// File: /workspace/github_c_makefile_star2_O3/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 0xb5790
movq %rdi, %r14
leaq 0x2a2b2f(%rip), %rdi    # 0x357e62
leaq 0x29d5eb(%rip), %rsi    # 0x352925
callq 0x107bfe
movq %rax, %rbx
movq 0x10(%r14), %rdx
leaq 0x29d2e7(%rip), %rdi    # 0x352634
leaq 0x29d2e8(%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 0x48(%r14), %rdx
leaq 0x29d2d9(%rip), %rdi    # 0x352655
leaq 0x29d2db(%rip), %rsi    # 0x35265e
movl $0x1, %ecx
movl $0x1, %r8d
callq 0x10a51f
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9c4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x4(%r14), %rdx
leaq 0x2d27c9(%rip), %rdi    # 0x387b7d
leaq 0x29d2fb(%rip), %rsi    # 0x3526b6
xorl %ecx, %ecx
movl $0x2, %r8d
callq 0x10a51f
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9c4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0xc(%r14), %rdx
leaq 0x29d567(%rip), %rdi    # 0x352950
leaq 0x29d56c(%rip), %rsi    # 0x35295c
movl $0x3, %ecx
movl $0x1, %r8d
callq 0x10a51f
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9c4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x8(%r14), %rdx
leaq 0x29d56b(%rip), %rdi    # 0x35298c
leaq 0x29d571(%rip), %rsi    # 0x352999
movl $0x64, %ecx
movl $0x1, %r8d
callq 0x10a51f
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9c4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x22(%r14), %rdx
leaq 0x2fa439(%rip), %rdi    # 0x3af892
leaq 0x29d560(%rip), %rsi    # 0x3529c0
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x20(%r14), %rdx
leaq 0x29d9af(%rip), %rdi    # 0x352e37
leaq 0x29d549(%rip), %rsi    # 0x3529d8
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9c4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x30(%r14), %rdx
leaq 0x29d572(%rip), %rdi    # 0x352a29
leaq 0x29d572(%rip), %rsi    # 0x352a30
movl $0x3, %ecx
callq 0x10a4fd
movq %rax, %r12
movq %rax, %rdi
callq 0x10a9c4
movq %r12, %rdi
movq %r15, %rsi
callq 0x10a9e4
movq %rbx, %rdi
movq %r12, %rsi
callq 0x107cc0
leaq 0x2c(%r14), %rdx
leaq 0x29d56c(%rip), %rdi    # 0x352a60
leaq 0x29d56d(%rip), %rsi    # 0x352a68
movl $0xa, %ecx
callq 0x10a4fd
movq %rax, %r12
movq %rax, %rdi
callq 0x10a9c4
movq %r12, %rdi
movq %r15, %rsi
callq 0x10a9e4
movq %rbx, %rdi
movq %r12, %rsi
callq 0x107cc0
leaq 0x34(%r14), %rdx
leaq 0x29d572(%rip), %rdi    # 0x352aa3
leaq 0x29d579(%rip), %rsi    # 0x352ab1
movl $0xa, %ecx
movl $0x1, %r8d
callq 0x10a51f
movq %rax, %r12
movq %rax, %rdi
callq 0x10a9c4
movq %r12, %rdi
movq %r15, %rsi
callq 0x10a9e4
movq %rbx, %rdi
movq %r12, %rsi
callq 0x107cc0
leaq 0x21(%r14), %rdx
leaq 0x29db70(%rip), %rdi    # 0x3530e4
leaq 0x29d59c(%rip), %rsi    # 0x352b17
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
movq 0x18(%r14), %rdx
leaq 0x2f7c66(%rip), %rdi    # 0x3ad209
leaq 0x29d5a6(%rip), %rsi    # 0x352b50
xorl %ecx, %ecx
callq 0x10a770
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
movq %r15, %rdi
callq 0x107bec
movq %rax, 0x38(%r14)
leaq 0x25(%r14), %rdx
leaq 0x29d5d5(%rip), %rdi    # 0x352bb3
leaq 0x29d5d1(%rip), %rsi    # 0x352bb6
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x26(%r14), %rdx
leaq 0x29d5ce(%rip), %rdi    # 0x352bdb
leaq 0x29d5cd(%rip), %rsi    # 0x352be1
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x50(%r14), %rdx
leaq 0x305918(%rip), %rdi    # 0x3baf54
leaq 0x29d5c5(%rip), %rsi    # 0x352c08
xorps %xmm0, %xmm0
callq 0x10a346
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x27(%r14), %rdx
leaq 0x2f7997(%rip), %rdi    # 0x3ad003
leaq 0x29d5d4(%rip), %rsi    # 0x352c47
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
movq %r14, %rdi
callq 0x10a257
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x107cc0
leaq 0x1(%r14), %rdx
leaq 0x2d0f97(%rip), %rdi    # 0x386648
leaq 0x29d07c(%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 0x24(%r14), %rdx
leaq 0x32a7e7(%rip), %rdi    # 0x3dfeca
leaq 0x29d5a5(%rip), %rsi    # 0x352c8f
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
leaq 0x23(%r14), %rdx
leaq 0x2dae00(%rip), %rdi    # 0x390512
leaq 0x29d596(%rip), %rsi    # 0x352caf
xorl %ecx, %ecx
callq 0x10a235
movq %rax, %r15
movq %rax, %rdi
callq 0x10a9d4
movq %rbx, %rdi
movq %r15, %rsi
callq 0x107cc0
addq $0x28, %r14
leaq 0x312d33(%rip), %rdi    # 0x3c8474
leaq 0x29d585(%rip), %rsi    # 0x352ccd
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 0x1257e1(%rip), %rsi    # 0x1daf50
movq %rbx, %rdi
callq 0x107d51
movq %rbx, %rdi
xorl %esi, %esi
callq 0x10873c
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r14
popq %r15
retq
callq 0x1d652