// File: /workspace/github_c_makefile_star2_O2/genometools[P]genometools/src/tools/gt_readjoiner_overlap.c
// Function: gt_readjoiner_overlap_option_parser_new
static GtOptionParser* gt_readjoiner_overlap_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerOverlapArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *optionparts, *optionmemlimit, *q_option, *v_option;

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...] [file]",
                            "Compute suffix prefix matches "
                            "from encoded sequence.");

  /* -readset */
  option = gt_option_new_string("readset", "specify the readset name",
                                arguments->encseqinput, NULL);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -l */
  option = gt_option_new_uint_min("l", "specify the minimum SPM length",
                                  &arguments->minmatchlength, 0, 2U);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -parts */
  optionparts = gt_option_new_uint("parts", "specify the number of parts",
                                  &arguments->numofparts, 0U);
  gt_option_parser_add_option(op, optionparts);

  /* -memlimit */
  optionmemlimit = gt_option_new_string("memlimit",
                       "specify maximal amount of memory to be used during "
                       "index construction (in bytes, the keywords 'MB' "
                       "and 'GB' are allowed)",
                       arguments->memlimitarg, NULL);
  gt_option_parser_add_option(op, optionmemlimit);
  gt_option_exclude(optionmemlimit, optionparts);
  arguments->refoptionmemlimit = gt_option_ref(optionmemlimit);

  /* -singlestrand */
  option = gt_option_new_bool("singlestrand", "do not use reverse complements "
      "of the reads", &arguments->singlestrand, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -elimtrans */
  option = gt_option_new_bool("elimtrans", "output only irreducible SPMs",
      &arguments->elimtrans, true);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -wmax */
  option = gt_option_new_uint("wmax", "specify the maximum width of w set;\n"
                              "use 0 to disable w set partitioning",
                              &arguments->w_maxsize, 32U);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -showspm */
  option = gt_option_new_bool("showspm", "show textual SPMs list on stdout",
      &arguments->showspm, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -phase2extra */
  option = gt_option_new_string("phase2extra",
                       "specify amount of additional space required for "
                       "the second phase of the computation involving the "
                       "processing of the intervals (in bytes, "
                       "the keywords 'MB' and 'GB' are allowed)",
                       arguments->phase2extraarg, NULL);
  gt_option_parser_add_option(op, option);
  arguments->refoptionphase2extra = gt_option_ref(option);
  gt_option_is_development_option(option);

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

  /* -q */
  q_option = gt_option_new_bool("q", "suppress standard output messages",
                             &arguments->quiet, false);
  gt_option_parser_add_option(op, q_option);
  gt_option_exclude(q_option, v_option);

  /* -radixparts */
  option = gt_option_new_uint("radixparts", "specify the radixpart parameter",
      &arguments->radixparts, 1U);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -radixsmall */
  option = gt_option_new_bool("radixsmall", "specify the radixsmall parameter",
      &arguments->radixsmall, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -onlyallfirstcodes */
  option = gt_option_new_bool("onlyallfirstcodes", "only determines allcodes",
                              &arguments->onlyallfirstcodes, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
  return op;
}

// Assembly:
pushq %rbp
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
testq %rdi, %rdi
je 0x3d075
movq %rdi, %r14
leaq 0x2ad8f0(%rip), %rdi    # 0x2ea6a1
leaq 0x2ad8fd(%rip), %rsi    # 0x2ea6b5
callq 0x97df5
movq %rax, %rbx
movq 0x28(%r14), %rdx
leaq 0x2b5879(%rip), %rdi    # 0x2f2644
leaq 0x2b587a(%rip), %rsi    # 0x2f264c
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9ae37
leaq 0x8(%r14), %rdx
leaq 0x2eb178(%rip), %rdi    # 0x327f72
leaq 0x2b58c5(%rip), %rsi    # 0x2f26c6
pushq $0x2
popq %r8
xorl %ecx, %ecx
callq 0x9abef
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9ae37
leaq 0xc(%r14), %rdx
leaq 0x2b9bca(%rip), %rdi    # 0x2f69f7
leaq 0x2ad8d1(%rip), %rsi    # 0x2ea705
xorl %ecx, %ecx
callq 0x9abcd
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq 0x30(%r14), %rdx
leaq 0x3480d4(%rip), %rdi    # 0x384f28
leaq 0x2ad8c6(%rip), %rsi    # 0x2ea721
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
movq %r15, %rsi
callq 0x9b38d
movq %r12, %rdi
callq 0x97db0
movq %rax, 0x40(%r14)
leaq 0x2ad92f(%rip), %rdi    # 0x2ea7bd
leaq 0x2b7184(%rip), %rsi    # 0x2f4019
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x1(%r14), %rdx
leaq 0x2b7185(%rip), %rdi    # 0x2f4045
leaq 0x2b7188(%rip), %rsi    # 0x2f404f
pushq $0x1
popq %rbp
movl %ebp, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x10(%r14), %rdx
leaq 0x2b717a(%rip), %rdi    # 0x2f406c
leaq 0x2b7178(%rip), %rsi    # 0x2f4071
pushq $0x20
popq %rcx
callq 0x9abcd
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x4(%r14), %rdx
leaq 0x2b7197(%rip), %rdi    # 0x2f40b9
leaq 0x2b7198(%rip), %rsi    # 0x2f40c1
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq 0x38(%r14), %rdx
leaq 0x2ad933(%rip), %rdi    # 0x2ea884
leaq 0x2b718a(%rip), %rsi    # 0x2f40e2
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x97db0
movq %rax, 0x48(%r14)
movq %r15, %rdi
callq 0x9b10a
leaq 0x2(%r14), %rdi
callq 0x9a9b6
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x3(%r14), %rdx
leaq 0x2e9aa5(%rip), %rdi    # 0x326a48
leaq 0x2b579a(%rip), %rsi    # 0x2f2744
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
movq %r15, %rsi
callq 0x9b38d
leaq 0x54(%r14), %rdx
leaq 0x2ad997(%rip), %rdi    # 0x2ea96c
leaq 0x2b71b7(%rip), %rsi    # 0x2f4193
movl %ebp, %ecx
callq 0x9abcd
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x50(%r14), %rdx
leaq 0x2b71af(%rip), %rdi    # 0x2f41b3
leaq 0x2b71b3(%rip), %rsi    # 0x2f41be
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
addq $0x58, %r14
leaq 0x2ad816(%rip), %rdi    # 0x2ea849
leaq 0x2ad821(%rip), %rsi    # 0x2ea85b
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r14
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r14, %rsi
callq 0x97f31
leaq 0x14b663(%rip), %rsi    # 0x1886c4
movq %rbx, %rdi
callq 0x9808c
movq %rbx, %rax
popq %rbx
popq %r12
popq %r14
popq %r15
popq %rbp
retq
movq 0x3faeec(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2a7f8d(%rip), %rsi    # 0x2e5013
leaq 0x30b5c6(%rip), %rdx    # 0x348653
leaq 0x2b6f5d(%rip), %rcx    # 0x2f3ff1
leaq 0x2b6f34(%rip), %r8     # 0x2f3fcf
pushq $0x58
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390