// File: /workspace/github_c_makefile_star2_O3/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 %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb9b2e
movq %rdi, %r14
leaq 0x290e41(%rip), %rdi    # 0x34a6a1
leaq 0x290e4e(%rip), %rsi    # 0x34a6b5
callq 0x107bfe
movq %rax, %rbx
movq 0x28(%r14), %rdx
leaq 0x298dba(%rip), %rdi    # 0x352634
leaq 0x298dbb(%rip), %rsi    # 0x35263c
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r15, %rdi
callq 0x10a87b
leaq 0x8(%r14), %rdx
leaq 0x2ce2d4(%rip), %rdi    # 0x387b7d
leaq 0x298e06(%rip), %rsi    # 0x3526b6
xorl %ecx, %ecx
movl $0x2, %r8d
callq 0x10a51f
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r15, %rdi
callq 0x10a87b
leaq 0xc(%r14), %rdx
leaq 0x29d109(%rip), %rdi    # 0x3569e7
leaq 0x290e20(%rip), %rsi    # 0x34a705
xorl %ecx, %ecx
callq 0x10a4fd
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq 0x30(%r14), %rdx
leaq 0x32b243(%rip), %rdi    # 0x3e4b48
leaq 0x290e15(%rip), %rsi    # 0x34a721
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r12, %rdi
movq %r15, %rsi
callq 0x10ab96
movq %r12, %rdi
callq 0x107bec
movq %rax, 0x40(%r14)
leaq 0x290e7e(%rip), %rdi    # 0x34a7bd
leaq 0x29a6c3(%rip), %rsi    # 0x354009
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x1(%r14), %rdx
leaq 0x29a6c4(%rip), %rdi    # 0x354035
leaq 0x29a6c7(%rip), %rsi    # 0x35403f
movl $0x1, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x10(%r14), %rdx
leaq 0x29a6b9(%rip), %rdi    # 0x35405c
leaq 0x29a6b7(%rip), %rsi    # 0x354061
movl $0x20, %ecx
callq 0x10a4fd
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x4(%r14), %rdx
leaq 0x29a6d4(%rip), %rdi    # 0x3540a9
leaq 0x29a6d5(%rip), %rsi    # 0x3540b1
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
movq 0x38(%r14), %rdx
leaq 0x290e80(%rip), %rdi    # 0x34a884
leaq 0x29a6c7(%rip), %rsi    # 0x3540d2
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r15, %rdi
callq 0x107bec
movq %rax, 0x48(%r14)
movq %r15, %rdi
callq 0x10a9d4
leaq 0x2(%r14), %rdi
callq 0x10a257
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x3(%r14), %rdx
leaq 0x2ccbf2(%rip), %rdi    # 0x386648
leaq 0x298cd7(%rip), %rsi    # 0x352734
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
movq %r12, %rdi
movq %r15, %rsi
callq 0x10ab96
leaq 0x54(%r14), %rdx
leaq 0x290ee4(%rip), %rdi    # 0x34a96c
leaq 0x29a6f4(%rip), %rsi    # 0x354183
movl $0x1, %ecx
callq 0x10a4fd
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x50(%r14), %rdx
leaq 0x29a6e9(%rip), %rdi    # 0x3541a3
leaq 0x29a6ed(%rip), %rsi    # 0x3541ae
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
addq $0x58, %r14
leaq 0x290d60(%rip), %rdi    # 0x34a849
leaq 0x290d6b(%rip), %rsi    # 0x34a85b
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r14
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r14, %rsi
callq 0x107cc0
leaq 0x121439(%rip), %rsi    # 0x1daf50
movq %rbx, %rdi
callq 0x107d51
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x1dc72