// File: /workspace/github_c_makefile_star2_O1/genometools[P]genometools/src/tools/gt_readjoiner_assembly.c
// Function: gt_readjoiner_assembly_option_parser_new
static GtOptionParser* gt_readjoiner_assembly_option_parser_new(
    void *tool_arguments)
{
  GtReadjoinerAssemblyArguments *arguments = tool_arguments;
  GtOptionParser *op;
  GtOption *option, *errors_option, *deadend_option, *v_option,
           *q_option, *bubble_option, *deadend_depth_option;
  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("[option ...]",
      "Construct string graph and output contigs.");

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

  /* -spmfiles */
  option = gt_option_new_uint_min("spmfiles", "number of SPM files to read\n"
      "this must be equal to the value of -j for the overlap phase",
      &arguments->nspmfiles, 1U, 1U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

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

  /* -depthcutoff */
  option = gt_option_new_uint_min("depthcutoff", "specify the minimal "
      "number of nodes in a contig",
      &arguments->depthcutoff, 3U, 1U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -lengthcutoff */
  option = gt_option_new_uint_min("lengthcutoff", "specify the minimal "
      "length of a contig",
      &arguments->lengthcutoff, 100U, 1U);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -redtrans */
  option = gt_option_new_bool("redtrans", "reduce transitive edges",
      &arguments->redtrans, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -errors */
  errors_option = gt_option_new_bool("errors", "search graph features which "
      "may originate from sequencing errors and remove them",
      &arguments->errors, false);
  gt_option_is_extended_option(errors_option);
  gt_option_parser_add_option(op, errors_option);

  /* -bubble */
  bubble_option = gt_option_new_uint("bubble", "number of rounds of p-bubble "
      "removal to perform", &arguments->bubble, 3U);
  gt_option_is_extended_option(bubble_option);
  gt_option_imply(bubble_option, errors_option);
  gt_option_parser_add_option(op, bubble_option);

  /* -deadend */
  deadend_option = gt_option_new_uint("deadend", "number of rounds of "
      "dead end removal to perform a dead end",
      &arguments->deadend, 10U);
  gt_option_is_extended_option(deadend_option);
  gt_option_imply(deadend_option, errors_option);
  gt_option_parser_add_option(op, deadend_option);

  /* -deadend-depth */
  deadend_depth_option = gt_option_new_uint_min("deadend-depth", "specify the "
      "maximal depth of a path to an end-vertex by which the path shall be "
      "considered a dead end",
      &arguments->deadend_depth, 10U, 1U);
  gt_option_is_extended_option(deadend_depth_option);
  gt_option_imply(deadend_depth_option, errors_option);
  gt_option_parser_add_option(op, deadend_depth_option);

  /* -paths2seq */
  option = gt_option_new_bool("paths2seq", "read <indexname>"
      GT_READJOINER_SUFFIX_CONTIG_PATHS " and write "
      "<indexname>" GT_READJOINER_SUFFIX_CONTIGS,
      &arguments->paths2seq, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -buffersize */
  option = gt_option_new_string("buffersize", "specify size for read buffer"
      " of paths2seq phase (in bytes, the keywords 'MB' and 'GB' are allowed)",
                       arguments->buffersizearg, NULL);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);
  arguments->refoptionbuffersize = gt_option_ref(option);

  /* -vd */
  option = gt_option_new_bool("vd", "use verbose descriptions for contigs",
      &arguments->vd, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -astat */
  option = gt_option_new_bool("astat", "calculate A-statistics for each contig",
      &arguments->astat, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -cov */
  option = gt_option_new_double("cov", "average coverage value to use for the "
      "A-statistics calculation", &arguments->coverage, (double)0);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -copynum */
  option = gt_option_new_bool("copynum", "load reads copy numbers list from "
      "file for the A-statistics calculation",
      &arguments->copynum, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, 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);

  /* -load */
  option = gt_option_new_bool("load", "save the string graph from file",
      &arguments->load, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -save */
  option = gt_option_new_bool("save", "save the string graph to file",
      &arguments->save, false);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -show_contigs_info */
  option = gt_option_new_bool("cinfo", "output additional files required "
      "for contigs graph construction (eqlen only)",
      &arguments->show_contigs_info, 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);
  gt_option_parser_set_max_args(op, 0);

  return op;
}

// Assembly:
pushq %r15
pushq %r14
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0xb7888
movq %rdi, %r14
leaq 0x2a9a8a(%rip), %rdi    # 0x360eb5
leaq 0x2a452b(%rip), %rsi    # 0x35b95d
callq 0x10cc4e
movq %rax, %rbx
movq 0x10(%r14), %rdx
leaq 0x2a4227(%rip), %rdi    # 0x35b66c
leaq 0x2a4228(%rip), %rsi    # 0x35b674
xorl %ecx, %ecx
callq 0x10f987
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r15, %rdi
callq 0x10fa96
leaq 0x48(%r14), %rdx
leaq 0x2a4219(%rip), %rdi    # 0x35b68d
leaq 0x2a421b(%rip), %rsi    # 0x35b696
movl $0x1, %ecx
movl $0x1, %r8d
callq 0x10f73b
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbdf
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x4(%r14), %rdx
leaq 0x2d9aaa(%rip), %rdi    # 0x390f56
leaq 0x2a423b(%rip), %rsi    # 0x35b6ee
xorl %ecx, %ecx
movl $0x2, %r8d
callq 0x10f73b
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbdf
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0xc(%r14), %rdx
leaq 0x2a44a7(%rip), %rdi    # 0x35b988
leaq 0x2a44ac(%rip), %rsi    # 0x35b994
movl $0x3, %ecx
movl $0x1, %r8d
callq 0x10f73b
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbdf
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x8(%r14), %rdx
leaq 0x2a44ab(%rip), %rdi    # 0x35b9c4
leaq 0x2a44b1(%rip), %rsi    # 0x35b9d1
movl $0x64, %ecx
movl $0x1, %r8d
callq 0x10f73b
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbdf
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x22(%r14), %rdx
leaq 0x301941(%rip), %rdi    # 0x3b8e92
leaq 0x2a44a0(%rip), %rsi    # 0x35b9f8
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x20(%r14), %rdx
leaq 0x2a48ef(%rip), %rdi    # 0x35be6f
leaq 0x2a4489(%rip), %rsi    # 0x35ba10
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbdf
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x30(%r14), %rdx
leaq 0x2a44b2(%rip), %rdi    # 0x35ba61
leaq 0x2a44b2(%rip), %rsi    # 0x35ba68
movl $0x3, %ecx
callq 0x10f719
movq %rax, %r12
movq %rax, %rdi
callq 0x10fbdf
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fbff
movq %rbx, %rdi
movq %r12, %rsi
callq 0x10cd10
leaq 0x2c(%r14), %rdx
leaq 0x2a44ac(%rip), %rdi    # 0x35ba98
leaq 0x2a44ad(%rip), %rsi    # 0x35baa0
movl $0xa, %ecx
callq 0x10f719
movq %rax, %r12
movq %rax, %rdi
callq 0x10fbdf
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fbff
movq %rbx, %rdi
movq %r12, %rsi
callq 0x10cd10
leaq 0x34(%r14), %rdx
leaq 0x2a44b2(%rip), %rdi    # 0x35badb
leaq 0x2a44b9(%rip), %rsi    # 0x35bae9
movl $0xa, %ecx
movl $0x1, %r8d
callq 0x10f73b
movq %rax, %r12
movq %rax, %rdi
callq 0x10fbdf
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fbff
movq %rbx, %rdi
movq %r12, %rsi
callq 0x10cd10
leaq 0x21(%r14), %rdx
leaq 0x2a4ab0(%rip), %rdi    # 0x35c11c
leaq 0x2a44dc(%rip), %rsi    # 0x35bb4f
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
movq 0x18(%r14), %rdx
leaq 0x2ff16e(%rip), %rdi    # 0x3b6809
leaq 0x2a44e6(%rip), %rsi    # 0x35bb88
xorl %ecx, %ecx
callq 0x10f987
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
movq %r15, %rdi
callq 0x10cc3c
movq %rax, 0x38(%r14)
leaq 0x25(%r14), %rdx
leaq 0x2a4515(%rip), %rdi    # 0x35bbeb
leaq 0x2a4511(%rip), %rsi    # 0x35bbee
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x26(%r14), %rdx
leaq 0x2a450e(%rip), %rdi    # 0x35bc13
leaq 0x2a450d(%rip), %rsi    # 0x35bc19
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x50(%r14), %rdx
leaq 0x30ce90(%rip), %rdi    # 0x3c45c4
leaq 0x2a4505(%rip), %rsi    # 0x35bc40
xorps %xmm0, %xmm0
callq 0x10f562
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x27(%r14), %rdx
leaq 0x2fee9f(%rip), %rdi    # 0x3b6603
leaq 0x2a4514(%rip), %rsi    # 0x35bc7f
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
movq %r14, %rdi
callq 0x10f473
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
leaq 0x1(%r14), %rdx
leaq 0x2d827f(%rip), %rdi    # 0x38fa28
leaq 0x2a3fbc(%rip), %rsi    # 0x35b76c
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x10cd10
movq %r12, %rdi
movq %r15, %rsi
callq 0x10fd9f
leaq 0x24(%r14), %rdx
leaq 0x331ddf(%rip), %rdi    # 0x3e95ba
leaq 0x2a44e5(%rip), %rsi    # 0x35bcc7
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
leaq 0x23(%r14), %rdx
leaq 0x2e2130(%rip), %rdi    # 0x39993a
leaq 0x2a44d6(%rip), %rsi    # 0x35bce7
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r15
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r15, %rsi
callq 0x10cd10
addq $0x28, %r14
leaq 0x31a363(%rip), %rdi    # 0x3d1b9c
leaq 0x2a44c5(%rip), %rsi    # 0x35bd05
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x10f451
movq %rax, %r14
movq %rax, %rdi
callq 0x10fbef
movq %rbx, %rdi
movq %r14, %rsi
callq 0x10cd10
leaq 0x12cf11(%rip), %rsi    # 0x1e4778
movq %rbx, %rdi
callq 0x10cda1
movq %rbx, %rdi
xorl %esi, %esi
callq 0x10d775
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x1d88a