// File: chhylp123[P]hifiasm/inter.cpp
// Function: worker_ul_rescall_pipeline(void*, int, void*)
static void *worker_ul_rescall_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;
		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; s->mm = p->mm;
        while ((ret = kseq_read(p->ks)) >= 0) 
        {
			if ((p->ks->seq.l < (uint64_t)p->opt->k) || (p->ks->seq.l < asm_opt.ul_min_base)) 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;
            MALLOC(s->seq[s->n], l);
            s->sum_len += l;
            memcpy(s->seq[s->n], p->ks->seq.s, l);
			// fprintf(stderr, "s->n->%d, l->%lu\n", s->n, l);
			// fprintf(stderr, "+++++rid->%lu, l->%lu, %.*s\n", 
			// 			s->id + s->n, l, (int32_t)p->ks->name.l, p->ks->name.s);
            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->mk, 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_rescall_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]); 
			kv_destroy(s->mk[i].idx); kv_destroy(s->mk[i].srt);
			//free(s->seq[i]);
		}
		free(s->hab); free(s->ll); free(s->mk); ///free(s->len); free(s->seq); 
		free(s->buf); free(s->gdp); free(s->mzs); free(s->sps); ///free(s);
		return s;
    } else if (step == 2) { // step 3: dump
		utepdat_t *s = (utepdat_t*)in; int64_t i, rid;
		// fprintf(stderr, "[M::%s::dump_start] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
		for (i = 0; i < s->n; ++i) {
			rid = s->id + i;
			if(UL_INF.a[rid].dd == 3 && p->ucr_s && p->ucr_s->flag == 1) {///for the scaffolding
				assert(s->seq[i]);
				// if(s->seq[i] == NULL) fprintf(stderr, "[M::%s::]rid->%ld, len->%lu\n", __func__, rid, s->len[i]);
				///for debug interval
				write_compress_base_disk(p->ucr_s->fp, rid, s->seq[i], s->len[i], &(p->ucr_s->u));
			}
			// if(UL_INF.a[rid].dd) fprintf(stderr, "rid->%ld\n", rid);
			free(s->seq[i]);
		}
		// fprintf(stderr, "[M::%s::dump_done] ==> s->id: %lu, s->n:% d\n", __func__, s->id, s->n);
		free(s->len); free(s->seq); free(s);
	}
    return 0;
}

// Assembly:
pushq %rbp
movq %rsp, %rbp
subq $0x70, %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 0x2f361f
movl $0x1, %edi
movl $0xd0, %esi
callq 0x2140
movq %rax, -0x40(%rbp)
movq -0x28(%rbp), %rax
movq (%rax), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x8(%rax)
movq -0x28(%rbp), %rax
movq 0x8(%rax), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x10(%rax)
movq -0x28(%rbp), %rax
movq 0x68(%rax), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x50(%rax)
movq -0x28(%rbp), %rax
movq 0x10(%rax), %rcx
movq -0x40(%rbp), %rax
movq %rcx, (%rax)
movq -0x28(%rbp), %rax
movq 0x30(%rax), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x30(%rax)
movq -0x28(%rbp), %rax
movq 0x28(%rax), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x28(%rax)
movq -0x28(%rbp), %rax
movq 0x20(%rax), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x20(%rax)
movq -0x28(%rbp), %rax
movq 0x38(%rax), %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0xa0(%rax)
movq -0x28(%rbp), %rax
movq 0x48(%rax), %rdi
callq 0x2cf590
movl %eax, -0x2c(%rbp)
cmpl $0x0, %eax
jl 0x2f35e4
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
jb 0x2f34ad
movq -0x28(%rbp), %rax
movq 0x48(%rax), %rax
movq 0x30(%rax), %rax
leaq 0xd1356(%rip), %rcx     # 0x3c47f8
movl 0x260(%rcx), %ecx
cmpq %rcx, %rax
jae 0x2f34af
jmp 0x2f3459
movq -0x40(%rbp), %rax
movl 0x38(%rax), %eax
movq -0x40(%rbp), %rcx
cmpl 0x3c(%rcx), %eax
jne 0x2f353a
movq -0x40(%rbp), %rax
cmpl $0x10, 0x3c(%rax)
jge 0x2f34d3
movl $0x10, %eax
movl %eax, -0x6c(%rbp)
jmp 0x2f34e8
movq -0x40(%rbp), %rax
movl 0x3c(%rax), %eax
movq -0x40(%rbp), %rcx
movl 0x38(%rcx), %ecx
sarl %ecx
addl %ecx, %eax
movl %eax, -0x6c(%rbp)
movl -0x6c(%rbp), %ecx
movq -0x40(%rbp), %rax
movl %ecx, 0x3c(%rax)
movq -0x40(%rbp), %rax
movq 0x48(%rax), %rdi
movq -0x40(%rbp), %rax
movslq 0x3c(%rax), %rsi
shlq $0x3, %rsi
callq 0x2360
movq %rax, %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x48(%rax)
movq -0x40(%rbp), %rax
movq 0x58(%rax), %rdi
movq -0x40(%rbp), %rax
movslq 0x3c(%rax), %rsi
shlq $0x3, %rsi
callq 0x2360
movq %rax, %rcx
movq -0x40(%rbp), %rax
movq %rcx, 0x58(%rax)
movq -0x28(%rbp), %rax
movq 0x48(%rax), %rax
movq 0x30(%rax), %rax
movq %rax, -0x38(%rbp)
movq -0x38(%rbp), %rdi
shlq $0x0, %rdi
callq 0x2270
movq %rax, %rdx
movq -0x40(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x40(%rbp), %rcx
movslq 0x38(%rcx), %rcx
movq %rdx, (%rax,%rcx,8)
movq -0x38(%rbp), %rdx
movq -0x40(%rbp), %rax
movslq 0x40(%rax), %rcx
addq %rdx, %rcx
movl %ecx, 0x40(%rax)
movq -0x40(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x40(%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 -0x40(%rbp), %rax
movq 0x48(%rax), %rax
movq -0x40(%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 -0x40(%rbp), %rax
movslq 0x40(%rax), %rax
movq -0x28(%rbp), %rcx
cmpq 0x50(%rcx), %rax
jl 0x2f35df
jmp 0x2f35e4
jmp 0x2f3459
movq -0x40(%rbp), %rax
movslq 0x38(%rax), %rcx
movq -0x28(%rbp), %rax
addq 0x68(%rax), %rcx
movq %rcx, 0x68(%rax)
movq -0x40(%rbp), %rax
cmpl $0x0, 0x40(%rax)
jne 0x2f360d
movq -0x40(%rbp), %rdi
callq 0x2210
jmp 0x2f361a
movq -0x40(%rbp), %rax
movq %rax, -0x8(%rbp)
jmp 0x2f3aa9
jmp 0x2f3aa1
cmpl $0x1, -0x14(%rbp)
jne 0x2f3961
movq -0x20(%rbp), %rax
movq %rax, -0x48(%rbp)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0xc0(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x8, %esi
callq 0x2140
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x80(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x68, %esi
callq 0x2140
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x88(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x8, %esi
callq 0x2140
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x78(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0xc0, %esi
callq 0x2140
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x90(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x10, %esi
callq 0x2140
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x60(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x18, %esi
callq 0x2140
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x68(%rax)
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rdi
movl $0x30, %esi
callq 0x2140
movq %rax, %rcx
movq -0x48(%rbp), %rax
movq %rcx, 0x98(%rax)
movq $0x0, -0x50(%rbp)
movq -0x50(%rbp), %rax
movq -0x28(%rbp), %rcx
cmpq 0x58(%rcx), %rax
jae 0x2f377b
xorl %esi, %esi
movl $0x1, %edx
movl %esi, %edi
callq 0x14c90
movq %rax, %rdx
movq -0x48(%rbp), %rax
movq 0x80(%rax), %rax
movq -0x50(%rbp), %rcx
movq %rdx, (%rax,%rcx,8)
callq 0x27e560
movq %rax, %rdx
movq -0x48(%rbp), %rax
movq 0x78(%rax), %rax
movq -0x50(%rbp), %rcx
movq %rdx, (%rax,%rcx,8)
movq -0x50(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x50(%rbp)
jmp 0x2f3723
movq -0x28(%rbp), %rax
movq 0x58(%rax), %rax
movl %eax, %edi
movq -0x48(%rbp), %rdx
movq -0x48(%rbp), %rax
movslq 0x38(%rax), %rcx
leaq 0x17bf8(%rip), %rsi     # 0x30b390
callq 0x16d710
movq $0x0, -0x50(%rbp)
movq -0x50(%rbp), %rax
movq -0x28(%rbp), %rcx
cmpq 0x58(%rcx), %rax
jae 0x2f38ed
movq -0x48(%rbp), %rax
movq 0x80(%rax), %rax
movq -0x50(%rbp), %rcx
movq (%rax,%rcx,8), %rax
movq 0xf0(%rax), %rcx
movq -0x28(%rbp), %rax
addq 0xd0(%rax), %rcx
movq %rcx, 0xd0(%rax)
movq -0x48(%rbp), %rax
movq 0x80(%rax), %rax
movq -0x50(%rbp), %rcx
movq (%rax,%rcx,8), %rax
movq 0xf8(%rax), %rcx
movq -0x28(%rbp), %rax
addq 0xd8(%rax), %rcx
movq %rcx, 0xd8(%rax)
movq -0x48(%rbp), %rax
movq 0x80(%rax), %rax
movq -0x50(%rbp), %rcx
movq (%rax,%rcx,8), %rdi
callq 0x14f00
movq -0x48(%rbp), %rax
movq 0x88(%rax), %rdi
imulq $0x68, -0x50(%rbp), %rax
addq %rax, %rdi
callq 0x282c10
movq -0x48(%rbp), %rax
movq 0x78(%rax), %rax
movq -0x50(%rbp), %rcx
movq (%rax,%rcx,8), %rdi
callq 0x27e5a0
movq -0x48(%rbp), %rax
movq 0x90(%rax), %rdi
imulq $0xc0, -0x50(%rbp), %rax
addq %rax, %rdi
callq 0x282c60
movq -0x48(%rbp), %rax
movq 0x60(%rax), %rax
movq -0x50(%rbp), %rcx
shlq $0x4, %rcx
addq %rcx, %rax
movq 0x8(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x68(%rax), %rax
imulq $0x18, -0x50(%rbp), %rcx
addq %rcx, %rax
movq 0x10(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x98(%rax), %rax
imulq $0x30, -0x50(%rbp), %rcx
addq %rcx, %rax
movq 0x10(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x98(%rax), %rax
imulq $0x30, -0x50(%rbp), %rcx
addq %rcx, %rax
movq 0x18(%rax), %rdi
callq 0x2210
movq -0x50(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x50(%rbp)
jmp 0x2f37a5
movq -0x48(%rbp), %rax
movq 0x80(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x88(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x98(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x78(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x90(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x60(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq 0x68(%rax), %rdi
callq 0x2210
movq -0x48(%rbp), %rax
movq %rax, -0x8(%rbp)
jmp 0x2f3aa9
cmpl $0x2, -0x14(%rbp)
jne 0x2f3a9d
movq -0x20(%rbp), %rax
movq %rax, -0x58(%rbp)
movq $0x0, -0x60(%rbp)
movq -0x60(%rbp), %rax
movq -0x58(%rbp), %rcx
movslq 0x38(%rcx), %rcx
cmpq %rcx, %rax
jge 0x2f3a7a
movq -0x58(%rbp), %rax
movq 0x50(%rax), %rax
addq -0x60(%rbp), %rax
movq %rax, -0x68(%rbp)
leaq 0xd1a11(%rip), %rax     # 0x3c53b8
movq 0x48(%rax), %rax
imulq $0x58, -0x68(%rbp), %rcx
addq %rcx, %rax
movzbl 0x50(%rax), %eax
cmpl $0x3, %eax
jne 0x2f3a54
movq -0x28(%rbp), %rax
cmpq $0x0, 0x40(%rax)
je 0x2f3a54
movq -0x28(%rbp), %rax
movq 0x40(%rax), %rax
cmpq $0x1, 0x60(%rax)
jne 0x2f3a54
movq -0x58(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x60(%rbp), %rcx
cmpq $0x0, (%rax,%rcx,8)
je 0x2f39f3
jmp 0x2f3a12
leaq 0xa2204(%rip), %rdi     # 0x395bfe
leaq 0x9ce2e(%rip), %rsi     # 0x39082f
movl $0x332f, %edx           # imm = 0x332F
leaq 0xa21fb(%rip), %rcx     # 0x395c08
callq 0x2130
movq -0x28(%rbp), %rax
movq 0x40(%rax), %rax
movq (%rax), %rdi
movq -0x68(%rbp), %rsi
movq -0x58(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x60(%rbp), %rcx
movq (%rax,%rcx,8), %rdx
movq -0x58(%rbp), %rax
movq 0x48(%rax), %rax
movq -0x60(%rbp), %rcx
movq (%rax,%rcx,8), %rax
movl %eax, %ecx
movq -0x28(%rbp), %rax
movq 0x40(%rax), %r8
addq $0x8, %r8
callq 0x13590
movq -0x58(%rbp), %rax
movq 0x58(%rax), %rax
movq -0x60(%rbp), %rcx
movq (%rax,%rcx,8), %rdi
callq 0x2210
movq -0x60(%rbp), %rax
addq $0x1, %rax
movq %rax, -0x60(%rbp)
jmp 0x2f397b
movq -0x58(%rbp), %rax
movq 0x48(%rax), %rdi
callq 0x2210
movq -0x58(%rbp), %rax
movq 0x58(%rax), %rdi
callq 0x2210
movq -0x58(%rbp), %rdi
callq 0x2210
jmp 0x2f3a9f
jmp 0x2f3aa1
movq $0x0, -0x8(%rbp)
movq -0x8(%rbp), %rax
addq $0x70, %rsp
popq %rbp
retq
nopw %cs:(%rax,%rax)