// File: /workspace/github_c_makefile_star2_O2/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 %rbp
pushq %r15
pushq %r14
pushq %r13
pushq %r12
pushq %rbx
pushq %rax
testq %rdi, %rdi
je 0x3900b
movq %rdi, %r14
leaq 0x2bf2b7(%rip), %rdi    # 0x2f7e72
leaq 0x2b9d73(%rip), %rsi    # 0x2f2935
callq 0x97df5
movq %rax, %rbx
movq 0x10(%r14), %rdx
leaq 0x2b9a6f(%rip), %rdi    # 0x2f2644
leaq 0x2b9a70(%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 0x48(%r14), %rdx
leaq 0x2b9a61(%rip), %rdi    # 0x2f2665
leaq 0x2b9a63(%rip), %rsi    # 0x2f266e
pushq $0x1
popq %rbp
movl %ebp, %ecx
movl %ebp, %r8d
callq 0x9abef
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x4(%r14), %rdx
leaq 0x2ef339(%rip), %rdi    # 0x327f72
leaq 0x2b9a86(%rip), %rsi    # 0x2f26c6
pushq $0x2
popq %r8
xorl %ecx, %ecx
callq 0x9abef
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0xc(%r14), %rdx
leaq 0x2b9cf4(%rip), %rdi    # 0x2f2960
leaq 0x2b9cf9(%rip), %rsi    # 0x2f296c
pushq $0x3
popq %r15
movl %r15d, %ecx
movl %ebp, %r8d
callq 0x9abef
movq %rax, %r12
movq %rax, %rdi
callq 0x9b0c7
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x8(%r14), %rdx
leaq 0x2b9cf9(%rip), %rdi    # 0x2f299c
leaq 0x2b9cff(%rip), %rsi    # 0x2f29a9
pushq $0x64
popq %rcx
movl %ebp, %r8d
callq 0x9abef
movq %rax, %r12
movq %rax, %rdi
callq 0x9b0c7
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x22(%r14), %rdx
leaq 0x317004(%rip), %rdi    # 0x34fcda
leaq 0x2b9cf3(%rip), %rsi    # 0x2f29d0
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r12
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x20(%r14), %rdx
leaq 0x2ba142(%rip), %rdi    # 0x2f2e47
leaq 0x2b9cdc(%rip), %rsi    # 0x2f29e8
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r12
movq %rax, %rdi
callq 0x9b0c7
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x30(%r14), %rdx
leaq 0x2b9d05(%rip), %rdi    # 0x2f2a39
leaq 0x2b9d05(%rip), %rsi    # 0x2f2a40
movl %r15d, %ecx
callq 0x9abcd
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r15, %rdi
movq %r12, %rsi
callq 0x9b14d
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x2c(%r14), %rdx
leaq 0x2b9d01(%rip), %rdi    # 0x2f2a70
leaq 0x2b9d02(%rip), %rsi    # 0x2f2a78
pushq $0xa
popq %r15
movl %r15d, %ecx
callq 0x9abcd
movq %rax, %r13
movq %rax, %rdi
callq 0x9b0c7
movq %r13, %rdi
movq %r12, %rsi
callq 0x9b14d
movq %rbx, %rdi
movq %r13, %rsi
callq 0x97f31
leaq 0x34(%r14), %rdx
leaq 0x2b9d05(%rip), %rdi    # 0x2f2ab3
leaq 0x2b9d0c(%rip), %rsi    # 0x2f2ac1
movl %r15d, %ecx
movl %ebp, %r8d
callq 0x9abef
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %r15, %rdi
movq %r12, %rsi
callq 0x9b14d
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x21(%r14), %rdx
leaq 0x2ba308(%rip), %rdi    # 0x2f30f4
leaq 0x2b9d34(%rip), %rsi    # 0x2f2b27
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq 0x18(%r14), %rdx
leaq 0x31473e(%rip), %rdi    # 0x34d559
leaq 0x2b9d3e(%rip), %rsi    # 0x2f2b60
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x97db0
movq %rax, 0x38(%r14)
leaq 0x25(%r14), %rdx
leaq 0x2b9d6d(%rip), %rdi    # 0x2f2bc3
leaq 0x2b9d69(%rip), %rsi    # 0x2f2bc6
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x26(%r14), %rdx
leaq 0x2b9d66(%rip), %rdi    # 0x2f2beb
leaq 0x2b9d65(%rip), %rsi    # 0x2f2bf1
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x50(%r14), %rdx
leaq 0x322500(%rip), %rdi    # 0x35b3b4
leaq 0x2b9d5d(%rip), %rsi    # 0x2f2c18
xorps %xmm0, %xmm0
callq 0x9aad7
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x27(%r14), %rdx
leaq 0x31446f(%rip), %rdi    # 0x34d353
leaq 0x2b9d6c(%rip), %rsi    # 0x2f2c57
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq %r14, %rdi
callq 0x9a9b6
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x1(%r14), %rdx
leaq 0x2edb1f(%rip), %rdi    # 0x326a48
leaq 0x2b9814(%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 0x24(%r14), %rdx
leaq 0x34731f(%rip), %rdi    # 0x38027a
leaq 0x2b9d3d(%rip), %rsi    # 0x2f2c9f
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x23(%r14), %rdx
leaq 0x2f78c6(%rip), %rdi    # 0x330850
leaq 0x2b9d2e(%rip), %rsi    # 0x2f2cbf
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
addq $0x28, %r14
leaq 0x32f8bb(%rip), %rdi    # 0x368874
leaq 0x2b9d1d(%rip), %rsi    # 0x2f2cdd
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 0x14f6dd(%rip), %rsi    # 0x1886c4
movq %rbx, %rdi
callq 0x9808c
movq %rbx, %rdi
xorl %esi, %esi
callq 0x98c29
movq %rbx, %rax
addq $0x8, %rsp
popq %rbx
popq %r12
popq %r13
popq %r14
popq %r15
popq %rbp
retq
movq 0x3fef56(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x2abff7(%rip), %rsi    # 0x2e5013
leaq 0x30f630(%rip), %rdx    # 0x348653
leaq 0x2b98e2(%rip), %rcx    # 0x2f290c
leaq 0x2b98b8(%rip), %r8     # 0x2f28e9
pushq $0x4c
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390