// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_seqcorrect.c
// Function: gt_seqcorrect_runner
static int gt_seqcorrect_runner(GT_UNUSED int argc,
    GT_UNUSED const char **argv,
    GT_UNUSED int parsed_args,
    void *tool_arguments,
    GtError *err)
{
  GtSeqcorrectArguments *arguments = tool_arguments;
  GtEncseqLoader *el = NULL;
  GtEncseq *encseq = NULL;
  GtTimer *timer = NULL;
  GtLogger *default_logger, *verbose_logger;
  bool haserr = false;

  gt_error_check(err);
  gt_assert(arguments);

  if (gt_showtime_enabled())
  {
    timer = gt_timer_new_with_progress_description("for initialization");
    gt_timer_show_cpu_time_by_progress(timer);
    gt_timer_start(timer);
  }
  default_logger =
    gt_logger_new(!arguments->quiet, GT_LOGGER_DEFLT_PREFIX, stdout);
  gt_logger_log(default_logger, "gt seqcorrect");
  verbose_logger =
    gt_logger_new(arguments->verbose, GT_LOGGER_DEFLT_PREFIX, stdout);
  gt_logger_log(verbose_logger, "verbose output enabled");

  if (gt_str_array_size(arguments->db) != 0)
  {
    haserr =
      gt_seqcorrect_encode(arguments, default_logger, verbose_logger, err);
  }
  else
  {
    gt_logger_log(verbose_logger, "input is an encseq: %s",
        gt_str_get(arguments->encseqinput));
  }
  if (!haserr)
  {
    el = gt_encseq_loader_new();
    gt_encseq_loader_drop_description_support(el);
    gt_encseq_loader_disable_autosupport(el);
    encseq = gt_encseq_loader_load(el, gt_str_get(arguments->encseqinput),
        err);
    if (encseq == NULL)
    {
      haserr = true;
    }
    if (!haserr)
    {
      if (gt_encseq_mirror(encseq, err) != 0)
      {
        haserr = true;
      }
      if (!haserr && gt_encseq_has_md5_support(encseq))
      {
        GtStr *md5path = gt_str_clone(arguments->encseqinput);
        gt_str_append_cstr(md5path, GT_MD5TABFILESUFFIX);
        gt_xunlink(gt_str_get(md5path));
        gt_warning("the input encseq %s had MD5 support, however sequence "
                   "invalidates the MD5 table, thus MD5 support will "
                   "be disabled", gt_str_get(arguments->encseqinput));
        gt_str_delete(md5path);
      }
    }
  }
  if (!haserr)
  {
    if (!arguments->find_seldom)
      haserr = gt_seqcorrect_correct(arguments, encseq, verbose_logger, timer,
          err);
    else
      haserr = gt_seqcorrect_find_seldom(arguments, encseq, verbose_logger,
          timer, err);
  }
  gt_encseq_delete(encseq);
  gt_encseq_loader_delete(el);
  if (timer != NULL)
  {
    gt_timer_show_progress_final(timer, stdout);
    gt_timer_delete(timer);
  }
  gt_logger_delete(default_logger);
  gt_logger_delete(verbose_logger);
  return haserr ? -1 : 0;
}

// Assembly:
subq $0x78, %rsp
movl %edi, 0x74(%rsp)
movq %rsi, 0x68(%rsp)
movl %edx, 0x64(%rsp)
movq %rcx, 0x58(%rsp)
movq %r8, 0x50(%rsp)
movq 0x58(%rsp), %rax
movq %rax, 0x48(%rsp)
movq $0x0, 0x40(%rsp)
movq $0x0, 0x38(%rsp)
movq $0x0, 0x30(%rsp)
movb $0x0, 0x1f(%rsp)
cmpq $0x0, 0x50(%rsp)
je 0x62825
movq 0x50(%rsp), %rdi
callq 0xd8a60
testb $0x1, %al
jne 0x627ed
jmp 0x62825
movq 0x5d97ac(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4b3815(%rip), %rsi    # 0x516013
leaq 0x4b39ba(%rip), %rdx    # 0x5161bf
leaq 0x4c69d1(%rip), %rcx    # 0x5291dd
leaq 0x4c66e0(%rip), %r8     # 0x528ef3
movl $0x2b9, %r9d            # imm = 0x2B9
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x62827
jmp 0x62829
cmpq $0x0, 0x48(%rsp)
jne 0x62869
movq 0x5d9768(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4b37d1(%rip), %rsi    # 0x516013
leaq 0x518316(%rip), %rdx    # 0x57ab5f
leaq 0x4c698d(%rip), %rcx    # 0x5291dd
leaq 0x4c669c(%rip), %r8     # 0x528ef3
movl $0x2ba, %r9d            # imm = 0x2BA
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x6286b
callq 0x11aa90
testb $0x1, %al
jne 0x62876
jmp 0x6289b
leaq 0x4c6975(%rip), %rdi    # 0x5291f2
callq 0x1213a0
movq %rax, 0x30(%rsp)
movq 0x30(%rsp), %rdi
callq 0x121ec0
movq 0x30(%rsp), %rdi
callq 0x1213f0
movq 0x48(%rsp), %rax
movb 0x2(%rax), %al
xorb $-0x1, %al
movq 0x5d968c(%rip), %rcx    # 0x63bf38
movq (%rcx), %rdx
movzbl %al, %edi
andl $0x1, %edi
leaq 0x4b5030(%rip), %rsi    # 0x5178ec
callq 0xe7870
movq %rax, 0x28(%rsp)
movq 0x28(%rsp), %rdi
leaq 0x4c6933(%rip), %rsi    # 0x529205
movb $0x0, %al
callq 0xe7cd0
movq 0x48(%rsp), %rax
movb 0x1(%rax), %al
movq 0x5d9650(%rip), %rcx    # 0x63bf38
movq (%rcx), %rdx
leaq 0x4b4ffa(%rip), %rsi    # 0x5178ec
andb $0x1, %al
movzbl %al, %edi
callq 0xe7870
movq %rax, 0x20(%rsp)
movq 0x20(%rsp), %rdi
leaq 0x4c6906(%rip), %rsi    # 0x529213
movb $0x0, %al
callq 0xe7cd0
movq 0x48(%rsp), %rax
movq 0x58(%rax), %rdi
callq 0x11fcc0
cmpq $0x0, %rax
je 0x62949
movq 0x48(%rsp), %rdi
movq 0x28(%rsp), %rsi
movq 0x20(%rsp), %rdx
movq 0x50(%rsp), %rcx
callq 0x62b40
andb $0x1, %al
movb %al, 0x1f(%rsp)
jmp 0x62977
movq 0x20(%rsp), %rax
movq %rax, 0x8(%rsp)
movq 0x48(%rsp), %rax
movq 0x38(%rax), %rdi
callq 0x11dee0
movq 0x8(%rsp), %rdi
movq %rax, %rdx
leaq 0x4c68ba(%rip), %rsi    # 0x52922a
movb $0x0, %al
callq 0xe7cd0
testb $0x1, 0x1f(%rsp)
jne 0x62a78
callq 0xb7a40
movq %rax, 0x40(%rsp)
movq 0x40(%rsp), %rdi
callq 0xba570
movq 0x40(%rsp), %rdi
callq 0xba760
movq 0x40(%rsp), %rax
movq %rax, (%rsp)
movq 0x48(%rsp), %rax
movq 0x38(%rax), %rdi
callq 0x11dee0
movq (%rsp), %rdi
movq %rax, %rsi
movq 0x50(%rsp), %rdx
callq 0xb7aa0
movq %rax, 0x38(%rsp)
cmpq $0x0, 0x38(%rsp)
jne 0x629da
movb $0x1, 0x1f(%rsp)
testb $0x1, 0x1f(%rsp)
jne 0x62a76
movq 0x38(%rsp), %rdi
movq 0x50(%rsp), %rsi
callq 0xbbd00
cmpl $0x0, %eax
je 0x629fe
movb $0x1, 0x1f(%rsp)
testb $0x1, 0x1f(%rsp)
jne 0x62a74
movq 0x38(%rsp), %rdi
callq 0xb3120
testb $0x1, %al
jne 0x62a15
jmp 0x62a74
movq 0x48(%rsp), %rax
movq 0x38(%rax), %rdi
callq 0x11e280
movq %rax, 0x10(%rsp)
movq 0x10(%rsp), %rdi
leaq 0x4b5018(%rip), %rsi    # 0x517a4c
callq 0x11d550
movq 0x10(%rsp), %rdi
callq 0x11dee0
movq %rax, %rdi
callq 0x127980
movq 0x48(%rsp), %rax
movq 0x38(%rax), %rdi
callq 0x11dee0
movq %rax, %rsi
leaq 0x4c67de(%rip), %rdi    # 0x529241
movb $0x0, %al
callq 0x1267d0
movq 0x10(%rsp), %rdi
callq 0x11f560
jmp 0x62a76
jmp 0x62a78
testb $0x1, 0x1f(%rsp)
jne 0x62ad6
movq 0x48(%rsp), %rax
testb $0x1, 0x8(%rax)
jne 0x62ab0
movq 0x48(%rsp), %rdi
movq 0x38(%rsp), %rsi
movq 0x20(%rsp), %rdx
movq 0x30(%rsp), %rcx
movq 0x50(%rsp), %r8
callq 0x63190
andb $0x1, %al
movb %al, 0x1f(%rsp)
jmp 0x62ad4
movq 0x48(%rsp), %rdi
movq 0x38(%rsp), %rsi
movq 0x20(%rsp), %rdx
movq 0x30(%rsp), %rcx
movq 0x50(%rsp), %r8
callq 0x63830
andb $0x1, %al
movb %al, 0x1f(%rsp)
jmp 0x62ad6
movq 0x38(%rsp), %rdi
callq 0xae070
movq 0x40(%rsp), %rdi
callq 0xb7e50
cmpq $0x0, 0x30(%rsp)
je 0x62b10
movq 0x30(%rsp), %rdi
movq 0x5d943a(%rip), %rax    # 0x63bf38
movq (%rax), %rsi
callq 0x121d70
movq 0x30(%rsp), %rdi
callq 0x121f00
movq 0x28(%rsp), %rdi
callq 0xe7ed0
movq 0x20(%rsp), %rdi
callq 0xe7ed0
movb 0x1f(%rsp), %dl
xorl %eax, %eax
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
testb $0x1, %dl
cmovnel %ecx, %eax
addq $0x78, %rsp
retq
nopw (%rax,%rax)