// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/ltr/gt_ltrharvest.c
// Function: gt_ltrharvest_arguments_check
static int gt_ltrharvest_arguments_check(GT_UNUSED int rest_argc,
                                           void *tool_arguments,
                                           GtError *err)
{
  LTRharvestArguments *arguments = tool_arguments;
  int had_err = 0;

  /* init */
  arguments->motif->firstleft   = (GtUchar) 't';
  arguments->motif->secondleft  = (GtUchar) 'g';
  arguments->motif->firstright  = (GtUchar) 'c';
  arguments->motif->secondright = (GtUchar) 'a';
  arguments->motif->allowedmismatches = arguments->allowedmismatches;

  if (gt_option_is_set(arguments->optionmotif))
  {
    if (gt_str_length(arguments->str_motif) != 4UL)
    {
      gt_error_set(err,
          "argument of -motif has not exactly 4 characters");
      had_err = -1;
    }
    if (!had_err) {
      arguments->motif->firstleft =
        (GtUchar) gt_str_get(arguments->str_motif)[0];
      arguments->motif->secondleft =
        (GtUchar) gt_str_get(arguments->str_motif)[1];
      arguments->motif->firstright =
        (GtUchar)  gt_str_get(arguments->str_motif)[2];
      arguments->motif->secondright =
        (GtUchar)  gt_str_get(arguments->str_motif)[3];
      /* default if motif specified */
      if (!gt_option_is_set(arguments->optionmotifmis))
      {
        arguments->motif->allowedmismatches = 0;
        arguments->allowedmismatches = 0;
      }
    }
  }
  if (!had_err) {
    if (gt_option_is_set(arguments->optionoverlaps))
    {
      if (strcmp(gt_str_get(arguments->str_overlaps), "no") == 0)
      {
        arguments->bestoverlaps = false;
        arguments->nooverlaps = true;
      }
      else if (strcmp(gt_str_get(arguments->str_overlaps), "best") == 0 )
      {
        arguments->bestoverlaps = true;
        arguments->nooverlaps = false;
      }
      else if (strcmp(gt_str_get(arguments->str_overlaps), "all") == 0 )
      {
        arguments->bestoverlaps = false;
        arguments->nooverlaps = false;
      }
      else
      {
        gt_assert(0); /* cannot happen */
      }
    }
    else
    {
      /* default is "best" */
      arguments->bestoverlaps = true;  /* take best prediction
                                          if overlap occurs, default */
      arguments->nooverlaps = false; /* overlapping predictions (not) allowed*/
    }
    /* if FASTA output is set */
    if (gt_option_is_set(arguments->optionout))
    {
      arguments->fastaoutput = true;
    }
    /* if FASTA output inner region is set */
    if (gt_option_is_set(arguments->optionoutinner))
    {
      arguments->fastaoutputinnerregion = true;
    }
    /* if GFF3 output is set */
    if (gt_option_is_set(arguments->optiongff3))
    {
      arguments->gff3output = true;
    }
  }
  return had_err;
}

// Assembly:
subq $0x28, %rsp
movl %edi, 0x24(%rsp)
movq %rsi, 0x18(%rsp)
movq %rdx, 0x10(%rsp)
movq 0x18(%rsp), %rax
movq %rax, 0x8(%rsp)
movl $0x0, 0x4(%rsp)
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movb $0x74, 0x8(%rax)
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movb $0x67, 0x9(%rax)
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movb $0x63, 0xa(%rax)
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movb $0x61, 0xb(%rax)
movq 0x8(%rsp), %rax
movl 0xac(%rax), %ecx
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movl %ecx, 0xc(%rax)
movq 0x8(%rsp), %rax
movq 0xc0(%rax), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x2fcd98
jmp 0x2fce8c
movq 0x8(%rsp), %rax
movq 0x18(%rax), %rdi
callq 0x11dfa0
cmpq $0x4, %rax
je 0x2fcdc7
movq 0x10(%rsp), %rdi
leaq 0x29540f(%rip), %rsi    # 0x5921c7
movb $0x0, %al
callq 0xd88c0
movl $0xffffffff, 0x4(%rsp)  # imm = 0xFFFFFFFF
cmpl $0x0, 0x4(%rsp)
jne 0x2fce8a
movq 0x8(%rsp), %rax
movq 0x18(%rax), %rdi
callq 0x11dee0
movb (%rax), %cl
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movb %cl, 0x8(%rax)
movq 0x8(%rsp), %rax
movq 0x18(%rax), %rdi
callq 0x11dee0
movb 0x1(%rax), %cl
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movb %cl, 0x9(%rax)
movq 0x8(%rsp), %rax
movq 0x18(%rax), %rdi
callq 0x11dee0
movb 0x2(%rax), %cl
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movb %cl, 0xa(%rax)
movq 0x8(%rsp), %rax
movq 0x18(%rax), %rdi
callq 0x11dee0
movb 0x3(%rax), %cl
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movb %cl, 0xb(%rax)
movq 0x8(%rsp), %rax
movq 0xc8(%rax), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x2fce88
movq 0x8(%rsp), %rax
movq 0xf0(%rax), %rax
movl $0x0, 0xc(%rax)
movq 0x8(%rsp), %rax
movl $0x0, 0xac(%rax)
jmp 0x2fce8a
jmp 0x2fce8c
cmpl $0x0, 0x4(%rsp)
jne 0x2fd02b
movq 0x8(%rsp), %rax
movq 0xd0(%rax), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x2fceb1
jmp 0x2fcfa8
movq 0x8(%rsp), %rax
movq 0x20(%rax), %rdi
callq 0x11dee0
movq %rax, %rdi
leaq 0x297cf2(%rip), %rsi    # 0x594bbb
callq 0x19980
cmpl $0x0, %eax
jne 0x2fcef0
movq 0x8(%rsp), %rax
movb $0x0, 0xb4(%rax)
movq 0x8(%rsp), %rax
movb $0x1, 0xb5(%rax)
jmp 0x2fcfa6
movq 0x8(%rsp), %rax
movq 0x20(%rax), %rdi
callq 0x11dee0
movq %rax, %rdi
leaq 0x263dc3(%rip), %rsi    # 0x560ccb
callq 0x19980
cmpl $0x0, %eax
jne 0x2fcf2c
movq 0x8(%rsp), %rax
movb $0x1, 0xb4(%rax)
movq 0x8(%rsp), %rax
movb $0x0, 0xb5(%rax)
jmp 0x2fcfa4
movq 0x8(%rsp), %rax
movq 0x20(%rax), %rdi
callq 0x11dee0
movq %rax, %rdi
leaq 0x24f5f9(%rip), %rsi    # 0x54c53d
callq 0x19980
cmpl $0x0, %eax
jne 0x2fcf68
movq 0x8(%rsp), %rax
movb $0x0, 0xb4(%rax)
movq 0x8(%rsp), %rax
movb $0x0, 0xb5(%rax)
jmp 0x2fcfa2
jmp 0x2fcf6a
movq 0x33f02f(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x219098(%rip), %rsi    # 0x516013
leaq 0x24376b(%rip), %rdx    # 0x5406ed
leaq 0x29526e(%rip), %rcx    # 0x5921f7
leaq 0x294e03(%rip), %r8     # 0x591d93
movl $0x223, %r9d            # imm = 0x223
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x2fcfa4
jmp 0x2fcfa6
jmp 0x2fcfc0
movq 0x8(%rsp), %rax
movb $0x1, 0xb4(%rax)
movq 0x8(%rsp), %rax
movb $0x0, 0xb5(%rax)
movq 0x8(%rsp), %rax
movq 0xd8(%rax), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x2fcfd7
jmp 0x2fcfe3
movq 0x8(%rsp), %rax
movb $0x1, 0xb6(%rax)
movq 0x8(%rsp), %rax
movq 0xe0(%rax), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x2fcffa
jmp 0x2fd006
movq 0x8(%rsp), %rax
movb $0x1, 0xb7(%rax)
movq 0x8(%rsp), %rax
movq 0xe8(%rax), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x2fd01d
jmp 0x2fd029
movq 0x8(%rsp), %rax
movb $0x1, 0xb8(%rax)
jmp 0x2fd02b
movl 0x4(%rsp), %eax
addq $0x28, %rsp
retq
nopw %cs:(%rax,%rax)