// File: /workspace/github_cpp_makefile_star2_O1/chhylp123[P]hifiasm/Assembly.cpp
// Function: ha_assemble_pair()
int ha_assemble_pair(void)
{
	extern void ha_extract_print_list(const All_reads *rs, int n_rounds, const char *o);
	int r = 0, hom_cov = -1, ovlp_loaded = 0; memset((&R_INF), 0, sizeof(R_INF));

	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) 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) {
        
        if(!append_All_reads(&R_INF, asm_opt.output_file_name, 0)) {
            fprintf(stderr, "[M::%s::] Cannot load %s.0\n", __func__, asm_opt.output_file_name); 
            exit(1);
        }

        if(!append_All_reads(&R_INF, asm_opt.output_file_name, 1)) {
            fprintf(stderr, "[M::%s::] Cannot load %s.1\n", __func__, asm_opt.output_file_name); 
            exit(1);
        }
        // Output_corrected_reads(); exit(0);

        ha_flt_tab = ha_idx = NULL; r = asm_opt.number_of_round - 1;
        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, 1);
            ha_opt_update_cov(&asm_opt, hom_cov);
        }
        // error correction
        assert(asm_opt.number_of_round > 0);
        ha_opt_reset_to_round(&asm_opt, r); // this update asm_opt.roundID and a few other fields
        ha_overlap_cal(r, 1);
        fprintf(stderr, "[M::%s] size of buffer: %.3fGB\n", __func__, asm_opt.mem_buf / 1073741824.0);
        fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> found overlaps for the final round\n", __func__, yak_realtime(),
				yak_cpu_usage(), yak_peakrss_in_gb());
        

        if (asm_opt.flag & HA_F_WRITE_EC) Output_corrected_reads();
        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);

	}
    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 $0x18, %rsp
movl $0xffffffff, 0x10(%rsp) # imm = 0xFFFFFFFF
leaq 0x24e86f(%rip), %rdi    # 0x28b230
movl $0x88, %edx
xorl %esi, %esi
callq 0x20e0
leaq 0x24dd84(%rip), %rbx    # 0x28a758
movl $0x1, %r12d
movb $0x1, %bpl
cmpl $0x0, 0xf0(%rbx)
je 0x3ca05
movq 0x10(%rbx), %rdx
leaq 0x24e8b7(%rip), %rdi    # 0x28b2a8
leaq 0x24e8b8(%rip), %rsi    # 0x28b2b0
callq 0xe01d6
testl %eax, %eax
jne 0x3cb91
testb $0x1, %bpl
jne 0x3caaf
movl 0xd0(%rbx), %esi
movq %rbx, %rdi
movl $0x64, %edx
callq 0x2fad
movl 0x118(%rbx), %edi
leaq 0x24e801(%rip), %r14    # 0x28b230
movq 0x24e872(%rip), %rsi    # 0x28b2a8
movq 0x24e873(%rip), %rdx    # 0x28b2b0
movq 0x24e83c(%rip), %rcx    # 0x28b280
movq 0x24e7fd(%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 $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x10(%rbx), %rsi
leaq 0x24e776(%rip), %rdi    # 0x28b230
xorl %edx, %edx
callq 0x32c5b
testl %eax, %eax
je 0x3cbb1
movq 0x10(%rbx), %rsi
leaq 0x24e75c(%rip), %rdi    # 0x28b230
movl $0x1, %edx
callq 0x32c5b
testl %eax, %eax
je 0x3cbb6
leaq 0x24e94b(%rip), %rax    # 0x28b438
xorl %ecx, %ecx
movq %rcx, (%rax)
leaq 0x24e937(%rip), %r13    # 0x28b430
movq %rcx, (%r13)
movl 0xf8(%rbx), %ebp
testb $0x4, (%rbx)
je 0x3cb39
movq 0x10(%rbx), %r8
leaq 0x24e91d(%rip), %rdi    # 0x28b430
leaq 0x24e91e(%rip), %rsi    # 0x28b438
leaq 0x24e70f(%rip), %rdx    # 0x28b230
movq %rbx, %rcx
callq 0x1156a7
movq 0x10(%rbx), %rsi
leaq 0x24e91c(%rip), %rdi    # 0x28b450
callq 0x115217
testb $0x2, (%rbx)
jne 0x3cb7a
cmpq $0x0, (%r13)
jne 0x3cb7a
leaq 0x24dc0c(%rip), %r14    # 0x28a758
leaq 0x24e6dd(%rip), %rsi    # 0x28b230
leaq 0x10(%rsp), %r15
movq %r14, %rdi
movq %r15, %rdx
xorl %ecx, %ecx
movl $0x1, %r8d
callq 0x14025
movq %rax, (%r13)
movl (%r15), %esi
movq %r14, %rdi
callq 0x2f59
cmpl $0x0, 0xf8(%rbx)
jle 0x3cbbb
decl %ebp
movl %ebp, %edi
callq 0x4b5f
jmp 0x3ca0f
leaq 0xf(%rsp), %r14
leaq 0x14(%rsp), %r15
movq %r14, %rdi
movq %r15, %rsi
callq 0x4aa9
movb (%r14), %bpl
movl (%r15), %r12d
jmp 0x3ca05
callq 0x4c84
callq 0x4c51
leaq 0x1e82f3(%rip), %rdi    # 0x224eb5
leaq 0x1e8308(%rip), %rsi    # 0x224ed1
leaq 0x1e84af(%rip), %rcx    # 0x22507f
movl $0x878, %edx            # imm = 0x878
callq 0x2110