// File: chhylp123[P]hifiasm/inter.cpp
// Function: worker_ul_recorrect_pipeline(void*, int, void*)
static void *worker_ul_recorrect_pipeline(void *data, int step, void *in) // callback for kt_pipeline()
{
    uldat_t *p = (uldat_t*)data;
    ///uint64_t total_base = 0, total_pair = 0;
    if (step == 0) { // step 1: read a block of sequences
        int ret;
        uint64_t l, rid;
		utepdat_t *s;
		CALLOC(s, 1);
        s->ha_flt_tab = p->ha_flt_tab; s->ha_idx = p->ha_idx; s->id = p->total_pair; 
		s->opt = p->opt; s->uu = p->uu; s->uopt = p->uopt; s->rg = p->rg;
        while ((ret = kseq_read(p->ks)) >= 0) 
        {
            if (p->ks->seq.l < (uint64_t)p->opt->k) continue;
            if (s->n == s->m) {
                s->m = s->m < 16? 16 : s->m + (s->n>>1);
                REALLOC(s->len, s->m);
                REALLOC(s->seq, s->m);
            }
			// append_ul_t(&UL_INF, NULL, p->ks->name.s, p->ks->name.l, NULL, 0, NULL, 0, P_CHAIN_COV, s->uopt);		
            l = p->ks->seq.l; s->seq[s->n] = NULL; rid = s->id + s->n;
			if(UL_INF.a[rid].rlen & ((uint32_t)(0x80000000))) {
				MALLOC(s->seq[s->n], l); memcpy(s->seq[s->n], p->ks->seq.s, l);
			}
            s->sum_len += l;
            s->len[s->n++] = l;
            if (s->sum_len >= p->chunk_size) break;            
        }
        p->total_pair += s->n;
        if (s->sum_len == 0) free(s);
		else return s;
    }
    else if (step == 1) { // step 2: alignment
        utepdat_t *s = (utepdat_t*)in;

		uint64_t i; s->n_thread = p->n_thread;
		CALLOC(s->hab, p->n_thread); CALLOC(s->ll, p->n_thread); CALLOC(s->buf, p->n_thread); 
		CALLOC(s->gdp, p->n_thread); CALLOC(s->mzs, p->n_thread); CALLOC(s->sps, p->n_thread); 

		// CALLOC(s->buf, p->n_thread);
		for (i = 0; i < p->n_thread; ++i) {
			s->hab[i] = ha_ovec_init(0, 0, 1); s->buf[i] = mg_tbuf_init();
		}
		fprintf(stderr, "[M::%s::Start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
		kt_for(p->n_thread, worker_for_ul_recorrect_alignment, s, s->n);
		fprintf(stderr, "[M::%s::Done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
		get_utepdat_t_mem(s, 1);

		for (i = 0; i < p->n_thread; ++i) {
			p->num_bases += s->hab[i]->num_read_base;
			p->num_corrected_bases += s->hab[i]->num_correct_base;

			// s->num_recorrected_bases += s->hab[i]->num_recorrect_base;
			ha_ovec_destroy(s->hab[i]); hc_glchain_destroy(&(s->ll[i]));
			mg_tbuf_destroy(s->buf[i]); hc_gdpchain_destroy(&(s->gdp[i])); 
			kv_destroy(s->mzs[i]); kv_destroy(s->sps[i]); free(s->seq[i]);
		}
		free(s->hab); free(s->ll); free(s->len); free(s->seq); 
		free(s->buf); free(s->gdp); free(s->mzs); free(s->sps); free(s);
    } 
    return 0;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x60, %rsp
movq %rdi, -0x10(%rbp)
movl %esi, -0x14(%rbp)
movq %rdx, -0x20(%rbp)
movq -0x10(%rbp), %rax
movq %rax, -0x28(%rbp)
cmpl $0x0, -0x14(%rbp)
jne 0x2f3ebd
movl $0x1, %edi
movl $0xd0, %esi
callq 0x2140
movq %rax, -0x48(%rbp)
movq -0x28(%rbp), %rax
movq (%rax), %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x28(%rbp), %rax
movq 0x8(%rax), %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x10(%rax)
movq -0x28(%rbp), %rax
movq 0x68(%rax), %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x50(%rax)
movq -0x28(%rbp), %rax
movq 0x10(%rax), %rcx
movq -0x48(%rbp), %rax
movq %rcx, (%rax)
movq -0x28(%rbp), %rax
movq 0x30(%rax), %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x30(%rax)
movq -0x28(%rbp), %rax
movq 0x28(%rax), %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x28(%rax)
movq -0x28(%rbp), %rax
movq 0x20(%rax), %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x20(%rax)
movq -0x28(%rbp), %rax
movq 0x48(%rax), %rdi
callq 0x2cf590
movl %eax, -0x2c(%rbp)
cmpl $0x0, %eax
jl 0x2f3e82
movq -0x28(%rbp), %rax
movq 0x48(%rax), %rax
movq 0x30(%rax), %rax
movq -0x28(%rbp), %rcx
movq 0x10(%rcx), %rcx
movslq 0x4(%rcx), %rcx
cmpq %rcx, %rax
jae 0x2f3cfe
jmp 0x2f3cc6
movq -0x48(%rbp), %rax
movl 0x38(%rax), %eax
movq -0x48(%rbp), %rcx
cmpl 0x3c(%rcx), %eax
jne 0x2f3d89
movq -0x48(%rbp), %rax
cmpl $0x10, 0x3c(%rax)
jge 0x2f3d22
movl $0x10, %eax
movl %eax, -0x5c(%rbp)
jmp 0x2f3d37
movq -0x48(%rbp), %rax
movl 0x3c(%rax), %eax
movq -0x48(%rbp), %rcx
movl 0x38(%rcx), %ecx
sarl %ecx
addl %ecx, %eax
movl %eax, -0x5c(%rbp)
movl -0x5c(%rbp), %ecx
movq -0x48(%rbp), %rax
movl %ecx, 0x3c(%rax)
movq -0x48(%rbp), %rax
movq 0x48(%rax), %rdi
movq -0x48(%rbp), %rax
movslq 0x3c(%rax), %rsi
shlq $0x3, %rsi
callq 0x2360
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x48(%rax)
movq -0x48(%rbp), %rax
movq 0x58(%rax), %rdi
movq -0x48(%rbp), %rax
movslq 0x3c(%rax), %rsi
shlq $0x3, %rsi
callq 0x2360
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x58(%rax)
movq -0x28(%rbp), %rax
movq 0x48(%rax), %rax
movq 0x30(%rax), %rax
movq %rax, -0x38(%rbp)
movq -0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x48(%rbp), %rcx
movslq 0x38(%rcx), %rcx
movq $0x0, (%rax,%rcx,8)
movq -0x48(%rbp), %rax
movq 0x50(%rax), %rax
movq -0x48(%rbp), %rcx
movslq 0x38(%rcx), %rcx
addq %rcx, %rax
movq %rax, -0x40(%rbp)
leaq 0xd15e9(%rip), %rax     # 0x3c53b8
movq 0x48(%rax), %rax
imulq $0x58, -0x40(%rbp), %rcx
addq %rcx, %rax
movl 0x18(%rax), %eax
andl $0x80000000, %eax       # imm = 0x80000000
cmpl $0x0, %eax
je 0x2f3e35
movq -0x38(%rbp), %rdi
shlq $0x0, %rdi
callq 0x2270
movq %rax, %rdx
movq -0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x48(%rbp), %rcx
movslq 0x38(%rcx), %rcx
movq %rdx, (%rax,%rcx,8)
movq -0x48(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x48(%rbp), %rcx
movslq 0x38(%rcx), %rcx
movq (%rax,%rcx,8), %rdi
movq -0x28(%rbp), %rax
movq 0x48(%rax), %rax
movq 0x40(%rax), %rsi
movq -0x38(%rbp), %rdx
callq 0x2180
movq -0x38(%rbp), %rdx
movq -0x48(%rbp), %rax
movslq 0x40(%rax), %rcx
addq %rdx, %rcx
movl %ecx, 0x40(%rax)
movq -0x38(%rbp), %rdx
movq -0x48(%rbp), %rax
movq 0x48(%rax), %rax
movq -0x48(%rbp), %rsi
movl 0x38(%rsi), %ecx
movl %ecx, %edi
addl $0x1, %edi
movl %edi, 0x38(%rsi)
movslq %ecx, %rcx
movq %rdx, (%rax,%rcx,8)
movq -0x48(%rbp), %rax
movslq 0x40(%rax), %rax
movq -0x28(%rbp), %rcx
cmpq 0x50(%rcx), %rax
jl 0x2f3e7d
jmp 0x2f3e82
jmp 0x2f3cc6
movq -0x48(%rbp), %rax
movslq 0x38(%rax), %rcx
movq -0x28(%rbp), %rax
addq 0x68(%rax), %rcx
movq %rcx, 0x68(%rax)
movq -0x48(%rbp), %rax
cmpl $0x0, 0x40(%rax)
jne 0x2f3eab
movq -0x48(%rbp), %rdi
callq 0x2210
jmp 0x2f3eb8
movq -0x48(%rbp), %rax
movq %rax, -0x8(%rbp)
jmp 0x2f4238
jmp 0x2f4230
cmpl $0x1, -0x14(%rbp)
jne 0x2f422e
movq -0x20(%rbp), %rax
movq %rax, -0x50(%rbp)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0xc0(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x8, %esi
callq 0x2140
movq %rax, %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x80(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x68, %esi
callq 0x2140
movq %rax, %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x88(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x8, %esi
callq 0x2140
movq %rax, %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x78(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0xc0, %esi
callq 0x2140
movq %rax, %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x90(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x10, %esi
callq 0x2140
movq %rax, %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x60(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x18, %esi
callq 0x2140
movq %rax, %rcx
movq -0x50(%rbp), %rax
movq %rcx, 0x68(%rax)
movq $0x0, -0x58(%rbp)
movq -0x58(%rbp), %rax
movq -0x28(%rbp), %rcx
cmpq 0x58(%rcx), %rax
jae 0x2f3ff9
xorl %esi, %esi
movl $0x1, %edx
movl %esi, %edi
callq 0x14c90
movq %rax, %rdx
movq -0x50(%rbp), %rax
movq 0x80(%rax), %rax
movq -0x58(%rbp), %rcx
movq %rdx, (%rax,%rcx,8)
callq 0x27e560
movq %rax, %rdx
movq -0x50(%rbp), %rax
movq 0x78(%rax), %rax
movq -0x58(%rbp), %rcx
movq %rdx, (%rax,%rcx,8)
movq -0x58(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x58(%rbp)
jmp 0x2f3fa1
movq 0xcffe0(%rip), %rax     # 0x3c3fe0
movq (%rax), %rdi
movq -0x50(%rbp), %rax
movq 0x50(%rax), %rcx
movq -0x50(%rbp), %rax
movl 0x38(%rax), %r8d
leaq 0xa1c24(%rip), %rsi     # 0x395c3e
leaq 0xa1c46(%rip), %rdx     # 0x395c67
movb $0x0, %al
callq 0x22a0
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rax
movl %eax, %edi
movq -0x50(%rbp), %rdx
movq -0x50(%rbp), %rax
movslq 0x38(%rax), %rcx
leaq 0x1843b(%rip), %rsi     # 0x30c480
callq 0x16d710
movq 0xcff8f(%rip), %rax     # 0x3c3fe0
movq (%rax), %rdi
movq -0x50(%rbp), %rax
movq 0x50(%rax), %rcx
movq -0x50(%rbp), %rax
movl 0x38(%rax), %r8d
leaq 0xa1c19(%rip), %rsi     # 0x395c84
leaq 0xa1bf5(%rip), %rdx     # 0x395c67
movb $0x0, %al
callq 0x22a0
movq -0x50(%rbp), %rdi
movl $0x1, %esi
callq 0x2ce380
movq $0x0, -0x58(%rbp)
movq -0x58(%rbp), %rax
movq -0x28(%rbp), %rcx
cmpq 0x58(%rcx), %rax
jae 0x2f41b4
movq -0x50(%rbp), %rax
movq 0x80(%rax), %rax
movq -0x58(%rbp), %rcx
movq (%rax,%rcx,8), %rax
movq 0xf0(%rax), %rcx
movq -0x28(%rbp), %rax
addq 0xd0(%rax), %rcx
movq %rcx, 0xd0(%rax)
movq -0x50(%rbp), %rax
movq 0x80(%rax), %rax
movq -0x58(%rbp), %rcx
movq (%rax,%rcx,8), %rax
movq 0xf8(%rax), %rcx
movq -0x28(%rbp), %rax
addq 0xd8(%rax), %rcx
movq %rcx, 0xd8(%rax)
movq -0x50(%rbp), %rax
movq 0x80(%rax), %rax
movq -0x58(%rbp), %rcx
movq (%rax,%rcx,8), %rdi
callq 0x14f00
movq -0x50(%rbp), %rax
movq 0x88(%rax), %rdi
imulq $0x68, -0x58(%rbp), %rax
addq %rax, %rdi
callq 0x282c10
movq -0x50(%rbp), %rax
movq 0x78(%rax), %rax
movq -0x58(%rbp), %rcx
movq (%rax,%rcx,8), %rdi
callq 0x27e5a0
movq -0x50(%rbp), %rax
movq 0x90(%rax), %rdi
imulq $0xc0, -0x58(%rbp), %rax
addq %rax, %rdi
callq 0x282c60
movq -0x50(%rbp), %rax
movq 0x60(%rax), %rax
movq -0x58(%rbp), %rcx
shlq $0x4, %rcx
addq %rcx, %rax
movq 0x8(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x68(%rax), %rax
imulq $0x18, -0x58(%rbp), %rcx
addq %rcx, %rax
movq 0x10(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x58(%rbp), %rcx
movq (%rax,%rcx,8), %rdi
callq 0x2210
movq -0x58(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x58(%rbp)
jmp 0x2f408f
movq -0x50(%rbp), %rax
movq 0x80(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x88(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x48(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x58(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x78(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x90(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x60(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
movq 0x68(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rdi
callq 0x2210
jmp 0x2f4230
movq $0x0, -0x8(%rbp)
movq -0x8(%rbp), %rax
addq $0x60, %rsp
popq %rbp
retq
nopw %cs:(%rax,%rax)