// File: /workspace/github_cpp_makefile_star2_O1/chhylp123[P]hifiasm/Overlaps.cpp
// Function: renew_g(ma_hit_t_alloc**, ma_hit_t_alloc**, long long*, unsigned long**, ma_sub_t**, R_to_U*, asg_t**, long, long, ug_opt_t*, long, double, double, long, bub_label_t*, unsigned int, char*, char const*, unsigned long, unsigned long, unsigned long)
void renew_g(ma_hit_t_alloc **sources, ma_hit_t_alloc **reverse_sources, long long *n_read, 
uint64_t **readLen, ma_sub_t **coverage_cut, R_to_U *ruIndex, asg_t **sg, int64_t mini_overlap_length, 
int64_t max_hang_length, ug_opt_t *uopt, int64_t clean_round, double min_ovlp_drop_ratio, 
double max_ovlp_drop_ratio, int64_t max_tip, bub_label_t *b_mask_t, uint32_t is_trio, 
char *o_file, const char *bin_file, uint64_t free_uld, uint64_t is_bridg, uint64_t deep_clean)
{
    ul_renew_t nopt; memset(&nopt, 0, sizeof(nopt));
    nopt.src = sources; nopt.r_src = reverse_sources; nopt.ruIndex = ruIndex;
    nopt.n_read = n_read; nopt.readLen = readLen; nopt.sg = sg;
    nopt.cov = coverage_cut; nopt.b_mask_t = b_mask_t;
    nopt.max_hang = max_hang_length; nopt.mini_ovlp = mini_overlap_length;
    ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 
        asm_opt.max_short_tip, asm_opt.max_short_ul_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file, &nopt, bin_file, free_uld, is_bridg, deep_clean);
    // ma_ug_t *iug = ul_realignment_gfa(uopt, *sg, clean_round, min_ovlp_drop_ratio, max_ovlp_drop_ratio, 
    //                                                                 asm_opt.max_short_tip, b_mask_t, ha_opt_triobin(&asm_opt), o_file);
    // asg_t *ng = gen_ng(iug, *sg, uopt, coverage_cut, ruIndex, 256);
    // ma_ug_destroy(iug); asg_destroy(*sg);
    // (*sources) = R_INF.paf; 
    // (*reverse_sources) = R_INF.reverse_paf;
    // (*n_read) = R_INF.total_reads;
    // (*readLen) = R_INF.read_length;
    // (*sg) = ng; 
    // ma_hit_contained_advance(*sources, *n_read, *coverage_cut, ruIndex, max_hang_length, mini_overlap_length);
    // post_rescue(uopt, *sg, (*sources), (*reverse_sources), ruIndex, b_mask_t, 0);
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
subq $0x58, %rsp
movq %r9, %rax
movq %rdx, %r10
movq 0xe0(%rsp), %r12
movq 0xd8(%rsp), %r15
movq 0xd0(%rsp), %r14
movq 0xc8(%rsp), %rbx
movq 0xc0(%rsp), %r11
movq 0xb0(%rsp), %r9
xorps %xmm2, %xmm2
movaps %xmm2, (%rsp)
movq %rdi, (%rsp)
movq 0xa0(%rsp), %rdx
movaps %xmm2, 0x20(%rsp)
movaps %xmm2, 0x10(%rsp)
movaps %xmm2, 0x30(%rsp)
movaps %xmm2, 0x40(%rsp)
movq %rsi, 0x8(%rsp)
movq 0x98(%rsp), %rdi
movq %rax, 0x28(%rsp)
movq 0x88(%rsp), %rax
movq %r10, 0x10(%rsp)
movq 0x90(%rsp), %rsi
movq %rcx, 0x18(%rsp)
movq 0x80(%rsp), %rcx
movq %rcx, 0x20(%rsp)
movq %r8, 0x30(%rsp)
movq %r9, 0x38(%rsp)
movq %rsi, 0x40(%rsp)
movq %rax, 0x48(%rsp)
movq (%rcx), %rsi
leaq 0x18a1cf(%rip), %r10    # 0x28a758
movslq 0x11c(%r10), %rcx
movslq 0x120(%r10), %r8
cmpq $0x0, 0x20(%r10)
je 0x1005aa
movl $0x1, %eax
cmpq $0x0, 0x28(%r10)
jne 0x1005bf
cmpq $0x0, 0x30(%r10)
je 0x1005bd
xorl %eax, %eax
cmpq $0x0, 0x38(%r10)
setne %al
jmp 0x1005bf
xorl %eax, %eax
subq $0x8, %rsp
leaq 0x8(%rsp), %r10
pushq %r12
pushq %r15
pushq %r14
pushq %rbx
pushq %r10
pushq %r11
pushq %rax
callq 0x2ef9c
addq $0x98, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq