// File: /workspace/github_cpp_makefile_star2_O3/chhylp123[P]hifiasm/Assembly.cpp
// Function: ha_assemble()
int ha_assemble(void)
{
    // debug_mc_g_t(MC_NAME);
    // debug_mc_gg_t(MC_NAME, 0, 0);
    // quick_debug_phasing(MC_NAME);
	extern void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o);
	int r, hom_cov = -1, ovlp_loaded = 0; uint64_t tot_b, tot_e;
	if (asm_opt.load_index_from_disk && load_all_data_from_disk(&R_INF.paf, &R_INF.reverse_paf, asm_opt.output_file_name)) {
		ovlp_loaded = 1;
		fprintf(stderr, "[M::%s::%.3f*%.2f] ==> loaded corrected reads and overlaps from disk\n", __func__, yak_realtime(), yak_cpu_usage());
		if (asm_opt.extract_list) {
			ha_extract_print_list(&R_INF, asm_opt.extract_iter, asm_opt.extract_list);
			exit(0);
		}
		if (asm_opt.flag & HA_F_WRITE_EC) {
            if(asm_opt.is_sc) Output_corrected_fastq();
            else Output_corrected_reads();
        }
		if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
        if (asm_opt.het_cov == -1024) hap_recalculate_peaks(asm_opt.output_file_name), ovlp_loaded = 2;
	}
	if (!ovlp_loaded) {
        ha_flt_tab = ha_idx = NULL;
        if((asm_opt.flag & HA_F_VERBOSE_GFA)) load_pt_index(&ha_flt_tab, &ha_idx, &R_INF, &asm_opt, asm_opt.output_file_name), load_ct_index(&ha_ct_table, asm_opt.output_file_name);

		// construct hash table for high occurrence k-mers
		if (!(asm_opt.flag & HA_F_NO_KMER_FLT) && ha_flt_tab == NULL) 
        {
			ha_flt_tab = ha_ft_gen(&asm_opt, &R_INF, &hom_cov, 0, 0);
			ha_opt_update_cov(&asm_opt, hom_cov);
		}
		// error correction
		assert(asm_opt.number_of_round > 0);
		for (r = ha_idx?asm_opt.number_of_round-1:0; r < asm_opt.number_of_round; ++r) {
			ha_opt_reset_to_round(&asm_opt, r); // this update asm_opt.roundID and a few other fields
            tot_b = tot_e = 0;
			// ha_overlap_and_correct(r);
            ha_ec(r, asm_opt.number_of_pround, (r<asm_opt.number_of_round-1)?1:0, &tot_b, &tot_e);
			fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> corrected reads for round %d\n", __func__, yak_realtime(),
					yak_cpu_usage(), yak_peakrss_in_gb(), r + 1);
            fprintf(stderr, "[M::%s] # bases: %lu; # corrected bases: %lu\n", __func__, tot_b, tot_e);
			// fprintf(stderr, "[M::%s] # bases: %lld; # corrected bases: %lld; # recorrected bases: %lld\n", __func__,
			// 		asm_opt.num_bases, asm_opt.num_corrected_bases, asm_opt.num_recorrected_bases);
			// fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
		}
		if (asm_opt.flag & HA_F_WRITE_EC) {
            if(asm_opt.is_sc) Output_corrected_fastq();
            else Output_corrected_reads();
        }
		// overlap between corrected reads
		ha_opt_reset_to_round(&asm_opt, asm_opt.number_of_round);
		// ha_overlap_final();
        ha_ec_ff(1/**0**/);
        fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb());
		// fprintf(stderr, "\n[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb());
		// ha_print_ovlp_stat(R_INF.paf, R_INF.reverse_paf, R_INF.total_reads);
		ha_ft_destroy(ha_flt_tab);
		if (asm_opt.flag & HA_F_WRITE_PAF) Output_PAF();
		ha_triobin(&asm_opt);

        // exit(1);
	}
    if(ovlp_loaded == 2) ovlp_loaded = 0;
    ha_opt_update_cov_min(&asm_opt, asm_opt.hom_cov, MIN_N_CHAIN);

    build_string_graph_without_clean(asm_opt.min_overlap_coverage, R_INF.paf, R_INF.reverse_paf, 
        R_INF.total_reads, R_INF.read_length, asm_opt.min_overlap_Len, asm_opt.max_hang_Len, asm_opt.clean_round, 
        asm_opt.gap_fuzz, asm_opt.min_drop_rate, asm_opt.max_drop_rate, asm_opt.output_file_name, asm_opt.large_pop_bubble_size, 0, !ovlp_loaded);
	destory_All_reads(&R_INF);
	return 0;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x18, %rsp
movl $0xffffffff, 0x4(%rsp)  # imm = 0xFFFFFFFF
leaq 0x259a5a(%rip), %rbx    # 0x295758
cmpl $0x0, 0xf0(%rbx)
je 0x3bd26
movq 0x10(%rbx), %rdx
leaq 0x25a596(%rip), %rdi    # 0x2962a8
leaq 0x25a597(%rip), %rsi    # 0x2962b0
callq 0xe1530
testl %eax, %eax
jne 0x3bddb
leaq 0x25a70b(%rip), %rax    # 0x296438
xorl %ecx, %ecx
movq %rcx, (%rax)
leaq 0x25a6f7(%rip), %r14    # 0x296430
movq %rcx, (%r14)
movl (%rbx), %ecx
movb $0x1, %al
testb $0x4, %cl
je 0x3bd7b
movq 0x10(%rbx), %r8
leaq 0x25a6e8(%rip), %rsi    # 0x296438
leaq 0x25a4d9(%rip), %rdx    # 0x296230
movq %r14, %rdi
movq %rbx, %rcx
callq 0x11b1e8
movq 0x10(%rbx), %rsi
leaq 0x25a6e3(%rip), %rdi    # 0x296450
callq 0x11ad58
movl (%rbx), %ecx
cmpq $0x0, (%r14)
sete %al
testb $0x2, %cl
jne 0x3bdb6
testb %al, %al
je 0x3bdb6
leaq 0x2599cd(%rip), %r15    # 0x295758
leaq 0x25a49e(%rip), %rsi    # 0x296230
leaq 0x4(%rsp), %r12
movq %r15, %rdi
movq %r12, %rdx
xorl %ecx, %ecx
xorl %r8d, %r8d
callq 0x1390f
movq %rax, (%r14)
movl (%r12), %esi
movq %r15, %rdi
callq 0x2f59
movl 0xf8(%rbx), %edi
testl %edi, %edi
jle 0x3be88
leaq 0x10(%rsp), %rsi
leaq 0x8(%rsp), %rdx
callq 0x4970
movl $0x1, %r15d
jmp 0x3bdeb
leaq 0x8(%rsp), %r14
movq %r14, %rdi
callq 0x48b9
movl (%r14), %r15d
movl 0xd0(%rbx), %esi
movq %rbx, %rdi
movl $0x64, %edx
callq 0x2fa8
movl 0x118(%rbx), %edi
leaq 0x25a425(%rip), %r14    # 0x296230
movq 0x25a496(%rip), %rsi    # 0x2962a8
movq 0x25a497(%rip), %rdx    # 0x2962b0
movq 0x25a460(%rip), %rcx    # 0x296280
movq 0x25a421(%rip), %r8     # 0x296248
movslq 0x114(%rbx), %r9
movslq 0x10c(%rbx), %rax
movslq 0x104(%rbx), %r10
movslq 0x110(%rbx), %r11
movss 0x15c(%rbx), %xmm0
movss 0x160(%rbx), %xmm1
subq $0x8, %rsp
pushq %r15
pushq $0x0
pushq 0x188(%rbx)
pushq 0x10(%rbx)
pushq %r11
pushq %r10
pushq %rax
callq 0x104e53
addq $0x40, %rsp
movq %r14, %rdi
callq 0x31ca8
xorl %eax, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
leaq 0x1f5066(%rip), %rdi    # 0x230ef5
leaq 0x1f507b(%rip), %rsi    # 0x230f11
leaq 0x1f511b(%rip), %rcx    # 0x230fb8
movl $0x827, %edx            # imm = 0x827
callq 0x2110