// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_select.c
// Function: gt_select_option_parser_new
static GtOptionParser* gt_select_option_parser_new(void *tool_arguments)
{
  SelectArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *contain_option, *overlap_option, *minaveragessp_option,
           *singleintron_option, *optiondroppedfile;
  gt_assert(arguments);

  static const char *filter_logic[] = {
    "AND",
    "OR",
    NULL
  };

  /* init */
  op = gt_option_parser_new("[option ...] [GFF3_file ...]",
                            "Select certain features (specified by the used "
                            "options) from given GFF3 file(s).");

  /* -retainids */
  option = gt_option_new_bool("retainids",
                              "when available, use the original IDs provided "
                              "in the source file\n"
                              "(memory consumption is proportional to the "
                              "input file size(s))", &arguments->retainids,
                              false);
  gt_option_parser_add_option(op, option);

  /* -seqid */
  option = gt_option_new_string("seqid", "select feature with the given "
                                "sequence ID (all comments are selected). ",
                                arguments->seqid, NULL);
  gt_option_parser_add_option(op, option);

  /* -source */
  option = gt_option_new_string("source", "select feature with the given "
                                "source (the source is column 2 in regular "
                                "GFF3 lines)" , arguments->source, NULL);
  gt_option_parser_add_option(op, option);

  /* -contain */
  contain_option = gt_option_new_range("contain", "select all features which "
                                       "are contained in the given range",
                                       &arguments->contain_range, NULL);
  gt_option_parser_add_option(op, contain_option);

  /* -overlap */
  overlap_option = gt_option_new_range("overlap", "select all features which "
                                       "do overlap with the given range",
                                       &arguments->overlap_range, NULL);
  gt_option_parser_add_option(op, overlap_option);

  /* -strand */
  option = gt_option_new_string(GT_STRAND_OPT, "select all top-level features"
                                "(i.e., features without parents) whose strand "
                                "equals the given one (must be one of '"
                                GT_STRAND_CHARS"')", arguments->gt_strand_char,
                                NULL);
  gt_option_parser_add_option(op, option);

  /* -targetstrand */
  option = gt_option_new_string(TARGETGT_STRAND_OPT, "select all top-level "
                                "features (i.e., features without parents) "
                                "which have exactly one target attribute whose "
                                "strand equals the given one (must be one of '"
                                GT_STRAND_CHARS"')",
                                arguments->targetgt_strand_char, NULL);
  gt_option_parser_add_option(op, option);

  /* -targetbest */
  option = gt_option_new_bool("targetbest", "if multiple top-level features "
                             "(i.e., features without parents) with exactly "
                             "one target attribute have the same target_id, "
                             "keep only the feature with the best score. If "
                             "-"TARGETGT_STRAND_OPT" is used at the same time, "
                             "this option is applied after "
                             "-"TARGETGT_STRAND_OPT".\n"
                             "Memory consumption is proportional to the input "
                             "file size(s).", &arguments->targetbest, false);
  gt_option_parser_add_option(op, option);

  /* -hascds */
  option = gt_option_new_bool("hascds", "select all top-level features which "
                              "do have a CDS child", &arguments->has_CDS,
                              false);
  gt_option_parser_add_option(op, option);

  /* -maxgenelength */
  option = gt_option_new_uword_min("maxgenelength", "select genes up to the "
                                   "given maximum length",
                                   &arguments->max_gene_length, GT_UNDEF_UWORD,
                                   1);
  gt_option_parser_add_option(op, option);

  /* -maxgenenum */
  option = gt_option_new_uword("maxgenenum", "select the first genes up to the "
                               "given maximum number", &arguments->max_gene_num,
                               GT_UNDEF_UWORD);
  gt_option_parser_add_option(op, option);

  /* -mingenescore */
  option = gt_option_new_double("mingenescore", "select genes with the given "
                                "minimum score", &arguments->min_gene_score,
                                GT_UNDEF_DOUBLE);
  gt_option_parser_add_option(op, option);

  /* -maxgenescore */
  option = gt_option_new_double("maxgenescore", "select genes with the given "
                                "maximum score", &arguments->max_gene_score,
                                GT_UNDEF_DOUBLE);
  gt_option_parser_add_option(op, option);

  /* -minaveragessp */
  minaveragessp_option =
    gt_option_new_probability("minaveragessp",
                              "set the minimum average splice site probability",
                              &arguments->min_average_splice_site_prob,
                              GT_UNDEF_DOUBLE);
  gt_option_parser_add_option(op, minaveragessp_option);

  /* -singleintronfactor */
  singleintron_option =
    gt_option_new_double_min("singleintronfactor",
                             "factor to multiplicate the average splice site "
                             "probability with for single introns before "
                             "comparing it to the minimum average splice site "
                             "probability", &arguments->single_intron_factor,
                             1.0, 1.0);
  gt_option_is_development_option(singleintron_option);
  gt_option_parser_add_option(op, singleintron_option);

  /* -featurenum */
  option = gt_option_new_uword_min("featurenum",
                                   "select feature tree occurring "
                                   "at given position in input",
                                   &arguments->feature_num, GT_UNDEF_UWORD, 1);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -filter_files */
  option = gt_option_new_filename_array("rule_files",
                                        "specify Lua filter rule files "
                                        "to be used for selection "
                                        "(terminate list with '--') ",
                                        arguments->filter_files);
  gt_option_parser_add_option(op, option);

  /* -filter_logic */
  option = gt_option_new_choice("rule_logic", "select how multiple Lua "
                                "files should be combined\nchoose from AND|OR",
                                arguments->filter_logic, filter_logic[0],
                                filter_logic);
  gt_option_parser_add_option(op, option);

  /* -nh_file */
  optiondroppedfile = gt_option_new_filename("dropped_file",
                                             "save non-selected features to "
                                             "file",
                                             arguments->dropped_file);
  gt_option_parser_add_option(op, optiondroppedfile);

  /* -v */
  option = gt_option_new_verbose(&arguments->verbose);
  gt_option_parser_add_option(op, option);

  /* option exclusions */
  gt_option_exclude(contain_option, overlap_option);

  /* option implications */
  gt_option_imply(singleintron_option, minaveragessp_option);

  /* output file options */
  gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);

  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);

  return op;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xc311a
movq %rdi, %rbx
leaq 0x29077a(%rip), %rdi    # 0x353509
leaq 0x29d44d(%rip), %rsi    # 0x3601e3
callq 0x10cc4e
movq %rax, %r14
leaq 0x3(%rbx), %rdx
leaq 0x326d42(%rip), %rdi    # 0x3e9aeb
leaq 0x293dba(%rip), %rsi    # 0x356b6a
xorl %ecx, %ecx
callq 0x10f451
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x8(%rbx), %rdx
leaq 0x2a5dca(%rip), %rdi    # 0x368b97
leaq 0x29d460(%rip), %rsi    # 0x360234
xorl %ecx, %ecx
callq 0x10f987
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x10(%rbx), %rdx
leaq 0x2c4075(%rip), %rdi    # 0x386e66
leaq 0x29d484(%rip), %rsi    # 0x36027c
xorl %ecx, %ecx
callq 0x10f987
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x28(%rbx), %rdx
leaq 0x29d4bb(%rip), %rdi    # 0x3602d0
leaq 0x29d4bc(%rip), %rsi    # 0x3602d8
xorl %ecx, %ecx
callq 0x10f913
movq %rax, (%rsp)
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x38(%rbx), %rdx
leaq 0x2b54cd(%rip), %rdi    # 0x37830a
leaq 0x29d4cf(%rip), %rsi    # 0x360313
xorl %ecx, %ecx
callq 0x10f913
movq %rax, %r12
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x18(%rbx), %rdx
leaq 0x29c9a2(%rip), %rdi    # 0x35f806
leaq 0x29d4e2(%rip), %rsi    # 0x36034d
xorl %ecx, %ecx
callq 0x10f987
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0x20(%rbx), %rdx
leaq 0x2d8b45(%rip), %rdi    # 0x39b9cd
leaq 0x29d536(%rip), %rsi    # 0x3603c5
xorl %ecx, %ecx
callq 0x10f987
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x2(%rbx), %rdx
leaq 0x2dcc5c(%rip), %rdi    # 0x39fb08
leaq 0x29d5b3(%rip), %rsi    # 0x360466
xorl %ecx, %ecx
callq 0x10f451
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x1(%rbx), %rdx
leaq 0x29d6d1(%rip), %rdi    # 0x3605a1
leaq 0x29d6d1(%rip), %rsi    # 0x3605a8
xorl %ecx, %ecx
callq 0x10f451
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x50(%rbx), %rdx
leaq 0x29d6ec(%rip), %rdi    # 0x3605e0
leaq 0x29d6f3(%rip), %rsi    # 0x3605ee
movl $0x1, %r8d
movq $-0x1, %rcx
callq 0x10f7ed
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x58(%rbx), %rdx
leaq 0x29d6f7(%rip), %rdi    # 0x36061a
leaq 0x29d6fb(%rip), %rsi    # 0x360625
movq $-0x1, %rcx
callq 0x10f4c7
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x68(%rbx), %rdx
leaq 0x29d70f(%rip), %rdi    # 0x36065b
leaq 0x29d715(%rip), %rsi    # 0x360668
movsd 0x28ddb5(%rip), %xmm0   # 0x350d10
callq 0x10f562
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x70(%rbx), %rdx
leaq 0x29d71c(%rip), %rdi    # 0x360692
leaq 0x29d722(%rip), %rsi    # 0x36069f
movsd 0x28dd8b(%rip), %xmm0   # 0x350d10
callq 0x10f562
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x78(%rbx), %rdx
leaq 0x29d729(%rip), %rdi    # 0x3606c9
leaq 0x29d730(%rip), %rsi    # 0x3606d7
movsd 0x28dd61(%rip), %xmm0   # 0x350d10
callq 0x10f627
movq %rax, %r13
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x80(%rbx), %rdx
leaq 0x29d737(%rip), %rdi    # 0x360707
leaq 0x29d743(%rip), %rsi    # 0x36071a
movsd 0x28c249(%rip), %xmm0   # 0x34f228
movaps %xmm0, %xmm1
callq 0x10f590
movq %rax, %rbp
movq %rax, %rdi
callq 0x10fbef
movq %r14, %rdi
movq %rbp, %rsi
callq 0x10cd10
leaq 0x60(%rbx), %rdx
leaq 0x29d7a8(%rip), %rdi    # 0x3607b0
leaq 0x29d7ac(%rip), %rsi    # 0x3607bb
movl $0x1, %r8d
movq $-0x1, %rcx
callq 0x10f7ed
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %r14, %rdi
movq %r15, %rsi
callq 0x10cd10
movq 0x98(%rbx), %rdx
leaq 0x29d7af(%rip), %rdi    # 0x3607f4
leaq 0x29d7b3(%rip), %rsi    # 0x3607ff
callq 0x10f9f6
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0xa0(%rbx), %rdx
movq 0x401906(%rip), %rcx    # 0x4c4970
leaq 0x4018ff(%rip), %r8     # 0x4c4970
leaq 0x29d7da(%rip), %rdi    # 0x360852
leaq 0x29d7de(%rip), %rsi    # 0x36085d
callq 0x10fa04
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq 0xa8(%rbx), %rdx
leaq 0x29d804(%rip), %rdi    # 0x3608a1
leaq 0x29d80a(%rip), %rsi    # 0x3608ae
callq 0x10f9c6
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %rbx, %rdi
callq 0x10f473
movq %r14, %rdi
movq %rax, %rsi
callq 0x10cd10
movq (%rsp), %rdi
movq %r12, %rsi
callq 0x10fd9f
movq %rbp, %rdi
movq %r13, %rsi
callq 0x10fbff
movq 0x88(%rbx), %rdi
addq $0x90, %rbx
movq %r14, %rsi
movq %rbx, %rdx
callq 0x10ffa3
leaq 0x90d9e(%rip), %rsi     # 0x153e9c
movq %r14, %rdi
xorl %edx, %edx
callq 0x10cd8d
movq %r14, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
callq 0x1ec81