// File: /workspace/github_c_makefile_star2_O0/genometools[P]genometools/src/tools/gt_genomediff.c
// Function: gt_genomediff_option_parser_new
static GtOptionParser* gt_genomediff_option_parser_new(void *tool_arguments)
{
  GtGenomediffArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *option_unitfile;
  static const char *indextypes[] = { "esa", "pck", "encseq", NULL };

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] "
                          "(INDEX | -indexname NAME SEQFILE SEQFILE [...]) ",
                          "Calculates Kr: pairwise distances between genomes.");

  /* options */
  option = gt_option_new_choice("indextype", "specify type of index, one of: "
                                "esa|pck|encseq. Where encseq is an encoded "
                                "sequence and an enhanced suffix array will be "
                                "constructed only in memory.",
                                arguments->indextype, indextypes[2],
                                indextypes);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_string("indexname", "Basename of encseq to construct.",
                                arguments->indexname, NULL);
  gt_option_parser_add_option(op, option);

  /*-unitfile*/
  option_unitfile =
    gt_option_new_filename("unitfile",
                           "specifies genomic units, "
                           "see below for description.",
                           arguments->unitfile);
  gt_option_parser_add_option(op, option_unitfile);
  arguments->ref_unitfile = gt_option_ref(option_unitfile);

  /* encseq options */
  arguments->loadopts =
    gt_encseq_options_register_loading(op, arguments->indexname);

  gt_option_is_development_option(
                        gt_encseq_options_lossless_option(arguments->loadopts));
  /* esa options */
  arguments->idxopts =
    gt_index_options_register_esa_noout(op);
  gt_option_is_development_option(
                            gt_index_options_spmopt_option(arguments->idxopts));

  /* scan */
  option = gt_option_new_bool("scan", "do not load esa index but scan "
                              "it sequentially.", &arguments->scanfile, true);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* dev options */
  /* -max_n */
  option = gt_option_new_uword("max_n", "Number of precalculated values "
                               "for ln(n!) and pmax(x).",
                               &arguments->max_ln_n_fac, 1000UL);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -maxdepth */
  option =  gt_option_new_int("maxdepth", "max depth of .pbi-file, use with "
                              "-indextype pck.",
                              &arguments->user_max_depth, -1);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* thresholds */
  /* divergence error */
  option = gt_option_new_double("thr",
                                "Threshold for difference (du, dl) in "
                                "divergence calculation.\n"
                                "default: 1e-9",
                                &arguments->divergence_threshold,
                                1e-9);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* expected shulen error */
  option = gt_option_new_double("abs_err",
                                "absolute error for expected shulen "
                                "calculation.\n"
                                "default: 1e-5",
                                &arguments->divergence_abs_err,
                                1e-5);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* relative expected shulen error */
  option = gt_option_new_double("rel_err",
                                "relative error for expected shulen "
                                "calculation.\n"
                                "default: 1e-3",
                                &arguments->divergence_rel_err,
                                1e-3);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* M */
  option = gt_option_new_double("M",
                                "threshold for minimum logarithm.\n"
                                "default: DBL_MIN",
                                &arguments->divergence_m,
                                DBL_MIN);
  gt_option_is_extended_option(option);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

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

  /* mail */
  gt_option_parser_set_mail_address(op, "<willrodt@zbh.uni-hamburg.de>");
  /* doc */
  gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
  return op;
}

// Assembly:
subq $0x28, %rsp
movq %rdi, 0x20(%rsp)
movq 0x20(%rsp), %rax
movq %rax, 0x18(%rsp)
cmpq $0x0, 0x18(%rsp)
jne 0x39eb3
movq 0x60211e(%rip), %rax    # 0x63bfa0
movq (%rax), %rdi
leaq 0x4dc187(%rip), %rsi    # 0x516013
leaq 0x540ccc(%rip), %rdx    # 0x57ab5f
leaq 0x4e4786(%rip), %rcx    # 0x51e620
leaq 0x4e4765(%rip), %r8     # 0x51e606
movl $0x4a, %r9d
movb $0x0, %al
callq 0x199f0
callq 0x19370
jmp 0x39eb5
leaq 0x4e4784(%rip), %rdi    # 0x51e640
leaq 0x4e4406(%rip), %rsi    # 0x51e2c9
callq 0xf1420
movq %rax, 0x10(%rsp)
movq 0x18(%rsp), %rax
movq 0x58(%rax), %rdx
movq 0x602963(%rip), %rcx    # 0x63c840
leaq 0x4e7ec6(%rip), %rdi    # 0x521daa
leaq 0x4e4793(%rip), %rsi    # 0x51e67e
leaq 0x60293e(%rip), %r8     # 0x63c830
callq 0xf6b30
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rax
movq 0x50(%rax), %rdx
leaq 0x4fcec4(%rip), %rdi    # 0x536ddf
leaq 0x4e43da(%rip), %rsi    # 0x51e2fc
xorl %eax, %eax
movl %eax, %ecx
callq 0xf69f0
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rax
movq 0x60(%rax), %rdx
leaq 0x4e43ce(%rip), %rdi    # 0x51e31d
leaq 0x4e47bc(%rip), %rsi    # 0x51e712
callq 0xf6aa0
movq %rax, (%rsp)
movq 0x10(%rsp), %rdi
movq (%rsp), %rsi
callq 0xf1600
movq (%rsp), %rdi
callq 0xf13c0
movq %rax, %rcx
movq 0x18(%rsp), %rax
movq %rcx, 0x48(%rax)
movq 0x10(%rsp), %rdi
movq 0x18(%rsp), %rax
movq 0x50(%rax), %rsi
callq 0xd7350
movq %rax, %rcx
movq 0x18(%rsp), %rax
movq %rcx, 0x38(%rax)
movq 0x18(%rsp), %rax
movq 0x38(%rax), %rdi
callq 0xd7700
movq %rax, %rdi
callq 0xf7040
movq 0x10(%rsp), %rdi
callq 0x25c6a0
movq %rax, %rcx
movq 0x18(%rsp), %rax
movq %rcx, 0x40(%rax)
movq 0x18(%rsp), %rax
movq 0x40(%rax), %rdi
callq 0x25cc60
movq %rax, %rdi
callq 0xf7040
movq 0x18(%rsp), %rdx
leaq 0x4e4567(%rip), %rdi    # 0x51e556
leaq 0x4e4750(%rip), %rsi    # 0x51e746
movl $0x1, %ecx
callq 0xf5f20
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x10, %rdx
leaq 0x4e432b(%rip), %rdi    # 0x51e359
leaq 0x4e4741(%rip), %rsi    # 0x51e776
movl $0x3e8, %ecx            # imm = 0x3E8
callq 0xf5fe0
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf7040
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x8, %rdx
leaq 0x4fee23(%rip), %rdi    # 0x538e90
leaq 0x4e4739(%rip), %rsi    # 0x51e7ad
movl $0xffffffff, %ecx       # imm = 0xFFFFFFFF
callq 0xf6310
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf7040
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x30, %rdx
leaq 0x4e42e9(%rip), %rdi    # 0x51e395
leaq 0x4e42e6(%rip), %rsi    # 0x51e399
movsd 0x4e41a5(%rip), %xmm0   # 0x51e260
callq 0xf6160
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x8(%rsp), %rdi
callq 0xf7400
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x18, %rdx
leaq 0x4e42ec(%rip), %rdi    # 0x51e3e4
leaq 0x4e42ed(%rip), %rsi    # 0x51e3ec
movsd 0x4e4151(%rip), %xmm0   # 0x51e258
callq 0xf6160
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x8(%rsp), %rdi
callq 0xf7400
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x28, %rdx
leaq 0x4e42e6(%rip), %rdi    # 0x51e42a
leaq 0x4e42e7(%rip), %rsi    # 0x51e432
movsd 0x4e40fd(%rip), %xmm0   # 0x51e250
callq 0xf6160
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x8(%rsp), %rdi
callq 0xf7400
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdx
addq $0x20, %rdx
leaq 0x4f4f2a(%rip), %rdi    # 0x52f0ba
leaq 0x4e42d9(%rip), %rsi    # 0x51e470
movsd 0x4e40a9(%rip), %xmm0   # 0x51e248
callq 0xf6160
movq %rax, 0x8(%rsp)
movq 0x8(%rsp), %rdi
callq 0xf6ff0
movq 0x8(%rsp), %rdi
callq 0xf7400
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x18(%rsp), %rdi
addq $0x1, %rdi
callq 0xf5f90
movq %rax, 0x8(%rsp)
movq 0x10(%rsp), %rdi
movq 0x8(%rsp), %rsi
callq 0xf1600
movq 0x10(%rsp), %rdi
leaq 0x4e42a8(%rip), %rsi    # 0x51e4a2
callq 0xf1a10
movq 0x10(%rsp), %rdi
leaq 0x147ad5(%rip), %rsi    # 0x181ce0
xorl %eax, %eax
movl %eax, %edx
callq 0xf1770
movq 0x10(%rsp), %rax
addq $0x28, %rsp
retq
nop