user: 提供的汇编代码用C语言表示会是什么样子:

```asm
<main>:
  endbr64
  push   %rbp
  mov    %rsp,%rbp
  push   %r15
  push   %r14
  push   %r13
  push   %r12
  push   %rbx
  sub    $0x88,%rsp
  mov    %rsi,%rbx
  mov    %fs:0x28,%rax
  mov    %rax,-0x38(%rbp)
  xor    %eax,%eax
  mov    %rsp,%rax
L365:
  cmp    %rax,%rsp
  je     L222
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L365
L222:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    %rsp,-0x98(%rbp)
  mov    0x8(%rbx),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  mov    %rsp,%rax
L282:
  cmp    %rax,%rsp
  je     L220
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L282
L220:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    %rsp,%r15
  mov    0x10(%rbx),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  mov    %rsp,%rax
L44:
  cmp    %rax,%rsp
  je     L280
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L44
L280:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    %rsp,-0x58(%rbp)
  mov    0x18(%rbx),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  mov    %rsp,%rax
L212:
  cmp    %rax,%rsp
  je     L493
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L212
L493:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    %rsp,-0xa0(%rbp)
  mov    0x20(%rbx),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  mov    %rsp,%rax
L352:
  cmp    %rax,%rsp
  je     L83
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L352
L83:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    -0x58(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  lea    D92(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D98(%rip),%rsi
  mov    %rsp,%rdi
  call   <fopen@plt>
  mov    %rax,-0xa8(%rbp)
  mov    %rsp,%rax
L573:
  cmp    %rax,%rsp
  je     L216
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L573
L216:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    -0x58(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  lea    D117(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r15,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D124(%rip),%rbx
  mov    %rbx,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    -0x98(%rbp),%r14
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D146(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r15,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %rbx,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D71(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    -0xa0(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D61(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D95(%rip),%rsi
  mov    %rsp,%rdi
  call   <fopen@plt>
  mov    %rax,-0x88(%rbp)
  mov    %rax,%rcx
  mov    $0x2a,%edx
  mov    $0x1,%esi
  lea    D132(%rip),%rdi
  call   <fwrite@plt>
  mov    %rsp,%rax
L205:
  cmp    %rax,%rsp
  je     L293
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L205
L293:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    %rsp,%rbx
  mov    -0x58(%rbp),%rsi
  mov    %rsp,%rdi
  call   <strcpy@plt>
  lea    D238(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    -0x98(%rbp),%r14
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D222(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  lea    D43(%rip),%rsi
  mov    %rsp,%rdi
  call   <strcat@plt>
  mov    %rsp,%rax
L531:
  cmp    %rax,%rsp
  je     L367
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L531
L367:
  sub    $0x3f0,%rsp
  orq    $0x0,0x3e8(%rsp)
  mov    %rsp,%r12
  lea    D97(%rip),%rsi
  mov    %rbx,%rdi
  call   <fopen@plt>
  mov    %rax,%r14
  mov    $0x0,%r13d
  test   %rax,%rax
  jne    L234
  mov    %rbx,%rdi
  call   <perror@plt>
  mov    $0x0,%r13d
  jmp    L321
L510:
  add    $0x1,%r13d
L234:
  mov    %r14,%rdx
  mov    $0x3e8,%esi
  mov    %r12,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  jne    L510
  mov    %r14,%rdi
  call   <fclose@plt>
L321:
  movslq %r13d,%rax
  imul   $0x3e8,%rax,%rax
  lea    0xf(%rax),%rdx
  mov    %rdx,%rsi
  and    $0xfffffffffffffff0,%rsi
  and    $0xfffffffffffff000,%rdx
  mov    %rsp,%rcx
  sub    %rdx,%rcx
L61:
  cmp    %rcx,%rsp
  je     L341
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L61
L341:
  mov    %rsi,%rdx
  and    $0xfff,%edx
  sub    %rdx,%rsp
  test   %rdx,%rdx
  je     L640
  orq    $0x0,-0x8(%rsp,%rdx,1)
L640:
  mov    %rsp,-0x90(%rbp)
  add    $0xf,%rax
  mov    %rax,%rdx
  and    $0xfffffffffffffff0,%rdx
  and    $0xfffffffffffff000,%rax
  mov    %rsp,%rcx
  sub    %rax,%rcx
L66:
  cmp    %rcx,%rsp
  je     L420
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L66
L420:
  mov    %rdx,%rax
  and    $0xfff,%eax
  sub    %rax,%rsp
  test   %rax,%rax
  je     L239
  orq    $0x0,-0x8(%rsp,%rax,1)
L239:
  mov    %rsp,%r14
  mov    %r14,-0x70(%rbp)
  lea    D97(%rip),%rsi
  mov    %rbx,%rdi
  call   <fopen@plt>
  mov    %rax,-0x48(%rbp)
  test   %rax,%rax
  je     L141
  mov    %r14,%rbx
  mov    -0x90(%rbp),%r13
  movl   $0x0,-0x4c(%rbp)
  lea    D124(%rip),%r14
  jmp    L131
L136:
  mov    %r12,%rsi
  mov    %r13,%rdi
  call   <strcpy@plt>
  mov    -0x58(%rbp),%rsi
  mov    %rbx,%rdi
  call   <strcpy@plt>
  lea    D117(%rip),%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    %r15,%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    -0x98(%rbp),%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  lea    D146(%rip),%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    %r15,%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  lea    D86(%rip),%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    -0xa0(%rbp),%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    %r14,%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  mov    %r12,%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  lea    D239(%rip),%rsi
  mov    %rbx,%rdi
  call   <strcat@plt>
  addl   $0x1,-0x4c(%rbp)
  add    $0x3e8,%r13
  add    $0x3e8,%rbx
L131:
  mov    -0x48(%rbp),%rdx
  mov    $0x3e8,%esi
  mov    %r12,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  je     L374
  mov    %r12,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  movslq %eax,%rdx
  cmpb   $0xa,(%r12,%rdx,1)
  jne    L136
  movb   $0x0,(%r12,%rdx,1)
  jmp    L136
L374:
  mov    -0x48(%rbp),%rdi
  call   <fclose@plt>
  lea    -0xf4000(%rsp),%rax
L435:
  cmp    %rax,%rsp
  je     L390
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L435
L390:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,-0x60(%rbp)
  lea    -0xf4000(%rsp),%rax
L599:
  cmp    %rax,%rsp
  je     L642
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L599
L642:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,-0x78(%rbp)
  movq   $0x0,-0x58(%rbp)
  movl   $0x0,-0x48(%rbp)
  cmpl   $0x0,-0x4c(%rbp)
  jg     L609
  jmp    L41
L141:
  mov    %rbx,%rdi
  call   <perror@plt>
L41:
  mov    -0xa0(%rbp),%r15
  mov    %r15,%rdx
  mov    -0x98(%rbp),%r14
  mov    %r14,%rsi
  lea    D34(%rip),%rbx
  mov    %rbx,%rdi
  call   <printf@plt>
  mov    %r15,%rcx
  mov    %r14,%rdx
  mov    %rbx,%rsi
  mov    -0xa8(%rbp),%rdi
  mov    $0x0,%eax
  call   <fprintf@plt>
  mov    -0x38(%rbp),%rax
  sub    %fs:0x28,%rax
  jne    L307
  mov    $0x0,%eax
  lea    -0x28(%rbp),%rsp
  pop    %rbx
  pop    %r12
  pop    %r13
  pop    %r14
  pop    %r15
  pop    %rbp
  ret
L401:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,%rbx
  jmp    L157
L104:
  mov    %rbx,%rsi
  mov    -0x60(%rbp),%rdi
  call   <strcpy@plt>
  mov    %r12,%rdi
  call   <fclose@plt>
L157:
  mov    %r12,%rdx
  mov    $0xf4240,%esi
  mov    %rbx,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  je     L63
  cmpb   $0x3e,(%rbx)
  je     L157
  mov    %rbx,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  movslq %eax,%rdx
  cmpb   $0xa,(%rbx,%rdx,1)
  jne    L104
  movb   $0x0,(%rbx,%rdx,1)
  jmp    L104
L63:
  mov    %r13,%rsp
L311:
  mov    -0x90(%rbp),%r15
  mov    %r15,%rax
  add    -0x58(%rbp),%rax
  mov    %rax,-0x68(%rbp)
  mov    -0x70(%rbp),%r14
  mov    $0x0,%ebx
  jmp    L618
L458:
  mov    %rbx,%rdi
  call   <perror@plt>
  jmp    L311
L152:
  sub    $0x240,%rsp
  orq    $0x0,0x238(%rsp)
  mov    %rsp,%r12
  jmp    L281
L13:
  mov    %r12,%rsi
  mov    -0x78(%rbp),%rdi
  call   <strcpy@plt>
  mov    %r13,%rdi
  call   <fclose@plt>
L281:
  mov    %r13,%rdx
  mov    $0xf4240,%esi
  mov    %r12,%rdi
  call   <fgets@plt>
  test   %rax,%rax
  je     L492
  cmpb   $0x3e,(%r12)
  je     L281
  mov    %r12,%rdi
  call   <strlen@plt>
  sub    $0x1,%eax
  movslq %eax,%rdx
  cmpb   $0xa,(%r12,%rdx,1)
  jne    L13
  movb   $0x0,(%r12,%rdx,1)
  jmp    L13
L492:
  mov    -0x80(%rbp),%rsp
L416:
  mov    -0x60(%rbp),%rdi
  call   <strlen@plt>
  mov    %eax,%r13d
  test   %eax,%eax
  jle    L247
  mov    %eax,%r8d
  mov    $0x0,%edx
  mov    $0x0,%edi
  mov    $0x0,%r12d
  mov    -0x60(%rbp),%rsi
  mov    -0x78(%rbp),%r9
  jmp    L569
L386:
  mov    %r14,%rdi
  call   <perror@plt>
  jmp    L416
L395:
  add    $0x1,%edi
L78:
  add    $0x1,%rdx
  cmp    %r8,%rdx
  je     L403
L569:
  movzbl (%rsi,%rdx,1),%eax
  cmp    $0x4e,%al
  je     L395
  movzbl (%r9,%rdx,1),%ecx
  cmp    $0x4e,%cl
  je     L395
  cmp    %cl,%al
  setne  %al
  movzbl %al,%eax
  add    %eax,%r12d
  jmp    L78
L247:
  mov    $0x0,%edi
  mov    $0x0,%r12d
L403:
  sub    %edi,%r13d
  pxor   %xmm0,%xmm0
  cvtsi2ss %r12d,%xmm0
  pxor   %xmm1,%xmm1
  cvtsi2ss %r13d,%xmm1
  divss  %xmm1,%xmm0
  mulss  D161(%rip),%xmm0
  movss  D65(%rip),%xmm1
  subss  %xmm0,%xmm1
  cvttss2si %xmm1,%edi
  call   <log@plt>
  mulss  D52(%rip),%xmm0
  cvtss2sd %xmm0,%xmm0
  mov    %r13d,%r9d
  mov    %r12d,%r8d
  mov    %r15,%rcx
  mov    -0x68(%rbp),%rdx
  lea    D120(%rip),%rsi
  mov    -0x88(%rbp),%rdi
  mov    $0x1,%eax
  call   <fprintf@plt>
L405:
  add    $0x1,%ebx
  add    $0x3e8,%r15
  add    $0x3e8,%r14
  cmp    %ebx,-0x4c(%rbp)
  je     L515
L618:
  cmp    %ebx,-0x48(%rbp)
  jle    L405
  lea    D97(%rip),%rsi
  mov    %r14,%rdi
  call   <fopen@plt>
  mov    %rax,%r13
  test   %rax,%rax
  je     L386
  mov    %rsp,-0x80(%rbp)
  lea    -0xf4000(%rsp),%rax
L229:
  cmp    %rax,%rsp
  je     L152
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L229
L515:
  addl   $0x1,-0x48(%rbp)
  mov    -0x48(%rbp),%eax
  addq   $0x3e8,-0x58(%rbp)
  cmp    %eax,-0x4c(%rbp)
  je     L41
L609:
  mov    -0x70(%rbp),%rbx
  add    -0x58(%rbp),%rbx
  lea    D97(%rip),%rsi
  mov    %rbx,%rdi
  call   <fopen@plt>
  mov    %rax,%r12
  test   %rax,%rax
  je     L458
  mov    %rsp,%r13
  lea    -0xf4000(%rsp),%rax
L634:
  cmp    %rax,%rsp
  je     L401
  sub    $0x1000,%rsp
  orq    $0x0,0xff8(%rsp)
  jmp    L634
L307:
  call   <__stack_chk_fail@plt>
```

tool_calls: name: retrieve_data
arguments: tag: D92
data_type: string
name: retrieve_data
arguments: tag: D98
data_type: string
name: retrieve_data
arguments: tag: D117
data_type: string
name: retrieve_data
arguments: tag: D124
data_type: string
name: retrieve_data
arguments: tag: D146
data_type: string
name: retrieve_data
arguments: tag: D71
data_type: string
name: retrieve_data
arguments: tag: D61
data_type: string
name: retrieve_data
arguments: tag: D95
data_type: string
name: retrieve_data
arguments: tag: D132
data_type: string
name: retrieve_data
arguments: tag: D238
data_type: string
name: retrieve_data
arguments: tag: D222
data_type: string
name: retrieve_data
arguments: tag: D43
data_type: string
name: retrieve_data
arguments: tag: D97
data_type: string
name: retrieve_data
arguments: tag: D86
data_type: string
name: retrieve_data
arguments: tag: D239
data_type: string
name: retrieve_data
arguments: tag: D34
data_type: string
name: retrieve_data
arguments: tag: D161
data_type: byte[4]
name: retrieve_data
arguments: tag: D65
data_type: byte[4]
name: retrieve_data
arguments: tag: D52
data_type: byte[4]
name: retrieve_data
arguments: tag: D120
data_type: string

tool: D92: /Analysis/log.txt

tool: D98: a

tool: D117: /Analysis/

tool: D124: /

tool: D146: _

tool: D71: _di_upstream_

tool: D61: .csv

tool: D95: w

tool: D132: Isolate_1,Isolate_2,SNPs,Sites,Divergence


tool: D238: /Analysis/Core_genome_alignment/

tool: D222: _Core_genome_alignment/

tool: D43: _isolates.txt

tool: D97: r

tool: D86: /Intergenic_files_upstream_

tool: D239: .fasta

tool: D34: %s di upstream %s calculated.


tool: {"D161": [0xab,0xaa,0xaa,0x3f]}

tool: {"D65": [0x00,0x00,0x80,0x3f]}

tool: {"D52": [0x00,0x00,0x40,0xbf]}

tool: D120: %s,%s,%i,%i,%0.6f


assistant: ```c
int main(int argc, char *argv[]) {
  int arg_len = 1000;
  char species[arg_len];
  strcpy(species, argv[1]);
  char analysis[arg_len];
  strcpy(analysis, argv[2]);
  char base_dir[arg_len];
  strcpy(base_dir, argv[3]);
  char upstream_len[arg_len];
  strcpy(upstream_len, argv[4]);
  char log_file_name[arg_len];
  strcpy(log_file_name, base_dir);
  strcat(log_file_name, "/Analysis/log.txt");
  FILE *log_file = fopen(log_file_name, "a");
  char output_file_name[arg_len];
  strcpy(output_file_name, base_dir);
  strcat(output_file_name, "/Analysis/");
  strcat(output_file_name, analysis);
  strcat(output_file_name, "/");
  strcat(output_file_name, species);
  strcat(output_file_name, "_");
  strcat(output_file_name, analysis);
  strcat(output_file_name, "/");
  strcat(output_file_name, species);
  strcat(output_file_name, "_di_upstream_");
  strcat(output_file_name, upstream_len);
  strcat(output_file_name, ".csv");
  FILE *output = fopen(output_file_name, "w");
  fprintf(output, "Isolate_1,Isolate_2,SNPs,Sites,Divergence\n");
  char isolates_file_name[arg_len];
  strcpy(isolates_file_name, base_dir);
  strcat(isolates_file_name, "/Analysis/Core_genome_alignment/");
  strcat(isolates_file_name, species);
  strcat(isolates_file_name, "_Core_genome_alignment/");
  strcat(isolates_file_name, species);
  strcat(isolates_file_name, "_isolates.txt");
  char isolate_name[arg_len];
  int isolate_count;
  isolate_count = 0;
  FILE *isolates_file = fopen(isolates_file_name, "r");
  if (isolates_file != NULL) {
    while (fgets(isolate_name, sizeof isolate_name, isolates_file) != NULL) {
      isolate_count++;
    }
    fclose(isolates_file);
  } else {
    perror(isolates_file_name);
  }
  char isolate_name_array[isolate_count][arg_len];
  char isolate_file_name_array[isolate_count][arg_len];
  isolate_count = 0;
  FILE *isolates_file_2 = fopen(isolates_file_name, "r");
  if (isolates_file_2 != NULL) {
    while (fgets(isolate_name, sizeof isolate_name, isolates_file_2) != NULL) {
      int isolate_name_len;
      isolate_name_len = strlen(isolate_name);
      if (isolate_name[(isolate_name_len - 1)] == '\n') {
        isolate_name[(isolate_name_len - 1)] = '\0';
      }
      strcpy(isolate_name_array[isolate_count], isolate_name);
      strcpy(isolate_file_name_array[isolate_count], base_dir);
      strcat(isolate_file_name_array[isolate_count], "/Analysis/");
      strcat(isolate_file_name_array[isolate_count], analysis);
      strcat(isolate_file_name_array[isolate_count], "/");
      strcat(isolate_file_name_array[isolate_count], species);
      strcat(isolate_file_name_array[isolate_count], "_");
      strcat(isolate_file_name_array[isolate_count], analysis);
      strcat(isolate_file_name_array[isolate_count], "/Intergenic_files_upstream_");
      strcat(isolate_file_name_array[isolate_count], upstream_len);
      strcat(isolate_file_name_array[isolate_count], "/");
      strcat(isolate_file_name_array[isolate_count], isolate_name);
      strcat(isolate_file_name_array[isolate_count], ".fasta");
      isolate_count++;
    }
    fclose(isolates_file_2);
  } else {
    perror(isolates_file_name);
  }
  int a;
  int b;
  int i;
  int genome_max = 1000000;
  char genome1[genome_max];
  char genome2[genome_max];
  int count;
  count = 0;
  for (a = 0; a < isolate_count; a++) {
    FILE *file1 = fopen(isolate_file_name_array[a], "r");
    if (file1 != NULL) {
      char line1[genome_max];
      while (fgets(line1, sizeof line1, file1) != NULL) {
        if (line1[0] != '>') {
          int line1_len = strlen(line1);
          line1_len = (line1_len - 1);
          if (line1[line1_len] == '\n') {
            line1[line1_len] = '\0';
          }
          strcpy(genome1, line1);
          fclose(file1);
        }
      }
    } else {
      perror(isolate_file_name_array[a]);
    }
    for (b = 0; b < isolate_count; b++) {
      if (a > b) {
        FILE *file2 = fopen(isolate_file_name_array[b], "r");
        if (file2 != NULL) {
          char line2[genome_max];
          while (fgets(line2, sizeof line2, file2) != NULL) {
            if (line2[0] != '>') {
              int line2_len = strlen(line2);
              line2_len = (line2_len - 1);
              if (line2[line2_len] == '\n') {
                line2[line2_len] = '\0';
              }
              strcpy(genome2, line2);
              fclose(file2);
            }
          }
        } else {
          perror(isolate_file_name_array[b]);
        }
        int genome_len;
        genome_len = strlen(genome1);
        int snp;
        snp = 0;
        int n;
        n = 0;
        for (i = 0; i < genome_len; i++) {
          if (genome1[i] == 'N' || genome2[i] == 'N') {
            n++;
          } else {
            if (genome1[i] != genome2[i]) {
              snp++;
            }
          }
        }
        int sites;
        sites = (genome_len - n);
        float div;
        div = ((float)snp / sites);
        float JC_div;
        JC_div = (((float)-3 / 4) * (log(1 - (((float)4 / 3) * div))));
        fprintf(output, "%s,%s,%i,%i,%0.6f\n", isolate_name_array[a], isolate_name_array[b], snp, sites, JC_div);
        count++;
      }
    }
  }
  printf("%s di upstream %s calculated.\n", species, upstream_len);
  fprintf(log_file, "%s di upstream %s calculated.\n", species, upstream_len);
  return 0;
}
```