// File: /workspace/github_cpp_makefile_star2_O1/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 %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
subq $0x28, %rsp
movl $0xffffffff, 0x4(%rsp)  # imm = 0xFFFFFFFF
leaq 0x24e030(%rip), %rbx    # 0x28a758
movl $0x1, %r12d
movb $0x1, %bpl
cmpl $0x0, 0xf0(%rbx)
je 0x3c759
movq 0x10(%rbx), %rdx
leaq 0x24eb63(%rip), %rdi    # 0x28b2a8
leaq 0x24eb64(%rip), %rsi    # 0x28b2b0
callq 0xe01d6
testl %eax, %eax
jne 0x3c8d6
testb $0x1, %bpl
jne 0x3c803
movl 0xd0(%rbx), %esi
movq %rbx, %rdi
movl $0x64, %edx
callq 0x2fad
movl 0x118(%rbx), %edi
leaq 0x24eaad(%rip), %r14    # 0x28b230
movq 0x24eb1e(%rip), %rsi    # 0x28b2a8
movq 0x24eb1f(%rip), %rdx    # 0x28b2b0
movq 0x24eae8(%rip), %rcx    # 0x28b280
movq 0x24eaa9(%rip), %r8     # 0x28b248
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 %r12
pushq $0x0
pushq 0x188(%rbx)
pushq 0x10(%rbx)
pushq %r11
pushq %r10
pushq %rax
callq 0x100b57
addq $0x40, %rsp
movq %r14, %rdi
callq 0x3259c
xorl %eax, %eax
addq $0x28, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
leaq 0x24ec2e(%rip), %rbp    # 0x28b438
xorl %eax, %eax
movq %rax, (%rbp)
leaq 0x24ec19(%rip), %r13    # 0x28b430
movq %rax, (%r13)
testb $0x4, (%rbx)
je 0x3c851
movq 0x10(%rbx), %r8
leaq 0x24ec05(%rip), %rdi    # 0x28b430
leaq 0x24ec06(%rip), %rsi    # 0x28b438
leaq 0x24e9f7(%rip), %rdx    # 0x28b230
movq %rbx, %rcx
callq 0x1156a7
movq 0x10(%rbx), %rsi
leaq 0x24ec04(%rip), %rdi    # 0x28b450
callq 0x115217
testb $0x2, (%rbx)
jne 0x3c88f
cmpq $0x0, (%r13)
jne 0x3c88f
leaq 0x24def4(%rip), %r14    # 0x28a758
leaq 0x24e9c5(%rip), %rsi    # 0x28b230
leaq 0x4(%rsp), %r15
movq %r14, %rdi
movq %r15, %rdx
xorl %ecx, %ecx
xorl %r8d, %r8d
callq 0x14025
movq %rax, (%r13)
movl (%r15), %esi
movq %r14, %rdi
callq 0x2f59
movl 0xf8(%rbx), %eax
testl %eax, %eax
jle 0x3c985
decl %eax
xorl %edi, %edi
cmpq $0x0, (%rbp)
cmovnel %eax, %edi
cmpl 0xf8(%rbx), %edi
jge 0x3c8c0
leaq 0x18(%rsp), %rsi
leaq 0x20(%rsp), %rdx
callq 0x49b8
testb $0x8, (%rbx)
je 0x3c8fb
cmpq $0x0, 0x2b0(%rbx)
jne 0x3c8f6
callq 0x399d0
jmp 0x3c8fb
leaq 0x18(%rsp), %r14
leaq 0x20(%rsp), %r15
movq %r14, %rdi
movq %r15, %rsi
callq 0x48f1
movb (%r14), %bpl
movl (%r15), %r12d
jmp 0x3c759
callq 0x39af3
movl 0xf8(%rbx), %esi
movq %rbx, %rdi
callq 0x3051a
movl $0x1, %edi
callq 0x3c2ee
movq 0x24d6c6(%rip), %rax    # 0x289fe0
movq (%rax), %r14
callq 0x1303c7
movsd %xmm0, 0x10(%rsp)
callq 0x130490
movsd %xmm0, 0x8(%rsp)
callq 0x13045d
movaps %xmm0, %xmm2
leaq 0x1e86b2(%rip), %rsi    # 0x224ff4
leaq 0x1e8623(%rip), %rdx    # 0x224f6c
movq %r14, %rdi
movsd 0x10(%rsp), %xmm0
movsd 0x8(%rsp), %xmm1
movb $0x3, %al
callq 0x22b0
movq (%r13), %rdi
callq 0x114a78
testb $0x10, (%rbx)
jne 0x3c97e
leaq 0x24dde4(%rip), %rdi    # 0x28a758
callq 0x10386a
jmp 0x3c763
callq 0x3c52
jmp 0x3c96d
leaq 0x1e8529(%rip), %rdi    # 0x224eb5
leaq 0x1e853e(%rip), %rsi    # 0x224ed1
leaq 0x1e85de(%rip), %rcx    # 0x224f78
movl $0x827, %edx            # imm = 0x827
callq 0x2110