#define NULL ((void *)0)
typedef unsigned long size_t; // Customize by platform.
typedef long intptr_t;
typedef unsigned long uintptr_t;
typedef long scalar_t__; // Either arithmetic or pointer type.
/* By default, we understand bool (as a convenience). */
typedef int bool;
#define false 0
#define true 1

/* Forward declarations */

/* Type definitions */
typedef int /*<<< orphan*/ FILE;

/* Variables and functions */
int /*<<< orphan*/ fclose(int /*<<< orphan*/ *);
int /*<<< orphan*/ *fgets(char *, int, int /*<<< orphan*/ *);
int /*<<< orphan*/ *fopen(char *, char *);
int /*<<< orphan*/ fprintf(int /*<<< orphan*/ *, char *, ...);
float log(int);
int /*<<< orphan*/ perror(char *);
int /*<<< orphan*/ printf(char *, char *);
int /*<<< orphan*/ strcat(char *, char *);
int /*<<< orphan*/ strcpy(char *, char *);
int strlen(char *);
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 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_simulated.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/");
  strcat(isolates_file_name, analysis);
  strcat(isolates_file_name, "/");
  strcat(isolates_file_name, species);
  strcat(isolates_file_name, "_");
  strcat(isolates_file_name, analysis);
  strcat(isolates_file_name, "/");
  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/");
      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 calculated.\n", species);
  fprintf(log_file, "%s di calculated.\n", species);
  return 0;
}


x86 assembly (clang, -O0):
<main>:
push   %rbp
mov    %rsp,%rbp
sub    $0x1d0,%rsp
movl   $0x0,-0x4(%rbp)
mov    %edi,-0x8(%rbp)
mov    %rsi,-0x10(%rbp)
movl   $0x3e8,-0x14(%rbp)
mov    -0x14(%rbp),%eax
mov    %rsp,%rcx
mov    %rcx,-0x20(%rbp)
mov    %rax,%rcx
add    $0xf,%rcx
and    $0xfffffffffffffff0,%rcx
mov    %rsp,%rdi
sub    %rcx,%rdi
mov    %rdi,-0x160(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x28(%rbp)
mov    -0x10(%rbp),%rax
mov    0x8(%rax),%rsi
call   1030 <strcpy@plt>
mov    -0x14(%rbp),%eax
mov    %rax,%rcx
add    $0xf,%rcx
and    $0xfffffffffffffff0,%rcx
mov    %rsp,%rdi
sub    %rcx,%rdi
mov    %rdi,-0x150(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x30(%rbp)
mov    -0x10(%rbp),%rax
mov    0x10(%rax),%rsi
call   1030 <strcpy@plt>
mov    -0x14(%rbp),%eax
mov    %rax,%rcx
add    $0xf,%rcx
and    $0xfffffffffffffff0,%rcx
mov    %rsp,%rdi
sub    %rcx,%rdi
mov    %rdi,-0x170(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x38(%rbp)
mov    -0x10(%rbp),%rax
mov    0x18(%rax),%rsi
call   1030 <strcpy@plt>
mov    -0x170(%rbp),%rsi
mov    -0x14(%rbp),%eax
mov    %rax,%rcx
add    $0xf,%rcx
and    $0xfffffffffffffff0,%rcx
mov    %rsp,%rdi
sub    %rcx,%rdi
mov    %rdi,-0x180(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x40(%rbp)
call   1030 <strcpy@plt>
mov    -0x180(%rbp),%rdi
lea    0xd7c(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x180(%rbp),%rdi
lea    0xdee(%rip),%rsi
call   10a0 <fopen@plt>
mov    -0x170(%rbp),%rsi
mov    %rax,-0x48(%rbp)
mov    -0x14(%rbp),%eax
mov    %rax,%rcx
add    $0xf,%rcx
and    $0xfffffffffffffff0,%rcx
mov    %rsp,%rdi
sub    %rcx,%rdi
mov    %rdi,-0x178(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x50(%rbp)
call   1030 <strcpy@plt>
mov    -0x178(%rbp),%rdi
lea    0xd36(%rip),%rsi
mov    %rsi,-0x168(%rbp)
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
mov    -0x150(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
lea    0xd75(%rip),%rsi
mov    %rsi,-0x148(%rbp)
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
mov    -0x160(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
lea    0xce7(%rip),%rsi
mov    %rsi,-0x158(%rbp)
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
mov    -0x150(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
mov    -0x148(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
mov    -0x160(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
lea    0xc96(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x178(%rbp),%rdi
lea    0xc95(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0x58(%rbp)
mov    -0x58(%rbp),%rdi
lea    0xc83(%rip),%rsi
xor    %eax,%eax
call   1080 <fprintf@plt>
mov    -0x170(%rbp),%rsi
mov    -0x14(%rbp),%eax
mov    %rax,%rcx
add    $0xf,%rcx
and    $0xfffffffffffffff0,%rcx
mov    %rsp,%rdi
sub    %rcx,%rdi
mov    %rdi,-0x140(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x60(%rbp)
call   1030 <strcpy@plt>
mov    -0x168(%rbp),%rsi
mov    -0x140(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x150(%rbp),%rsi
mov    -0x140(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x148(%rbp),%rsi
mov    -0x140(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x160(%rbp),%rsi
mov    -0x140(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x158(%rbp),%rsi
mov    -0x140(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x150(%rbp),%rsi
mov    -0x140(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x148(%rbp),%rsi
mov    -0x140(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x140(%rbp),%rdi
lea    0xbe6(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x140(%rbp),%rdi
mov    -0x14(%rbp),%eax
mov    %rax,-0x138(%rbp)
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x130(%rbp)
mov    %rcx,%rsp
mov    %rax,-0x68(%rbp)
movl   $0x0,-0x6c(%rbp)
lea    0xbb0(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0x78(%rbp)
cmpq   $0x0,-0x78(%rbp)
je     151f <main+0x37f>
jmp    14e0 <main+0x340>
mov    -0x130(%rbp),%rdi
mov    -0x138(%rbp),%rax
mov    %eax,%esi
mov    -0x78(%rbp),%rdx
call   1070 <fgets@plt>
cmp    $0x0,%rax
je     1511 <main+0x371>
mov    -0x6c(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x6c(%rbp)
jmp    14e0 <main+0x340>
mov    -0x78(%rbp),%rdi
call   1040 <fclose@plt>
jmp    152b <main+0x38b>
mov    -0x140(%rbp),%rdi
call   10b0 <perror@plt>
mov    -0x140(%rbp),%rdi
mov    -0x6c(%rbp),%eax
mov    %eax,%ecx
mov    -0x14(%rbp),%eax
mov    %rax,-0x1a0(%rbp)
mov    %rcx,%rsi
imul   %rax,%rsi
add    $0xf,%rsi
and    $0xfffffffffffffff0,%rsi
mov    %rsp,%rdx
sub    %rsi,%rdx
mov    %rdx,-0x198(%rbp)
mov    %rdx,%rsp
mov    %rcx,-0x80(%rbp)
mov    %rax,-0x88(%rbp)
mov    -0x6c(%rbp),%eax
mov    %eax,%ecx
mov    -0x14(%rbp),%eax
mov    %rax,-0x190(%rbp)
mov    %rcx,%rsi
imul   %rax,%rsi
add    $0xf,%rsi
and    $0xfffffffffffffff0,%rsi
mov    %rsp,%rdx
sub    %rsi,%rdx
mov    %rdx,-0x188(%rbp)
mov    %rdx,%rsp
mov    %rcx,-0x90(%rbp)
mov    %rax,-0x98(%rbp)
movl   $0x0,-0x6c(%rbp)
lea    0xac2(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0xa0(%rbp)
cmpq   $0x0,-0xa0(%rbp)
je     17fb <main+0x65b>
jmp    15d4 <main+0x434>
mov    -0x130(%rbp),%rdi
mov    -0x138(%rbp),%rax
mov    %eax,%esi
mov    -0xa0(%rbp),%rdx
call   1070 <fgets@plt>
cmp    $0x0,%rax
je     17ea <main+0x64a>
mov    -0x130(%rbp),%rdi
call   1050 <strlen@plt>
mov    %eax,%ecx
mov    -0x130(%rbp),%rax
mov    %ecx,-0xa4(%rbp)
mov    -0xa4(%rbp),%ecx
sub    $0x1,%ecx
movslq %ecx,%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0xa,%eax
jne    1645 <main+0x4a5>
mov    -0x130(%rbp),%rax
mov    -0xa4(%rbp),%ecx
sub    $0x1,%ecx
movslq %ecx,%rcx
movb   $0x0,(%rax,%rcx,1)
mov    -0x130(%rbp),%rsi
mov    -0x198(%rbp),%rdi
mov    -0x1a0(%rbp),%rcx
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   1030 <strcpy@plt>
mov    -0x170(%rbp),%rsi
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   1030 <strcpy@plt>
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x96f(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x150(%rbp),%rsi
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x991(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x160(%rbp),%rsi
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x8e6(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x150(%rbp),%rsi
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x8ec(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x130(%rbp),%rsi
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x190(%rbp),%rcx
mov    -0x188(%rbp),%rdi
movslq -0x6c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x8b5(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x6c(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x6c(%rbp)
jmp    15d4 <main+0x434>
mov    -0xa0(%rbp),%rdi
call   1040 <fclose@plt>
jmp    1807 <main+0x667>
mov    -0x140(%rbp),%rdi
call   10b0 <perror@plt>
movl   $0xf4240,-0xb4(%rbp)
mov    -0xb4(%rbp),%eax
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x1b0(%rbp)
mov    %rcx,%rsp
mov    %rax,-0xc0(%rbp)
mov    -0xb4(%rbp),%eax
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x1a8(%rbp)
mov    %rcx,%rsp
mov    %rax,-0xc8(%rbp)
movl   $0x0,-0xcc(%rbp)
movl   $0x0,-0xa8(%rbp)
mov    -0xa8(%rbp),%eax
cmp    -0x6c(%rbp),%eax
jge    1d42 <main+0xba2>
mov    -0x188(%rbp),%rdi
mov    -0x190(%rbp),%rcx
movslq -0xa8(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x7d0(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0xd8(%rbp)
cmpq   $0x0,-0xd8(%rbp)
je     19b6 <main+0x816>
mov    -0xb4(%rbp),%eax
mov    %rax,-0x1c0(%rbp)
mov    %rsp,%rcx
mov    %rcx,-0xe0(%rbp)
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x1b8(%rbp)
mov    %rcx,%rsp
mov    %rax,-0xe8(%rbp)
mov    -0x1b8(%rbp),%rdi
mov    -0x1c0(%rbp),%rax
mov    %eax,%esi
mov    -0xd8(%rbp),%rdx
call   1070 <fgets@plt>
cmp    $0x0,%rax
je     19a7 <main+0x807>
mov    -0x1b8(%rbp),%rax
movsbl (%rax),%eax
cmp    $0x3e,%eax
je     19a2 <main+0x802>
mov    -0x1b8(%rbp),%rdi
call   1050 <strlen@plt>
mov    %eax,%ecx
mov    -0x1b8(%rbp),%rax
mov    %ecx,-0xec(%rbp)
mov    -0xec(%rbp),%ecx
sub    $0x1,%ecx
mov    %ecx,-0xec(%rbp)
movslq -0xec(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0xa,%eax
jne    1983 <main+0x7e3>
mov    -0x1b8(%rbp),%rax
movslq -0xec(%rbp),%rcx
movb   $0x0,(%rax,%rcx,1)
mov    -0x1b8(%rbp),%rsi
mov    -0x1b0(%rbp),%rdi
call   1030 <strcpy@plt>
mov    -0xd8(%rbp),%rdi
call   1040 <fclose@plt>
jmp    18fa <main+0x75a>
mov    -0xe0(%rbp),%rax
mov    %rax,%rsp
jmp    19d7 <main+0x837>
mov    -0x188(%rbp),%rdi
mov    -0x190(%rbp),%rcx
movslq -0xa8(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10b0 <perror@plt>
movl   $0x0,-0xac(%rbp)
mov    -0xac(%rbp),%eax
cmp    -0x6c(%rbp),%eax
jge    1d29 <main+0xb89>
mov    -0xa8(%rbp),%eax
cmp    -0xac(%rbp),%eax
jle    1d10 <main+0xb70>
mov    -0x188(%rbp),%rdi
mov    -0x190(%rbp),%rcx
movslq -0xac(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x652(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0xf8(%rbp)
cmpq   $0x0,-0xf8(%rbp)
je     1b34 <main+0x994>
mov    -0xb4(%rbp),%eax
mov    %rax,-0x1d0(%rbp)
mov    %rsp,%rcx
mov    %rcx,-0x100(%rbp)
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x1c8(%rbp)
mov    %rcx,%rsp
mov    %rax,-0x108(%rbp)
mov    -0x1c8(%rbp),%rdi
mov    -0x1d0(%rbp),%rax
mov    %eax,%esi
mov    -0xf8(%rbp),%rdx
call   1070 <fgets@plt>
cmp    $0x0,%rax
je     1b25 <main+0x985>
mov    -0x1c8(%rbp),%rax
movsbl (%rax),%eax
cmp    $0x3e,%eax
je     1b20 <main+0x980>
mov    -0x1c8(%rbp),%rdi
call   1050 <strlen@plt>
mov    %eax,%ecx
mov    -0x1c8(%rbp),%rax
mov    %ecx,-0x10c(%rbp)
mov    -0x10c(%rbp),%ecx
sub    $0x1,%ecx
mov    %ecx,-0x10c(%rbp)
movslq -0x10c(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0xa,%eax
jne    1b01 <main+0x961>
mov    -0x1c8(%rbp),%rax
movslq -0x10c(%rbp),%rcx
movb   $0x0,(%rax,%rcx,1)
mov    -0x1c8(%rbp),%rsi
mov    -0x1a8(%rbp),%rdi
call   1030 <strcpy@plt>
mov    -0xf8(%rbp),%rdi
call   1040 <fclose@plt>
jmp    1a78 <main+0x8d8>
mov    -0x100(%rbp),%rax
mov    %rax,%rsp
jmp    1b55 <main+0x9b5>
mov    -0x188(%rbp),%rdi
mov    -0x190(%rbp),%rcx
movslq -0xac(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10b0 <perror@plt>
mov    -0x1b0(%rbp),%rdi
call   1050 <strlen@plt>
mov    %eax,-0x110(%rbp)
movl   $0x0,-0x114(%rbp)
movl   $0x0,-0x118(%rbp)
movl   $0x0,-0xb0(%rbp)
mov    -0xb0(%rbp),%eax
cmp    -0x110(%rbp),%eax
jge    1c3a <main+0xa9a>
mov    -0x1b0(%rbp),%rax
movslq -0xb0(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0x4e,%eax
je     1bcd <main+0xa2d>
mov    -0x1a8(%rbp),%rax
movslq -0xb0(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0x4e,%eax
jne    1be1 <main+0xa41>
mov    -0x118(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x118(%rbp)
jmp    1c21 <main+0xa81>
mov    -0x1a8(%rbp),%rcx
mov    -0x1b0(%rbp),%rax
movslq -0xb0(%rbp),%rdx
movsbl (%rax,%rdx,1),%eax
movslq -0xb0(%rbp),%rdx
movsbl (%rcx,%rdx,1),%ecx
cmp    %ecx,%eax
je     1c1c <main+0xa7c>
mov    -0x114(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x114(%rbp)
jmp    1c21 <main+0xa81>
jmp    1c26 <main+0xa86>
mov    -0xb0(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0xb0(%rbp)
jmp    1b85 <main+0x9e5>
mov    -0x110(%rbp),%eax
sub    -0x118(%rbp),%eax
mov    %eax,-0x11c(%rbp)
cvtsi2ssl -0x114(%rbp),%xmm0
ff
cvtsi2ssl -0x11c(%rbp),%xmm1
ff
divss  %xmm1,%xmm0
movss  %xmm0,-0x120(%rbp)
ff
movss  -0x120(%rbp),%xmm0
ff
movss  0x38c(%rip),%xmm1
mulss  %xmm1,%xmm0
movss  0x384(%rip),%xmm1
addss  %xmm1,%xmm0
cvttss2si %xmm0,%edi
call   1090 <log@plt>
mov    -0x1a0(%rbp),%rsi
mov    -0x198(%rbp),%rcx
movaps %xmm0,%xmm1
movss  0x356(%rip),%xmm0
mulss  %xmm1,%xmm0
movss  %xmm0,-0x124(%rbp)
ff
mov    -0x58(%rbp),%rdi
movslq -0xa8(%rbp),%rax
imul   %rsi,%rax
mov    %rcx,%rdx
add    %rax,%rdx
movslq -0xac(%rbp),%rax
imul   %rsi,%rax
add    %rax,%rcx
mov    -0x114(%rbp),%r8d
mov    -0x11c(%rbp),%r9d
movss  -0x124(%rbp),%xmm0
ff
cvtss2sd %xmm0,%xmm0
lea    0x399(%rip),%rsi
mov    $0x1,%al
call   1080 <fprintf@plt>
mov    -0xcc(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0xcc(%rbp)
jmp    1d15 <main+0xb75>
mov    -0xac(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0xac(%rbp)
jmp    19e1 <main+0x841>
jmp    1d2e <main+0xb8e>
mov    -0xa8(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0xa8(%rbp)
jmp    1875 <main+0x6d5>
mov    -0x160(%rbp),%rsi
lea    0x356(%rip),%rdi
call   1060 <printf@plt>
mov    -0x160(%rbp),%rdx
mov    -0x48(%rbp),%rdi
lea    0x33f(%rip),%rsi
mov    $0x0,%al
call   1080 <fprintf@plt>
movl   $0x0,-0x4(%rbp)
mov    -0x20(%rbp),%rax
mov    %rax,%rsp
mov    -0x4(%rbp),%eax
mov    %rbp,%rsp
pop    %rbp
ret

x86 assembly (clang, -O2):
<main>:
push   %rbp
mov    %rsp,%rbp
push   %r15
push   %r14
push   %r13
push   %r12
push   %rbx
sub    $0x1bd8,%rsp
mov    %rsi,%rbx
mov    0x8(%rsi),%rsi
lea    -0x460(%rbp),%rdi
call   1030 <strcpy@plt>
mov    0x10(%rbx),%rsi
lea    -0x1420(%rbp),%r15
mov    %r15,%rdi
call   1030 <strcpy@plt>
mov    0x18(%rbx),%rsi
lea    -0x1030(%rbp),%r12
mov    %r12,%rdi
call   1030 <strcpy@plt>
lea    -0x1c00(%rbp),%rbx
mov    %rbx,%rdi
mov    %r12,%rsi
call   1030 <strcpy@plt>
lea    0xdf6(%rip),%rsi
mov    %rbx,%rdi
call   10c0 <strcat@plt>
lea    0xe6c(%rip),%rsi
mov    %rbx,%rdi
call   10a0 <fopen@plt>
mov    %rax,-0x58(%rbp)
lea    -0x1810(%rbp),%r13
mov    %r13,%rdi
mov    %r12,%rsi
call   1030 <strcpy@plt>
lea    0xdd4(%rip),%rsi
mov    %r13,%rdi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %r15,%rsi
call   10c0 <strcat@plt>
lea    0xe26(%rip),%r14
mov    %r13,%rdi
mov    %r14,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
lea    -0x460(%rbp),%rbx
mov    %rbx,%rsi
call   10c0 <strcat@plt>
lea    0xda1(%rip),%rsi
mov    %r13,%rdi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %r15,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %r14,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %rbx,%rsi
call   10c0 <strcat@plt>
lea    0xd73(%rip),%rsi
mov    %r13,%rdi
call   10c0 <strcat@plt>
lea    0xd76(%rip),%rsi
mov    %r13,%rdi
call   10a0 <fopen@plt>
lea    0xd69(%rip),%rdi
mov    $0x2a,%esi
mov    $0x1,%edx
mov    %rax,-0x60(%rbp)
mov    %rax,%rcx
call   10d0 <fwrite@plt>
lea    -0x850(%rbp),%rbx
mov    %rbx,%rdi
mov    %r12,%rsi
call   1030 <strcpy@plt>
mov    %rbx,%rdi
lea    0xd16(%rip),%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    %r15,%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    %r14,%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
lea    -0x460(%rbp),%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
lea    0xced(%rip),%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    %r15,%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    %r14,%rsi
call   10c0 <strcat@plt>
lea    0xd0c(%rip),%rsi
mov    %rbx,%rdi
call   10c0 <strcat@plt>
lea    0xd0a(%rip),%rsi
mov    %rbx,%rdi
call   10a0 <fopen@plt>
test   %rax,%rax
je     1828 <main+0x678>
mov    %rax,%r15
mov    $0xffffffff,%ebx
lea    -0xc40(%rbp),%r14
nopl   (%rax)
mov    %r14,%rdi
mov    $0x3e8,%esi
mov    %r15,%rdx
call   1070 <fgets@plt>
add    $0x1,%ebx
test   %rax,%rax
jne    1390 <main+0x1e0>
mov    %r15,%rdi
call   1040 <fclose@plt>
mov    %ebx,%eax
imul   $0x3e8,%rax,%rax
mov    %rsp,%rcx
add    $0xf,%rax
and    $0xfffffffffffffff0,%rax
sub    %rax,%rcx
mov    %rcx,-0x40(%rbp)
mov    %rcx,%rsp
mov    %rsp,%rcx
sub    %rax,%rcx
mov    %rcx,-0x38(%rbp)
mov    %rcx,%rsp
lea    0xc95(%rip),%rsi
lea    -0x850(%rbp),%rdi
call   10a0 <fopen@plt>
test   %rax,%rax
je     183b <main+0x68b>
lea    -0xc40(%rbp),%rbx
mov    %rbx,%rdi
mov    $0x3e8,%esi
mov    %rax,-0x30(%rbp)
mov    %rax,%rdx
call   1070 <fgets@plt>
xor    %r14d,%r14d
test   %rax,%rax
je     151f <main+0x36f>
lea    -0x1420(%rbp),%r13
mov    -0x40(%rbp),%r12
mov    -0x38(%rbp),%r15
jmp    14fd <main+0x34d>
cs nopw 0x0(%rax,%rax,1)
nopl   0x0(%rax)
mov    %r12,%rdi
mov    %rbx,%rsi
call   1030 <strcpy@plt>
mov    %r15,%rdi
lea    -0x1030(%rbp),%rsi
call   1030 <strcpy@plt>
mov    %r15,%rdi
lea    0xbba(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
mov    %r13,%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xc0c(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    -0x460(%rbp),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xb8d(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
mov    %r13,%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xbc3(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
mov    %rbx,%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xbbc(%rip),%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    $0x3e8,%esi
mov    -0x30(%rbp),%rdx
call   1070 <fgets@plt>
add    $0x3e8,%r15
add    $0x3e8,%r12
add    $0x1,%r14d
test   %rax,%rax
je     151f <main+0x36f>
mov    %rbx,%rdi
call   1050 <strlen@plt>
cltq
cmpb   $0xa,-0x1(%rax,%rbx,1)
jne    1440 <main+0x290>
movb   $0x0,-0xc41(%rbp,%rax,1)
jmp    1440 <main+0x290>
mov    -0x30(%rbp),%rdi
call   1040 <fclose@plt>
mov    %rsp,%r13
add    $0xfffffffffff0bdc0,%r13
mov    %r13,%rsp
mov    %rsp,%r12
add    $0xfffffffffff0bdc0,%r12
mov    %r12,%rsp
test   %r14d,%r14d
je     1847 <main+0x697>
mov    %r14d,%eax
mov    %rax,-0x30(%rbp)
xor    %eax,%eax
jmp    156e <main+0x3be>
cs nopw 0x0(%rax,%rax,1)
add    $0x1,%rax
cmp    -0x30(%rbp),%rax
je     1847 <main+0x697>
mov    %rax,-0x48(%rbp)
imul   $0x3e8,%rax,%rcx
mov    -0x38(%rbp),%rax
mov    %rcx,-0x50(%rbp)
lea    (%rax,%rcx,1),%rbx
mov    %rbx,%rdi
lea    0xae8(%rip),%rsi
call   10a0 <fopen@plt>
test   %rax,%rax
je     181b <main+0x66b>
mov    %rax,%r14
mov    %rsp,%r15
mov    %rsp,%rbx
add    $0xfffffffffff0bdc0,%rbx
mov    %rbx,%rsp
jmp    15d3 <main+0x423>
cs nopw 0x0(%rax,%rax,1)
nopl   0x0(%rax)
mov    %r13,%rdi
mov    %rbx,%rsi
call   1030 <strcpy@plt>
mov    %r14,%rdi
call   1040 <fclose@plt>
mov    %rbx,%rdi
mov    $0xf4240,%esi
mov    %r14,%rdx
call   1070 <fgets@plt>
test   %rax,%rax
je     1610 <main+0x460>
cmpb   $0x3e,(%rbx)
je     15d3 <main+0x423>
mov    %rbx,%rdi
call   1050 <strlen@plt>
cltq
cmpb   $0xa,-0x1(%rax,%rbx,1)
jne    15c0 <main+0x410>
movb   $0x0,-0x1(%rbx,%rax,1)
jmp    15c0 <main+0x410>
cs nopw 0x0(%rax,%rax,1)
nop
mov    %r15,%rsp
mov    -0x48(%rbp),%rax
mov    -0x50(%rbp),%rcx
add    -0x40(%rbp),%rcx
mov    %rcx,-0x50(%rbp)
xor    %r15d,%r15d
jmp    169f <main+0x4ef>
xor    %r14d,%r14d
xor    %esi,%esi
sub    %esi,%eax
xorps  %xmm0,%xmm0
cvtsi2ss %r14d,%xmm0
xorps  %xmm1,%xmm1
cvtsi2ss %eax,%xmm1
divss  %xmm1,%xmm0
mulss  0x9b6(%rip),%xmm0
addss  0x9b2(%rip),%xmm0
cvttss2si %xmm0,%edi
mov    %eax,%ebx
call   1090 <log@plt>
mulss  0x9a3(%rip),%xmm0
mov    -0x70(%rbp),%rcx
add    -0x40(%rbp),%rcx
cvtss2sd %xmm0,%xmm0
mov    -0x60(%rbp),%rdi
lea    0xa17(%rip),%rsi
mov    -0x50(%rbp),%rdx
mov    %r14d,%r8d
mov    %ebx,%r9d
mov    $0x1,%al
call   1080 <fprintf@plt>
mov    -0x48(%rbp),%rax
add    $0x1,%r15
cmp    -0x30(%rbp),%r15
je     1560 <main+0x3b0>
cmp    %r15,%rax
jbe    1691 <main+0x4e1>
imul   $0x3e8,%r15,%rcx
mov    -0x38(%rbp),%rax
mov    %rcx,-0x70(%rbp)
lea    (%rax,%rcx,1),%rbx
mov    %rbx,%rdi
lea    0x9b6(%rip),%rsi
call   10a0 <fopen@plt>
test   %rax,%rax
je     180e <main+0x65e>
mov    %rax,%r14
mov    %rsp,-0x68(%rbp)
mov    %rsp,%rbx
add    $0xfffffffffff0bdc0,%rbx
mov    %rbx,%rsp
jmp    1703 <main+0x553>
cs nopw 0x0(%rax,%rax,1)
nop
mov    %r12,%rdi
mov    %rbx,%rsi
call   1030 <strcpy@plt>
mov    %r14,%rdi
call   1040 <fclose@plt>
mov    %rbx,%rdi
mov    $0xf4240,%esi
mov    %r14,%rdx
call   1070 <fgets@plt>
test   %rax,%rax
je     1740 <main+0x590>
cmpb   $0x3e,(%rbx)
je     1703 <main+0x553>
mov    %rbx,%rdi
call   1050 <strlen@plt>
cltq
cmpb   $0xa,-0x1(%rax,%rbx,1)
jne    16f0 <main+0x540>
movb   $0x0,-0x1(%rbx,%rax,1)
jmp    16f0 <main+0x540>
cs nopw 0x0(%rax,%rax,1)
nop
mov    -0x68(%rbp),%rsp
mov    %r13,%rdi
call   1050 <strlen@plt>
test   %eax,%eax
jle    1628 <main+0x478>
mov    %eax,%r8d
cmp    $0x1,%eax
jne    1788 <main+0x5d8>
xor    %ecx,%ecx
xor    %esi,%esi
xor    %r14d,%r14d
test   $0x1,%r8b
je     162d <main+0x47d>
mov    0x0(%r13,%rcx,1),%dl
cmp    $0x4e,%dl
je     1780 <main+0x5d0>
mov    (%r12,%rcx,1),%cl
cmp    $0x4e,%cl
jne    17fe <main+0x64e>
add    $0x1,%esi
jmp    162d <main+0x47d>
mov    %r8d,%r9d
and    $0xfffffffe,%r9d
xor    %ecx,%ecx
xor    %esi,%esi
xor    %r14d,%r14d
jmp    17ac <main+0x5fc>
nopl   0x0(%rax,%rax,1)
add    $0x1,%esi
add    $0x2,%rcx
cmp    %rcx,%r9
je     1763 <main+0x5b3>
movzbl 0x0(%r13,%rcx,1),%edx
cmp    $0x4e,%dl
je     17c1 <main+0x611>
movzbl (%r12,%rcx,1),%ebx
cmp    $0x4e,%bl
jne    17d0 <main+0x620>
add    $0x1,%esi
jmp    17db <main+0x62b>
cs nopw 0x0(%rax,%rax,1)
xor    %edi,%edi
cmp    %bl,%dl
setne  %dil
add    %edi,%r14d
movzbl 0x1(%r13,%rcx,1),%edx
cmp    $0x4e,%dl
je     17a0 <main+0x5f0>
movzbl 0x1(%r12,%rcx,1),%ebx
cmp    $0x4e,%bl
je     17a0 <main+0x5f0>
xor    %edi,%edi
cmp    %bl,%dl
setne  %dil
add    %edi,%r14d
jmp    17a3 <main+0x5f3>
xor    %edi,%edi
cmp    %cl,%dl
setne  %dil
add    %edi,%r14d
jmp    162d <main+0x47d>
mov    %rbx,%rdi
call   10b0 <perror@plt>
jmp    1744 <main+0x594>
mov    %rbx,%rdi
call   10b0 <perror@plt>
jmp    1613 <main+0x463>
lea    -0x850(%rbp),%rdi
call   10b0 <perror@plt>
xor    %ebx,%ebx
jmp    13b0 <main+0x200>
lea    -0x850(%rbp),%rdi
call   10b0 <perror@plt>
lea    0x858(%rip),%rbx
lea    -0x460(%rbp),%r14
mov    %rbx,%rdi
mov    %r14,%rsi
call   1060 <printf@plt>
mov    -0x58(%rbp),%rdi
mov    %rbx,%rsi
mov    %r14,%rdx
xor    %eax,%eax
call   1080 <fprintf@plt>
xor    %eax,%eax
lea    -0x28(%rbp),%rsp
pop    %rbx
pop    %r12
pop    %r13
pop    %r14
pop    %r15
pop    %rbp
ret

LLVM IR (-O0):
@.str = [18 x i8] c"/Analysis/log.txt\00"
@.str.1 = [2 x i8] c"a\00"
@.str.2 = [11 x i8] c"/Analysis/\00"
@.str.3 = [2 x i8] c"/\00"
@.str.4 = [2 x i8] c"_\00"
@.str.5 = [18 x i8] c"_di_simulated.csv\00"
@.str.6 = [2 x i8] c"w\00"
@.str.7 = [43 x i8] c"Isolate_1,Isolate_2,SNPs,Sites,Divergence\0A\00"
@.str.8 = [13 x i8] c"Isolates.txt\00"
@.str.9 = [2 x i8] c"r\00"
@.str.10 = [19 x i8] c"/Intergenic_files/\00"
@.str.11 = [7 x i8] c".fasta\00"
@.str.12 = [19 x i8] c"%s,%s,%i,%i,%0.6f\0A\00"
@.str.13 = [19 x i8] c"%s di calculated.\0A\00"
define i32 @main(i32 %0, i8** %1) {
%3 = alloca i32
%4 = alloca i32
%5 = alloca i8**
%6 = alloca i32
%7 = alloca i8*
%8 = alloca i64
%9 = alloca i64
%10 = alloca i64
%11 = alloca i64
%12 = alloca i32*
%13 = alloca i64
%14 = alloca i32*
%15 = alloca i64
%16 = alloca i64
%17 = alloca i32
%18 = alloca i32*
%19 = alloca i64
%20 = alloca i64
%21 = alloca i64
%22 = alloca i64
%23 = alloca i32*
%24 = alloca i32
%25 = alloca i32
%26 = alloca i32
%27 = alloca i32
%28 = alloca i32
%29 = alloca i64
%30 = alloca i64
%31 = alloca i32
%32 = alloca i32*
%33 = alloca i8*
%34 = alloca i64
%35 = alloca i32
%36 = alloca i32*
%37 = alloca i8*
%38 = alloca i64
%39 = alloca i32
%40 = alloca i32
%41 = alloca i32
%42 = alloca i32
%43 = alloca i32
%44 = alloca float
%45 = alloca float
store i32 0, i32* %3
store i32 %0, i32* %4
store i8** %1, i8*** %5
store i32 1000, i32* %6
%46 = load i32, i32* %6
%47 = zext i32 %46 to i64
%48 = call i8* @llvm.stacksave()
store i8* %48, i8** %7
%49 = alloca i8, i64 %47
store i64 %47, i64* %8
%50 = load i8**, i8*** %5
%51 = getelementptr inbounds i8*, i8** %50, i64 1
%52 = load i8*, i8** %51
%53 = call i32 @strcpy(i8* %49, i8* %52)
%54 = load i32, i32* %6
%55 = zext i32 %54 to i64
%56 = alloca i8, i64 %55
store i64 %55, i64* %9
%57 = load i8**, i8*** %5
%58 = getelementptr inbounds i8*, i8** %57, i64 2
%59 = load i8*, i8** %58
%60 = call i32 @strcpy(i8* %56, i8* %59)
%61 = load i32, i32* %6
%62 = zext i32 %61 to i64
%63 = alloca i8, i64 %62
store i64 %62, i64* %10
%64 = load i8**, i8*** %5
%65 = getelementptr inbounds i8*, i8** %64, i64 3
%66 = load i8*, i8** %65
%67 = call i32 @strcpy(i8* %63, i8* %66)
%68 = load i32, i32* %6
%69 = zext i32 %68 to i64
%70 = alloca i8, i64 %69
store i64 %69, i64* %11
%71 = call i32 @strcpy(i8* %70, i8* %63)
%72 = call i32 @strcat(i8* %70, i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str, i64 0, i64 0))
%73 = call i32* @fopen(i8* %70, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.1, i64 0, i64 0))
store i32* %73, i32** %12
%74 = load i32, i32* %6
%75 = zext i32 %74 to i64
%76 = alloca i8, i64 %75
store i64 %75, i64* %13
%77 = call i32 @strcpy(i8* %76, i8* %63)
%78 = call i32 @strcat(i8* %76, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%79 = call i32 @strcat(i8* %76, i8* %56)
%80 = call i32 @strcat(i8* %76, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%81 = call i32 @strcat(i8* %76, i8* %49)
%82 = call i32 @strcat(i8* %76, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%83 = call i32 @strcat(i8* %76, i8* %56)
%84 = call i32 @strcat(i8* %76, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%85 = call i32 @strcat(i8* %76, i8* %49)
%86 = call i32 @strcat(i8* %76, i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str.5, i64 0, i64 0))
%87 = call i32* @fopen(i8* %76, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.6, i64 0, i64 0))
store i32* %87, i32** %14
%88 = load i32*, i32** %14
%89 = call i32 (i32*, i8*, ...) @fprintf(i32* %88, i8* getelementptr inbounds ([43 x i8], [43 x i8]* @.str.7, i64 0, i64 0))
%90 = load i32, i32* %6
%91 = zext i32 %90 to i64
%92 = alloca i8, i64 %91
store i64 %91, i64* %15
%93 = call i32 @strcpy(i8* %92, i8* %63)
%94 = call i32 @strcat(i8* %92, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%95 = call i32 @strcat(i8* %92, i8* %56)
%96 = call i32 @strcat(i8* %92, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%97 = call i32 @strcat(i8* %92, i8* %49)
%98 = call i32 @strcat(i8* %92, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%99 = call i32 @strcat(i8* %92, i8* %56)
%100 = call i32 @strcat(i8* %92, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%101 = call i32 @strcat(i8* %92, i8* getelementptr inbounds ([13 x i8], [13 x i8]* @.str.8, i64 0, i64 0))
%102 = load i32, i32* %6
%103 = zext i32 %102 to i64
%104 = alloca i8, i64 %103
store i64 %103, i64* %16
store i32 0, i32* %17
%105 = call i32* @fopen(i8* %92, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
store i32* %105, i32** %18
%106 = load i32*, i32** %18
%107 = icmp ne i32* %106, null
br i1 %107, label %108, label %120
108: ; preds = %2
br label %109
109: ; preds = %114, %108
%110 = trunc i64 %103 to i32
%111 = load i32*, i32** %18
%112 = call i32* @fgets(i8* %104, i32 %110, i32* %111)
%113 = icmp ne i32* %112, null
br i1 %113, label %114, label %117
114: ; preds = %109
%115 = load i32, i32* %17
%116 = add nsw i32 %115, 1
store i32 %116, i32* %17
br label %109
117: ; preds = %109
%118 = load i32*, i32** %18
%119 = call i32 @fclose(i32* %118)
br label %122
120: ; preds = %2
%121 = call i32 @perror(i8* %92)
br label %122
122: ; preds = %120, %117
%123 = load i32, i32* %17
%124 = zext i32 %123 to i64
%125 = load i32, i32* %6
%126 = zext i32 %125 to i64
%127 = mul nuw i64 %124, %126
%128 = alloca i8, i64 %127
store i64 %124, i64* %19
store i64 %126, i64* %20
%129 = load i32, i32* %17
%130 = zext i32 %129 to i64
%131 = load i32, i32* %6
%132 = zext i32 %131 to i64
%133 = mul nuw i64 %130, %132
%134 = alloca i8, i64 %133
store i64 %130, i64* %21
store i64 %132, i64* %22
store i32 0, i32* %17
%135 = call i32* @fopen(i8* %92, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
store i32* %135, i32** %23
%136 = load i32*, i32** %23
%137 = icmp ne i32* %136, null
br i1 %137, label %138, label %219
138: ; preds = %122
br label %139
139: ; preds = %158, %138
%140 = trunc i64 %103 to i32
%141 = load i32*, i32** %23
%142 = call i32* @fgets(i8* %104, i32 %140, i32* %141)
%143 = icmp ne i32* %142, null
br i1 %143, label %144, label %216
144: ; preds = %139
%145 = call i32 @strlen(i8* %104)
store i32 %145, i32* %24
%146 = load i32, i32* %24
%147 = sub nsw i32 %146, 1
%148 = sext i32 %147 to i64
%149 = getelementptr inbounds i8, i8* %104, i64 %148
%150 = load i8, i8* %149
%151 = sext i8 %150 to i32
%152 = icmp eq i32 %151, 10
br i1 %152, label %153, label %158
153: ; preds = %144
%154 = load i32, i32* %24
%155 = sub nsw i32 %154, 1
%156 = sext i32 %155 to i64
%157 = getelementptr inbounds i8, i8* %104, i64 %156
store i8 0, i8* %157
br label %158
158: ; preds = %153, %144
%159 = load i32, i32* %17
%160 = sext i32 %159 to i64
%161 = mul nsw i64 %160, %126
%162 = getelementptr inbounds i8, i8* %128, i64 %161
%163 = call i32 @strcpy(i8* %162, i8* %104)
%164 = load i32, i32* %17
%165 = sext i32 %164 to i64
%166 = mul nsw i64 %165, %132
%167 = getelementptr inbounds i8, i8* %134, i64 %166
%168 = call i32 @strcpy(i8* %167, i8* %63)
%169 = load i32, i32* %17
%170 = sext i32 %169 to i64
%171 = mul nsw i64 %170, %132
%172 = getelementptr inbounds i8, i8* %134, i64 %171
%173 = call i32 @strcat(i8* %172, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%174 = load i32, i32* %17
%175 = sext i32 %174 to i64
%176 = mul nsw i64 %175, %132
%177 = getelementptr inbounds i8, i8* %134, i64 %176
%178 = call i32 @strcat(i8* %177, i8* %56)
%179 = load i32, i32* %17
%180 = sext i32 %179 to i64
%181 = mul nsw i64 %180, %132
%182 = getelementptr inbounds i8, i8* %134, i64 %181
%183 = call i32 @strcat(i8* %182, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%184 = load i32, i32* %17
%185 = sext i32 %184 to i64
%186 = mul nsw i64 %185, %132
%187 = getelementptr inbounds i8, i8* %134, i64 %186
%188 = call i32 @strcat(i8* %187, i8* %49)
%189 = load i32, i32* %17
%190 = sext i32 %189 to i64
%191 = mul nsw i64 %190, %132
%192 = getelementptr inbounds i8, i8* %134, i64 %191
%193 = call i32 @strcat(i8* %192, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%194 = load i32, i32* %17
%195 = sext i32 %194 to i64
%196 = mul nsw i64 %195, %132
%197 = getelementptr inbounds i8, i8* %134, i64 %196
%198 = call i32 @strcat(i8* %197, i8* %56)
%199 = load i32, i32* %17
%200 = sext i32 %199 to i64
%201 = mul nsw i64 %200, %132
%202 = getelementptr inbounds i8, i8* %134, i64 %201
%203 = call i32 @strcat(i8* %202, i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.10, i64 0, i64 0))
%204 = load i32, i32* %17
%205 = sext i32 %204 to i64
%206 = mul nsw i64 %205, %132
%207 = getelementptr inbounds i8, i8* %134, i64 %206
%208 = call i32 @strcat(i8* %207, i8* %104)
%209 = load i32, i32* %17
%210 = sext i32 %209 to i64
%211 = mul nsw i64 %210, %132
%212 = getelementptr inbounds i8, i8* %134, i64 %211
%213 = call i32 @strcat(i8* %212, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.11, i64 0, i64 0))
%214 = load i32, i32* %17
%215 = add nsw i32 %214, 1
store i32 %215, i32* %17
br label %139
216: ; preds = %139
%217 = load i32*, i32** %23
%218 = call i32 @fclose(i32* %217)
br label %221
219: ; preds = %122
%220 = call i32 @perror(i8* %92)
br label %221
221: ; preds = %219, %216
store i32 1000000, i32* %28
%222 = load i32, i32* %28
%223 = zext i32 %222 to i64
%224 = alloca i8, i64 %223
store i64 %223, i64* %29
%225 = load i32, i32* %28
%226 = zext i32 %225 to i64
%227 = alloca i8, i64 %226
store i64 %226, i64* %30
store i32 0, i32* %31
store i32 0, i32* %25
br label %228
228: ; preds = %419, %221
%229 = load i32, i32* %25
%230 = load i32, i32* %17
%231 = icmp slt i32 %229, %230
br i1 %231, label %232, label %422
232: ; preds = %228
%233 = load i32, i32* %25
%234 = sext i32 %233 to i64
%235 = mul nsw i64 %234, %132
%236 = getelementptr inbounds i8, i8* %134, i64 %235
%237 = call i32* @fopen(i8* %236, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
store i32* %237, i32** %32
%238 = load i32*, i32** %32
%239 = icmp ne i32* %238, null
br i1 %239, label %240, label %276
240: ; preds = %232
%241 = load i32, i32* %28
%242 = zext i32 %241 to i64
%243 = call i8* @llvm.stacksave()
store i8* %243, i8** %33
%244 = alloca i8, i64 %242
store i64 %242, i64* %34
br label %245
245: ; preds = %273, %240
%246 = trunc i64 %242 to i32
%247 = load i32*, i32** %32
%248 = call i32* @fgets(i8* %244, i32 %246, i32* %247)
%249 = icmp ne i32* %248, null
br i1 %249, label %250, label %274
250: ; preds = %245
%251 = getelementptr inbounds i8, i8* %244, i64 0
%252 = load i8, i8* %251
%253 = sext i8 %252 to i32
%254 = icmp ne i32 %253, 62
br i1 %254, label %255, label %273
255: ; preds = %250
%256 = call i32 @strlen(i8* %244)
store i32 %256, i32* %35
%257 = load i32, i32* %35
%258 = sub nsw i32 %257, 1
store i32 %258, i32* %35
%259 = load i32, i32* %35
%260 = sext i32 %259 to i64
%261 = getelementptr inbounds i8, i8* %244, i64 %260
%262 = load i8, i8* %261
%263 = sext i8 %262 to i32
%264 = icmp eq i32 %263, 10
br i1 %264, label %265, label %269
265: ; preds = %255
%266 = load i32, i32* %35
%267 = sext i32 %266 to i64
%268 = getelementptr inbounds i8, i8* %244, i64 %267
store i8 0, i8* %268
br label %269
269: ; preds = %265, %255
%270 = call i32 @strcpy(i8* %224, i8* %244)
%271 = load i32*, i32** %32
%272 = call i32 @fclose(i32* %271)
br label %273
273: ; preds = %269, %250
br label %245
274: ; preds = %245
%275 = load i8*, i8** %33
br label %282
276: ; preds = %232
%277 = load i32, i32* %25
%278 = sext i32 %277 to i64
%279 = mul nsw i64 %278, %132
%280 = getelementptr inbounds i8, i8* %134, i64 %279
%281 = call i32 @perror(i8* %280)
br label %282
282: ; preds = %276, %274
store i32 0, i32* %26
br label %283
283: ; preds = %415, %282
%284 = load i32, i32* %26
%285 = load i32, i32* %17
%286 = icmp slt i32 %284, %285
br i1 %286, label %287, label %418
287: ; preds = %283
%288 = load i32, i32* %25
%289 = load i32, i32* %26
%290 = icmp sgt i32 %288, %289
br i1 %290, label %291, label %414
291: ; preds = %287
%292 = load i32, i32* %26
%293 = sext i32 %292 to i64
%294 = mul nsw i64 %293, %132
%295 = getelementptr inbounds i8, i8* %134, i64 %294
%296 = call i32* @fopen(i8* %295, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
store i32* %296, i32** %36
%297 = load i32*, i32** %36
%298 = icmp ne i32* %297, null
br i1 %298, label %299, label %335
299: ; preds = %291
%300 = load i32, i32* %28
%301 = zext i32 %300 to i64
%302 = call i8* @llvm.stacksave()
store i8* %302, i8** %37
%303 = alloca i8, i64 %301
store i64 %301, i64* %38
br label %304
304: ; preds = %332, %299
%305 = trunc i64 %301 to i32
%306 = load i32*, i32** %36
%307 = call i32* @fgets(i8* %303, i32 %305, i32* %306)
%308 = icmp ne i32* %307, null
br i1 %308, label %309, label %333
309: ; preds = %304
%310 = getelementptr inbounds i8, i8* %303, i64 0
%311 = load i8, i8* %310
%312 = sext i8 %311 to i32
%313 = icmp ne i32 %312, 62
br i1 %313, label %314, label %332
314: ; preds = %309
%315 = call i32 @strlen(i8* %303)
store i32 %315, i32* %39
%316 = load i32, i32* %39
%317 = sub nsw i32 %316, 1
store i32 %317, i32* %39
%318 = load i32, i32* %39
%319 = sext i32 %318 to i64
%320 = getelementptr inbounds i8, i8* %303, i64 %319
%321 = load i8, i8* %320
%322 = sext i8 %321 to i32
%323 = icmp eq i32 %322, 10
br i1 %323, label %324, label %328
324: ; preds = %314
%325 = load i32, i32* %39
%326 = sext i32 %325 to i64
%327 = getelementptr inbounds i8, i8* %303, i64 %326
store i8 0, i8* %327
br label %328
328: ; preds = %324, %314
%329 = call i32 @strcpy(i8* %227, i8* %303)
%330 = load i32*, i32** %36
%331 = call i32 @fclose(i32* %330)
br label %332
332: ; preds = %328, %309
br label %304
333: ; preds = %304
%334 = load i8*, i8** %37
br label %341
335: ; preds = %291
%336 = load i32, i32* %26
%337 = sext i32 %336 to i64
%338 = mul nsw i64 %337, %132
%339 = getelementptr inbounds i8, i8* %134, i64 %338
%340 = call i32 @perror(i8* %339)
br label %341
341: ; preds = %335, %333
%342 = call i32 @strlen(i8* %224)
store i32 %342, i32* %40
store i32 0, i32* %41
store i32 0, i32* %42
store i32 0, i32* %27
br label %343
343: ; preds = %381, %341
%344 = load i32, i32* %27
%345 = load i32, i32* %40
%346 = icmp slt i32 %344, %345
br i1 %346, label %347, label %384
347: ; preds = %343
%348 = load i32, i32* %27
%349 = sext i32 %348 to i64
%350 = getelementptr inbounds i8, i8* %224, i64 %349
%351 = load i8, i8* %350
%352 = sext i8 %351 to i32
%353 = icmp eq i32 %352, 78
br i1 %353, label %361, label %354
354: ; preds = %347
%355 = load i32, i32* %27
%356 = sext i32 %355 to i64
%357 = getelementptr inbounds i8, i8* %227, i64 %356
%358 = load i8, i8* %357
%359 = sext i8 %358 to i32
%360 = icmp eq i32 %359, 78
br i1 %360, label %361, label %364
361: ; preds = %354, %347
%362 = load i32, i32* %42
%363 = add nsw i32 %362, 1
store i32 %363, i32* %42
br label %380
364: ; preds = %354
%365 = load i32, i32* %27
%366 = sext i32 %365 to i64
%367 = getelementptr inbounds i8, i8* %224, i64 %366
%368 = load i8, i8* %367
%369 = sext i8 %368 to i32
%370 = load i32, i32* %27
%371 = sext i32 %370 to i64
%372 = getelementptr inbounds i8, i8* %227, i64 %371
%373 = load i8, i8* %372
%374 = sext i8 %373 to i32
%375 = icmp ne i32 %369, %374
br i1 %375, label %376, label %379
376: ; preds = %364
%377 = load i32, i32* %41
%378 = add nsw i32 %377, 1
store i32 %378, i32* %41
br label %379
379: ; preds = %376, %364
br label %380
380: ; preds = %379, %361
br label %381
381: ; preds = %380
%382 = load i32, i32* %27
%383 = add nsw i32 %382, 1
store i32 %383, i32* %27
br label %343
384: ; preds = %343
%385 = load i32, i32* %40
%386 = load i32, i32* %42
%387 = sub nsw i32 %385, %386
store i32 %387, i32* %43
%388 = load i32, i32* %41
%389 = sitofp i32 %388 to float
%390 = load i32, i32* %43
%391 = sitofp i32 %390 to float
%392 = fdiv float %389, %391
store float %392, float* %44
%393 = load float, float* %44
%394 = call float @llvm.fmuladd.f32(float 0xBFF5555560000000, float %393, float 1.000000e+00)
%395 = fptosi float %394 to i32
%396 = call float @log(i32 %395)
%397 = fmul float -7.500000e-01, %396
store float %397, float* %45
%398 = load i32*, i32** %14
%399 = load i32, i32* %25
%400 = sext i32 %399 to i64
%401 = mul nsw i64 %400, %126
%402 = getelementptr inbounds i8, i8* %128, i64 %401
%403 = load i32, i32* %26
%404 = sext i32 %403 to i64
%405 = mul nsw i64 %404, %126
%406 = getelementptr inbounds i8, i8* %128, i64 %405
%407 = load i32, i32* %41
%408 = load i32, i32* %43
%409 = load float, float* %45
%410 = fpext float %409 to double
%411 = call i32 (i32*, i8*, ...) @fprintf(i32* %398, i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.12, i64 0, i64 0), i8* %402, i8* %406, i32 %407, i32 %408, double %410)
%412 = load i32, i32* %31
%413 = add nsw i32 %412, 1
store i32 %413, i32* %31
br label %414
414: ; preds = %384, %287
br label %415
415: ; preds = %414
%416 = load i32, i32* %26
%417 = add nsw i32 %416, 1
store i32 %417, i32* %26
br label %283
418: ; preds = %283
br label %419
419: ; preds = %418
%420 = load i32, i32* %25
%421 = add nsw i32 %420, 1
store i32 %421, i32* %25
br label %228
422: ; preds = %228
%423 = call i32 @printf(i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.13, i64 0, i64 0), i8* %49)
%424 = load i32*, i32** %12
%425 = call i32 (i32*, i8*, ...) @fprintf(i32* %424, i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.13, i64 0, i64 0), i8* %49)
store i32 0, i32* %3
%426 = load i8*, i8** %7
%427 = load i32, i32* %3
ret i32 %427
}

LLVM IR (-O2):
@.str = [18 x i8] c"/Analysis/log.txt\00"
@.str.1 = [2 x i8] c"a\00"
@.str.2 = [11 x i8] c"/Analysis/\00"
@.str.3 = [2 x i8] c"/\00"
@.str.4 = [2 x i8] c"_\00"
@.str.5 = [18 x i8] c"_di_simulated.csv\00"
@.str.6 = [2 x i8] c"w\00"
@.str.7 = [43 x i8] c"Isolate_1,Isolate_2,SNPs,Sites,Divergence\0A\00"
@.str.8 = [13 x i8] c"Isolates.txt\00"
@.str.9 = [2 x i8] c"r\00"
@.str.10 = [19 x i8] c"/Intergenic_files/\00"
@.str.11 = [7 x i8] c".fasta\00"
@.str.12 = [19 x i8] c"%s,%s,%i,%i,%0.6f\0A\00"
@.str.13 = [19 x i8] c"%s di calculated.\0A\00"
define i32 @main(i32 %0, i8** nocapture %1) {
%3 = alloca [1000 x i8]
%4 = getelementptr inbounds [1000 x i8], [1000 x i8]* %3, i64 0, i64 0
%5 = getelementptr inbounds i8*, i8** %1, i64 1
%6 = load i8*, i8** %5
%7 = call i32 @strcpy(i8* %4, i8* %6)
%8 = alloca [1000 x i8]
%9 = getelementptr inbounds [1000 x i8], [1000 x i8]* %8, i64 0, i64 0
%10 = getelementptr inbounds i8*, i8** %1, i64 2
%11 = load i8*, i8** %10
%12 = call i32 @strcpy(i8* %9, i8* %11)
%13 = alloca [1000 x i8]
%14 = getelementptr inbounds [1000 x i8], [1000 x i8]* %13, i64 0, i64 0
%15 = getelementptr inbounds i8*, i8** %1, i64 3
%16 = load i8*, i8** %15
%17 = call i32 @strcpy(i8* %14, i8* %16)
%18 = alloca [1000 x i8]
%19 = getelementptr inbounds [1000 x i8], [1000 x i8]* %18, i64 0, i64 0
%20 = call i32 @strcpy(i8* %19, i8* %14)
%21 = call i32 @strcat(i8* %19, i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str, i64 0, i64 0))
%22 = call i32* @fopen(i8* %19, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.1, i64 0, i64 0))
%23 = alloca [1000 x i8]
%24 = getelementptr inbounds [1000 x i8], [1000 x i8]* %23, i64 0, i64 0
%25 = call i32 @strcpy(i8* %24, i8* %14)
%26 = call i32 @strcat(i8* %24, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%27 = call i32 @strcat(i8* %24, i8* %9)
%28 = call i32 @strcat(i8* %24, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%29 = call i32 @strcat(i8* %24, i8* %4)
%30 = call i32 @strcat(i8* %24, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%31 = call i32 @strcat(i8* %24, i8* %9)
%32 = call i32 @strcat(i8* %24, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%33 = call i32 @strcat(i8* %24, i8* %4)
%34 = call i32 @strcat(i8* %24, i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str.5, i64 0, i64 0))
%35 = call i32* @fopen(i8* %24, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.6, i64 0, i64 0))
%36 = call i64 @fwrite(i8* getelementptr inbounds ([43 x i8], [43 x i8]* @.str.7, i64 0, i64 0), i64 42, i64 1, i32* %35)
%37 = alloca [1000 x i8]
%38 = getelementptr inbounds [1000 x i8], [1000 x i8]* %37, i64 0, i64 0
%39 = call i32 @strcpy(i8* %38, i8* %14)
%40 = call i32 @strcat(i8* %38, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%41 = call i32 @strcat(i8* %38, i8* %9)
%42 = call i32 @strcat(i8* %38, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%43 = call i32 @strcat(i8* %38, i8* %4)
%44 = call i32 @strcat(i8* %38, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%45 = call i32 @strcat(i8* %38, i8* %9)
%46 = call i32 @strcat(i8* %38, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%47 = call i32 @strcat(i8* %38, i8* getelementptr inbounds ([13 x i8], [13 x i8]* @.str.8, i64 0, i64 0))
%48 = alloca [1000 x i8]
%49 = getelementptr inbounds [1000 x i8], [1000 x i8]* %48, i64 0, i64 0
%50 = call i32* @fopen(i8* %38, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
%51 = icmp eq i32* %50, null
br i1 %51, label %59, label %52
52: ; preds = %2, %52
%53 = phi i32 [ %56, %52 ], [ 0, %2 ]
%54 = call i32* @fgets(i8* %49, i32 1000, i32* %50)
%55 = icmp eq i32* %54, null
%56 = add nuw nsw i32 %53, 1
br i1 %55, label %57, label %52
57: ; preds = %52
%58 = call i32 @fclose(i32* %50)
br label %61
59: ; preds = %2
%60 = call i32 @perror(i8* %38)
br label %61
61: ; preds = %59, %57
%62 = phi i32 [ %53, %57 ], [ 0, %59 ]
%63 = zext i32 %62 to i64
%64 = mul nuw nsw i64 %63, 1000
%65 = alloca i8, i64 %64
%66 = alloca i8, i64 %64
%67 = call i32* @fopen(i8* %38, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
%68 = icmp eq i32* %67, null
br i1 %68, label %101, label %69
69: ; preds = %61
%70 = call i32* @fgets(i8* %49, i32 1000, i32* %67)
%71 = icmp eq i32* %70, null
br i1 %71, label %103, label %72
72: ; preds = %69, %81
%73 = phi i64 [ %96, %81 ], [ 0, %69 ]
%74 = call i32 @strlen(i8* %49)
%75 = add nsw i32 %74, -1
%76 = sext i32 %75 to i64
%77 = getelementptr inbounds [1000 x i8], [1000 x i8]* %48, i64 0, i64 %76
%78 = load i8, i8* %77
%79 = icmp eq i8 %78, 10
br i1 %79, label %80, label %81
80: ; preds = %72
store i8 0, i8* %77
br label %81
81: ; preds = %80, %72
%82 = mul nuw nsw i64 %73, 1000
%83 = getelementptr inbounds i8, i8* %65, i64 %82
%84 = call i32 @strcpy(i8* %83, i8* %49)
%85 = getelementptr inbounds i8, i8* %66, i64 %82
%86 = call i32 @strcpy(i8* %85, i8* %14)
%87 = call i32 @strcat(i8* %85, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%88 = call i32 @strcat(i8* %85, i8* %9)
%89 = call i32 @strcat(i8* %85, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%90 = call i32 @strcat(i8* %85, i8* %4)
%91 = call i32 @strcat(i8* %85, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%92 = call i32 @strcat(i8* %85, i8* %9)
%93 = call i32 @strcat(i8* %85, i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.10, i64 0, i64 0))
%94 = call i32 @strcat(i8* %85, i8* %49)
%95 = call i32 @strcat(i8* %85, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.11, i64 0, i64 0))
%96 = add nuw i64 %73, 1
%97 = call i32* @fgets(i8* %49, i32 1000, i32* %67)
%98 = icmp eq i32* %97, null
br i1 %98, label %99, label %72
99: ; preds = %81
%100 = trunc i64 %96 to i32
br label %103
101: ; preds = %61
%102 = call i32 @perror(i8* %38)
br label %272
103: ; preds = %69, %99
%104 = phi i32 [ 0, %69 ], [ %100, %99 ]
%105 = call i32 @fclose(i32* %67)
%106 = alloca [1000000 x i8]
%107 = alloca [1000000 x i8]
%108 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %107, i64 0, i64 0
%109 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %106, i64 0, i64 0
%110 = icmp eq i32 %104, 0
br i1 %110, label %272, label %111
111: ; preds = %103
%112 = zext i32 %104 to i64
br label %113
113: ; preds = %111, %269
%114 = phi i64 [ 0, %111 ], [ %270, %269 ]
%115 = mul nuw nsw i64 %114, 1000
%116 = getelementptr inbounds i8, i8* %66, i64 %115
%117 = call i32* @fopen(i8* %116, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
%118 = icmp eq i32* %117, null
br i1 %118, label %143, label %119
119: ; preds = %113
%120 = call i8* @llvm.stacksave()
%121 = alloca [1000000 x i8]
%122 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %121, i64 0, i64 0
%123 = call i32* @fgets(i8* %122, i32 1000000, i32* %117)
%124 = icmp eq i32* %123, null
br i1 %124, label %142, label %125
125: ; preds = %119, %139
%126 = load i8, i8* %122
%127 = icmp eq i8 %126, 62
br i1 %127, label %139, label %128
128: ; preds = %125
%129 = call i32 @strlen(i8* %122)
%130 = add nsw i32 %129, -1
%131 = sext i32 %130 to i64
%132 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %121, i64 0, i64 %131
%133 = load i8, i8* %132
%134 = icmp eq i8 %133, 10
br i1 %134, label %135, label %136
135: ; preds = %128
store i8 0, i8* %132
br label %136
136: ; preds = %135, %128
%137 = call i32 @strcpy(i8* %109, i8* %122)
%138 = call i32 @fclose(i32* %117)
br label %139
139: ; preds = %136, %125
%140 = call i32* @fgets(i8* %122, i32 1000000, i32* %117)
%141 = icmp eq i32* %140, null
br i1 %141, label %142, label %125
142: ; preds = %139, %119
br label %145
143: ; preds = %113
%144 = call i32 @perror(i8* %116)
br label %145
145: ; preds = %143, %142
%146 = getelementptr inbounds i8, i8* %65, i64 %115
br label %147
147: ; preds = %145, %266
%148 = phi i64 [ 0, %145 ], [ %267, %266 ]
%149 = icmp ugt i64 %114, %148
br i1 %149, label %150, label %266
150: ; preds = %147
%151 = mul nuw nsw i64 %148, 1000
%152 = getelementptr inbounds i8, i8* %66, i64 %151
%153 = call i32* @fopen(i8* %152, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
%154 = icmp eq i32* %153, null
br i1 %154, label %179, label %155
155: ; preds = %150
%156 = call i8* @llvm.stacksave()
%157 = alloca [1000000 x i8]
%158 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %157, i64 0, i64 0
%159 = call i32* @fgets(i8* %158, i32 1000000, i32* %153)
%160 = icmp eq i32* %159, null
br i1 %160, label %178, label %161
161: ; preds = %155, %175
%162 = load i8, i8* %158
%163 = icmp eq i8 %162, 62
br i1 %163, label %175, label %164
164: ; preds = %161
%165 = call i32 @strlen(i8* %158)
%166 = add nsw i32 %165, -1
%167 = sext i32 %166 to i64
%168 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %157, i64 0, i64 %167
%169 = load i8, i8* %168
%170 = icmp eq i8 %169, 10
br i1 %170, label %171, label %172
171: ; preds = %164
store i8 0, i8* %168
br label %172
172: ; preds = %171, %164
%173 = call i32 @strcpy(i8* %108, i8* %158)
%174 = call i32 @fclose(i32* %153)
br label %175
175: ; preds = %172, %161
%176 = call i32* @fgets(i8* %158, i32 1000000, i32* %153)
%177 = icmp eq i32* %176, null
br i1 %177, label %178, label %161
178: ; preds = %175, %155
br label %181
179: ; preds = %150
%180 = call i32 @perror(i8* %152)
br label %181
181: ; preds = %179, %178
%182 = call i32 @strlen(i8* %109)
%183 = icmp sgt i32 %182, 0
br i1 %183, label %184, label %252
184: ; preds = %181
%185 = zext i32 %182 to i64
%186 = and i64 %185, 1
%187 = icmp eq i32 %182, 1
br i1 %187, label %231, label %188
188: ; preds = %184
%189 = and i64 %185, 4294967294
br label %190
190: ; preds = %225, %188
%191 = phi i64 [ 0, %188 ], [ %228, %225 ]
%192 = phi i32 [ 0, %188 ], [ %227, %225 ]
%193 = phi i32 [ 0, %188 ], [ %226, %225 ]
%194 = phi i64 [ 0, %188 ], [ %229, %225 ]
%195 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %106, i64 0, i64 %191
%196 = load i8, i8* %195
%197 = icmp eq i8 %196, 78
br i1 %197, label %202, label %198
198: ; preds = %190
%199 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %107, i64 0, i64 %191
%200 = load i8, i8* %199
%201 = icmp eq i8 %200, 78
br i1 %201, label %202, label %204
202: ; preds = %198, %190
%203 = add nsw i32 %192, 1
br label %208
204: ; preds = %198
%205 = icmp ne i8 %196, %200
%206 = zext i1 %205 to i32
%207 = add nsw i32 %193, %206
br label %208
208: ; preds = %204, %202
%209 = phi i32 [ %193, %202 ], [ %207, %204 ]
%210 = phi i32 [ %203, %202 ], [ %192, %204 ]
%211 = or i64 %191, 1
%212 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %106, i64 0, i64 %211
%213 = load i8, i8* %212
%214 = icmp eq i8 %213, 78
br i1 %214, label %223, label %215
215: ; preds = %208
%216 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %107, i64 0, i64 %211
%217 = load i8, i8* %216
%218 = icmp eq i8 %217, 78
br i1 %218, label %223, label %219
219: ; preds = %215
%220 = icmp ne i8 %213, %217
%221 = zext i1 %220 to i32
%222 = add nsw i32 %209, %221
br label %225
223: ; preds = %215, %208
%224 = add nsw i32 %210, 1
br label %225
225: ; preds = %223, %219
%226 = phi i32 [ %209, %223 ], [ %222, %219 ]
%227 = phi i32 [ %224, %223 ], [ %210, %219 ]
%228 = add nuw nsw i64 %191, 2
%229 = add i64 %194, 2
%230 = icmp eq i64 %229, %189
br i1 %230, label %231, label %190
231: ; preds = %225, %184
%232 = phi i32 [ undef, %184 ], [ %226, %225 ]
%233 = phi i32 [ undef, %184 ], [ %227, %225 ]
%234 = phi i64 [ 0, %184 ], [ %228, %225 ]
%235 = phi i32 [ 0, %184 ], [ %227, %225 ]
%236 = phi i32 [ 0, %184 ], [ %226, %225 ]
%237 = icmp eq i64 %186, 0
br i1 %237, label %252, label %238
238: ; preds = %231
%239 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %106, i64 0, i64 %234
%240 = load i8, i8* %239
%241 = icmp eq i8 %240, 78
br i1 %241, label %250, label %242
242: ; preds = %238
%243 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %107, i64 0, i64 %234
%244 = load i8, i8* %243
%245 = icmp eq i8 %244, 78
br i1 %245, label %250, label %246
246: ; preds = %242
%247 = icmp ne i8 %240, %244
%248 = zext i1 %247 to i32
%249 = add nsw i32 %236, %248
br label %252
250: ; preds = %242, %238
%251 = add nsw i32 %235, 1
br label %252
252: ; preds = %231, %250, %246, %181
%253 = phi i32 [ 0, %181 ], [ %232, %231 ], [ %236, %250 ], [ %249, %246 ]
%254 = phi i32 [ 0, %181 ], [ %233, %231 ], [ %251, %250 ], [ %235, %246 ]
%255 = sub nsw i32 %182, %254
%256 = sitofp i32 %253 to float
%257 = sitofp i32 %255 to float
%258 = fdiv float %256, %257
%259 = call float @llvm.fmuladd.f32(float %258, float 0xBFF5555560000000, float 1.000000e+00)
%260 = fptosi float %259 to i32
%261 = call float @log(i32 %260)
%262 = fmul float %261, -7.500000e-01
%263 = getelementptr inbounds i8, i8* %65, i64 %151
%264 = fpext float %262 to double
%265 = call i32 (i32*, i8*, ...) @fprintf(i32* %35, i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.12, i64 0, i64 0), i8* %146, i8* %263, i32 %253, i32 %255, double %264)
br label %266
266: ; preds = %147, %252
%267 = add nuw nsw i64 %148, 1
%268 = icmp eq i64 %267, %112
br i1 %268, label %269, label %147
269: ; preds = %266
%270 = add nuw nsw i64 %114, 1
%271 = icmp eq i64 %270, %112
br i1 %271, label %272, label %113
272: ; preds = %269, %101, %103
%273 = call i32 @printf(i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.13, i64 0, i64 0), i8* %4)
%274 = call i32 (i32*, i8*, ...) @fprintf(i32* %22, i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.13, i64 0, i64 0), i8* %4)
ret i32 0
}