#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 *, 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 category[arg_len];
  strcpy(category, argv[4]);
  char category_file[arg_len];
  strcpy(category_file, argv[5]);
  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, "_");
  strcat(output_file_name, category_file);
  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_");
      strcat(isolate_file_name_array[isolate_count], category_file);
      strcat(isolate_file_name_array[isolate_count], "_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 intergenic annotation %s di calculated.\n", species,
         category_file);
  fprintf(log_file, "%s intergenic annotation %s di calculated.\n", species,
          category_file);
  return 0;
}


x86 assembly (clang, -O0):
<main>:
push   %rbp
mov    %rsp,%rbp
sub    $0x1f0,%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,-0x170(%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,-0x160(%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,-0x180(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x38(%rbp)
mov    -0x10(%rbp),%rax
mov    0x18(%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,%rsp
mov    %rax,-0x40(%rbp)
mov    -0x10(%rbp),%rax
mov    0x20(%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,-0x190(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x48(%rbp)
mov    -0x10(%rbp),%rax
mov    0x28(%rax),%rsi
call   1030 <strcpy@plt>
mov    -0x180(%rbp),%rsi
mov    -0x14(%rbp),%eax
mov    %rax,%rcx
add    $0xf,%rcx
and    $0xfffffffffffffff0,%rcx
mov    %rsp,%rdi
sub    %rcx,%rdi
mov    %rdi,-0x198(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x50(%rbp)
call   1030 <strcpy@plt>
mov    -0x198(%rbp),%rdi
lea    0xd25(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x198(%rbp),%rdi
lea    0xd97(%rip),%rsi
call   10a0 <fopen@plt>
mov    -0x180(%rbp),%rsi
mov    %rax,-0x58(%rbp)
mov    -0x14(%rbp),%eax
mov    %rax,%rcx
add    $0xf,%rcx
and    $0xfffffffffffffff0,%rcx
mov    %rsp,%rdi
sub    %rcx,%rdi
mov    %rdi,-0x188(%rbp)
mov    %rdi,%rsp
mov    %rax,-0x60(%rbp)
call   1030 <strcpy@plt>
mov    -0x188(%rbp),%rdi
lea    0xcdf(%rip),%rsi
mov    %rsi,-0x178(%rbp)
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
mov    -0x160(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
lea    0xd1e(%rip),%rsi
mov    %rsi,-0x158(%rbp)
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
mov    -0x170(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
lea    0xce9(%rip),%rsi
mov    %rsi,-0x168(%rbp)
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
mov    -0x160(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
mov    -0x158(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
mov    -0x170(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
mov    -0x168(%rbp),%rsi
call   10c0 <strcat@plt>
mov    -0x190(%rbp),%rsi
mov    -0x188(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
lea    0xc17(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x188(%rbp),%rdi
lea    0xc16(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0x68(%rbp)
mov    -0x68(%rbp),%rdi
lea    0xc04(%rip),%rsi
xor    %eax,%eax
call   1080 <fprintf@plt>
mov    -0x180(%rbp),%rsi
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,-0x70(%rbp)
call   1030 <strcpy@plt>
mov    -0x178(%rbp),%rsi
mov    -0x150(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x160(%rbp),%rsi
mov    -0x150(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x158(%rbp),%rsi
mov    -0x150(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x170(%rbp),%rsi
mov    -0x150(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x168(%rbp),%rsi
mov    -0x150(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x160(%rbp),%rsi
mov    -0x150(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x158(%rbp),%rsi
mov    -0x150(%rbp),%rdi
call   10c0 <strcat@plt>
mov    -0x150(%rbp),%rdi
lea    0xb67(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x150(%rbp),%rdi
mov    -0x14(%rbp),%eax
mov    %rax,-0x148(%rbp)
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x140(%rbp)
mov    %rcx,%rsp
mov    %rax,-0x78(%rbp)
movl   $0x0,-0x7c(%rbp)
lea    0xb31(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0x88(%rbp)
cmpq   $0x0,-0x88(%rbp)
je     15a8 <main+0x408>
jmp    1563 <main+0x3c3>
mov    -0x140(%rbp),%rdi
mov    -0x148(%rbp),%rax
mov    %eax,%esi
mov    -0x88(%rbp),%rdx
call   1070 <fgets@plt>
cmp    $0x0,%rax
je     1597 <main+0x3f7>
mov    -0x7c(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x7c(%rbp)
jmp    1563 <main+0x3c3>
mov    -0x88(%rbp),%rdi
call   1040 <fclose@plt>
jmp    15b4 <main+0x414>
mov    -0x150(%rbp),%rdi
call   10b0 <perror@plt>
mov    -0x150(%rbp),%rdi
mov    -0x7c(%rbp),%eax
mov    %eax,%ecx
mov    -0x14(%rbp),%eax
mov    %rax,-0x1b8(%rbp)
mov    %rcx,%rsi
imul   %rax,%rsi
add    $0xf,%rsi
and    $0xfffffffffffffff0,%rsi
mov    %rsp,%rdx
sub    %rsi,%rdx
mov    %rdx,-0x1b0(%rbp)
mov    %rdx,%rsp
mov    %rcx,-0x90(%rbp)
mov    %rax,-0x98(%rbp)
mov    -0x7c(%rbp),%eax
mov    %eax,%ecx
mov    -0x14(%rbp),%eax
mov    %rax,-0x1a8(%rbp)
mov    %rcx,%rsi
imul   %rax,%rsi
add    $0xf,%rsi
and    $0xfffffffffffffff0,%rsi
mov    %rsp,%rdx
sub    %rsi,%rdx
mov    %rdx,-0x1a0(%rbp)
mov    %rdx,%rsp
mov    %rcx,-0xa0(%rbp)
mov    %rax,-0xa8(%rbp)
movl   $0x0,-0x7c(%rbp)
lea    0xa34(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0xb0(%rbp)
cmpq   $0x0,-0xb0(%rbp)
je     18d1 <main+0x731>
jmp    1660 <main+0x4c0>
mov    -0x140(%rbp),%rdi
mov    -0x148(%rbp),%rax
mov    %eax,%esi
mov    -0xb0(%rbp),%rdx
call   1070 <fgets@plt>
cmp    $0x0,%rax
je     18c0 <main+0x720>
mov    -0x140(%rbp),%rdi
call   1050 <strlen@plt>
mov    %eax,%ecx
mov    -0x140(%rbp),%rax
mov    %ecx,-0xb4(%rbp)
mov    -0xb4(%rbp),%ecx
sub    $0x1,%ecx
movslq %ecx,%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0xa,%eax
jne    16d1 <main+0x531>
mov    -0x140(%rbp),%rax
mov    -0xb4(%rbp),%ecx
sub    $0x1,%ecx
movslq %ecx,%rcx
movb   $0x0,(%rax,%rcx,1)
mov    -0x140(%rbp),%rsi
mov    -0x1b0(%rbp),%rdi
mov    -0x1b8(%rbp),%rcx
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   1030 <strcpy@plt>
mov    -0x180(%rbp),%rsi
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   1030 <strcpy@plt>
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x8e3(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x160(%rbp),%rsi
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x905(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x170(%rbp),%rsi
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x8b3(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x160(%rbp),%rsi
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x85e(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x190(%rbp),%rsi
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x821(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x140(%rbp),%rsi
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10c0 <strcat@plt>
mov    -0x1a8(%rbp),%rcx
mov    -0x1a0(%rbp),%rdi
movslq -0x7c(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x7df(%rip),%rsi
call   10c0 <strcat@plt>
mov    -0x7c(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x7c(%rbp)
jmp    1660 <main+0x4c0>
mov    -0xb0(%rbp),%rdi
call   1040 <fclose@plt>
jmp    18dd <main+0x73d>
mov    -0x150(%rbp),%rdi
call   10b0 <perror@plt>
movl   $0xf4240,-0xc4(%rbp)
mov    -0xc4(%rbp),%eax
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x1c8(%rbp)
mov    %rcx,%rsp
mov    %rax,-0xd0(%rbp)
mov    -0xc4(%rbp),%eax
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x1c0(%rbp)
mov    %rcx,%rsp
mov    %rax,-0xd8(%rbp)
movl   $0x0,-0xdc(%rbp)
movl   $0x0,-0xb8(%rbp)
mov    -0xb8(%rbp),%eax
cmp    -0x7c(%rbp),%eax
jge    1e18 <main+0xc78>
mov    -0x1a0(%rbp),%rdi
mov    -0x1a8(%rbp),%rcx
movslq -0xb8(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x6f8(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0xe8(%rbp)
cmpq   $0x0,-0xe8(%rbp)
je     1a8c <main+0x8ec>
mov    -0xc4(%rbp),%eax
mov    %rax,-0x1d8(%rbp)
mov    %rsp,%rcx
mov    %rcx,-0xf0(%rbp)
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x1d0(%rbp)
mov    %rcx,%rsp
mov    %rax,-0xf8(%rbp)
mov    -0x1d0(%rbp),%rdi
mov    -0x1d8(%rbp),%rax
mov    %eax,%esi
mov    -0xe8(%rbp),%rdx
call   1070 <fgets@plt>
cmp    $0x0,%rax
je     1a7d <main+0x8dd>
mov    -0x1d0(%rbp),%rax
movsbl (%rax),%eax
cmp    $0x3e,%eax
je     1a78 <main+0x8d8>
mov    -0x1d0(%rbp),%rdi
call   1050 <strlen@plt>
mov    %eax,%ecx
mov    -0x1d0(%rbp),%rax
mov    %ecx,-0xfc(%rbp)
mov    -0xfc(%rbp),%ecx
sub    $0x1,%ecx
mov    %ecx,-0xfc(%rbp)
movslq -0xfc(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0xa,%eax
jne    1a59 <main+0x8b9>
mov    -0x1d0(%rbp),%rax
movslq -0xfc(%rbp),%rcx
movb   $0x0,(%rax,%rcx,1)
mov    -0x1d0(%rbp),%rsi
mov    -0x1c8(%rbp),%rdi
call   1030 <strcpy@plt>
mov    -0xe8(%rbp),%rdi
call   1040 <fclose@plt>
jmp    19d0 <main+0x830>
mov    -0xf0(%rbp),%rax
mov    %rax,%rsp
jmp    1aad <main+0x90d>
mov    -0x1a0(%rbp),%rdi
mov    -0x1a8(%rbp),%rcx
movslq -0xb8(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10b0 <perror@plt>
movl   $0x0,-0xbc(%rbp)
mov    -0xbc(%rbp),%eax
cmp    -0x7c(%rbp),%eax
jge    1dff <main+0xc5f>
mov    -0xb8(%rbp),%eax
cmp    -0xbc(%rbp),%eax
jle    1de6 <main+0xc46>
mov    -0x1a0(%rbp),%rdi
mov    -0x1a8(%rbp),%rcx
movslq -0xbc(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
lea    0x57a(%rip),%rsi
call   10a0 <fopen@plt>
mov    %rax,-0x108(%rbp)
cmpq   $0x0,-0x108(%rbp)
je     1c0a <main+0xa6a>
mov    -0xc4(%rbp),%eax
mov    %rax,-0x1e8(%rbp)
mov    %rsp,%rcx
mov    %rcx,-0x110(%rbp)
mov    %rax,%rdx
add    $0xf,%rdx
and    $0xfffffffffffffff0,%rdx
mov    %rsp,%rcx
sub    %rdx,%rcx
mov    %rcx,-0x1e0(%rbp)
mov    %rcx,%rsp
mov    %rax,-0x118(%rbp)
mov    -0x1e0(%rbp),%rdi
mov    -0x1e8(%rbp),%rax
mov    %eax,%esi
mov    -0x108(%rbp),%rdx
call   1070 <fgets@plt>
cmp    $0x0,%rax
je     1bfb <main+0xa5b>
mov    -0x1e0(%rbp),%rax
movsbl (%rax),%eax
cmp    $0x3e,%eax
je     1bf6 <main+0xa56>
mov    -0x1e0(%rbp),%rdi
call   1050 <strlen@plt>
mov    %eax,%ecx
mov    -0x1e0(%rbp),%rax
mov    %ecx,-0x11c(%rbp)
mov    -0x11c(%rbp),%ecx
sub    $0x1,%ecx
mov    %ecx,-0x11c(%rbp)
movslq -0x11c(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0xa,%eax
jne    1bd7 <main+0xa37>
mov    -0x1e0(%rbp),%rax
movslq -0x11c(%rbp),%rcx
movb   $0x0,(%rax,%rcx,1)
mov    -0x1e0(%rbp),%rsi
mov    -0x1c0(%rbp),%rdi
call   1030 <strcpy@plt>
mov    -0x108(%rbp),%rdi
call   1040 <fclose@plt>
jmp    1b4e <main+0x9ae>
mov    -0x110(%rbp),%rax
mov    %rax,%rsp
jmp    1c2b <main+0xa8b>
mov    -0x1a0(%rbp),%rdi
mov    -0x1a8(%rbp),%rcx
movslq -0xbc(%rbp),%rax
imul   %rcx,%rax
add    %rax,%rdi
call   10b0 <perror@plt>
mov    -0x1c8(%rbp),%rdi
call   1050 <strlen@plt>
mov    %eax,-0x120(%rbp)
movl   $0x0,-0x124(%rbp)
movl   $0x0,-0x128(%rbp)
movl   $0x0,-0xc0(%rbp)
mov    -0xc0(%rbp),%eax
cmp    -0x120(%rbp),%eax
jge    1d10 <main+0xb70>
mov    -0x1c8(%rbp),%rax
movslq -0xc0(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0x4e,%eax
je     1ca3 <main+0xb03>
mov    -0x1c0(%rbp),%rax
movslq -0xc0(%rbp),%rcx
movsbl (%rax,%rcx,1),%eax
cmp    $0x4e,%eax
jne    1cb7 <main+0xb17>
mov    -0x128(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x128(%rbp)
jmp    1cf7 <main+0xb57>
mov    -0x1c0(%rbp),%rcx
mov    -0x1c8(%rbp),%rax
movslq -0xc0(%rbp),%rdx
movsbl (%rax,%rdx,1),%eax
movslq -0xc0(%rbp),%rdx
movsbl (%rcx,%rdx,1),%ecx
cmp    %ecx,%eax
je     1cf2 <main+0xb52>
mov    -0x124(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0x124(%rbp)
jmp    1cf7 <main+0xb57>
jmp    1cfc <main+0xb5c>
mov    -0xc0(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0xc0(%rbp)
jmp    1c5b <main+0xabb>
mov    -0x120(%rbp),%eax
sub    -0x128(%rbp),%eax
mov    %eax,-0x12c(%rbp)
cvtsi2ssl -0x124(%rbp),%xmm0
ff
cvtsi2ssl -0x12c(%rbp),%xmm1
ff
divss  %xmm1,%xmm0
movss  %xmm0,-0x130(%rbp)
ff
movss  -0x130(%rbp),%xmm0
ff
movss  0x2b6(%rip),%xmm1
mulss  %xmm1,%xmm0
movss  0x2ae(%rip),%xmm1
addss  %xmm1,%xmm0
cvttss2si %xmm0,%edi
call   1090 <log@plt>
mov    -0x1b8(%rbp),%rsi
mov    -0x1b0(%rbp),%rcx
movaps %xmm0,%xmm1
movss  0x280(%rip),%xmm0
mulss  %xmm1,%xmm0
movss  %xmm0,-0x134(%rbp)
ff
mov    -0x68(%rbp),%rdi
movslq -0xb8(%rbp),%rax
imul   %rsi,%rax
mov    %rcx,%rdx
add    %rax,%rdx
movslq -0xbc(%rbp),%rax
imul   %rsi,%rax
add    %rax,%rcx
mov    -0x124(%rbp),%r8d
mov    -0x12c(%rbp),%r9d
movss  -0x134(%rbp),%xmm0
ff
cvtss2sd %xmm0,%xmm0
lea    0x2c3(%rip),%rsi
mov    $0x1,%al
call   1080 <fprintf@plt>
mov    -0xdc(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0xdc(%rbp)
jmp    1deb <main+0xc4b>
mov    -0xbc(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0xbc(%rbp)
jmp    1ab7 <main+0x917>
jmp    1e04 <main+0xc64>
mov    -0xb8(%rbp),%eax
add    $0x1,%eax
mov    %eax,-0xb8(%rbp)
jmp    194b <main+0x7ab>
mov    -0x190(%rbp),%rdx
mov    -0x170(%rbp),%rsi
lea    0x279(%rip),%rdi
call   1060 <printf@plt>
mov    -0x170(%rbp),%rdx
mov    -0x190(%rbp),%rcx
mov    -0x58(%rbp),%rdi
lea    0x25b(%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    $0x23b8,%rsp
mov    %rsi,%rbx
mov    0x8(%rsi),%rsi
lea    -0xc40(%rbp),%r12
mov    %r12,%rdi
call   1030 <strcpy@plt>
mov    0x10(%rbx),%rsi
lea    -0x1810(%rbp),%rdi
mov    %rdi,%r14
call   1030 <strcpy@plt>
mov    0x18(%rbx),%rsi
lea    -0x1420(%rbp),%r15
mov    %r15,%rdi
call   1030 <strcpy@plt>
mov    0x20(%rbx),%rsi
lea    -0x23e0(%rbp),%rdi
call   1030 <strcpy@plt>
mov    0x28(%rbx),%rsi
lea    -0x850(%rbp),%rdi
call   1030 <strcpy@plt>
lea    -0x1ff0(%rbp),%rbx
mov    %rbx,%rdi
mov    %r15,%rsi
call   1030 <strcpy@plt>
lea    0xdd3(%rip),%rsi
mov    %rbx,%rdi
call   10c0 <strcat@plt>
lea    0xe49(%rip),%rsi
mov    %rbx,%rdi
call   10a0 <fopen@plt>
mov    %rax,-0x58(%rbp)
lea    -0x1c00(%rbp),%r13
mov    %r13,%rdi
mov    %r15,%rsi
call   1030 <strcpy@plt>
lea    0xdb1(%rip),%rsi
mov    %r13,%rdi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %r14,%rbx
mov    %r14,%rsi
call   10c0 <strcat@plt>
lea    0xe00(%rip),%r15
mov    %r13,%rdi
mov    %r15,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %r12,%rsi
call   10c0 <strcat@plt>
lea    0xddb(%rip),%r14
mov    %r13,%rdi
mov    %r14,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %rbx,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %r15,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %r12,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
mov    %r14,%rsi
call   10c0 <strcat@plt>
mov    %r13,%rdi
lea    -0x850(%rbp),%rsi
call   10c0 <strcat@plt>
lea    0xd35(%rip),%rsi
mov    %r13,%rdi
call   10c0 <strcat@plt>
lea    0xd38(%rip),%rsi
mov    %r13,%rdi
call   10a0 <fopen@plt>
lea    0xd2b(%rip),%rdi
mov    $0x2a,%esi
mov    $0x1,%edx
mov    %rax,-0x60(%rbp)
mov    %rax,%rcx
call   10d0 <fwrite@plt>
lea    -0x460(%rbp),%rbx
mov    %rbx,%rdi
lea    -0x1420(%rbp),%rsi
call   1030 <strcpy@plt>
mov    %rbx,%rdi
lea    0xcd6(%rip),%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
lea    -0x1810(%rbp),%r12
mov    %r12,%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    %r15,%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
lea    -0xc40(%rbp),%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    %r14,%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    %r12,%rsi
call   10c0 <strcat@plt>
mov    %rbx,%rdi
mov    %r15,%rsi
call   10c0 <strcat@plt>
lea    0xcc7(%rip),%rsi
mov    %rbx,%rdi
call   10c0 <strcat@plt>
lea    0xcc5(%rip),%rsi
mov    %rbx,%rdi
call   10a0 <fopen@plt>
test   %rax,%rax
je     1888 <main+0x6d8>
mov    %rax,%r15
mov    $0xffffffff,%ebx
lea    -0x1030(%rbp),%r14
mov    %r14,%rdi
mov    $0x3e8,%esi
mov    %r15,%rdx
call   1070 <fgets@plt>
add    $0x1,%ebx
test   %rax,%rax
jne    13d0 <main+0x220>
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    0xc53(%rip),%rsi
lea    -0x460(%rbp),%rdi
call   10a0 <fopen@plt>
test   %rax,%rax
je     189b <main+0x6eb>
lea    -0x1030(%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     157d <main+0x3cd>
lea    -0x1810(%rbp),%r13
mov    -0x40(%rbp),%r12
mov    -0x38(%rbp),%r15
jmp    155b <main+0x3ab>
cs nopw 0x0(%rax,%rax,1)
nopl   0x0(%rax)
mov    %r12,%rdi
mov    %rbx,%rsi
call   1030 <strcpy@plt>
mov    %r15,%rdi
lea    -0x1420(%rbp),%rsi
call   1030 <strcpy@plt>
mov    %r15,%rdi
lea    0xb7a(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
mov    %r13,%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xbcc(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    -0xc40(%rbp),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xba6(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
mov    %r13,%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xb81(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    -0x850(%rbp),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xb70(%rip),%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
mov    %rbx,%rsi
call   10c0 <strcat@plt>
mov    %r15,%rdi
lea    0xb5e(%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     157d <main+0x3cd>
mov    %rbx,%rdi
call   1050 <strlen@plt>
cltq
cmpb   $0xa,-0x1(%rax,%rbx,1)
jne    1480 <main+0x2d0>
movb   $0x0,-0x1031(%rbp,%rax,1)
jmp    1480 <main+0x2d0>
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     18a7 <main+0x6f7>
mov    %r14d,%eax
mov    %rax,-0x30(%rbp)
xor    %eax,%eax
jmp    15ce <main+0x41e>
cs nopw 0x0(%rax,%rax,1)
xchg   %ax,%ax
add    $0x1,%rax
cmp    -0x30(%rbp),%rax
je     18a7 <main+0x6f7>
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    0xa86(%rip),%rsi
call   10a0 <fopen@plt>
test   %rax,%rax
je     187b <main+0x6cb>
mov    %rax,%r14
mov    %rsp,%r15
mov    %rsp,%rbx
add    $0xfffffffffff0bdc0,%rbx
mov    %rbx,%rsp
jmp    1633 <main+0x483>
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     1670 <main+0x4c0>
cmpb   $0x3e,(%rbx)
je     1633 <main+0x483>
mov    %rbx,%rdi
call   1050 <strlen@plt>
cltq
cmpb   $0xa,-0x1(%rax,%rbx,1)
jne    1620 <main+0x470>
movb   $0x0,-0x1(%rbx,%rax,1)
jmp    1620 <main+0x470>
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    16ff <main+0x54f>
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  0x956(%rip),%xmm0
addss  0x952(%rip),%xmm0
cvttss2si %xmm0,%edi
mov    %eax,%ebx
call   1090 <log@plt>
mulss  0x943(%rip),%xmm0
mov    -0x70(%rbp),%rcx
add    -0x40(%rbp),%rcx
cvtss2sd %xmm0,%xmm0
mov    -0x60(%rbp),%rdi
lea    0x9b7(%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     15c0 <main+0x410>
cmp    %r15,%rax
jbe    16f1 <main+0x541>
imul   $0x3e8,%r15,%rcx
mov    -0x38(%rbp),%rax
mov    %rcx,-0x70(%rbp)
lea    (%rax,%rcx,1),%rbx
mov    %rbx,%rdi
lea    0x954(%rip),%rsi
call   10a0 <fopen@plt>
test   %rax,%rax
je     186e <main+0x6be>
mov    %rax,%r14
mov    %rsp,-0x68(%rbp)
mov    %rsp,%rbx
add    $0xfffffffffff0bdc0,%rbx
mov    %rbx,%rsp
jmp    1763 <main+0x5b3>
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     17a0 <main+0x5f0>
cmpb   $0x3e,(%rbx)
je     1763 <main+0x5b3>
mov    %rbx,%rdi
call   1050 <strlen@plt>
cltq
cmpb   $0xa,-0x1(%rax,%rbx,1)
jne    1750 <main+0x5a0>
movb   $0x0,-0x1(%rbx,%rax,1)
jmp    1750 <main+0x5a0>
cs nopw 0x0(%rax,%rax,1)
nop
mov    -0x68(%rbp),%rsp
mov    %r13,%rdi
call   1050 <strlen@plt>
test   %eax,%eax
jle    1688 <main+0x4d8>
mov    %eax,%r8d
cmp    $0x1,%eax
jne    17e8 <main+0x638>
xor    %ecx,%ecx
xor    %esi,%esi
xor    %r14d,%r14d
test   $0x1,%r8b
je     168d <main+0x4dd>
mov    0x0(%r13,%rcx,1),%dl
cmp    $0x4e,%dl
je     17e0 <main+0x630>
mov    (%r12,%rcx,1),%cl
cmp    $0x4e,%cl
jne    185e <main+0x6ae>
add    $0x1,%esi
jmp    168d <main+0x4dd>
mov    %r8d,%r9d
and    $0xfffffffe,%r9d
xor    %ecx,%ecx
xor    %esi,%esi
xor    %r14d,%r14d
jmp    180c <main+0x65c>
nopl   0x0(%rax,%rax,1)
add    $0x1,%esi
add    $0x2,%rcx
cmp    %rcx,%r9
je     17c3 <main+0x613>
movzbl 0x0(%r13,%rcx,1),%edx
cmp    $0x4e,%dl
je     1821 <main+0x671>
movzbl (%r12,%rcx,1),%ebx
cmp    $0x4e,%bl
jne    1830 <main+0x680>
add    $0x1,%esi
jmp    183b <main+0x68b>
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     1800 <main+0x650>
movzbl 0x1(%r12,%rcx,1),%ebx
cmp    $0x4e,%bl
je     1800 <main+0x650>
xor    %edi,%edi
cmp    %bl,%dl
setne  %dil
add    %edi,%r14d
jmp    1803 <main+0x653>
xor    %edi,%edi
cmp    %cl,%dl
setne  %dil
add    %edi,%r14d
jmp    168d <main+0x4dd>
mov    %rbx,%rdi
call   10b0 <perror@plt>
jmp    17a4 <main+0x5f4>
mov    %rbx,%rdi
call   10b0 <perror@plt>
jmp    1673 <main+0x4c3>
lea    -0x460(%rbp),%rdi
call   10b0 <perror@plt>
xor    %ebx,%ebx
jmp    13f0 <main+0x240>
lea    -0x460(%rbp),%rdi
call   10b0 <perror@plt>
lea    0x7f8(%rip),%rbx
lea    -0xc40(%rbp),%r14
lea    -0x850(%rbp),%r15
mov    %rbx,%rdi
mov    %r14,%rsi
mov    %r15,%rdx
call   1060 <printf@plt>
mov    -0x58(%rbp),%rdi
mov    %rbx,%rsi
mov    %r14,%rdx
mov    %r15,%rcx
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 = [13 x i8] c"/Intergenic_\00"
@.str.11 = [8 x i8] c"_files/\00"
@.str.12 = [7 x i8] c".fasta\00"
@.str.13 = [19 x i8] c"%s,%s,%i,%i,%0.6f\0A\00"
@.str.14 = [44 x i8] c"%s intergenic annotation %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 i64
%13 = alloca i64
%14 = alloca i32*
%15 = alloca i64
%16 = alloca i32*
%17 = alloca i64
%18 = alloca i64
%19 = alloca i32
%20 = alloca i32*
%21 = alloca i64
%22 = alloca i64
%23 = alloca i64
%24 = alloca i64
%25 = alloca i32*
%26 = alloca i32
%27 = alloca i32
%28 = alloca i32
%29 = alloca i32
%30 = alloca i32
%31 = alloca i64
%32 = alloca i64
%33 = alloca i32
%34 = alloca i32*
%35 = alloca i8*
%36 = alloca i64
%37 = alloca i32
%38 = alloca i32*
%39 = alloca i8*
%40 = alloca i64
%41 = alloca i32
%42 = alloca i32
%43 = alloca i32
%44 = alloca i32
%45 = alloca i32
%46 = alloca float
%47 = alloca float
store i32 0, i32* %3
store i32 %0, i32* %4
store i8** %1, i8*** %5
store i32 1000, i32* %6
%48 = load i32, i32* %6
%49 = zext i32 %48 to i64
%50 = call i8* @llvm.stacksave()
store i8* %50, i8** %7
%51 = alloca i8, i64 %49
store i64 %49, i64* %8
%52 = load i8**, i8*** %5
%53 = getelementptr inbounds i8*, i8** %52, i64 1
%54 = load i8*, i8** %53
%55 = call i32 @strcpy(i8* %51, i8* %54)
%56 = load i32, i32* %6
%57 = zext i32 %56 to i64
%58 = alloca i8, i64 %57
store i64 %57, i64* %9
%59 = load i8**, i8*** %5
%60 = getelementptr inbounds i8*, i8** %59, i64 2
%61 = load i8*, i8** %60
%62 = call i32 @strcpy(i8* %58, i8* %61)
%63 = load i32, i32* %6
%64 = zext i32 %63 to i64
%65 = alloca i8, i64 %64
store i64 %64, i64* %10
%66 = load i8**, i8*** %5
%67 = getelementptr inbounds i8*, i8** %66, i64 3
%68 = load i8*, i8** %67
%69 = call i32 @strcpy(i8* %65, i8* %68)
%70 = load i32, i32* %6
%71 = zext i32 %70 to i64
%72 = alloca i8, i64 %71
store i64 %71, i64* %11
%73 = load i8**, i8*** %5
%74 = getelementptr inbounds i8*, i8** %73, i64 4
%75 = load i8*, i8** %74
%76 = call i32 @strcpy(i8* %72, i8* %75)
%77 = load i32, i32* %6
%78 = zext i32 %77 to i64
%79 = alloca i8, i64 %78
store i64 %78, i64* %12
%80 = load i8**, i8*** %5
%81 = getelementptr inbounds i8*, i8** %80, i64 5
%82 = load i8*, i8** %81
%83 = call i32 @strcpy(i8* %79, i8* %82)
%84 = load i32, i32* %6
%85 = zext i32 %84 to i64
%86 = alloca i8, i64 %85
store i64 %85, i64* %13
%87 = call i32 @strcpy(i8* %86, i8* %65)
%88 = call i32 @strcat(i8* %86, i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str, i64 0, i64 0))
%89 = call i32* @fopen(i8* %86, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.1, i64 0, i64 0))
store i32* %89, i32** %14
%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* %65)
%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* %58)
%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* %51)
%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* %58)
%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* %51)
%102 = call i32 @strcat(i8* %92, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%103 = call i32 @strcat(i8* %92, i8* %79)
%104 = call i32 @strcat(i8* %92, i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str.5, i64 0, i64 0))
%105 = call i32* @fopen(i8* %92, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.6, i64 0, i64 0))
store i32* %105, i32** %16
%106 = load i32*, i32** %16
%107 = call i32 (i32*, i8*, ...) @fprintf(i32* %106, i8* getelementptr inbounds ([43 x i8], [43 x i8]* @.str.7, i64 0, i64 0))
%108 = load i32, i32* %6
%109 = zext i32 %108 to i64
%110 = alloca i8, i64 %109
store i64 %109, i64* %17
%111 = call i32 @strcpy(i8* %110, i8* %65)
%112 = call i32 @strcat(i8* %110, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%113 = call i32 @strcat(i8* %110, i8* %58)
%114 = call i32 @strcat(i8* %110, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%115 = call i32 @strcat(i8* %110, i8* %51)
%116 = call i32 @strcat(i8* %110, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%117 = call i32 @strcat(i8* %110, i8* %58)
%118 = call i32 @strcat(i8* %110, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%119 = call i32 @strcat(i8* %110, i8* getelementptr inbounds ([13 x i8], [13 x i8]* @.str.8, i64 0, i64 0))
%120 = load i32, i32* %6
%121 = zext i32 %120 to i64
%122 = alloca i8, i64 %121
store i64 %121, i64* %18
store i32 0, i32* %19
%123 = call i32* @fopen(i8* %110, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
store i32* %123, i32** %20
%124 = load i32*, i32** %20
%125 = icmp ne i32* %124, null
br i1 %125, label %126, label %138
126: ; preds = %2
br label %127
127: ; preds = %132, %126
%128 = trunc i64 %121 to i32
%129 = load i32*, i32** %20
%130 = call i32* @fgets(i8* %122, i32 %128, i32* %129)
%131 = icmp ne i32* %130, null
br i1 %131, label %132, label %135
132: ; preds = %127
%133 = load i32, i32* %19
%134 = add nsw i32 %133, 1
store i32 %134, i32* %19
br label %127
135: ; preds = %127
%136 = load i32*, i32** %20
%137 = call i32 @fclose(i32* %136)
br label %140
138: ; preds = %2
%139 = call i32 @perror(i8* %110)
br label %140
140: ; preds = %138, %135
%141 = load i32, i32* %19
%142 = zext i32 %141 to i64
%143 = load i32, i32* %6
%144 = zext i32 %143 to i64
%145 = mul nuw i64 %142, %144
%146 = alloca i8, i64 %145
store i64 %142, i64* %21
store i64 %144, i64* %22
%147 = load i32, i32* %19
%148 = zext i32 %147 to i64
%149 = load i32, i32* %6
%150 = zext i32 %149 to i64
%151 = mul nuw i64 %148, %150
%152 = alloca i8, i64 %151
store i64 %148, i64* %23
store i64 %150, i64* %24
store i32 0, i32* %19
%153 = call i32* @fopen(i8* %110, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
store i32* %153, i32** %25
%154 = load i32*, i32** %25
%155 = icmp ne i32* %154, null
br i1 %155, label %156, label %247
156: ; preds = %140
br label %157
157: ; preds = %176, %156
%158 = trunc i64 %121 to i32
%159 = load i32*, i32** %25
%160 = call i32* @fgets(i8* %122, i32 %158, i32* %159)
%161 = icmp ne i32* %160, null
br i1 %161, label %162, label %244
162: ; preds = %157
%163 = call i32 @strlen(i8* %122)
store i32 %163, i32* %26
%164 = load i32, i32* %26
%165 = sub nsw i32 %164, 1
%166 = sext i32 %165 to i64
%167 = getelementptr inbounds i8, i8* %122, i64 %166
%168 = load i8, i8* %167
%169 = sext i8 %168 to i32
%170 = icmp eq i32 %169, 10
br i1 %170, label %171, label %176
171: ; preds = %162
%172 = load i32, i32* %26
%173 = sub nsw i32 %172, 1
%174 = sext i32 %173 to i64
%175 = getelementptr inbounds i8, i8* %122, i64 %174
store i8 0, i8* %175
br label %176
176: ; preds = %171, %162
%177 = load i32, i32* %19
%178 = sext i32 %177 to i64
%179 = mul nsw i64 %178, %144
%180 = getelementptr inbounds i8, i8* %146, i64 %179
%181 = call i32 @strcpy(i8* %180, i8* %122)
%182 = load i32, i32* %19
%183 = sext i32 %182 to i64
%184 = mul nsw i64 %183, %150
%185 = getelementptr inbounds i8, i8* %152, i64 %184
%186 = call i32 @strcpy(i8* %185, i8* %65)
%187 = load i32, i32* %19
%188 = sext i32 %187 to i64
%189 = mul nsw i64 %188, %150
%190 = getelementptr inbounds i8, i8* %152, i64 %189
%191 = call i32 @strcat(i8* %190, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%192 = load i32, i32* %19
%193 = sext i32 %192 to i64
%194 = mul nsw i64 %193, %150
%195 = getelementptr inbounds i8, i8* %152, i64 %194
%196 = call i32 @strcat(i8* %195, i8* %58)
%197 = load i32, i32* %19
%198 = sext i32 %197 to i64
%199 = mul nsw i64 %198, %150
%200 = getelementptr inbounds i8, i8* %152, i64 %199
%201 = call i32 @strcat(i8* %200, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%202 = load i32, i32* %19
%203 = sext i32 %202 to i64
%204 = mul nsw i64 %203, %150
%205 = getelementptr inbounds i8, i8* %152, i64 %204
%206 = call i32 @strcat(i8* %205, i8* %51)
%207 = load i32, i32* %19
%208 = sext i32 %207 to i64
%209 = mul nsw i64 %208, %150
%210 = getelementptr inbounds i8, i8* %152, i64 %209
%211 = call i32 @strcat(i8* %210, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%212 = load i32, i32* %19
%213 = sext i32 %212 to i64
%214 = mul nsw i64 %213, %150
%215 = getelementptr inbounds i8, i8* %152, i64 %214
%216 = call i32 @strcat(i8* %215, i8* %58)
%217 = load i32, i32* %19
%218 = sext i32 %217 to i64
%219 = mul nsw i64 %218, %150
%220 = getelementptr inbounds i8, i8* %152, i64 %219
%221 = call i32 @strcat(i8* %220, i8* getelementptr inbounds ([13 x i8], [13 x i8]* @.str.10, i64 0, i64 0))
%222 = load i32, i32* %19
%223 = sext i32 %222 to i64
%224 = mul nsw i64 %223, %150
%225 = getelementptr inbounds i8, i8* %152, i64 %224
%226 = call i32 @strcat(i8* %225, i8* %79)
%227 = load i32, i32* %19
%228 = sext i32 %227 to i64
%229 = mul nsw i64 %228, %150
%230 = getelementptr inbounds i8, i8* %152, i64 %229
%231 = call i32 @strcat(i8* %230, i8* getelementptr inbounds ([8 x i8], [8 x i8]* @.str.11, i64 0, i64 0))
%232 = load i32, i32* %19
%233 = sext i32 %232 to i64
%234 = mul nsw i64 %233, %150
%235 = getelementptr inbounds i8, i8* %152, i64 %234
%236 = call i32 @strcat(i8* %235, i8* %122)
%237 = load i32, i32* %19
%238 = sext i32 %237 to i64
%239 = mul nsw i64 %238, %150
%240 = getelementptr inbounds i8, i8* %152, i64 %239
%241 = call i32 @strcat(i8* %240, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.12, i64 0, i64 0))
%242 = load i32, i32* %19
%243 = add nsw i32 %242, 1
store i32 %243, i32* %19
br label %157
244: ; preds = %157
%245 = load i32*, i32** %25
%246 = call i32 @fclose(i32* %245)
br label %249
247: ; preds = %140
%248 = call i32 @perror(i8* %110)
br label %249
249: ; preds = %247, %244
store i32 1000000, i32* %30
%250 = load i32, i32* %30
%251 = zext i32 %250 to i64
%252 = alloca i8, i64 %251
store i64 %251, i64* %31
%253 = load i32, i32* %30
%254 = zext i32 %253 to i64
%255 = alloca i8, i64 %254
store i64 %254, i64* %32
store i32 0, i32* %33
store i32 0, i32* %27
br label %256
256: ; preds = %447, %249
%257 = load i32, i32* %27
%258 = load i32, i32* %19
%259 = icmp slt i32 %257, %258
br i1 %259, label %260, label %450
260: ; preds = %256
%261 = load i32, i32* %27
%262 = sext i32 %261 to i64
%263 = mul nsw i64 %262, %150
%264 = getelementptr inbounds i8, i8* %152, i64 %263
%265 = call i32* @fopen(i8* %264, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
store i32* %265, i32** %34
%266 = load i32*, i32** %34
%267 = icmp ne i32* %266, null
br i1 %267, label %268, label %304
268: ; preds = %260
%269 = load i32, i32* %30
%270 = zext i32 %269 to i64
%271 = call i8* @llvm.stacksave()
store i8* %271, i8** %35
%272 = alloca i8, i64 %270
store i64 %270, i64* %36
br label %273
273: ; preds = %301, %268
%274 = trunc i64 %270 to i32
%275 = load i32*, i32** %34
%276 = call i32* @fgets(i8* %272, i32 %274, i32* %275)
%277 = icmp ne i32* %276, null
br i1 %277, label %278, label %302
278: ; preds = %273
%279 = getelementptr inbounds i8, i8* %272, i64 0
%280 = load i8, i8* %279
%281 = sext i8 %280 to i32
%282 = icmp ne i32 %281, 62
br i1 %282, label %283, label %301
283: ; preds = %278
%284 = call i32 @strlen(i8* %272)
store i32 %284, i32* %37
%285 = load i32, i32* %37
%286 = sub nsw i32 %285, 1
store i32 %286, i32* %37
%287 = load i32, i32* %37
%288 = sext i32 %287 to i64
%289 = getelementptr inbounds i8, i8* %272, i64 %288
%290 = load i8, i8* %289
%291 = sext i8 %290 to i32
%292 = icmp eq i32 %291, 10
br i1 %292, label %293, label %297
293: ; preds = %283
%294 = load i32, i32* %37
%295 = sext i32 %294 to i64
%296 = getelementptr inbounds i8, i8* %272, i64 %295
store i8 0, i8* %296
br label %297
297: ; preds = %293, %283
%298 = call i32 @strcpy(i8* %252, i8* %272)
%299 = load i32*, i32** %34
%300 = call i32 @fclose(i32* %299)
br label %301
301: ; preds = %297, %278
br label %273
302: ; preds = %273
%303 = load i8*, i8** %35
br label %310
304: ; preds = %260
%305 = load i32, i32* %27
%306 = sext i32 %305 to i64
%307 = mul nsw i64 %306, %150
%308 = getelementptr inbounds i8, i8* %152, i64 %307
%309 = call i32 @perror(i8* %308)
br label %310
310: ; preds = %304, %302
store i32 0, i32* %28
br label %311
311: ; preds = %443, %310
%312 = load i32, i32* %28
%313 = load i32, i32* %19
%314 = icmp slt i32 %312, %313
br i1 %314, label %315, label %446
315: ; preds = %311
%316 = load i32, i32* %27
%317 = load i32, i32* %28
%318 = icmp sgt i32 %316, %317
br i1 %318, label %319, label %442
319: ; preds = %315
%320 = load i32, i32* %28
%321 = sext i32 %320 to i64
%322 = mul nsw i64 %321, %150
%323 = getelementptr inbounds i8, i8* %152, i64 %322
%324 = call i32* @fopen(i8* %323, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
store i32* %324, i32** %38
%325 = load i32*, i32** %38
%326 = icmp ne i32* %325, null
br i1 %326, label %327, label %363
327: ; preds = %319
%328 = load i32, i32* %30
%329 = zext i32 %328 to i64
%330 = call i8* @llvm.stacksave()
store i8* %330, i8** %39
%331 = alloca i8, i64 %329
store i64 %329, i64* %40
br label %332
332: ; preds = %360, %327
%333 = trunc i64 %329 to i32
%334 = load i32*, i32** %38
%335 = call i32* @fgets(i8* %331, i32 %333, i32* %334)
%336 = icmp ne i32* %335, null
br i1 %336, label %337, label %361
337: ; preds = %332
%338 = getelementptr inbounds i8, i8* %331, i64 0
%339 = load i8, i8* %338
%340 = sext i8 %339 to i32
%341 = icmp ne i32 %340, 62
br i1 %341, label %342, label %360
342: ; preds = %337
%343 = call i32 @strlen(i8* %331)
store i32 %343, i32* %41
%344 = load i32, i32* %41
%345 = sub nsw i32 %344, 1
store i32 %345, i32* %41
%346 = load i32, i32* %41
%347 = sext i32 %346 to i64
%348 = getelementptr inbounds i8, i8* %331, i64 %347
%349 = load i8, i8* %348
%350 = sext i8 %349 to i32
%351 = icmp eq i32 %350, 10
br i1 %351, label %352, label %356
352: ; preds = %342
%353 = load i32, i32* %41
%354 = sext i32 %353 to i64
%355 = getelementptr inbounds i8, i8* %331, i64 %354
store i8 0, i8* %355
br label %356
356: ; preds = %352, %342
%357 = call i32 @strcpy(i8* %255, i8* %331)
%358 = load i32*, i32** %38
%359 = call i32 @fclose(i32* %358)
br label %360
360: ; preds = %356, %337
br label %332
361: ; preds = %332
%362 = load i8*, i8** %39
br label %369
363: ; preds = %319
%364 = load i32, i32* %28
%365 = sext i32 %364 to i64
%366 = mul nsw i64 %365, %150
%367 = getelementptr inbounds i8, i8* %152, i64 %366
%368 = call i32 @perror(i8* %367)
br label %369
369: ; preds = %363, %361
%370 = call i32 @strlen(i8* %252)
store i32 %370, i32* %42
store i32 0, i32* %43
store i32 0, i32* %44
store i32 0, i32* %29
br label %371
371: ; preds = %409, %369
%372 = load i32, i32* %29
%373 = load i32, i32* %42
%374 = icmp slt i32 %372, %373
br i1 %374, label %375, label %412
375: ; preds = %371
%376 = load i32, i32* %29
%377 = sext i32 %376 to i64
%378 = getelementptr inbounds i8, i8* %252, i64 %377
%379 = load i8, i8* %378
%380 = sext i8 %379 to i32
%381 = icmp eq i32 %380, 78
br i1 %381, label %389, label %382
382: ; preds = %375
%383 = load i32, i32* %29
%384 = sext i32 %383 to i64
%385 = getelementptr inbounds i8, i8* %255, i64 %384
%386 = load i8, i8* %385
%387 = sext i8 %386 to i32
%388 = icmp eq i32 %387, 78
br i1 %388, label %389, label %392
389: ; preds = %382, %375
%390 = load i32, i32* %44
%391 = add nsw i32 %390, 1
store i32 %391, i32* %44
br label %408
392: ; preds = %382
%393 = load i32, i32* %29
%394 = sext i32 %393 to i64
%395 = getelementptr inbounds i8, i8* %252, i64 %394
%396 = load i8, i8* %395
%397 = sext i8 %396 to i32
%398 = load i32, i32* %29
%399 = sext i32 %398 to i64
%400 = getelementptr inbounds i8, i8* %255, i64 %399
%401 = load i8, i8* %400
%402 = sext i8 %401 to i32
%403 = icmp ne i32 %397, %402
br i1 %403, label %404, label %407
404: ; preds = %392
%405 = load i32, i32* %43
%406 = add nsw i32 %405, 1
store i32 %406, i32* %43
br label %407
407: ; preds = %404, %392
br label %408
408: ; preds = %407, %389
br label %409
409: ; preds = %408
%410 = load i32, i32* %29
%411 = add nsw i32 %410, 1
store i32 %411, i32* %29
br label %371
412: ; preds = %371
%413 = load i32, i32* %42
%414 = load i32, i32* %44
%415 = sub nsw i32 %413, %414
store i32 %415, i32* %45
%416 = load i32, i32* %43
%417 = sitofp i32 %416 to float
%418 = load i32, i32* %45
%419 = sitofp i32 %418 to float
%420 = fdiv float %417, %419
store float %420, float* %46
%421 = load float, float* %46
%422 = call float @llvm.fmuladd.f32(float 0xBFF5555560000000, float %421, float 1.000000e+00)
%423 = fptosi float %422 to i32
%424 = call float @log(i32 %423)
%425 = fmul float -7.500000e-01, %424
store float %425, float* %47
%426 = load i32*, i32** %16
%427 = load i32, i32* %27
%428 = sext i32 %427 to i64
%429 = mul nsw i64 %428, %144
%430 = getelementptr inbounds i8, i8* %146, i64 %429
%431 = load i32, i32* %28
%432 = sext i32 %431 to i64
%433 = mul nsw i64 %432, %144
%434 = getelementptr inbounds i8, i8* %146, i64 %433
%435 = load i32, i32* %43
%436 = load i32, i32* %45
%437 = load float, float* %47
%438 = fpext float %437 to double
%439 = call i32 (i32*, i8*, ...) @fprintf(i32* %426, i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.13, i64 0, i64 0), i8* %430, i8* %434, i32 %435, i32 %436, double %438)
%440 = load i32, i32* %33
%441 = add nsw i32 %440, 1
store i32 %441, i32* %33
br label %442
442: ; preds = %412, %315
br label %443
443: ; preds = %442
%444 = load i32, i32* %28
%445 = add nsw i32 %444, 1
store i32 %445, i32* %28
br label %311
446: ; preds = %311
br label %447
447: ; preds = %446
%448 = load i32, i32* %27
%449 = add nsw i32 %448, 1
store i32 %449, i32* %27
br label %256
450: ; preds = %256
%451 = call i32 @printf(i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.14, i64 0, i64 0), i8* %51, i8* %79)
%452 = load i32*, i32** %14
%453 = call i32 (i32*, i8*, ...) @fprintf(i32* %452, i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.14, i64 0, i64 0), i8* %51, i8* %79)
store i32 0, i32* %3
%454 = load i8*, i8** %7
%455 = load i32, i32* %3
ret i32 %455
}

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 = [13 x i8] c"/Intergenic_\00"
@.str.11 = [8 x i8] c"_files/\00"
@.str.12 = [7 x i8] c".fasta\00"
@.str.13 = [19 x i8] c"%s,%s,%i,%i,%0.6f\0A\00"
@.str.14 = [44 x i8] c"%s intergenic annotation %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 = getelementptr inbounds i8*, i8** %1, i64 4
%21 = load i8*, i8** %20
%22 = call i32 @strcpy(i8* %19, i8* %21)
%23 = alloca [1000 x i8]
%24 = getelementptr inbounds [1000 x i8], [1000 x i8]* %23, i64 0, i64 0
%25 = getelementptr inbounds i8*, i8** %1, i64 5
%26 = load i8*, i8** %25
%27 = call i32 @strcpy(i8* %24, i8* %26)
%28 = alloca [1000 x i8]
%29 = getelementptr inbounds [1000 x i8], [1000 x i8]* %28, i64 0, i64 0
%30 = call i32 @strcpy(i8* %29, i8* %14)
%31 = call i32 @strcat(i8* %29, i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str, i64 0, i64 0))
%32 = call i32* @fopen(i8* %29, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.1, i64 0, i64 0))
%33 = alloca [1000 x i8]
%34 = getelementptr inbounds [1000 x i8], [1000 x i8]* %33, i64 0, i64 0
%35 = call i32 @strcpy(i8* %34, i8* %14)
%36 = call i32 @strcat(i8* %34, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%37 = call i32 @strcat(i8* %34, i8* %9)
%38 = call i32 @strcat(i8* %34, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%39 = call i32 @strcat(i8* %34, i8* %4)
%40 = call i32 @strcat(i8* %34, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%41 = call i32 @strcat(i8* %34, i8* %9)
%42 = call i32 @strcat(i8* %34, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%43 = call i32 @strcat(i8* %34, i8* %4)
%44 = call i32 @strcat(i8* %34, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%45 = call i32 @strcat(i8* %34, i8* %24)
%46 = call i32 @strcat(i8* %34, i8* getelementptr inbounds ([18 x i8], [18 x i8]* @.str.5, i64 0, i64 0))
%47 = call i32* @fopen(i8* %34, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.6, i64 0, i64 0))
%48 = call i64 @fwrite(i8* getelementptr inbounds ([43 x i8], [43 x i8]* @.str.7, i64 0, i64 0), i64 42, i64 1, i32* %47)
%49 = alloca [1000 x i8]
%50 = getelementptr inbounds [1000 x i8], [1000 x i8]* %49, i64 0, i64 0
%51 = call i32 @strcpy(i8* %50, i8* %14)
%52 = call i32 @strcat(i8* %50, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%53 = call i32 @strcat(i8* %50, i8* %9)
%54 = call i32 @strcat(i8* %50, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%55 = call i32 @strcat(i8* %50, i8* %4)
%56 = call i32 @strcat(i8* %50, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%57 = call i32 @strcat(i8* %50, i8* %9)
%58 = call i32 @strcat(i8* %50, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%59 = call i32 @strcat(i8* %50, i8* getelementptr inbounds ([13 x i8], [13 x i8]* @.str.8, i64 0, i64 0))
%60 = alloca [1000 x i8]
%61 = getelementptr inbounds [1000 x i8], [1000 x i8]* %60, i64 0, i64 0
%62 = call i32* @fopen(i8* %50, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
%63 = icmp eq i32* %62, null
br i1 %63, label %71, label %64
64: ; preds = %2, %64
%65 = phi i32 [ %68, %64 ], [ 0, %2 ]
%66 = call i32* @fgets(i8* %61, i32 1000, i32* %62)
%67 = icmp eq i32* %66, null
%68 = add nuw nsw i32 %65, 1
br i1 %67, label %69, label %64
69: ; preds = %64
%70 = call i32 @fclose(i32* %62)
br label %73
71: ; preds = %2
%72 = call i32 @perror(i8* %50)
br label %73
73: ; preds = %71, %69
%74 = phi i32 [ %65, %69 ], [ 0, %71 ]
%75 = zext i32 %74 to i64
%76 = mul nuw nsw i64 %75, 1000
%77 = alloca i8, i64 %76
%78 = alloca i8, i64 %76
%79 = call i32* @fopen(i8* %50, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
%80 = icmp eq i32* %79, null
br i1 %80, label %115, label %81
81: ; preds = %73
%82 = call i32* @fgets(i8* %61, i32 1000, i32* %79)
%83 = icmp eq i32* %82, null
br i1 %83, label %117, label %84
84: ; preds = %81, %93
%85 = phi i64 [ %110, %93 ], [ 0, %81 ]
%86 = call i32 @strlen(i8* %61)
%87 = add nsw i32 %86, -1
%88 = sext i32 %87 to i64
%89 = getelementptr inbounds [1000 x i8], [1000 x i8]* %60, i64 0, i64 %88
%90 = load i8, i8* %89
%91 = icmp eq i8 %90, 10
br i1 %91, label %92, label %93
92: ; preds = %84
store i8 0, i8* %89
br label %93
93: ; preds = %92, %84
%94 = mul nuw nsw i64 %85, 1000
%95 = getelementptr inbounds i8, i8* %77, i64 %94
%96 = call i32 @strcpy(i8* %95, i8* %61)
%97 = getelementptr inbounds i8, i8* %78, i64 %94
%98 = call i32 @strcpy(i8* %97, i8* %14)
%99 = call i32 @strcat(i8* %97, i8* getelementptr inbounds ([11 x i8], [11 x i8]* @.str.2, i64 0, i64 0))
%100 = call i32 @strcat(i8* %97, i8* %9)
%101 = call i32 @strcat(i8* %97, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.3, i64 0, i64 0))
%102 = call i32 @strcat(i8* %97, i8* %4)
%103 = call i32 @strcat(i8* %97, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.4, i64 0, i64 0))
%104 = call i32 @strcat(i8* %97, i8* %9)
%105 = call i32 @strcat(i8* %97, i8* getelementptr inbounds ([13 x i8], [13 x i8]* @.str.10, i64 0, i64 0))
%106 = call i32 @strcat(i8* %97, i8* %24)
%107 = call i32 @strcat(i8* %97, i8* getelementptr inbounds ([8 x i8], [8 x i8]* @.str.11, i64 0, i64 0))
%108 = call i32 @strcat(i8* %97, i8* %61)
%109 = call i32 @strcat(i8* %97, i8* getelementptr inbounds ([7 x i8], [7 x i8]* @.str.12, i64 0, i64 0))
%110 = add nuw i64 %85, 1
%111 = call i32* @fgets(i8* %61, i32 1000, i32* %79)
%112 = icmp eq i32* %111, null
br i1 %112, label %113, label %84
113: ; preds = %93
%114 = trunc i64 %110 to i32
br label %117
115: ; preds = %73
%116 = call i32 @perror(i8* %50)
br label %286
117: ; preds = %81, %113
%118 = phi i32 [ 0, %81 ], [ %114, %113 ]
%119 = call i32 @fclose(i32* %79)
%120 = alloca [1000000 x i8]
%121 = alloca [1000000 x i8]
%122 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %121, i64 0, i64 0
%123 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %120, i64 0, i64 0
%124 = icmp eq i32 %118, 0
br i1 %124, label %286, label %125
125: ; preds = %117
%126 = zext i32 %118 to i64
br label %127
127: ; preds = %125, %283
%128 = phi i64 [ 0, %125 ], [ %284, %283 ]
%129 = mul nuw nsw i64 %128, 1000
%130 = getelementptr inbounds i8, i8* %78, i64 %129
%131 = call i32* @fopen(i8* %130, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
%132 = icmp eq i32* %131, null
br i1 %132, label %157, label %133
133: ; preds = %127
%134 = call i8* @llvm.stacksave()
%135 = alloca [1000000 x i8]
%136 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %135, i64 0, i64 0
%137 = call i32* @fgets(i8* %136, i32 1000000, i32* %131)
%138 = icmp eq i32* %137, null
br i1 %138, label %156, label %139
139: ; preds = %133, %153
%140 = load i8, i8* %136
%141 = icmp eq i8 %140, 62
br i1 %141, label %153, label %142
142: ; preds = %139
%143 = call i32 @strlen(i8* %136)
%144 = add nsw i32 %143, -1
%145 = sext i32 %144 to i64
%146 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %135, i64 0, i64 %145
%147 = load i8, i8* %146
%148 = icmp eq i8 %147, 10
br i1 %148, label %149, label %150
149: ; preds = %142
store i8 0, i8* %146
br label %150
150: ; preds = %149, %142
%151 = call i32 @strcpy(i8* %123, i8* %136)
%152 = call i32 @fclose(i32* %131)
br label %153
153: ; preds = %150, %139
%154 = call i32* @fgets(i8* %136, i32 1000000, i32* %131)
%155 = icmp eq i32* %154, null
br i1 %155, label %156, label %139
156: ; preds = %153, %133
br label %159
157: ; preds = %127
%158 = call i32 @perror(i8* %130)
br label %159
159: ; preds = %157, %156
%160 = getelementptr inbounds i8, i8* %77, i64 %129
br label %161
161: ; preds = %159, %280
%162 = phi i64 [ 0, %159 ], [ %281, %280 ]
%163 = icmp ugt i64 %128, %162
br i1 %163, label %164, label %280
164: ; preds = %161
%165 = mul nuw nsw i64 %162, 1000
%166 = getelementptr inbounds i8, i8* %78, i64 %165
%167 = call i32* @fopen(i8* %166, i8* getelementptr inbounds ([2 x i8], [2 x i8]* @.str.9, i64 0, i64 0))
%168 = icmp eq i32* %167, null
br i1 %168, label %193, label %169
169: ; preds = %164
%170 = call i8* @llvm.stacksave()
%171 = alloca [1000000 x i8]
%172 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %171, i64 0, i64 0
%173 = call i32* @fgets(i8* %172, i32 1000000, i32* %167)
%174 = icmp eq i32* %173, null
br i1 %174, label %192, label %175
175: ; preds = %169, %189
%176 = load i8, i8* %172
%177 = icmp eq i8 %176, 62
br i1 %177, label %189, label %178
178: ; preds = %175
%179 = call i32 @strlen(i8* %172)
%180 = add nsw i32 %179, -1
%181 = sext i32 %180 to i64
%182 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %171, i64 0, i64 %181
%183 = load i8, i8* %182
%184 = icmp eq i8 %183, 10
br i1 %184, label %185, label %186
185: ; preds = %178
store i8 0, i8* %182
br label %186
186: ; preds = %185, %178
%187 = call i32 @strcpy(i8* %122, i8* %172)
%188 = call i32 @fclose(i32* %167)
br label %189
189: ; preds = %186, %175
%190 = call i32* @fgets(i8* %172, i32 1000000, i32* %167)
%191 = icmp eq i32* %190, null
br i1 %191, label %192, label %175
192: ; preds = %189, %169
br label %195
193: ; preds = %164
%194 = call i32 @perror(i8* %166)
br label %195
195: ; preds = %193, %192
%196 = call i32 @strlen(i8* %123)
%197 = icmp sgt i32 %196, 0
br i1 %197, label %198, label %266
198: ; preds = %195
%199 = zext i32 %196 to i64
%200 = and i64 %199, 1
%201 = icmp eq i32 %196, 1
br i1 %201, label %245, label %202
202: ; preds = %198
%203 = and i64 %199, 4294967294
br label %204
204: ; preds = %239, %202
%205 = phi i64 [ 0, %202 ], [ %242, %239 ]
%206 = phi i32 [ 0, %202 ], [ %241, %239 ]
%207 = phi i32 [ 0, %202 ], [ %240, %239 ]
%208 = phi i64 [ 0, %202 ], [ %243, %239 ]
%209 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %120, i64 0, i64 %205
%210 = load i8, i8* %209
%211 = icmp eq i8 %210, 78
br i1 %211, label %216, label %212
212: ; preds = %204
%213 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %121, i64 0, i64 %205
%214 = load i8, i8* %213
%215 = icmp eq i8 %214, 78
br i1 %215, label %216, label %218
216: ; preds = %212, %204
%217 = add nsw i32 %206, 1
br label %222
218: ; preds = %212
%219 = icmp ne i8 %210, %214
%220 = zext i1 %219 to i32
%221 = add nsw i32 %207, %220
br label %222
222: ; preds = %218, %216
%223 = phi i32 [ %207, %216 ], [ %221, %218 ]
%224 = phi i32 [ %217, %216 ], [ %206, %218 ]
%225 = or i64 %205, 1
%226 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %120, i64 0, i64 %225
%227 = load i8, i8* %226
%228 = icmp eq i8 %227, 78
br i1 %228, label %237, label %229
229: ; preds = %222
%230 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %121, i64 0, i64 %225
%231 = load i8, i8* %230
%232 = icmp eq i8 %231, 78
br i1 %232, label %237, label %233
233: ; preds = %229
%234 = icmp ne i8 %227, %231
%235 = zext i1 %234 to i32
%236 = add nsw i32 %223, %235
br label %239
237: ; preds = %229, %222
%238 = add nsw i32 %224, 1
br label %239
239: ; preds = %237, %233
%240 = phi i32 [ %223, %237 ], [ %236, %233 ]
%241 = phi i32 [ %238, %237 ], [ %224, %233 ]
%242 = add nuw nsw i64 %205, 2
%243 = add i64 %208, 2
%244 = icmp eq i64 %243, %203
br i1 %244, label %245, label %204
245: ; preds = %239, %198
%246 = phi i32 [ undef, %198 ], [ %240, %239 ]
%247 = phi i32 [ undef, %198 ], [ %241, %239 ]
%248 = phi i64 [ 0, %198 ], [ %242, %239 ]
%249 = phi i32 [ 0, %198 ], [ %241, %239 ]
%250 = phi i32 [ 0, %198 ], [ %240, %239 ]
%251 = icmp eq i64 %200, 0
br i1 %251, label %266, label %252
252: ; preds = %245
%253 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %120, i64 0, i64 %248
%254 = load i8, i8* %253
%255 = icmp eq i8 %254, 78
br i1 %255, label %264, label %256
256: ; preds = %252
%257 = getelementptr inbounds [1000000 x i8], [1000000 x i8]* %121, i64 0, i64 %248
%258 = load i8, i8* %257
%259 = icmp eq i8 %258, 78
br i1 %259, label %264, label %260
260: ; preds = %256
%261 = icmp ne i8 %254, %258
%262 = zext i1 %261 to i32
%263 = add nsw i32 %250, %262
br label %266
264: ; preds = %256, %252
%265 = add nsw i32 %249, 1
br label %266
266: ; preds = %245, %264, %260, %195
%267 = phi i32 [ 0, %195 ], [ %246, %245 ], [ %250, %264 ], [ %263, %260 ]
%268 = phi i32 [ 0, %195 ], [ %247, %245 ], [ %265, %264 ], [ %249, %260 ]
%269 = sub nsw i32 %196, %268
%270 = sitofp i32 %267 to float
%271 = sitofp i32 %269 to float
%272 = fdiv float %270, %271
%273 = call float @llvm.fmuladd.f32(float %272, float 0xBFF5555560000000, float 1.000000e+00)
%274 = fptosi float %273 to i32
%275 = call float @log(i32 %274)
%276 = fmul float %275, -7.500000e-01
%277 = getelementptr inbounds i8, i8* %77, i64 %165
%278 = fpext float %276 to double
%279 = call i32 (i32*, i8*, ...) @fprintf(i32* %47, i8* getelementptr inbounds ([19 x i8], [19 x i8]* @.str.13, i64 0, i64 0), i8* %160, i8* %277, i32 %267, i32 %269, double %278)
br label %280
280: ; preds = %161, %266
%281 = add nuw nsw i64 %162, 1
%282 = icmp eq i64 %281, %126
br i1 %282, label %283, label %161
283: ; preds = %280
%284 = add nuw nsw i64 %128, 1
%285 = icmp eq i64 %284, %126
br i1 %285, label %286, label %127
286: ; preds = %283, %115, %117
%287 = call i32 @printf(i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.14, i64 0, i64 0), i8* %4, i8* %24)
%288 = call i32 (i32*, i8*, ...) @fprintf(i32* %32, i8* getelementptr inbounds ([44 x i8], [44 x i8]* @.str.14, i64 0, i64 0), i8* %4, i8* %24)
ret i32 0
}