// File: /workspace/github_cpp_makefile_star2_O2/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
orl $-0x1, 0xc(%rsp)
leaq 0x243e99(%rip), %rdi    # 0x254230
movl $0x88, %edx
xorl %esi, %esi
callq 0x20e0
leaq 0x2433ae(%rip), %rbx    # 0x253758
cmpl $0x0, 0xf0(%rbx)
je 0x103d2
movq 0x10(%rbx), %rdx
leaq 0x243eea(%rip), %rdi    # 0x2542a8
leaq 0x243eeb(%rip), %rsi    # 0x2542b0
callq 0xa4465
testl %eax, %eax
jne 0x10618
movq 0x10(%rbx), %rsi
leaq 0x243e53(%rip), %rdi    # 0x254230
xorl %edx, %edx
callq 0x61a6
testl %eax, %eax
je 0x10699
movq 0x10(%rbx), %rsi
leaq 0x243e39(%rip), %rdi    # 0x254230
pushq $0x1
popq %rdx
callq 0x61a6
testl %eax, %eax
je 0x106b0
leaq 0x24402a(%rip), %rax    # 0x254438
andq $0x0, (%rax)
leaq 0x244017(%rip), %r14    # 0x254430
andq $0x0, (%r14)
movl (%rbx), %eax
movl 0xf8(%rbx), %ebp
movb $0x1, %cl
testb $0x4, %al
je 0x10461
movq 0x10(%rbx), %r8
leaq 0x244002(%rip), %rsi    # 0x254438
leaq 0x243df3(%rip), %rdx    # 0x254230
movq %r14, %rdi
movq %rbx, %rcx
callq 0xd755f
movq 0x10(%rbx), %rsi
leaq 0x243ffd(%rip), %rdi    # 0x254450
callq 0xd6e4f
movl (%rbx), %eax
cmpq $0x0, (%r14)
sete %cl
testb $0x2, %al
jne 0x1049c
testb %cl, %cl
je 0x1049c
leaq 0x2432e8(%rip), %r15    # 0x253758
leaq 0x243db9(%rip), %rsi    # 0x254230
leaq 0xc(%rsp), %r12
pushq $0x1
popq %r8
movq %r15, %rdi
movq %r12, %rdx
xorl %ecx, %ecx
callq 0xd61b1
movq %rax, (%r14)
movl (%r12), %esi
movq %r15, %rdi
callq 0x3430
cmpl $0x0, 0xf8(%rbx)
jle 0x106db
decl %ebp
movq %rbx, %rdi
movl %ebp, %esi
callq 0x3418
pushq $0x1
popq %r15
movl %ebp, %edi
movl %r15d, %esi
callq 0xdf2c
movq 0x242b16(%rip), %r13    # 0x252fe0
movq (%r13), %rdi
cvtsi2sdq 0x1a8(%rbx), %xmm0
mulsd 0x1d2729(%rip), %xmm0   # 0x1e2c08
leaq 0x1d2a3f(%rip), %rsi    # 0x1e2f25
leaq 0x1d2b79(%rip), %r12    # 0x1e3066
movq %r12, %rdx
movb $0x1, %al
callq 0x22b0
movq (%r13), %r13
callq 0xefea7
movsd %xmm0, (%rsp)
callq 0xefef4
movsd %xmm0, 0x10(%rsp)
callq 0xefedf
movapd %xmm0, %xmm2
leaq 0x1d2b04(%rip), %rsi    # 0x1e3024
movq %r13, %rdi
movq %r12, %rdx
movsd (%rsp), %xmm0
movsd 0x10(%rsp), %xmm1
movb $0x3, %al
callq 0x22b0
testb $0x8, (%rbx)
je 0x10542
callq 0xc9ba
movq 0x243d5f(%rip), %rdi    # 0x2542a8
movq 0x243d60(%rip), %rsi    # 0x2542b0
movq 0x243d29(%rip), %rdx    # 0x254280
callq 0xe95b
movq (%r14), %rdi
callq 0xd5c37
testb $0x10, (%rbx)
je 0x1056e
callq 0xed58
leaq 0x2431e3(%rip), %rdi    # 0x253758
callq 0xc55cf
movl 0xd0(%rbx), %esi
pushq $0x64
popq %rdx
movq %rbx, %rdi
callq 0x347f
movl 0x118(%rbx), %edi
leaq 0x243c98(%rip), %r14    # 0x254230
movq 0x243d09(%rip), %rsi    # 0x2542a8
movq 0x243d0a(%rip), %rdx    # 0x2542b0
movq 0x243cd3(%rip), %rcx    # 0x254280
movq 0x243c94(%rip), %r8     # 0x254248
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 0xc28fd
addq $0x40, %rsp
movq %r14, %rdi
callq 0x5891
xorl %eax, %eax
addq $0x18, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x2429c1(%rip), %rax    # 0x252fe0
movq (%rax), %r14
callq 0xefea7
movsd %xmm0, (%rsp)
callq 0xefef4
movaps %xmm0, %xmm1
leaq 0x1d291b(%rip), %rsi    # 0x1e2f56
leaq 0x1d2a24(%rip), %rdx    # 0x1e3066
movq %r14, %rdi
movsd (%rsp), %xmm0
movb $0x2, %al
callq 0x22b0
movq 0x48(%rbx), %rdx
testq %rdx, %rdx
jne 0x106fa
movl (%rbx), %eax
testb $0x8, %al
je 0x1066b
callq 0xc9ba
movl (%rbx), %eax
testb $0x10, %al
je 0x10674
callq 0xed58
xorl %r15d, %r15d
cmpl $0xfffffc00, 0xd4(%rbx) # imm = 0xFFFFFC00
jne 0x1057a
movq 0x10(%rbx), %rdi
callq 0xf733
pushq $0x1
popq %r15
jmp 0x1057a
movq 0x242940(%rip), %rax    # 0x252fe0
movq (%rax), %rdi
movq 0x10(%rbx), %rcx
leaq 0x1d29c9(%rip), %rsi    # 0x1e3077
jmp 0x106c5
movq 0x242929(%rip), %rax    # 0x252fe0
movq (%rax), %rdi
movq 0x10(%rbx), %rcx
leaq 0x1d29ce(%rip), %rsi    # 0x1e3093
leaq 0x1d299a(%rip), %rdx    # 0x1e3066
xorl %eax, %eax
callq 0x22b0
pushq $0x1
popq %rdi
callq 0x2250
leaq 0x1d2803(%rip), %rdi    # 0x1e2ee5
leaq 0x1d2818(%rip), %rsi    # 0x1e2f01
leaq 0x1d29bf(%rip), %rcx    # 0x1e30af
movl $0x878, %edx            # imm = 0x878
callq 0x2110
movl 0x78(%rbx), %esi
leaq 0x243b2c(%rip), %rdi    # 0x254230
callq 0xefd48
xorl %edi, %edi
callq 0x2250