// File: /workspace/github_c_makefile_star2_O1/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 %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xd204b
movq %rdi, %rbx
leaq 0x294aec(%rip), %rdi    # 0x366694
leaq 0x294b03(%rip), %rsi    # 0x3666b2
callq 0x10cc4e
movq %rax, %r14
movq (%rbx), %rdx
leaq 0x2c450d(%rip), %rdi    # 0x3960ce
leaq 0x294b34(%rip), %rsi    # 0x3666fc
xorl %ecx, %ecx
callq 0x10f987
movq %rax, %r15
movq %rax, %rdi
callq 0x10fa96
movq %r14, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x20(%rbx), %rdx
leaq 0x28ca80(%rip), %rdi    # 0x35e670
leaq 0x294b45(%rip), %rsi    # 0x36673c
movl $0x14, %ecx
movl $0x5, %r8d
callq 0x10f7ed
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x28(%rbx), %rdx
leaq 0x294b4d(%rip), %rdi    # 0x36676a
leaq 0x294b50(%rip), %rsi    # 0x366774
movl $0x64, %ecx
movl $0x1, %r8d
movq $-0x1, %r9
callq 0x10f81b
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x30(%rbx), %rdx
leaq 0x294b47(%rip), %rdi    # 0x366798
leaq 0x294b4a(%rip), %rsi    # 0x3667a2
movl $0x3e8, %ecx            # imm = 0x3E8
movl $0x1, %r8d
movq $-0x1, %r9
callq 0x10f81b
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x38(%rbx), %rdx
leaq 0x294b41(%rip), %rdi    # 0x3667c6
leaq 0x294b45(%rip), %rsi    # 0x3667d1
movl $0x1f4, %ecx            # imm = 0x1F4
movl $0x1, %r8d
movq $-0x1, %r9
callq 0x10f81b
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x40(%rbx), %rdx
leaq 0x294b39(%rip), %rdi    # 0x3667f2
leaq 0x294b3d(%rip), %rsi    # 0x3667fd
movl $0x2710, %ecx           # imm = 0x2710
movl $0x1, %r8d
movq $-0x1, %r9
callq 0x10f81b
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x60(%rbx), %rdx
leaq 0x292f6a(%rip), %rdi    # 0x364c57
leaq 0x294b2a(%rip), %rsi    # 0x36681e
movl $0x2, %ecx
movl $0x1, %r8d
callq 0x10f68b
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x64(%rbx), %rdx
leaq 0x2f676a(%rip), %rdi    # 0x3c8484
leaq 0x294b28(%rip), %rsi    # 0x366849
movl $0xfffffffe, %ecx       # imm = 0xFFFFFFFE
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
callq 0x10f6b4
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x68(%rbx), %rdx
leaq 0x2d632f(%rip), %rdi    # 0x3a8076
leaq 0x294b29(%rip), %rsi    # 0x366877
movl $0xfffffffd, %ecx       # imm = 0xFFFFFFFD
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
callq 0x10f6b4
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x6c(%rbx), %rdx
leaq 0x2f4a20(%rip), %rdi    # 0x3c6794
leaq 0x294b2b(%rip), %rsi    # 0x3668a6
movl $0xfffffffd, %ecx       # imm = 0xFFFFFFFD
movl $0xffffffff, %r8d       # imm = 0xFFFFFFFF
callq 0x10f6b4
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x70(%rbx), %rdx
leaq 0x2b12b6(%rip), %rdi    # 0x383057
leaq 0x294b2c(%rip), %rsi    # 0x3668d4
movl $0x5, %ecx
xorl %r8d, %r8d
callq 0x10f68b
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x78(%rbx), %rdx
leaq 0x2b57fe(%rip), %rdi    # 0x3875c9
leaq 0x294b32(%rip), %rsi    # 0x366904
movsd 0x29486e(%rip), %xmm0   # 0x366648
movsd 0x280a0e(%rip), %xmm2   # 0x3527f0
xorps %xmm1, %xmm1
callq 0x10f5d1
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x10(%rbx), %rdx
movq 0x3f2bf0(%rip), %rcx    # 0x4c49f0
leaq 0x3f2be9(%rip), %r8     # 0x4c49f0
leaq 0x2ce210(%rip), %rdi    # 0x3a001e
leaq 0x294b26(%rip), %rsi    # 0x36693b
callq 0x10fa04
movq %rax, %r15
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r15, %rdi
callq 0x10cc3c
movq %rax, 0x98(%rbx)
leaq 0x48(%rbx), %rdx
leaq 0x294b15(%rip), %rdi    # 0x366957
leaq 0x294b15(%rip), %rsi    # 0x36695e
movl $0x2, %ecx
movl $0xffffffff, %r9d       # imm = 0xFFFFFFFF
xorl %r8d, %r8d
callq 0x10f81b
movq %rax, %r15
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x50(%rbx), %rdx
leaq 0x294b0d(%rip), %rdi    # 0x366982
leaq 0x294b0d(%rip), %rsi    # 0x366989
movl $0xb, %ecx
movl $0xffffffff, %r9d       # imm = 0xFFFFFFFF
xorl %r8d, %r8d
callq 0x10f81b
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fbff
leaq 0x58(%rbx), %rdx
leaq 0x294afa(%rip), %rdi    # 0x3669ad
leaq 0x294af7(%rip), %rsi    # 0x3669b1
movl $0x3c, %ecx
movl $0x1, %r8d
movl $0x1f4, %r9d            # imm = 0x1F4
callq 0x10f81b
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0xa0(%rbx), %rdx
leaq 0x294b54(%rip), %rdi    # 0x366a3d
leaq 0x294b52(%rip), %rsi    # 0x366a42
callq 0x10f9f6
movq %rax, %r15
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x80(%rbx), %rdx
leaq 0x294bb8(%rip), %rdi    # 0x366ac9
leaq 0x294bc0(%rip), %rsi    # 0x366ad8
movsd 0x294730(%rip), %xmm0   # 0x366650
callq 0x10f627
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r12, %rdi
callq 0x10fe32
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fbff
movq 0x8(%rbx), %rdx
movq 0x3f2ad7(%rip), %rcx    # 0x4c4a28
leaq 0x3f2ac8(%rip), %r8     # 0x4c4a20
leaq 0x294bac(%rip), %rdi    # 0x366b0b
leaq 0x294bb0(%rip), %rsi    # 0x366b16
callq 0x10fa04
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fbff
leaq 0x90(%rbx), %rdx
leaq 0x294bec(%rip), %rdi    # 0x366b7e
leaq 0x294bef(%rip), %rsi    # 0x366b88
movl $0x32, %ecx
callq 0x10f719
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r12, %rdi
callq 0x10fbdf
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fbff
movq 0x18(%rbx), %rdx
leaq 0x294c22(%rip), %rdi    # 0x366bf1
leaq 0x294c23(%rip), %rsi    # 0x366bf9
xorl %ecx, %ecx
callq 0x10f987
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x8b(%rbx), %rdx
leaq 0x2ca36d(%rip), %rdi    # 0x39c363
leaq 0x294c41(%rip), %rsi    # 0x366c3e
movl $0x1, %ecx
callq 0x10f451
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
addq $0x8c, %rbx
leaq 0x2a3684(%rip), %rdi    # 0x3756a4
leaq 0x294c5c(%rip), %rsi    # 0x366c83
movq %rbx, %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x21c11