// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_tir.c
// Function: gt_tir_option_parser_new
static GtOptionParser* gt_tir_option_parser_new(void *tool_arguments)
{
  GtTirArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *optionindex,      /* index */
           *optionseed,       /* minseedlength */
           *optionminlentir,  /* minimal length of TIR */
           *optionmaxlentir,  /* maximal length of TIR */
           *optionmindisttir, /* minimal distance of TIRs */
           *optionmaxdisttir, /* maximal distance of TIRs */
           *optionmat,        /* arbitrary scores */
           *optionmis,
           *optionins,
           *optiondel,
           *optionxdrop,      /* xdropbelowscore for extension alignment */
           *optionsimilar,    /* similarity threshold */
           *optionoverlaps,   /* for overlaps */
           *optionmintsd,     /* minimal length for Target Site Duplication */
           *optionmaxtsd,     /* maximal length for Target Site Duplication */
           *optionvicinity,   /* vicinity around TIRs to be searched for TSDs */
           *optionhmms,
           *optionrefseqfile,
           *optionevalcutoff,
           *optionpdomcutoff,
           *optionmaxgap,
           *optionseqids,
           *optionmd5;
  static const char *overlaps[] = {
    "best", /* default */
    "longest",
    "no",
    "all",
    NULL
  };
  static const char *cutoffs[] = {
    "NONE",
    "GA",
    "TC",
    NULL
  };
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] -index INDEXNAME",
                            "Identify Terminal Inverted Repeat (TIR) elements,"
                            "such as DNA transposons.");

  /* -index */
  optionindex = gt_option_new_string("index",
                                     "specify the name of the enhanced suffix "
                                     "array index (mandatory)",
                                     arguments->str_indexname, NULL);
  gt_option_is_mandatory(optionindex);
  gt_option_parser_add_option(op, optionindex);

   /* -seed */
  optionseed = gt_option_new_uword_min("seed",
                                       "specify minimum seed length for "
                                       "exact repeats",
                                       &arguments->min_seed_length, 20UL, 5UL);
  gt_option_parser_add_option(op, optionseed);

  /* -minlentir */
  optionminlentir = gt_option_new_uword_min_max("mintirlen",
                                                "specify minimum length for "
                                                "each TIR",
                                                &arguments->min_TIR_length,
                                                100UL, 1UL, GT_UNDEF_UWORD);
  gt_option_parser_add_option(op, optionminlentir);

  /* -maxlentir */
  optionmaxlentir = gt_option_new_uword_min_max("maxtirlen",
                                                "specify maximum length for "
                                                "each TIR",
                                                &arguments->max_TIR_length,
                                                1000UL, 1UL, GT_UNDEF_UWORD);
  gt_option_parser_add_option(op, optionmaxlentir);

  /* -mindisttir */
  optionmindisttir = gt_option_new_uword_min_max("mintirdist",
                                                 "specify minimum distance of "
                                                 "TIRs",
                                                 &arguments->min_TIR_distance,
                                                 500UL, 1UL, GT_UNDEF_UWORD);
  gt_option_parser_add_option(op, optionmindisttir);

  /* -maxdisttir */
  optionmaxdisttir = gt_option_new_uword_min_max("maxtirdist",
                                                 "specify maximum distance of "
                                                 "TIRs",
                                                 &arguments->max_TIR_distance,
                                                 10000UL, 1UL, GT_UNDEF_UWORD);
  gt_option_parser_add_option(op, optionmaxdisttir);

  optionmat = gt_option_new_int_min("mat",
                                    "specify matchscore for "
                                    "extension-alignment",
                                    &arguments->arbit_scores.mat, 2, 1);
  gt_option_parser_add_option(op, optionmat);

  /* -mis */
  optionmis = gt_option_new_int_max("mis",
                                    "specify mismatchscore for "
                                    "extension-alignment",
                                    &arguments->arbit_scores.mis, -2, -1);
  gt_option_parser_add_option(op, optionmis);

  /* -ins */
  optionins = gt_option_new_int_max("ins",
                                    "specify insertionscore for "
                                    "extension-alignment",
                                    &arguments->arbit_scores.ins, -3, -1);
  gt_option_parser_add_option(op, optionins);

  /* -del */
  optiondel = gt_option_new_int_max("del",
                                    "specify deletionscore for "
                                    "extension-alignment",
                                    &arguments->arbit_scores.del, -3, -1);
  gt_option_parser_add_option(op, optiondel);

  /* -xdrop */
  optionxdrop = gt_option_new_int_min("xdrop",
                                      "specify xdropbelowscore for "
                                      "extension-alignment",
                                      &arguments->xdrop_belowscore, (int) 5,
                                      (int) 0);
  gt_option_parser_add_option(op, optionxdrop);

  /* -similar */
  optionsimilar = gt_option_new_double_min_max("similar",
                                               "specify TIR similarity "
                                               "threshold in the"
                                               "range [1..100%]",
                                               &arguments->similarity_threshold,
                                               (double) 85.0, (double) 0.0,
                                               100.0);
  gt_option_parser_add_option(op, optionsimilar);

  /* -overlaps */
  optionoverlaps = gt_option_new_choice("overlaps",
                                        "specify no|best|longest|all",
                                        arguments->str_overlaps,
                                        overlaps[0], overlaps);
  gt_option_parser_add_option(op, optionoverlaps);
  arguments->optionoverlaps = gt_option_ref(optionoverlaps);

  /* -mintsd */
  optionmintsd = gt_option_new_uword_min_max("mintsd",
                                             "specify minimum length for each "
                                             "TSD",
                                             &arguments->min_TSD_length,
                                             2U, 0, GT_UNDEF_UINT);
  gt_option_parser_add_option(op, optionmintsd);

  /* -maxtsd */
  optionmaxtsd = gt_option_new_uword_min_max("maxtsd",
                                             "specify maximum length for each "
                                             "TSD",
                                             &arguments->max_TSD_length,
                                             11U, 0, GT_UNDEF_UINT);
  gt_option_parser_add_option(op, optionmaxtsd);
  gt_option_imply(optionmaxtsd, optionmintsd);

  /* -vicinity */
  optionvicinity = gt_option_new_uword_min_max("vic",
                                               "specify the number of "
                                               "nucleotides (to the left and "
                                               "to the right) that will be "
                                               "searched for TSDs around 5' "
                                               "and 3' boundary of predicted "
                                               "TIRs",
                                               &arguments->vicinity,
                                               60U, 1U, 500U);
  gt_option_parser_add_option(op, optionvicinity);

  optionhmms = gt_option_new_filename_array("hmms",
                                    "profile HMM models for domain detection "
                                    "(separate by spaces, finish with --) in "
                                    "HMMER3 format\n"
                                    "Omit this option to disable pHMM search.",
                                    arguments->hmm_files);
  gt_option_parser_add_option(op, optionhmms);

  optionevalcutoff = gt_option_new_probability("pdomevalcutoff",
                                    "global E-value cutoff for pHMM search\n"
                                    "default 1E-6",
                                    &arguments->evalue_cutoff,
                                    0.000001);
  gt_option_parser_add_option(op, optionevalcutoff);
  gt_option_hide_default(optionevalcutoff);
  gt_option_imply(optionevalcutoff, optionhmms);

  optionpdomcutoff = gt_option_new_choice("pdomcutoff",
                                       "model-specific score cutoff\n"
                                       "choose from TC (trusted cutoff) | "
                                       "GA (gathering cutoff) | "
                                       "NONE (no cutoffs)",
                             arguments->cutoffs, cutoffs[1], cutoffs);
  gt_option_parser_add_option(op, optionpdomcutoff);
  gt_option_imply(optionpdomcutoff, optionhmms);

  /* XXX: make -pdomcutoff and -pdomevalcutoff mutually exclusive */

  optionmaxgap = gt_option_new_uint("maxgaplen",
                         "maximal allowed gap size between fragments (in amino "
                         "acids) when chaining pHMM hits for a protein domain",
                         &arguments->chain_max_gap_length,
                         50U);
  gt_option_parser_add_option(op, optionmaxgap);
  gt_option_is_extended_option(optionmaxgap);
  gt_option_imply(optionmaxgap, optionhmms);

  optionrefseqfile = gt_option_new_string("refseqs",
                                     "specify the name of the gene sequences "
                                     "to scan for inside candidates",
                                     arguments->refseq_file, NULL);
  gt_option_parser_add_option(op, optionrefseqfile);

  optionseqids = gt_option_new_bool("seqids",
                                    "use sequence descriptions instead of "
                                    "sequence numbers in GFF3 output",
                                    &arguments->seqids,
                                    true);
  gt_option_parser_add_option(op, optionseqids);

  optionmd5 = gt_option_new_bool("md5",
                                 "add MD5 hashes to seqids in GFF3 output",
                                 &arguments->md5,
                                 false);
  gt_option_parser_add_option(op, optionmd5);

  return op;
}

// Assembly:
subq $0xd8, %rsp
movq %rdi, 0xd0(%rsp)
movq 0xd0(%rsp), %rax
movq %rax, 0xc8(%rsp)
cmpq $0x0, 0xc8(%rsp)
jne 0x7b5d2
movq 0x5c09ff(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x49aa68(%rip), %rsi    # 0x516013
leaq 0x4ff5ad(%rip), %rdx    # 0x57ab5f
leaq 0x4b3182(%rip), %rcx    # 0x52e73b
leaq 0x4b3160(%rip), %r8     # 0x52e720
movl $0x7e, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x7b5d4
leaq 0x4b3179(%rip), %rdi    # 0x52e754
leaq 0x4b3190(%rip), %rsi    # 0x52e772
callq 0xf1420
movq %rax, 0xc0(%rsp)
movq 0xc8(%rsp), %rax
movq (%rax), %rdx
leaq 0x4e3f4d(%rip), %rdi    # 0x55f54e
leaq 0x4b31b4(%rip), %rsi    # 0x52e7bc
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0xb8(%rsp)
movq 0xb8(%rsp), %rdi
callq 0xf6ca0
movq 0xc0(%rsp), %rdi
movq 0xb8(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x20, %rdx
leaq 0x4ab0b2(%rip), %rdi    # 0x526700
leaq 0x4b31a7(%rip), %rsi    # 0x52e7fc
movl $0x14, %ecx
movl $0x5, %r8d
callq 0xf66b0
movq %rax, 0xb0(%rsp)
movq 0xc0(%rsp), %rdi
movq 0xb0(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x28, %rdx
leaq 0x4b3195(%rip), %rdi    # 0x52e82a
leaq 0x4b3198(%rip), %rsi    # 0x52e834
movl $0x64, %ecx
movl $0x1, %r8d
movq $-0x1, %r9
callq 0xf6710
movq %rax, 0xa8(%rsp)
movq 0xc0(%rsp), %rdi
movq 0xa8(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x30, %rdx
leaq 0x4b3175(%rip), %rdi    # 0x52e858
leaq 0x4b3178(%rip), %rsi    # 0x52e862
movl $0x3e8, %ecx            # imm = 0x3E8
movl $0x1, %r8d
movq $-0x1, %r9
callq 0xf6710
movq %rax, 0xa0(%rsp)
movq 0xc0(%rsp), %rdi
movq 0xa0(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x38, %rdx
leaq 0x4b3155(%rip), %rdi    # 0x52e886
leaq 0x4b3159(%rip), %rsi    # 0x52e891
movl $0x1f4, %ecx            # imm = 0x1F4
movl $0x1, %r8d
movq $-0x1, %r9
callq 0xf6710
movq %rax, 0x98(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x98(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x40, %rdx
leaq 0x4b3133(%rip), %rdi    # 0x52e8b2
leaq 0x4b3137(%rip), %rsi    # 0x52e8bd
movl $0x2710, %ecx           # imm = 0x2710
movl $0x1, %r8d
movq $-0x1, %r9
callq 0xf6710
movq %rax, 0x90(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x90(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x60, %rdx
leaq 0x4b1537(%rip), %rdi    # 0x52cd04
leaq 0x4b310a(%rip), %rsi    # 0x52e8de
movl $0x2, %ecx
movl $0x1, %r8d
callq 0xf6370
movq %rax, 0x88(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x88(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x60, %rdx
addq $0x4, %rdx
leaq 0x51677c(%rip), %rdi    # 0x591f94
leaq 0x4b30ea(%rip), %rsi    # 0x52e909
movl $0xfffffffe, %ecx       # imm = 0xFFFFFFFE
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
callq 0xf63d0
movq %rax, 0x80(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x80(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x60, %rdx
addq $0x8, %rdx
leaq 0x4f5dd3(%rip), %rdi    # 0x571636
leaq 0x4b30cd(%rip), %rsi    # 0x52e937
movl $0xfffffffd, %ecx       # imm = 0xFFFFFFFD
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
callq 0xf63d0
movq %rax, 0x78(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x78(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x60, %rdx
addq $0xc, %rdx
leaq 0x514a0d(%rip), %rdi    # 0x5902b5
leaq 0x4b30b7(%rip), %rsi    # 0x52e966
movl $0xfffffffd, %ecx       # imm = 0xFFFFFFFD
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
callq 0xf63d0
movq %rax, 0x70(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x70(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x70, %rdx
leaq 0x4d07b8(%rip), %rdi    # 0x54c0a1
leaq 0x4b30a4(%rip), %rsi    # 0x52e994
movl $0x5, %ecx
xorl %r8d, %r8d
callq 0xf6370
movq %rax, 0x68(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x68(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x78, %rdx
leaq 0x4d4ed2(%rip), %rdi    # 0x5507f9
leaq 0x4b3096(%rip), %rsi    # 0x52e9c4
movsd 0x4b2dda(%rip), %xmm0   # 0x52e710
xorps %xmm1, %xmm1
movsd 0x49eef7(%rip), %xmm2   # 0x51a838
callq 0xf6240
movq %rax, 0x60(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x60(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rax
movq 0x10(%rax), %rdx
movq 0x5c10a0(%rip), %rcx    # 0x63ca10
leaq 0x4edbb1(%rip), %rdi    # 0x569528
leaq 0x4b307d(%rip), %rsi    # 0x52e9fb
leaq 0x5c108b(%rip), %r8     # 0x63ca10
callq 0xf6b30
movq %rax, 0x58(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x58(%rsp), %rsi
callq 0xf1600
movq 0x58(%rsp), %rdi
callq 0xf13c0
movq %rax, %rcx
movq 0xc8(%rsp), %rax
movq %rcx, 0x98(%rax)
movq 0xc8(%rsp), %rdx
addq $0x48, %rdx
leaq 0x4b3047(%rip), %rdi    # 0x52ea17
leaq 0x4b3047(%rip), %rsi    # 0x52ea1e
movl $0x2, %ecx
xorl %eax, %eax
movl %eax, %r8d
movl $0xffffffff, %r9d       # imm = 0xFFFFFFFF
callq 0xf6710
movq %rax, 0x50(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x50(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x50, %rdx
leaq 0x4b302c(%rip), %rdi    # 0x52ea42
leaq 0x4b302c(%rip), %rsi    # 0x52ea49
movl $0xb, %ecx
xorl %eax, %eax
movl %eax, %r8d
movl $0xffffffff, %r9d       # imm = 0xFFFFFFFF
callq 0xf6710
movq %rax, 0x48(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x48(%rsp), %rsi
callq 0xf1600
movq 0x48(%rsp), %rdi
movq 0x50(%rsp), %rsi
callq 0xf7090
movq 0xc8(%rsp), %rdx
addq $0x58, %rdx
leaq 0x4b3002(%rip), %rdi    # 0x52ea6d
leaq 0x4b2fff(%rip), %rsi    # 0x52ea71
movl $0x3c, %ecx
movl $0x1, %r8d
movl $0x1f4, %r9d            # imm = 0x1F4
callq 0xf6710
movq %rax, 0x40(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x40(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rax
movq 0xa0(%rax), %rdx
leaq 0x4b3048(%rip), %rdi    # 0x52eafd
leaq 0x4b3046(%rip), %rsi    # 0x52eb02
callq 0xf6b00
movq %rax, 0x38(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x38(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x80, %rdx
leaq 0x4b309b(%rip), %rdi    # 0x52eb89
leaq 0x4b30a3(%rip), %rsi    # 0x52eb98
movsd 0x4b2c0b(%rip), %xmm0   # 0x52e708
callq 0xf62c0
movq %rax, 0x28(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x28(%rsp), %rsi
callq 0xf1600
movq 0x28(%rsp), %rdi
callq 0xf7400
movq 0x28(%rsp), %rdi
movq 0x38(%rsp), %rsi
callq 0xf7090
movq 0xc8(%rsp), %rax
movq 0x8(%rax), %rdx
movq 0x5c0f03(%rip), %rcx    # 0x63ca48
leaq 0x4b307f(%rip), %rdi    # 0x52ebcb
leaq 0x4b3083(%rip), %rsi    # 0x52ebd6
leaq 0x5c0ee6(%rip), %r8     # 0x63ca40
callq 0xf6b30
movq %rax, 0x20(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x20(%rsp), %rsi
callq 0xf1600
movq 0x20(%rsp), %rdi
movq 0x38(%rsp), %rsi
callq 0xf7090
movq 0xc8(%rsp), %rdx
addq $0x90, %rdx
leaq 0x4b30a3(%rip), %rdi    # 0x52ec3e
leaq 0x4b30a6(%rip), %rsi    # 0x52ec48
movl $0x32, %ecx
callq 0xf64b0
movq %rax, 0x18(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x18(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdi
callq 0xf6ff0
movq 0x18(%rsp), %rdi
movq 0x38(%rsp), %rsi
callq 0xf7090
movq 0xc8(%rsp), %rax
movq 0x18(%rax), %rdx
leaq 0x4b30c2(%rip), %rdi    # 0x52ecb1
leaq 0x4b30c3(%rip), %rsi    # 0x52ecb9
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x30(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x30(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x8b, %rdx
leaq 0x4e9bcb(%rip), %rdi    # 0x5657f7
leaq 0x4b30cb(%rip), %rsi    # 0x52ecfe
movl $0x1, %ecx
callq 0xf5f20
movq %rax, 0x10(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x10(%rsp), %rsi
callq 0xf1600
movq 0xc8(%rsp), %rdx
addq $0x8c, %rdx
leaq 0x4c24e1(%rip), %rdi    # 0x53e14b
leaq 0x4b30d2(%rip), %rsi    # 0x52ed43
xorl %ecx, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0xc0(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0xc0(%rsp), %rax
addq $0xd8, %rsp
retq
nop