// File: chhylp123[P]hifiasm/anchor.cpp
// Function: minimizers_gen(ha_abufl_s*, char*, long, unsigned long, unsigned long, Candidates_list*, kvec_t_u8_warp*, void*, ha_pt_s*, kvec_t_u64_warp*, st_mt_t*, unsigned int*, unsigned int*)
void minimizers_gen(ha_abufl_t *ab, char* rs, int64_t rl, uint64_t mz_w, uint64_t mz_k, Candidates_list *cl, kvec_t_u8_warp* k_flag, 
void *ha_flt_tab, ha_pt_t *ha_idx, kvec_t_u64_warp* dbg_ct, st_mt_t *sp, uint32_t *high_occ, uint32_t *low_occ)
{
	// fprintf(stderr, "+[M::%s]\n", __func__);
	uint64_t i, k, l, max_cnt = UINT32_MAX, min_cnt = 0; int n, j; ha_mzl_t *z; seedl_t *s; 
	if(high_occ) {
		max_cnt = (*high_occ);
		if(max_cnt < 2) max_cnt = 2;
	}
	if(low_occ) {
		min_cnt = (*low_occ);
		if(min_cnt < 2) min_cnt = 2;
	}
	clear_Candidates_list(cl); ab->mz.n = 0, ab->n_a = 0;
	
	// get the list of anchors
	mz2_ha_sketch(rs, rl, mz_w, mz_k, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, asm_opt.mz_sample_dist, k_flag, dbg_ct, NULL, -1, asm_opt.dp_min_len, -1, sp, asm_opt.mz_rewin, 0, NULL);

	// minimizer of queried read
	if (ab->mz.m > ab->old_mz_m) {
		ab->old_mz_m = ab->mz.m;
		REALLOC(ab->seed, ab->old_mz_m);
	}

	for (i = 0, ab->n_a = 0; i < ab->mz.n; ++i) {
		ab->seed[i].a = ha_ptl_get(ha_idx, ab->mz.a[i].x, &n);
		ab->seed[i].n = n;
		ab->n_a += n;
	}

	if (ab->n_a > ab->m_a) {
		ab->m_a = ab->n_a;
		REALLOC(ab->a, ab->m_a);
	}

	for (i = 0, k = 0; i < ab->mz.n; ++i) {
		///z is one of the minimizer
		z = &ab->mz.a[i]; s = &ab->seed[i];
		for (j = 0; j < s->n; ++j) {
			const ha_idxposl_t *y = &s->a[j];
			anchor1_t *an = &ab->a[k++];
			uint8_t rev = z->rev == y->rev? 0 : 1;
			an->other_off = y->pos;
			an->self_off = rev? rl - 1 - (z->pos + 1 - z->span) : z->pos;
			///an->cnt: cnt<<8|span
			an->cnt = s->n; if(an->cnt > ((uint32_t)(0xffffffu))) an->cnt = 0xffffffu;
			an->cnt <<= 8; an->cnt |= ((z->span <= ((uint32_t)(0xffu)))?z->span:((uint32_t)(0xffu)));
			an->srt = (uint64_t)y->rid<<33 | (uint64_t)rev<<32 | an->other_off;
		}
	}

	radix_sort_ha_an1(ab->a, ab->a + ab->n_a);
	for (k = 1, l = 0; k <= ab->n_a; ++k) {
		if (k == ab->n_a || ab->a[k].srt != ab->a[l].srt) {
			if (k - l > 1)
				radix_sort_ha_an2(ab->a + l, ab->a + k);
			l = k;
		}
	}

	// copy over to _cl_
	if (ab->m_a >= (uint64_t)cl->size) {
		cl->size = ab->m_a;
		REALLOC(cl->list, cl->size);
	}

	for (k = 0; k < ab->n_a; ++k) {
		k_mer_hit *p = &cl->list[k];
		p->readID = ab->a[k].srt >> 33;
		p->strand = ab->a[k].srt >> 32 & 1;
		p->offset = ab->a[k].other_off;
		p->self_offset = ab->a[k].self_off;
		if(((ab->a[k].cnt>>8) < max_cnt) && ((ab->a[k].cnt>>8) > min_cnt)){
			p->cnt = 1;
		} else if((ab->a[k].cnt>>8) <= min_cnt) {
			p->cnt = 2;
		} else{
			p->cnt = 1 + (((ab->a[k].cnt>>8) + (max_cnt<<1) - 1)/(max_cnt<<1));
			p->cnt = pow(p->cnt, 1.1);
		}
		if(p->cnt > ((uint32_t)(0xffffffu))) p->cnt = 0xffffffu;
		p->cnt <<= 8; p->cnt |= (((uint32_t)(0xffu))&(ab->a[k].cnt));
	}
	cl->length = ab->n_a;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x108, %rsp            # imm = 0x108
movq 0x40(%rbp), %rax
movq 0x38(%rbp), %rax
movq 0x30(%rbp), %rax
movq 0x28(%rbp), %rax
movq 0x20(%rbp), %rax
movq 0x18(%rbp), %rax
movq 0x10(%rbp), %rax
movq %rdi, -0x30(%rbp)
movq %rsi, -0x38(%rbp)
movq %rdx, -0x40(%rbp)
movq %rcx, -0x48(%rbp)
movq %r8, -0x50(%rbp)
movq %r9, -0x58(%rbp)
movl $0xffffffff, %eax       # imm = 0xFFFFFFFF
movq %rax, -0x78(%rbp)
movq $0x0, -0x80(%rbp)
cmpq $0x0, 0x38(%rbp)
je 0x1a3d0b
movq 0x38(%rbp), %rax
movl (%rax), %eax
movq %rax, -0x78(%rbp)
cmpq $0x2, -0x78(%rbp)
jae 0x1a3d09
movq $0x2, -0x78(%rbp)
jmp 0x1a3d0b
cmpq $0x0, 0x40(%rbp)
je 0x1a3d2d
movq 0x40(%rbp), %rax
movl (%rax), %eax
movq %rax, -0x80(%rbp)
cmpq $0x2, -0x80(%rbp)
jae 0x1a3d2b
movq $0x2, -0x80(%rbp)
jmp 0x1a3d2d
movq -0x58(%rbp), %rdi
callq 0x23090
movq -0x30(%rbp), %rax
movl $0x0, 0x18(%rax)
movq -0x30(%rbp), %rax
movq $0x0, (%rax)
movq -0x38(%rbp), %rdi
movq -0x40(%rbp), %rax
movl %eax, %esi
movq -0x48(%rbp), %rax
movl %eax, %edx
movq -0x50(%rbp), %rax
movl %eax, %ecx
leaq 0x220a8f(%rip), %rax    # 0x3c47f8
movl (%rax), %eax
andl $0x1, %eax
cmpl $0x0, %eax
setne %al
xorb $-0x1, %al
andb $0x1, %al
movzbl %al, %r9d
movq -0x30(%rbp), %r13
addq $0x18, %r13
movq 0x18(%rbp), %r12
leaq 0x220a69(%rip), %rax    # 0x3c47f8
movl 0xa8(%rax), %r15d
movq 0x10(%rbp), %r14
movq 0x28(%rbp), %rbx
leaq 0x220a53(%rip), %rax    # 0x3c47f8
movl 0x1f8(%rax), %r11d
movq 0x30(%rbp), %r10
leaq 0x220a41(%rip), %rax    # 0x3c47f8
movl 0xa0(%rax), %eax
movl %eax, -0xbc(%rbp)
xorl %r8d, %r8d
xorl %eax, %eax
movl -0xbc(%rbp), %eax
movss 0x1db29a(%rip), %xmm0   # 0x37f070
movq %r13, (%rsp)
movq %r12, 0x8(%rsp)
movl %r15d, 0x10(%rsp)
movq %r14, 0x18(%rsp)
movq %rbx, 0x20(%rsp)
movq $0x0, 0x28(%rsp)
movl $0xffffffff, 0x30(%rsp) # imm = 0xFFFFFFFF
movl %r11d, 0x38(%rsp)
movq %r10, 0x40(%rsp)
movl %eax, 0x48(%rsp)
movl $0x0, 0x50(%rsp)
movq $0x0, 0x58(%rsp)
callq 0x1995e0
movq -0x30(%rbp), %rax
movl 0x1c(%rax), %eax
movq -0x30(%rbp), %rcx
cmpl 0x10(%rcx), %eax
jbe 0x1a3e66
movq -0x30(%rbp), %rax
movl 0x1c(%rax), %ecx
movq -0x30(%rbp), %rax
movl %ecx, 0x10(%rax)
movq -0x30(%rbp), %rax
movq 0x28(%rax), %rdi
movq -0x30(%rbp), %rax
movl 0x10(%rax), %eax
movl %eax, %esi
shlq $0x4, %rsi
callq 0x2360
movq %rax, %rcx
movq -0x30(%rbp), %rax
movq %rcx, 0x28(%rax)
movq $0x0, -0x60(%rbp)
movq -0x30(%rbp), %rax
movq $0x0, (%rax)
movq -0x60(%rbp), %rax
movq -0x30(%rbp), %rcx
movl 0x18(%rcx), %ecx
cmpq %rcx, %rax
jae 0x1a3f03
movq 0x20(%rbp), %rdi
movq -0x30(%rbp), %rax
movq 0x20(%rax), %rax
imulq $0x18, -0x60(%rbp), %rcx
addq %rcx, %rax
movq (%rax), %rsi
leaq -0x84(%rbp), %rdx
callq 0x1878d0
movq %rax, %rcx
movq -0x30(%rbp), %rax
movq 0x28(%rax), %rax
movq -0x60(%rbp), %rdx
shlq $0x4, %rdx
addq %rdx, %rax
movq %rcx, 0x8(%rax)
movl -0x84(%rbp), %ecx
movq -0x30(%rbp), %rax
movq 0x28(%rax), %rax
movq -0x60(%rbp), %rdx
shlq $0x4, %rdx
addq %rdx, %rax
movl %ecx, (%rax)
movslq -0x84(%rbp), %rcx
movq -0x30(%rbp), %rax
addq (%rax), %rcx
movq %rcx, (%rax)
movq -0x60(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x60(%rbp)
jmp 0x1a3e79
movq -0x30(%rbp), %rax
movq (%rax), %rax
movq -0x30(%rbp), %rcx
cmpq 0x8(%rcx), %rax
jbe 0x1a3f44
movq -0x30(%rbp), %rax
movq (%rax), %rcx
movq -0x30(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rdi
movq -0x30(%rbp), %rax
imulq $0x18, 0x8(%rax), %rsi
callq 0x2360
movq %rax, %rcx
movq -0x30(%rbp), %rax
movq %rcx, 0x30(%rax)
movq $0x0, -0x60(%rbp)
movq $0x0, -0x68(%rbp)
movq -0x60(%rbp), %rax
movq -0x30(%rbp), %rcx
movl 0x18(%rcx), %ecx
cmpq %rcx, %rax
jae 0x1a41a0
movq -0x30(%rbp), %rax
movq 0x20(%rax), %rax
imulq $0x18, -0x60(%rbp), %rcx
addq %rcx, %rax
movq %rax, -0x90(%rbp)
movq -0x30(%rbp), %rax
movq 0x28(%rax), %rax
movq -0x60(%rbp), %rcx
shlq $0x4, %rcx
addq %rcx, %rax
movq %rax, -0x98(%rbp)
movl $0x0, -0x88(%rbp)
movl -0x88(%rbp), %eax
movq -0x98(%rbp), %rcx
cmpl (%rcx), %eax
jge 0x1a418d
movq -0x98(%rbp), %rax
movq 0x8(%rax), %rax
movslq -0x88(%rbp), %rcx
shlq $0x4, %rcx
addq %rcx, %rax
movq %rax, -0xa0(%rbp)
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
movq -0x68(%rbp), %rcx
movq %rcx, %rdx
addq $0x1, %rdx
movq %rdx, -0x68(%rbp)
imulq $0x18, %rcx, %rcx
addq %rcx, %rax
movq %rax, -0xa8(%rbp)
movq -0x90(%rbp), %rax
movq 0x8(%rax), %rax
shrq $0x1f, %rax
andq $0x1, %rax
movl %eax, %edx
movq -0xa0(%rbp), %rax
movq (%rax), %rax
shrq $0x1f, %rax
andq $0x1, %rax
movl %eax, %esi
movl $0x1, %eax
xorl %ecx, %ecx
cmpl %esi, %edx
cmovel %ecx, %eax
movb %al, -0xa9(%rbp)
movq -0xa0(%rbp), %rax
movq (%rax), %rax
shrq $0x20, %rax
movl %eax, %ecx
movq -0xa8(%rbp), %rax
movl %ecx, 0xc(%rax)
cmpb $0x0, -0xa9(%rbp)
je 0x1a4090
movq -0x40(%rbp), %rax
subq $0x1, %rax
movq -0x90(%rbp), %rcx
movq 0x8(%rcx), %rcx
shrq $0x20, %rcx
addl $0x1, %ecx
movq -0x90(%rbp), %rdx
movzbl 0x10(%rdx), %edx
subl %edx, %ecx
movl %ecx, %ecx
subq %rcx, %rax
movq %rax, -0xc8(%rbp)
jmp 0x1a40a6
movq -0x90(%rbp), %rax
movq 0x8(%rax), %rax
shrq $0x20, %rax
movq %rax, -0xc8(%rbp)
movq -0xc8(%rbp), %rax
movl %eax, %ecx
movq -0xa8(%rbp), %rax
movl %ecx, 0x8(%rax)
movq -0x98(%rbp), %rax
movl (%rax), %ecx
movq -0xa8(%rbp), %rax
movl %ecx, 0x10(%rax)
movq -0xa8(%rbp), %rax
cmpl $0xffffff, 0x10(%rax)   # imm = 0xFFFFFF
jbe 0x1a40ea
movq -0xa8(%rbp), %rax
movl $0xffffff, 0x10(%rax)   # imm = 0xFFFFFF
movq -0xa8(%rbp), %rax
movl 0x10(%rax), %ecx
shll $0x8, %ecx
movl %ecx, 0x10(%rax)
movq -0x90(%rbp), %rax
movzbl 0x10(%rax), %eax
cmpl $0xff, %eax
ja 0x1a411f
movq -0x90(%rbp), %rax
movzbl 0x10(%rax), %eax
movl %eax, -0xcc(%rbp)
jmp 0x1a412c
movl $0xff, %eax
movl %eax, -0xcc(%rbp)
jmp 0x1a412c
movl -0xcc(%rbp), %ecx
movq -0xa8(%rbp), %rax
orl 0x10(%rax), %ecx
movl %ecx, 0x10(%rax)
movq -0xa0(%rbp), %rax
movq (%rax), %rcx
andq $0x7fffffff, %rcx       # imm = 0x7FFFFFFF
shlq $0x21, %rcx
movzbl -0xa9(%rbp), %eax
shlq $0x20, %rax
orq %rax, %rcx
movq -0xa8(%rbp), %rax
movl 0xc(%rax), %eax
orq %rax, %rcx
movq -0xa8(%rbp), %rax
movq %rcx, (%rax)
movl -0x88(%rbp), %eax
addl $0x1, %eax
movl %eax, -0x88(%rbp)
jmp 0x1a3fa3
jmp 0x1a418f
movq -0x60(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x60(%rbp)
jmp 0x1a3f54
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rdi
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rsi
movq -0x30(%rbp), %rax
imulq $0x18, (%rax), %rax
addq %rax, %rsi
callq 0x19c150
movq $0x1, -0x68(%rbp)
movq $0x0, -0x70(%rbp)
movq -0x68(%rbp), %rax
movq -0x30(%rbp), %rcx
cmpq (%rcx), %rax
ja 0x1a4264
movq -0x68(%rbp), %rax
movq -0x30(%rbp), %rcx
cmpq (%rcx), %rax
je 0x1a4216
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movq (%rax), %rax
movq -0x30(%rbp), %rcx
movq 0x30(%rcx), %rcx
imulq $0x18, -0x70(%rbp), %rdx
addq %rdx, %rcx
cmpq (%rcx), %rax
je 0x1a4251
movq -0x68(%rbp), %rax
subq -0x70(%rbp), %rax
cmpq $0x1, %rax
jbe 0x1a4249
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rdi
imulq $0x18, -0x70(%rbp), %rax
addq %rax, %rdi
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rsi
imulq $0x18, -0x68(%rbp), %rax
addq %rax, %rsi
callq 0x19c660
movq -0x68(%rbp), %rax
movq %rax, -0x70(%rbp)
jmp 0x1a4253
movq -0x68(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x68(%rbp)
jmp 0x1a41d0
movq -0x30(%rbp), %rax
movq 0x8(%rax), %rax
movq -0x58(%rbp), %rcx
cmpq 0x10(%rcx), %rax
jb 0x1a42a8
movq -0x30(%rbp), %rax
movq 0x8(%rax), %rcx
movq -0x58(%rbp), %rax
movq %rcx, 0x10(%rax)
movq -0x58(%rbp), %rax
movq (%rax), %rdi
movq -0x58(%rbp), %rax
movq 0x10(%rax), %rsi
shlq $0x4, %rsi
callq 0x2360
movq %rax, %rcx
movq -0x58(%rbp), %rax
movq %rcx, (%rax)
movq $0x0, -0x68(%rbp)
movq -0x68(%rbp), %rax
movq -0x30(%rbp), %rcx
cmpq (%rcx), %rax
jae 0x1a44c1
movq -0x58(%rbp), %rax
movq (%rax), %rax
movq -0x68(%rbp), %rcx
shlq $0x4, %rcx
addq %rcx, %rax
movq %rax, -0xb8(%rbp)
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movq (%rax), %rax
shrq $0x21, %rax
movl %eax, %edx
movq -0xb8(%rbp), %rax
movl (%rax), %ecx
andl $0x7fffffff, %edx       # imm = 0x7FFFFFFF
andl $0x80000000, %ecx       # imm = 0x80000000
orl %edx, %ecx
movl %ecx, (%rax)
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movq (%rax), %rax
shrq $0x20, %rax
andq $0x1, %rax
movl %eax, %edx
movq -0xb8(%rbp), %rax
movl (%rax), %ecx
andl $0x1, %edx
shll $0x1f, %edx
andl $0x7fffffff, %ecx       # imm = 0x7FFFFFFF
orl %edx, %ecx
movl %ecx, (%rax)
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movl 0xc(%rax), %ecx
movq -0xb8(%rbp), %rax
movl %ecx, 0x4(%rax)
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movl 0x8(%rax), %ecx
movq -0xb8(%rbp), %rax
movl %ecx, 0x8(%rax)
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movl 0x10(%rax), %eax
shrl $0x8, %eax
movl %eax, %eax
cmpq -0x78(%rbp), %rax
jae 0x1a43cb
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movl 0x10(%rax), %eax
shrl $0x8, %eax
movl %eax, %eax
cmpq -0x80(%rbp), %rax
jbe 0x1a43cb
movq -0xb8(%rbp), %rax
movl $0x1, 0xc(%rax)
jmp 0x1a445c
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movl 0x10(%rax), %eax
shrl $0x8, %eax
movl %eax, %eax
cmpq -0x80(%rbp), %rax
ja 0x1a43f9
movq -0xb8(%rbp), %rax
movl $0x2, 0xc(%rax)
jmp 0x1a445a
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
movq -0x68(%rbp), %rcx
leaq (%rcx,%rcx,2), %rcx
movl 0x10(%rax,%rcx,8), %eax
shrl $0x8, %eax
movq -0x78(%rbp), %rdx
movq %rdx, %rcx
addq %rcx, %rcx
leaq -0x1(%rax,%rdx,2), %rax
xorl %edx, %edx
divq %rcx
movl %eax, %ecx
incl %ecx
movq -0xb8(%rbp), %rax
movl %ecx, 0xc(%rax)
movq -0xb8(%rbp), %rax
movl 0xc(%rax), %edi
movsd 0x1e2404(%rip), %xmm0   # 0x386848
callq 0x1b4690
cvttsd2si %xmm0, %rax
movl %eax, %ecx
movq -0xb8(%rbp), %rax
movl %ecx, 0xc(%rax)
jmp 0x1a445c
movq -0xb8(%rbp), %rax
cmpl $0xffffff, 0xc(%rax)    # imm = 0xFFFFFF
jbe 0x1a447a
movq -0xb8(%rbp), %rax
movl $0xffffff, 0xc(%rax)    # imm = 0xFFFFFF
movq -0xb8(%rbp), %rax
movl 0xc(%rax), %ecx
shll $0x8, %ecx
movl %ecx, 0xc(%rax)
movq -0x30(%rbp), %rax
movq 0x30(%rax), %rax
imulq $0x18, -0x68(%rbp), %rcx
addq %rcx, %rax
movl 0x10(%rax), %ecx
andl $0xff, %ecx
movq -0xb8(%rbp), %rax
orl 0xc(%rax), %ecx
movl %ecx, 0xc(%rax)
movq -0x68(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x68(%rbp)
jmp 0x1a42b0
movq -0x30(%rbp), %rax
movq (%rax), %rcx
movq -0x58(%rbp), %rax
movq %rcx, 0x8(%rax)
addq $0x108, %rsp            # imm = 0x108
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
nopw %cs:(%rax,%rax)