// File: /workspace/github_c_makefile_star2_O2/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:
pushq %r15
pushq %r14
pushq %rbx
testq %rdi, %rdi
je 0x2c403
movq %rdi, %r14
leaq 0x2c1431(%rip), %rdi    # 0x2ed5a0
leaq 0x2c10b3(%rip), %rsi    # 0x2ed229
callq 0x97df5
movq %rax, %rbx
movq 0x58(%r14), %rdx
movq 0x40c6c7(%rip), %rcx    # 0x438850
leaq 0x40c6b0(%rip), %r8     # 0x438840
leaq 0x2c4ba8(%rip), %rdi    # 0x2f0d3f
leaq 0x2c1440(%rip), %rsi    # 0x2ed5de
callq 0x9ad83
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq 0x50(%r14), %rdx
leaq 0x2d98a4(%rip), %rdi    # 0x305a5d
leaq 0x2c109c(%rip), %rsi    # 0x2ed25c
xorl %ecx, %ecx
callq 0x9ad12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq 0x60(%r14), %rdx
leaq 0x2c10a0(%rip), %rdi    # 0x2ed27d
leaq 0x2c148e(%rip), %rsi    # 0x2ed672
callq 0x9ad51
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x97db0
movq %rax, 0x48(%r14)
movq 0x50(%r14), %rsi
movq %rbx, %rdi
callq 0x88f82
movq %rax, 0x38(%r14)
movq %rax, %rdi
callq 0x8925a
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
callq 0x163fd2
movq %rax, 0x40(%r14)
movq %rax, %rdi
callq 0x1643fe
movq %rax, %rdi
callq 0x9b10a
leaq 0x2c1270(%rip), %rdi    # 0x2ed4b6
leaq 0x2c1459(%rip), %rsi    # 0x2ed6a6
pushq $0x1
popq %rcx
movq %r14, %rdx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x10(%r14), %rdx
leaq 0x2c1040(%rip), %rdi    # 0x2ed2b9
leaq 0x2c1456(%rip), %rsi    # 0x2ed6d6
movl $0x3e8, %ecx            # imm = 0x3E8
callq 0x9a9e6
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x8(%r14), %rdx
leaq 0x2db7b0(%rip), %rdi    # 0x307a5b
leaq 0x2c145b(%rip), %rsi    # 0x2ed70d
pushq $-0x1
popq %rcx
callq 0x9ab66
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x30(%r14), %rdx
leaq 0x2c101a(%rip), %rdi    # 0x2ed2f5
leaq 0x2c1017(%rip), %rsi    # 0x2ed2f9
movsd 0x2c0ebe(%rip), %xmm0   # 0x2ed1a8
callq 0x9aad7
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r15, %rdi
callq 0x9b445
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x18(%r14), %rdx
leaq 0x2c102c(%rip), %rdi    # 0x2ed344
leaq 0x2c102d(%rip), %rsi    # 0x2ed34c
movsd 0x2c0e89(%rip), %xmm0   # 0x2ed1b0
callq 0x9aad7
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r15, %rdi
callq 0x9b445
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x28(%r14), %rdx
leaq 0x2c1035(%rip), %rdi    # 0x2ed38a
leaq 0x2c1036(%rip), %rsi    # 0x2ed392
movsd 0x2c0e54(%rip), %xmm0   # 0x2ed1b8
callq 0x9aad7
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r15, %rdi
callq 0x9b445
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x20(%r14), %rdx
leaq 0x2d1b20(%rip), %rdi    # 0x2fdeb2
leaq 0x2c1037(%rip), %rsi    # 0x2ed3d0
movsd 0x2c0e1f(%rip), %xmm0   # 0x2ed1c0
callq 0x9aad7
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r15, %rdi
callq 0x9b445
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
incq %r14
movq %r14, %rdi
callq 0x9a9b6
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x2c1021(%rip), %rsi    # 0x2ed402
movq %rbx, %rdi
callq 0x98288
leaq 0xbb0fc(%rip), %rsi     # 0xe74ec
movq %rbx, %rdi
xorl %edx, %edx
callq 0x98045
movq %rbx, %rax
popq %rbx
popq %r14
popq %r15
retq
movq 0x40bb5e(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2b8bff(%rip), %rsi    # 0x2e5013
leaq 0x31c238(%rip), %rdx    # 0x348653
leaq 0x2c115e(%rip), %rcx    # 0x2ed580
leaq 0x2c113d(%rip), %r8     # 0x2ed566
pushq $0x4a
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390