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

  gt_assert(arguments);

  /* init */
  op = gt_option_parser_new("(-ii <indexname>|-db <filenames>) "
      "-k <kmersize> [option ...]", "K-mer based sequence correction.");

  /* -db */
  db_option = gt_option_new_filename_array("db",
      GT_READS2TWOBIT_LIBSPEC_HELPMSG, arguments->db);
  gt_option_hide_default(db_option);
  gt_option_parser_add_option(op, db_option);

  /* -indexname */
  option = gt_option_new_string("indexname", "specify the indexname to use "
      "for the input\ndefault: first argument of the -db option",
      arguments->indexname, NULL);
  gt_option_hide_default(option);
  gt_option_parser_add_option(op, option);

  /* -ii */
  option = gt_option_new_string("ii", "specify the input enseq index",
                                arguments->encseqinput, NULL);
  gt_option_is_mandatory_either(option, db_option);
  gt_option_exclude(option, db_option);
  gt_option_parser_add_option(op, option);

  /* -k */
  option = gt_option_new_uint_min("k", "specify the kmer size for the "
      "correction algorithm", &arguments->correction_kmersize, 31U, 2U);
  gt_option_parser_add_option(op, option);
  gt_option_is_mandatory(option);

  /* -c */
  option = gt_option_new_uint_min("c", "specify the trusted count threshold",
      &arguments->trusted_count, 3U, 2U);
  gt_option_parser_add_option(op, option);

  /* -find-seldom */
  option = gt_option_new_bool("find-seldom", "do not try to correct, only "
      "prepare a list of all reads containing seldom k-mers",
      &arguments->find_seldom, false);
  gt_option_parser_add_option(op, option);

  /* -iter */
  option = gt_option_new_uint_min("iter", "specify the number of iterations",
      &arguments->iterations, 1U, 1U);
  gt_option_parser_add_option(op, option);

  /* -sf */
  option = gt_option_new_uint_min("sf", "specify the sampling factor",
                                  &arguments->samplingfactor, 50U, 1U);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(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);

  /* -forcek */
  option = gt_option_new_uint("forcek", "specify the kmersize for the bucket "
      "keys", &arguments->forcek, 0);
  gt_option_is_development_option(option);
  gt_option_parser_add_option(op, option);

  /* -usefirstcodes */
  option = gt_option_new_bool("usefirstcodes", "use first codes instead of "
      "random sampled codes", &arguments->usefirstcodes, false);
  gt_option_parser_add_option(op, 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_exclude(q_option, v_option);
  gt_option_parser_add_option(op, q_option);

  /* -maxlow */
  maxlow_option = gt_option_new_uword("maxlow",
      "maximal number of low-quality positions in a read\n"
      "default: infinite",
      &arguments->maxlow, GT_UNDEF_UWORD);
  gt_option_hide_default(maxlow_option);
  gt_option_is_extended_option(maxlow_option);
  gt_option_parser_add_option(op, maxlow_option);

  /* -lowqual */
  option = gt_option_new_uint_max("lowqual",
      "maximal quality for a position to be considered low-quality",
      &arguments->lowqual, 3U, 127U);
  gt_option_is_extended_option(option);
  gt_option_imply(option, maxlow_option);
  gt_option_parser_add_option(op, option);

  /* -phred64 */
  option = gt_option_new_bool("phred64", "use phred64 scores for FastQ format",
      &arguments->phred64, false);
  gt_option_is_extended_option(option);
  gt_option_parser_add_option(op, option);

  /* -usemaxdepth */
  option = gt_option_new_bool("usemaxdepth", "use maxdepth in sortremaining",
                             &arguments->usemaxdepth, true);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -checksuftab */
  option = gt_option_new_bool("checksuftab", "check the suffix table",
                             &arguments->checksuftab, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -onlyaccum */
  option = gt_option_new_bool("onlyaccum", "only accumulate codes",
                             &arguments->onlyaccum, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

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

  /* -addbscachedepth */
  option = gt_option_new_uint("addbscachedepth", "only determines allcodes",
                              &arguments->addbscache_depth, 5U);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -radixlarge */
  option = gt_option_new_bool("radixlarge", "use large tables for radixsort",
                              &arguments->radixlarge, false);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  /* -radixparts */
  option = gt_option_new_uint("radixparts", "specify the number of parts "
                              "for radixsort",
                              &arguments->radixparts, 1U);
  gt_option_parser_add_option(op, option);
  gt_option_is_development_option(option);

  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 0x45fc9
movq %rdi, %r14
leaq 0x2b231d(%rip), %rdi    # 0x2f7e42
leaq 0x2b2353(%rip), %rsi    # 0x2f7e7f
callq 0x97df5
movq %rax, %rbx
movq 0x58(%r14), %rdx
leaq 0x2cfcca(%rip), %rdi    # 0x315809
leaq 0x2ae86b(%rip), %rsi    # 0x2f43b1
callq 0x9ad7e
movq %rax, %r15
movq %rax, %rdi
callq 0x9b445
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
movq 0x48(%r14), %rdx
leaq 0x2bfef1(%rip), %rdi    # 0x305a5d
leaq 0x2b232d(%rip), %rsi    # 0x2f7ea0
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r12
movq %rax, %rdi
callq 0x9b445
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
movq 0x38(%r14), %rdx
leaq 0x30dd38(%rip), %rdi    # 0x3538d3
leaq 0x2b2353(%rip), %rsi    # 0x2f7ef5
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r12
movq %rax, %rdi
movq %r15, %rsi
callq 0x9ae7a
movq %r12, %rdi
movq %r15, %rsi
callq 0x9b38d
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0xc(%r14), %rdx
leaq 0x2a4e48(%rip), %rdi    # 0x2eaa20
leaq 0x2b2334(%rip), %rsi    # 0x2f7f13
pushq $0x1f
popq %rcx
pushq $0x2
popq %rbp
movl %ebp, %r8d
callq 0x9abef
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9ae37
leaq 0x14(%r14), %rdx
leaq 0x31ea3a(%rip), %rdi    # 0x364648
leaq 0x2b2331(%rip), %rsi    # 0x2f7f46
pushq $0x3
popq %r15
movl %r15d, %ecx
movl %ebp, %r8d
callq 0x9abef
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x8(%r14), %rdx
leaq 0x2b2330(%rip), %rdi    # 0x2f7f6a
leaq 0x2b2335(%rip), %rsi    # 0x2f7f76
xorl %ecx, %ecx
callq 0x9a997
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x28(%r14), %rdx
leaq 0x2dd3ee(%rip), %rdi    # 0x32304c
leaq 0x2b2362(%rip), %rsi    # 0x2f7fc7
pushq $0x1
popq %rbp
movl %ebp, %ecx
movl %ebp, %r8d
callq 0x9abef
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x10(%r14), %rdx
leaq 0x2e1c50(%rip), %rdi    # 0x3278d8
leaq 0x2b2359(%rip), %rsi    # 0x2f7fe8
pushq $0x32
popq %rcx
movl %ebp, %r8d
callq 0x9abef
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
callq 0x9b10a
leaq 0x18(%r14), %rdx
leaq 0x2b0d3c(%rip), %rdi    # 0x2f69f7
leaq 0x2a4a43(%rip), %rsi    # 0x2ea705
xorl %ecx, %ecx
callq 0x9abcd
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq 0x40(%r14), %rdx
leaq 0x33f246(%rip), %rdi    # 0x384f28
leaq 0x2a4a38(%rip), %rsi    # 0x2ea721
xorl %ecx, %ecx
callq 0x9ad12
movq %rax, %r13
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r13, %rdi
movq %r12, %rsi
callq 0x9b38d
movq %r13, %rdi
callq 0x97db0
movq %rax, 0x50(%r14)
leaq 0x24(%r14), %rdx
leaq 0x2a4ce4(%rip), %rdi    # 0x2eaa04
leaq 0x2b22dd(%rip), %rsi    # 0x2f8004
xorl %ecx, %ecx
callq 0x9abcd
movq %rax, %r12
movq %rax, %rdi
callq 0x9b10a
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x2b22e2(%rip), %rdi    # 0x2f802d
leaq 0x2b22e9(%rip), %rsi    # 0x2f803b
movq %r14, %rdx
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
callq 0x9b10a
leaq 0x1(%r14), %rdi
callq 0x9a9b6
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
leaq 0x2(%r14), %rdx
leaq 0x2e0cb4(%rip), %rdi    # 0x326a48
leaq 0x2ac9a9(%rip), %rsi    # 0x2f2744
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r13
movq %rax, %rdi
movq %r12, %rsi
callq 0x9b38d
movq %rbx, %rdi
movq %r13, %rsi
callq 0x97f31
leaq 0x68(%r14), %rdx
leaq 0x2ae89f(%rip), %rdi    # 0x2f4665
leaq 0x2ae89f(%rip), %rsi    # 0x2f466c
pushq $-0x1
popq %rcx
callq 0x9a9e6
movq %rax, %r12
movq %rax, %rdi
callq 0x9b445
movq %r12, %rdi
callq 0x9b0c7
movq %rbx, %rdi
movq %r12, %rsi
callq 0x97f31
leaq 0x70(%r14), %rdx
leaq 0x2ae8b2(%rip), %rdi    # 0x2f46b0
leaq 0x2ae8b3(%rip), %rsi    # 0x2f46b8
pushq $0x7f
popq %r8
movl %r15d, %ecx
callq 0x9ac01
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 0x60(%r14), %rdx
leaq 0x30c9e4(%rip), %rdi    # 0x352821
leaq 0x2ae8b0(%rip), %rsi    # 0x2f46f4
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rax, %rdi
callq 0x9b0c7
movq %rbx, %rdi
movq %r15, %rsi
callq 0x97f31
leaq 0x7(%r14), %rdx
leaq 0x2b21ff(%rip), %rdi    # 0x2f806b
leaq 0x2b2204(%rip), %rsi    # 0x2f8077
movl %ebp, %ecx
callq 0x9a997
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9b10a
leaq 0x6(%r14), %rdx
leaq 0x2a48ff(%rip), %rdi    # 0x2ea79a
leaq 0x2a4904(%rip), %rsi    # 0x2ea7a6
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9b10a
leaq 0x3(%r14), %rdx
leaq 0x2a495f(%rip), %rdi    # 0x2ea829
leaq 0x2a4962(%rip), %rsi    # 0x2ea833
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9b10a
leaq 0x4(%r14), %rdx
leaq 0x2b219c(%rip), %rdi    # 0x2f8095
leaq 0x2a495b(%rip), %r15    # 0x2ea85b
movq %r15, %rsi
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r12
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r12, %rdi
callq 0x9b10a
leaq 0x20(%r14), %rdx
leaq 0x2a4949(%rip), %rdi    # 0x2ea874
pushq $0x5
popq %rcx
movq %r15, %rsi
callq 0x9abcd
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9b10a
leaq 0x5(%r14), %rdx
leaq 0x2a49eb(%rip), %rdi    # 0x2ea942
leaq 0x2a49ef(%rip), %rsi    # 0x2ea94d
xorl %ecx, %ecx
callq 0x9a997
movq %rax, %r15
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r15, %rdi
callq 0x9b10a
addq $0x1c, %r14
leaq 0x2a49e6(%rip), %rdi    # 0x2ea96c
leaq 0x2a49ea(%rip), %rsi    # 0x2ea977
movq %r14, %rdx
movl %ebp, %ecx
callq 0x9abcd
movq %rax, %r14
movq %rbx, %rdi
movq %rax, %rsi
callq 0x97f31
movq %r14, %rdi
callq 0x9b10a
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 0x3f1f98(%rip), %rax    # 0x437f68
movq (%rax), %rdi
leaq 0x29f039(%rip), %rsi    # 0x2e5013
leaq 0x302672(%rip), %rdx    # 0x348653
leaq 0x2b1e3a(%rip), %rcx    # 0x2f7e22
leaq 0x2b1e19(%rip), %r8     # 0x2f7e08
pushq $0x6e
popq %r9
xorl %eax, %eax
callq 0x17a50
callq 0x17390