// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_gdiffcalc.c
// Function: gt_gdiffcalc_option_parser_new
static GtOptionParser* gt_gdiffcalc_option_parser_new(void *tool_arguments)
{
  GtGenomediffArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *option_unitfile;

  gt_assert(arguments);

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

  /* options */
  option = gt_option_new_string("indexname", "Basename of encseq to construct.",
                                arguments->indexname, NULL);
  gt_option_is_mandatory(option);
  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));

  /* 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);

  /* 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 0x2b95b
movq %rdi, %r14
leaq 0x2c1a99(%rip), %rdi    # 0x2ed200
leaq 0x2c1abb(%rip), %rsi    # 0x2ed229
callq 0x97df5
movq %rax, %rbx
movq 0x50(%r14), %rdx
leaq 0x2da2dc(%rip), %rdi    # 0x305a5d
leaq 0x2c1ad4(%rip), %rsi    # 0x2ed25c
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r15
movq %rax, %rdi
callq 0x9ae37
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq 0x60(%r14), %rdx
leaq 0x2c1acd(%rip), %rdi    # 0x2ed27d
leaq 0x2c1acf(%rip), %rsi    # 0x2ed286
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
leaq 0x10(%r14), %rdx
leaq 0x2c1ab8(%rip), %rdi    # 0x2ed2b9
leaq 0x2c1ab7(%rip), %rsi    # 0x2ed2bf
movl $0x3e8, %ecx            # imm = 0x3E8
callq 0x9a9e6
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x30(%r14), %rdx
leaq 0x2c1ac2(%rip), %rdi    # 0x2ed2f5
leaq 0x2c1abf(%rip), %rsi    # 0x2ed2f9
movsd 0x2c1966(%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 0x2c1ad4(%rip), %rdi    # 0x2ed344
leaq 0x2c1ad5(%rip), %rsi    # 0x2ed34c
movsd 0x2c1931(%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 0x2c1add(%rip), %rdi    # 0x2ed38a
leaq 0x2c1ade(%rip), %rsi    # 0x2ed392
movsd 0x2c18fc(%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 0x2d25c8(%rip), %rdi    # 0x2fdeb2
leaq 0x2c1adf(%rip), %rsi    # 0x2ed3d0
movsd 0x2c18c7(%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 0x2c1ac9(%rip), %rsi    # 0x2ed402
movq %rbx, %rdi
callq 0x98288
leaq 0xbbba4(%rip), %rsi     # 0xe74ec
movq %rbx, %rdi
xorl %edx, %edx
callq 0x98045
movq %rbx, %rax
popq %rbx
popq %r14
popq %r15
retq
movq 0x40c606(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2b96a7(%rip), %rsi    # 0x2e5013
leaq 0x31cce0(%rip), %rdx    # 0x348653
leaq 0x2c1867(%rip), %rcx    # 0x2ed1e1
leaq 0x2c1847(%rip), %r8     # 0x2ed1c8
pushq $0x4b
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390