// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_paircmp.c
// Function: parse_options
static GtOPrval parse_options(int *parsed_args,
                              Cmppairwiseopt *pw,
                              int argc, const char **argv, GtError *err)
{
  GtOptionParser *op;
  GtOption *optionstrings,
         *optionfiles,
         *optioncharlistlen,
         *optiontext,
         *optionshowedist,
         *optionprint;
  GtStrArray *charlistlen;
  GtOPrval oprval;

  gt_error_check(err);
  charlistlen = gt_str_array_new();
  pw->strings = gt_str_array_new();
  pw->files = gt_str_array_new();
  pw->text = gt_str_new();
  pw->charlistlen = NULL;
  pw->fastasequences0 = NULL;
  pw->fastasequences1 = NULL;
  pw->showedist = false;
  pw->print = false;
  pw->fasta = false;
  op = gt_option_parser_new("options", "Apply function to pairs of strings.");
  gt_option_parser_set_mail_address(op, "<kurtz@zbh.uni-hamburg.de>");

  optionstrings = gt_option_new_string_array("ss", "use two strings",
                                             pw->strings);
  gt_option_parser_add_option(op, optionstrings);

  optionfiles = gt_option_new_filename_array("ff", "use two files",
                                             pw->files);
  gt_option_parser_add_option(op, optionfiles);

  optioncharlistlen = gt_option_new_string_array("a",
                                             "use character list and length",
                                             charlistlen);
  gt_option_parser_add_option(op, optioncharlistlen);

  optiontext = gt_option_new_string("t", "use text", pw->text, NULL);
  gt_option_parser_add_option(op, optiontext);

  optionshowedist = gt_option_new_bool("e", "output unit edit distance",
                      &pw->showedist, false);
  gt_option_parser_add_option(op, optionshowedist);

  optionprint = gt_option_new_bool("p", "print edist alignment",
                      &pw->print, false);
  gt_option_parser_add_option(op, optionprint);

  gt_option_exclude(optionstrings, optionfiles);
  gt_option_exclude(optionstrings, optioncharlistlen);
  gt_option_exclude(optionstrings, optiontext);
  gt_option_exclude(optionfiles, optioncharlistlen);
  gt_option_exclude(optionfiles, optiontext);
  gt_option_exclude(optioncharlistlen, optiontext);
  gt_option_imply(optionshowedist, optionstrings);
  gt_option_imply(optionprint, optionstrings);

  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);
  if (oprval == GT_OPTION_PARSER_OK)
  {
    if (gt_option_is_set(optionstrings))
    {
      if (gt_str_array_size(pw->strings) != 2UL)
      {
        gt_error_set(err, "option -ss requires two string arguments");
        oprval = GT_OPTION_PARSER_ERROR;
      }
    } else
    {
      if (gt_option_is_set(optionfiles))
      {
        if (gt_str_array_size(pw->files) != 2UL)
        {
          if (gt_str_array_size(pw->files) == 3UL &&
              !strcmp(gt_str_array_get(pw->files,0),"fasta"))
          {
            pw->fasta = true;
          }
          if (!pw->fasta)
          {
            gt_error_set(err, "option -ff requires two filename arguments or "
                              "keyword fasta and two filename arguments in "
                              "FASTA format");
            oprval = GT_OPTION_PARSER_ERROR;
          }
        }
      } else
      {
        if (gt_option_is_set(optioncharlistlen))
        {
          GtWord readint;
          if (gt_str_array_size(charlistlen) != 2UL)
          {
            gt_error_set(err,
                         "option -a requires charlist and length argument");
            oprval = GT_OPTION_PARSER_ERROR;
          }else
          {
            pw->charlistlen = gt_malloc(sizeof *pw->charlistlen);
            pw->charlistlen->charlist =
              gt_str_ref(gt_str_array_get_str(charlistlen,
                                                                    0));
            if (sscanf(gt_str_array_get(charlistlen,1UL), GT_WD, &readint) != 1
                || readint < 1L)
            {
              gt_error_set(err,
                           "option -a requires charlist and length argument");
              oprval = GT_OPTION_PARSER_ERROR;
            }
            pw->charlistlen->len = (GtUword) readint;
          }
        } else
        {
          if (!gt_option_is_set(optiontext))
          {
            gt_error_set(err,
                         "use exactly one of the options -ss, -ff, -a, -t");
            oprval = GT_OPTION_PARSER_ERROR;
          }
        }
      }
    }
  }
  gt_option_parser_delete(op);
  if (oprval == GT_OPTION_PARSER_OK && *parsed_args != argc)
  {
    gt_error_set(err, "superfluous program parameters");
    oprval = GT_OPTION_PARSER_ERROR;
  }
  gt_str_array_delete(charlistlen);
  return oprval;
}

// Assembly:
subq $0x78, %rsp
movq %rdi, 0x70(%rsp)
movq %rsi, 0x68(%rsp)
movl %edx, 0x64(%rsp)
movq %rcx, 0x58(%rsp)
movq %r8, 0x50(%rsp)
cmpq $0x0, 0x50(%rsp)
je 0x4a48c
movq 0x50(%rsp), %rdi
callq 0xd8a60
testb $0x1, %al
jne 0x4a454
jmp 0x4a48c
movq 0x5f1b45(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4cbbae(%rip), %rsi    # 0x516013
leaq 0x4cbd53(%rip), %rdx    # 0x5161bf
leaq 0x54aa1f(%rip), %rcx    # 0x594e92
leaq 0x4d8a5c(%rip), %r8     # 0x522ed6
movl $0x6a, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x4a48e
callq 0x11f5c0
movq %rax, 0x10(%rsp)
callq 0x11f5c0
movq %rax, %rcx
movq 0x68(%rsp), %rax
movq %rcx, (%rax)
callq 0x11f5c0
movq %rax, %rcx
movq 0x68(%rsp), %rax
movq %rcx, 0x8(%rax)
callq 0x11d4a0
movq %rax, %rcx
movq 0x68(%rsp), %rax
movq %rcx, 0x28(%rax)
movq 0x68(%rsp), %rax
movq $0x0, 0x20(%rax)
movq 0x68(%rsp), %rax
movq $0x0, 0x10(%rax)
movq 0x68(%rsp), %rax
movq $0x0, 0x18(%rax)
movq 0x68(%rsp), %rax
movb $0x0, 0x31(%rax)
movq 0x68(%rsp), %rax
movb $0x0, 0x32(%rax)
movq 0x68(%rsp), %rax
movb $0x0, 0x30(%rax)
leaq 0x4d00d3(%rip), %rdi    # 0x51a5e6
leaq 0x4d8b46(%rip), %rsi    # 0x523060
callq 0xf1420
movq %rax, 0x48(%rsp)
movq 0x48(%rsp), %rdi
leaq 0x4ccdb4(%rip), %rsi    # 0x5172e4
callq 0xf1a10
movq 0x68(%rsp), %rax
movq (%rax), %rdx
leaq 0x56c278(%rip), %rdi    # 0x5b67bc
leaq 0x4d68a6(%rip), %rsi    # 0x520df1
callq 0xf6a50
movq %rax, 0x40(%rsp)
movq 0x48(%rsp), %rdi
movq 0x40(%rsp), %rsi
callq 0xf1600
movq 0x68(%rsp), %rax
movq 0x8(%rax), %rdx
leaq 0x4f1e2d(%rip), %rdi    # 0x53c3a1
leaq 0x4d688d(%rip), %rsi    # 0x520e08
callq 0xf6b00
movq %rax, 0x38(%rsp)
movq 0x48(%rsp), %rdi
movq 0x38(%rsp), %rsi
callq 0xf1600
movq 0x10(%rsp), %rdx
leaq 0x4e94be(%rip), %rdi    # 0x533a5e
leaq 0x4d8add(%rip), %rsi    # 0x523084
callq 0xf6a50
movq %rax, 0x30(%rsp)
movq 0x48(%rsp), %rdi
movq 0x30(%rsp), %rsi
callq 0xf1600
movq 0x68(%rsp), %rax
movq 0x28(%rax), %rdx
leaq 0x54d883(%rip), %rdi    # 0x597e53
leaq 0x4d8acb(%rip), %rsi    # 0x5230a2
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x28(%rsp)
movq 0x48(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x68(%rsp), %rdx
addq $0x31, %rdx
leaq 0x548aa4(%rip), %rdi    # 0x5930a8
leaq 0x4d8aa0(%rip), %rsi    # 0x5230ab
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x20(%rsp)
movq 0x48(%rsp), %rdi
movq 0x20(%rsp), %rsi
callq 0xf1600
movq 0x68(%rsp), %rdx
addq $0x32, %rdx
leaq 0x51db0c(%rip), %rdi    # 0x568142
leaq 0x4d8a88(%rip), %rsi    # 0x5230c5
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x18(%rsp)
movq 0x48(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf1600
movq 0x40(%rsp), %rdi
movq 0x38(%rsp), %rsi
callq 0xf7320
movq 0x40(%rsp), %rdi
movq 0x30(%rsp), %rsi
callq 0xf7320
movq 0x40(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf7320
movq 0x38(%rsp), %rdi
movq 0x30(%rsp), %rsi
callq 0xf7320
movq 0x38(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf7320
movq 0x30(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf7320
movq 0x20(%rsp), %rdi
movq 0x40(%rsp), %rsi
callq 0xf7090
movq 0x18(%rsp), %rdi
movq 0x40(%rsp), %rsi
callq 0xf7090
movq 0x48(%rsp), %rdi
movq 0x70(%rsp), %rsi
movl 0x64(%rsp), %edx
movq 0x58(%rsp), %rcx
movq 0x50(%rsp), %r9
leaq 0xdc041(%rip), %r8      # 0x126730
callq 0xf2ab0
movl %eax, 0xc(%rsp)
cmpl $0x0, 0xc(%rsp)
jne 0x4a8f5
movq 0x40(%rsp), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x4a713
jmp 0x4a746
movq 0x68(%rsp), %rax
movq (%rax), %rdi
callq 0x11fcc0
cmpq $0x2, %rax
je 0x4a741
movq 0x50(%rsp), %rdi
leaq 0x4d68d5(%rip), %rsi    # 0x521007
movb $0x0, %al
callq 0xd88c0
movl $0x1, 0xc(%rsp)
jmp 0x4a8f3
movq 0x38(%rsp), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x4a759
jmp 0x4a7dd
movq 0x68(%rsp), %rax
movq 0x8(%rax), %rdi
callq 0x11fcc0
cmpq $0x2, %rax
je 0x4a7d8
movq 0x68(%rsp), %rax
movq 0x8(%rax), %rdi
callq 0x11fcc0
cmpq $0x3, %rax
jne 0x4a7b0
movq 0x68(%rsp), %rax
movq 0x8(%rax), %rdi
xorl %eax, %eax
movl %eax, %esi
callq 0x11f8c0
movq %rax, %rdi
leaq 0x5016db(%rip), %rsi    # 0x54be78
callq 0x19980
cmpl $0x0, %eax
jne 0x4a7b0
movq 0x68(%rsp), %rax
movb $0x1, 0x30(%rax)
movq 0x68(%rsp), %rax
testb $0x1, 0x30(%rax)
jne 0x4a7d6
movq 0x50(%rsp), %rdi
leaq 0x4d8914(%rip), %rsi    # 0x5230db
movb $0x0, %al
callq 0xd88c0
movl $0x1, 0xc(%rsp)
jmp 0x4a7d8
jmp 0x4a8f1
movq 0x30(%rsp), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x4a7f0
jmp 0x4a8c4
movq 0x10(%rsp), %rdi
callq 0x11fcc0
cmpq $0x2, %rax
je 0x4a820
movq 0x50(%rsp), %rdi
leaq 0x4d8936(%rip), %rsi    # 0x523142
movb $0x0, %al
callq 0xd88c0
movl $0x1, 0xc(%rsp)
jmp 0x4a8c2
movl $0x10, %edi
leaq 0x4d86aa(%rip), %rsi    # 0x522ed6
movl $0xc3, %edx
callq 0xe80f0
movq %rax, %rcx
movq 0x68(%rsp), %rax
movq %rcx, 0x20(%rax)
movq 0x10(%rsp), %rdi
xorl %eax, %eax
movl %eax, %esi
callq 0x11f960
movq %rax, %rdi
callq 0x11e360
movq %rax, %rcx
movq 0x68(%rsp), %rax
movq 0x20(%rax), %rax
movq %rcx, (%rax)
movq 0x10(%rsp), %rdi
movl $0x1, %esi
callq 0x11f8c0
movq %rax, %rdi
leaq 0x503fef(%rip), %rsi    # 0x54e86f
movq %rsp, %rdx
movb $0x0, %al
callq 0x19770
cmpl $0x1, %eax
jne 0x4a896
cmpq $0x1, (%rsp)
jge 0x4a8b1
movq 0x50(%rsp), %rdi
leaq 0x4d88a0(%rip), %rsi    # 0x523142
movb $0x0, %al
callq 0xd88c0
movl $0x1, 0xc(%rsp)
movq (%rsp), %rcx
movq 0x68(%rsp), %rax
movq 0x20(%rax), %rax
movq %rcx, 0x8(%rax)
jmp 0x4a8ef
movq 0x28(%rsp), %rdi
callq 0xf74a0
testb $0x1, %al
jne 0x4a8ed
movq 0x50(%rsp), %rdi
leaq 0x4d8894(%rip), %rsi    # 0x523172
movb $0x0, %al
callq 0xd88c0
movl $0x1, 0xc(%rsp)
jmp 0x4a8ef
jmp 0x4a8f1
jmp 0x4a8f3
jmp 0x4a8f5
movq 0x48(%rsp), %rdi
callq 0xf5cf0
cmpl $0x0, 0xc(%rsp)
jne 0x4a92e
movq 0x70(%rsp), %rax
movl (%rax), %eax
cmpl 0x64(%rsp), %eax
je 0x4a92e
movq 0x50(%rsp), %rdi
leaq 0x4d8883(%rip), %rsi    # 0x5231a2
movb $0x0, %al
callq 0xd88c0
movl $0x1, 0xc(%rsp)
movq 0x10(%rsp), %rdi
callq 0x11fd20
movl 0xc(%rsp), %eax
addq $0x78, %rsp
retq
nopw %cs:(%rax,%rax)