// File: /workspace/github_c_makefile_star2_O2/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:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x550dc
movq %rdi, %rbx
leaq 0x2a88e3(%rip), %rdi    # 0x2fd54c
leaq 0x2a88fa(%rip), %rsi    # 0x2fd56a
callq 0x97df5
movq %rax, %r14
movq (%rbx), %rdx
leaq 0x2d845c(%rip), %rdi    # 0x32d0de
leaq 0x2a892b(%rip), %rsi    # 0x2fd5b4
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r15
movq %rax, %rdi
callq 0x9ae37
movq %r14, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x20(%rbx), %rdx
leaq 0x2a099f(%rip), %rdi    # 0x2f5650
leaq 0x2a893c(%rip), %rsi    # 0x2fd5f4
pushq $0x14
popq %rcx
pushq $0x5
popq %r8
callq 0x9ac58
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x28(%rbx), %rdx
leaq 0x2a8948(%rip), %rdi    # 0x2fd622
leaq 0x2a894b(%rip), %rsi    # 0x2fd62c
pushq $0x64
popq %rcx
pushq $0x1
popq %r15
pushq $-0x1
popq %r12
movq %r15, %r8
movq %r12, %r9
callq 0x9ac6b
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x30(%rbx), %rdx
leaq 0x2a8943(%rip), %rdi    # 0x2fd650
leaq 0x2a8946(%rip), %rsi    # 0x2fd65a
movl $0x3e8, %ecx            # imm = 0x3E8
movq %r15, %r8
movq %r12, %r9
callq 0x9ac6b
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x38(%rbx), %rdx
leaq 0x2a8944(%rip), %rdi    # 0x2fd67e
leaq 0x2a8948(%rip), %rsi    # 0x2fd689
movl $0x1f4, %ecx            # imm = 0x1F4
movq %r15, %r8
movq %r12, %r9
callq 0x9ac6b
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x40(%rbx), %rdx
leaq 0x2a8943(%rip), %rdi    # 0x2fd6aa
leaq 0x2a8947(%rip), %rsi    # 0x2fd6b5
movl $0x2710, %ecx           # imm = 0x2710
movq %r15, %r8
movq %r12, %r9
callq 0x9ac6b
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x60(%rbx), %rdx
leaq 0x2a6d79(%rip), %rdi    # 0x2fbb0d
leaq 0x2a893b(%rip), %rsi    # 0x2fd6d6
pushq $0x2
popq %rcx
pushq $0x1
popq %rbp
movl %ebp, %r8d
callq 0x9ab88
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x64(%rbx), %rdx
leaq 0x30a495(%rip), %rdi    # 0x35f254
leaq 0x2a893b(%rip), %rsi    # 0x2fd701
pushq $-0x2
popq %rcx
pushq $-0x1
popq %r12
movl %r12d, %r8d
callq 0x9ab9a
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x68(%rbx), %rdx
leaq 0x2ea0bb(%rip), %rdi    # 0x33eea6
leaq 0x2a893d(%rip), %rsi    # 0x2fd72f
pushq $-0x3
popq %r13
movl %r13d, %ecx
movl %r12d, %r8d
callq 0x9ab9a
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x6c(%rbx), %rdx
leaq 0x308750(%rip), %rdi    # 0x35d567
leaq 0x2a8940(%rip), %rsi    # 0x2fd75e
movl %r13d, %ecx
movl %r12d, %r8d
callq 0x9ab9a
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x70(%rbx), %rdx
leaq 0x2c5248(%rip), %rdi    # 0x31a087
leaq 0x2a8946(%rip), %rsi    # 0x2fd78c
pushq $0x5
popq %rcx
xorl %r8d, %r8d
callq 0x9ab88
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x78(%rbx), %rdx
leaq 0x2c97fa(%rip), %rdi    # 0x31e661
leaq 0x2a894e(%rip), %rsi    # 0x2fd7bc
movsd 0x2a868a(%rip), %xmm0   # 0x2fd500
movsd 0x294962(%rip), %xmm2   # 0x2e97e0
xorps %xmm1, %xmm1
callq 0x9ab20
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq 0x10(%rbx), %rdx
movq 0x3e3b04(%rip), %rcx    # 0x4389a0
leaq 0x3e3afd(%rip), %r8     # 0x4389a0
leaq 0x2e201d(%rip), %rdi    # 0x336ec7
leaq 0x2a8942(%rip), %rsi    # 0x2fd7f3
callq 0x9ad83
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
callq 0x97db0
movq %rax, 0x98(%rbx)
leaq 0x48(%rbx), %rdx
leaq 0x2a8931(%rip), %rdi    # 0x2fd80f
leaq 0x2a8931(%rip), %rsi    # 0x2fd816
pushq $0x2
popq %rcx
movl $0xffffffff, %r9d       # imm = 0xFFFFFFFF
xorl %r8d, %r8d
callq 0x9ac6b
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x50(%rbx), %rdx
leaq 0x2a892b(%rip), %rdi    # 0x2fd83a
leaq 0x2a892b(%rip), %rsi    # 0x2fd841
pushq $0xb
popq %rcx
movl $0xffffffff, %r9d       # imm = 0xFFFFFFFF
xorl %r8d, %r8d
callq 0x9ac6b
movq %rax, %r13
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r13, %rdi
movq %r12, %rsi
callq 0x9b14d
leaq 0x58(%rbx), %rdx
leaq 0x2a891a(%rip), %rdi    # 0x2fd865
leaq 0x2a8917(%rip), %rsi    # 0x2fd869
pushq $0x3c
popq %rcx
movl $0x1f4, %r9d            # imm = 0x1F4
movq %r15, %r8
callq 0x9ac6b
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq 0xa0(%rbx), %rdx
leaq 0x2a8979(%rip), %rdi    # 0x2fd8f5
leaq 0x2a8977(%rip), %rsi    # 0x2fd8fa
callq 0x9ad7e
movq %rax, %r15
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x80(%rbx), %rdx
leaq 0x2a89dd(%rip), %rdi    # 0x2fd981
leaq 0x2a89e5(%rip), %rsi    # 0x2fd990
movsd 0x2a8555(%rip), %xmm0   # 0x2fd508
callq 0x9ab56
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
callq 0x9b445
movq %r12, %rdi
movq %r15, %rsi
callq 0x9b14d
movq 0x8(%rbx), %rdx
movq 0x3e39f4(%rip), %rcx    # 0x4389d8
leaq 0x3e39e5(%rip), %r8     # 0x4389d0
leaq 0x2a89d1(%rip), %rdi    # 0x2fd9c3
leaq 0x2a89d5(%rip), %rsi    # 0x2fd9ce
callq 0x9ad83
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
movq %r15, %rsi
callq 0x9b14d
leaq 0x90(%rbx), %rdx
leaq 0x2a8a11(%rip), %rdi    # 0x2fda36
leaq 0x2a8a14(%rip), %rsi    # 0x2fda40
pushq $0x32
popq %rcx
callq 0x9abcd
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
callq 0x9b0c7
movq %r12, %rdi
movq %r15, %rsi
callq 0x9b14d
movq 0x18(%rbx), %rdx
leaq 0x2a8a49(%rip), %rdi    # 0x2fdaa9
leaq 0x2a8a4a(%rip), %rsi    # 0x2fdab1
xorl %ecx, %ecx
callq 0x9ad12
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x8b(%rbx), %rdx
leaq 0x2de1cc(%rip), %rdi    # 0x333253
leaq 0x2a8a68(%rip), %rsi    # 0x2fdaf6
movl %ebp, %ecx
callq 0x9a997
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
addq $0x8c, %rbx
leaq 0x2b76cb(%rip), %rdi    # 0x30c779
leaq 0x2a8a86(%rip), %rsi    # 0x2fdb3b
movq %rbx, %rdx
xorl %ecx, %ecx
callq 0x9a997
movq %r14, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x3e2e85(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x28ff26(%rip), %rsi    # 0x2e5013
leaq 0x2f355f(%rip), %rdx    # 0x348653
leaq 0x2a8438(%rip), %rcx    # 0x2fd533
leaq 0x2a8416(%rip), %r8     # 0x2fd518
pushq $0x7e
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390