm0, %xmm0
movups %xmm0, (%rbx)
movq %rax, 0x10(%rbx)
movups %xmm0, 0xa8(%rbx)
movq $-0x1, 0xa0(%rbx)
movups %xmm0, 0x70(%rbx)
movq %rax, 0x80(%rbx)
popq %rbx
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/POA.cpp
// Function: addUnmatchedSeqToGraph(Graph*, char*, long long, long long*, long long*)
void addUnmatchedSeqToGraph(Graph* g, char* g_read_seq, long long g_read_length, long long* startID, long long* endID)
{
    long long firstID, lastID, nodeID, i;
    firstID = -1;
    lastID = -1;

    if(g_read_length == 0)
        return;

    ///start node
    nodeID  = add_Node_Graph(g, 'S');
    firstID = nodeID;
    lastID = nodeID;


    for (i = 0; i < g_read_length; i++)
    {
        nodeID = add_Node_Graph(g, g_read_seq[i]);
        
        if (firstID == -1)
        {
            firstID = nodeID;
        }
        if (lastID != -1)
        {
            ///the legnth of match edge is 0, while the length of musmatch is 1
            append_Edge_alloc(&(g->g_nodes.list[lastID].mismatch_edges), lastID, nodeID, 1, 0);
        }

        lastID = nodeID; 
    }

    *startID = firstID;
    *endID = lastID;

    g->s_start_nodeID = firstID;
    g->s_end_nodeID = lastID;
    
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movq %rsi, 0x20(%rsp)
testq %rdx, %rdx
je 0x44a68
movq %rdx, %r12
movq %rcx, 0x8(%rsp)
movq %r8, 0x18(%rsp)
movq %rdi, 0x10(%rsp)
leaq 0x18(%rdi), %rbp
movq %rbp, %rdi
movl $0x53, %esi
callq 0x44796
movq %rax, %rbx
testq %r12, %r12
jle 0x44a3f
xorl %r13d, %r13d
movq %rbx, %r14
movq 0x20(%rsp), %rax
movsbl (%rax,%r13), %esi
movq %rbp, %rdi
callq 0x44796
movq %rax, %r15
cmpq $-0x1, %r14
cmoveq %rax, %r14
cmpq $-0x1, %rbx
je 0x44a32
movq (%rbp), %rax
movq %rbx, %rcx
shlq $0x7, %rcx
leaq (%rax,%rcx), %rdi
addq $0x20, %rdi
movl $0x1, %ecx
movq %rbx, %rsi
movq %r15, %rdx
xorl %r8d, %r8d
callq 0x442e2
incq %r13
movq %r15, %rbx
cmpq %r13, %r12
jne 0x449e9
jmp 0x44a45
movq %rbx, %r14
movq %rbx, %r15
movq 0x8(%rsp), %rax
movq %r14, (%rax)
movq 0x18(%rsp), %rax
movq %r15, (%rax)
movq 0x10(%rsp), %rax
movq %r14, 0xa8(%rax)
movq %r15, 0xb0(%rax)
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: print_string(char*, int)
void print_string(char* s, int l)
{
    int i;
    for (i = 0; i < l; i++)
    {
        fprintf(stderr, "%c", s[i]);
    }

    fprintf(stderr, "\n");
    
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testl %esi, %esi
jle 0x4782e
movq %rdi, %rbx
movl %esi, %r14d
xorl %r15d, %r15d
movq 0x24d7c8(%rip), %r12    # 0x294fe0
movq (%r12), %rsi
movsbl (%rbx,%r15), %edi
callq 0x2270
incq %r15
cmpq %r15, %r14
jne 0x47818
movq 0x24d7ab(%rip), %rax    # 0x294fe0
movq (%rax), %rsi
movl $0xa, %edi
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
jmp 0x2270
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: init_waln(long, long, long, long, long*, long*, long*, long*)
int32_t init_waln(int64_t err, int64_t s, int64_t l, int64_t w_l, int64_t* aux_beg, int64_t* aux_end, int64_t* r_s, int64_t* r_l)
{
    (*aux_beg) = (*aux_end) = (*r_s) = (*r_l) = -1;
    ///since w_l == x_len + (err << 1)
    if((s < 0) || (s >= l) || ((l-s+(2*err)+THRESHOLD_MAX_SIZE) < w_l)) return 0;
    (*aux_beg) = (*aux_end) = 0;
    ///s might be less than 0
    (*r_s) = s - err; 
    (*r_l) = l-(*r_s); if((*r_l) > w_l) (*r_l) = w_l;
    (*aux_end) = w_l - (*r_l);

    if ((*r_s) < 0) {
        (*aux_beg) = -(*r_s); (*r_s) = 0; (*r_l) -= (*aux_beg);
    }
    return 1;
}

// Assembly:
pushq %rbp
pushq %rbx
movq 0x20(%rsp), %r10
movq 0x18(%rsp), %r11
movq $-0x1, %rax
movq %rax, (%r10)
movq %rax, (%r11)
movq %rax, (%r9)
movq %rax, (%r8)
testq %rsi, %rsi
sets %bl
cmpq %rdx, %rsi
setge %bpl
xorl %eax, %eax
orb %bl, %bpl
jne 0x48ea2
leaq (%rdi,%rdi), %rbx
subq %rsi, %rbx
addq %rdx, %rbx
addq $0x1f, %rbx
cmpq %rcx, %rbx
jl 0x48ea2
movq $0x0, (%r8)
subq %rdi, %rsi
movq %rsi, (%r11)
subq %rsi, %rdx
cmpq %rcx, %rdx
cmovgeq %rcx, %rdx
movq %rdx, (%r10)
subq %rdx, %rcx
movq %rcx, (%r9)
movq (%r11), %rcx
movl $0x1, %eax
testq %rcx, %rcx
jns 0x48ea2
negq %rcx
movq %rcx, (%r8)
movq $0x0, (%r11)
movq (%r8), %rcx
subq %rcx, (%r10)
popq %rbx
popq %rbp
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: check_coverage_gap(unsigned long*, unsigned long, unsigned long, long)
int64_t check_coverage_gap(uint64_t *v_idx, uint64_t w_s, uint64_t w_e, int64_t block_s)
{
    int64_t wid = w_s/block_s, a_n = (uint32_t)(v_idx[wid]), k;
    uint64_t *a = v_idx + (v_idx[wid]>>32);
    for (k = 0; k < a_n; k++) {
        if(((a[k]>>32) == w_s) && (((uint32_t)(a[k])) == w_e)) return 1;
    }
    return 0;
}

// Assembly:
movq %rdx, %r8
xorl %r9d, %r9d
movq %rsi, %rax
xorl %edx, %edx
divq %rcx
movq (%rdi,%rax,8), %rcx
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
andq %rcx, %rax
je 0x4975c
shrq $0x20, %rcx
leaq (%rdi,%rcx,8), %rcx
xorl %r9d, %r9d
xorl %edx, %edx
movq (%rcx,%rdx,8), %rdi
movl %edi, %r10d
shrq $0x20, %rdi
xorq %rsi, %rdi
xorq %r8, %r10
orq %rdi, %r10
je 0x49756
incq %rdx
cmpq %rdx, %rax
jne 0x49736
jmp 0x4975c
movl $0x1, %r9d
movq %r9, %rax
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: get_adjust_winid(overlap_region*, long, long)
int64_t get_adjust_winid(overlap_region *z, int64_t win_beg, int64_t win_len)
{   
    int64_t win_id, k;
    win_id = (win_beg-((z->x_pos_s/win_len)*win_len))/win_len;
    if((uint64_t)win_id < z->w_list.n && z->w_list.a[win_id].x_start == win_beg) return win_id;
    if(z->w_list.n == 0) return -1;
    // if(z->w_list.a[win_id].x_start <= win_beg) {
    //     fprintf(stderr, "z->w_list.n::%u, z->w_list.a[%ld].x_start::%d, win_beg::%ld\n", 
    //     (uint32_t)z->w_list.n, win_id, z->w_list.a[win_id].x_start, win_beg);
    // }
    if((uint64_t)win_id > z->w_list.n) win_id = z->w_list.n;
    // assert((z->w_list.a[win_id].x_start > win_beg);
    for (k = win_id - 1; k >= 0; k--) {
        // if(k < 0 || k >= (int64_t)z->w_list.n) fprintf(stderr, "win_id::%ld, k::%ld, z->w_list.n::%ld\n", win_id, k, (int64_t)z->w_list.n);
        if(z->w_list.a[k].x_start == win_beg) return k;
        if(z->w_list.a[k].x_start < win_beg) return -1;
    }
    return -1;
}

// Assembly:
movq %rdx, %rcx
movl 0x4(%rdi), %r8d
movq %r8, %rax
xorl %edx, %edx
idivq %rcx
leaq (%rdx,%rsi), %rax
subq %r8, %rax
cqto
idivq %rcx
movq 0x48(%rdi), %rcx
cmpq %rcx, %rax
jae 0x4accc
movq 0x58(%rdi), %rdx
movq %rax, %r8
shlq $0x5, %r8
movslq (%rdx,%r8), %rdx
cmpq %rsi, %rdx
jne 0x4acd1
retq
testq %rcx, %rcx
je 0x4ad0a
cmpq %rcx, %rax
cmovbq %rax, %rcx
movq %rcx, %rdx
shlq $0x5, %rdx
addq $-0x20, %rdx
movq $-0x1, %rax
testq %rcx, %rcx
jle 0x4accb
movq 0x58(%rdi), %r8
movslq (%r8,%rdx), %r8
cmpq %rsi, %r8
je 0x4ad12
addq $-0x20, %rdx
decq %rcx
cmpq %rsi, %r8
jge 0x4acea
jmp 0x4accb
movq $-0x1, %rax
retq
decq %rcx
movq %rcx, %rax
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: cmp_snp_stats(void const*, void const*)
int cmp_snp_stats(const void * a, const void * b)
{
    if ((*(SnpStats*)a).score != (*(SnpStats*)b).score)
    {
        return (*(SnpStats*)a).score < (*(SnpStats*)b).score ? 1 : -1; 
    }
    else
    {
        if ((*(SnpStats*)a).occ_2 != (*(SnpStats*)b).occ_2)
        {
            return (*(SnpStats*)a).occ_2 > (*(SnpStats*)b).occ_2 ? 1 : -1; 
        }
        else
        {
            return 0;
        }   
    }
}

// Assembly:
movl 0x1c(%rsi), %eax
cmpl %eax, 0x1c(%rdi)
jne 0x4fcfd
movl 0x10(%rdi), %ecx
movl 0x10(%rsi), %edx
xorl %eax, %eax
cmpl %edx, %ecx
je 0x4fcfc
xorl %eax, %eax
cmpl %ecx, %edx
adcl $-0x1, %eax
orl $0x1, %eax
retq
setl %al
movzbl %al, %eax
leal -0x1(,%rax,2), %eax
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: add_to_result_snp_vector(haplotype_evdience_alloc*, signed char*, int)
void add_to_result_snp_vector(haplotype_evdience_alloc* hap, int8_t *new_vector, int Len)
{
    int8_t *r_vector = Get_Result_SNP_Vector((*hap));
    int j;
    for (j = 0; j < Len; j++)
    {
        if(r_vector[j] == -1)
        {
            if(new_vector[j] == 0)
            {
                hap->result_stat.occ_0++;
                r_vector[j] = new_vector[j];
            }
            else if(new_vector[j] == 1)
            {
                hap->result_stat.occ_1++;
                r_vector[j] = new_vector[j];
            }
        }
        ///can debug here
    }

    hap->result_stat.overlap_num = hap->result_stat.occ_0 + hap->result_stat.occ_1;
}

// Assembly:
testl %edx, %edx
jle 0x4ff16
movq 0x1e0(%rdi), %rax
leaq 0x1f8(%rdi), %rcx
leaq 0x1f4(%rdi), %r8
movl %edx, %edx
xorl %r9d, %r9d
cmpb $-0x1, (%rax,%r9)
jne 0x4ff0e
movzbl (%rsi,%r9), %r10d
movq %r8, %r11
testl %r10d, %r10d
je 0x4ff03
cmpl $0x1, %r10d
jne 0x4ff0e
movq %rcx, %r11
incl (%r11)
movb (%rsi,%r9), %r10b
movb %r10b, (%rax,%r9)
incq %r9
cmpq %r9, %rdx
jne 0x4fee6
movl 0x1f8(%rdi), %eax
addl 0x1f4(%rdi), %eax
movl %eax, 0x1f0(%rdi)
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: debug_add_to_result_snp_vector(haplotype_evdience_alloc*, signed char*, int)
int debug_add_to_result_snp_vector(haplotype_evdience_alloc* hap, int8_t *new_vector, int Len)
{
    int8_t *r_vector = Get_Result_SNP_Vector((*hap));
    int j;
    for (j = 0; j < Len; j++)
    {
        if(r_vector[j] == -1)
        {
            if(new_vector[j] == 0)
            {
                hap->result_stat.occ_0++;
                r_vector[j] = new_vector[j];
            }
            else if(new_vector[j] == 1)
            {
                hap->result_stat.occ_1++;
                r_vector[j] = new_vector[j];
            }
        }
        else ///can debug here
        {
            ///if((new_vector[j] != -1 && new_vector[j] != 2 && new_vector[j] != r_vector[j]))
            if((new_vector[j] == 0 || new_vector[j] == 1) && new_vector[j] != r_vector[j])
            {
                return j;
            }
        }
    }

    return -1;

}

// Assembly:
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
testl %edx, %edx
jle 0x4ff9a
pushq %rbx
movq 0x1e0(%rdi), %rcx
leaq 0x1f8(%rdi), %r8
addq $0x1f4, %rdi            # imm = 0x1F4
movl %edx, %r9d
xorl %edx, %edx
movb (%rcx,%rdx), %r11b
movzbl (%rsi,%rdx), %r10d
cmpb $-0x1, %r11b
je 0x4ff71
cmpb $0x2, %r10b
setae %bl
cmpb %r11b, %r10b
sete %r10b
orb %bl, %r10b
jne 0x4ff8d
jmp 0x4ff97
movq %rdi, %r11
testl %r10d, %r10d
je 0x4ff82
movq %r8, %r11
cmpl $0x1, %r10d
jne 0x4ff8d
incl (%r11)
movb (%rsi,%rdx), %r10b
movb %r10b, (%rcx,%rdx)
incq %rdx
cmpq %rdx, %r9
jne 0x4ff4d
jmp 0x4ff99
movl %edx, %eax
popq %rbx
retq
// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Correct.cpp
// Function: merge_snp_vectors_and_test(haplotype_evdience_alloc*, int)
int merge_snp_vectors_and_test(haplotype_evdience_alloc* hap, int diff_vector_ID)
{
    int8_t *r_vector = Get_Result_SNP_Vector((*hap));
    int vectorLen = Get_SNP_Vector_Length((*hap));
    memset(r_vector, -1, vectorLen);
    hap->result_stat.occ_0 = 0;
    hap->result_stat.occ_1 = 0;

    int8_t* vector;
    int vectorID;
    int i, j;

    for (i = 0; i < (int)hap->core_snp; i++)
    {
        if(i == diff_vector_ID)
        {
            continue;
        }

        vectorID = hap->snp_stat.a[i].id;
        vector = Get_SNP_Vector((*hap), vectorID);

        for (j = 0; j < vectorLen; j++)
        {
            if(r_vector[j] == -1)
            {
                if(vector[j] == 0)
                {
                    hap->result_stat.occ_0++;
                    r_vector[j] = vector[j];
                }
                else if(vector[j] == 1)
                {
                    hap->result_stat.occ_1++;
                    r_vector[j] = vector[j];
                }
            }
            else ///can debug here
            {
                ///has confilict
                if(vector[j] != -1 && vector[j] != 2 && vector[j] != r_vector[j])
                {
                    return 0;
                }
            }
        }
    }

    hap->result_stat.overlap_num = hap->result_stat.occ_0 + hap->result_stat.occ_1;

    return 1;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %rbx
pushq %rax
movl %esi, %ebp
movq %rdi, %rbx
movq 0x1e0(%rdi), %r14
movslq 0x1c8(%rdi), %r15
movq %r14, %rdi
movl $0xff, %esi
movq %r15, %rdx
callq 0x20e0
movq $0x0, 0x1f4(%rbx)
movl 0x1c4(%rbx), %r8d
testl %r8d, %r8d
jle 0x50088
movl %r15d, %ecx
leaq 0x1f4(%rbx), %rax
leaq 0x1f8(%rbx), %rdx
movl %ebp, %esi
xorl %edi, %edi
cmpq %rsi, %rdi
je 0x5006f
testl %ecx, %ecx
jle 0x5006f
movq 0x218(%rbx), %r9
leaq (%rdi,%rdi,4), %r10
movl 0x1c8(%rbx), %r8d
imull (%r9,%r10,8), %r8d
addq 0x1d0(%rbx), %r8
xorl %r9d, %r9d
movb (%r14,%r9), %r11b
movzbl (%r8,%r9), %r10d
cmpb $-0x1, %r11b
je 0x50044
cmpl $0x2, %r10d
je 0x50060
cmpl $0xff, %r10d
je 0x50060
cmpb %r11b, %r10b
je 0x50060
jmp 0x50084
movq %rax, %r11
testl %r10d, %r10d
je 0x50055
movq %rdx, %r11
cmpl $0x1, %r10d
jne 0x50060
incl (%r11)
movb (%r8,%r9), %r10b
movb %r10b, (%r14,%r9)
incq %r9
cmpq %r9, %rcx
jne 0x5001f
movl 0x1c4(%rbx), %r8d
incq %rdi
movslq %r8d, %r9
cmpq %r9, %rdi
jl 0x4fff5
movl (%rdx), %ecx
addl (%rax), %ecx
jmp 0x5008a
xorl %eax, %eax
jmp 0x50095
xorl %ecx, %ecx
movl %ecx, 0x1f0(%rbx)
movl $0x1, %eax
addq $0x8, %rsp
popq %rbx
popq %r14
popq %r15
popq %rbp
retq