C++ (Cpp) gt_registerPackedIndexOptions 예제들

예제 #1

파일: index_options.c 프로젝트: AlexWoroschilow/uni_hamburg

static GtIndexOptions*
gt_index_options_register_generic_output(GtOptionParser *op,
                                         GtIndexOptions *idxo,
                                         GtStr *indexname,
                                         GtEncseqOptions *encopts)
{
  gt_assert(idxo != NULL);
  gt_assert(op != NULL && idxo->type != GT_INDEX_OPTIONS_UNDEFINED &&
            encopts != NULL);
  idxo->encopts = encopts;
  idxo->indexname = indexname != NULL ? gt_str_ref(indexname) : NULL;
  idxo->optionkys = gt_option_new_string("kys",
                                   "output/sort according to keys of the form "
                                   "|key| in fasta header",
                                   idxo->kysargumentstring,
                                   "nosort");
  gt_option_argument_is_optional(idxo->optionkys);
  gt_option_imply(idxo->optionkys, gt_encseq_options_sds_option(idxo->encopts));
  gt_option_parser_add_option(op, idxo->optionkys);

  gt_encseq_options_add_readmode_option(op, idxo->dir);

  if (idxo->type == GT_INDEX_OPTIONS_ESA)
  {
    idxo->optionoutsuftab = gt_option_new_bool("suf",
                                   "output suffix array (suftab) to file",
                                   &idxo->outsuftab,
                                   false);
    gt_option_parser_add_option(op, idxo->optionoutsuftab);

    idxo->optionoutlcptab = gt_option_new_bool("lcp",
                                   "output lcp table (lcptab) to file",
                                   &idxo->outlcptab,
                                   false);
    gt_option_parser_add_option(op, idxo->optionoutlcptab);

    idxo->option = gt_option_new_bool("lcpdist",
                              "output distributions of values in lcptab",
                              &idxo->lcpdist,
                              false);
    gt_option_is_extended_option(idxo->option);
    gt_option_imply(idxo->option, idxo->optionoutlcptab);
    gt_option_parser_add_option(op, idxo->option);

    idxo->option = gt_option_new_bool("swallow-tail",
                              "swallow the tail of the suffix array and lcptab",
                              &idxo->swallow_tail,
                              false);
    gt_option_is_development_option(idxo->option);
    gt_option_parser_add_option(op, idxo->option);

    idxo->optionoutbwttab = gt_option_new_bool("bwt",
                                   "output Burrows-Wheeler Transformation "
                                   "(bwttab) to file",
                                   &idxo->outbwttab,
                                   false);
    gt_option_exclude(idxo->optionspmopt, idxo->optionoutbwttab);
    gt_option_parser_add_option(op, idxo->optionoutbwttab);

    idxo->optionoutbcktab = gt_option_new_bool("bck",
                                "output bucket table to file",
                                &idxo->outbcktab,
                                false);
    gt_option_parser_add_option(op, idxo->optionoutbcktab);
  } else {
    idxo->optionoutsuftab
      = idxo->optionoutlcptab = idxo->optionoutbwttab = NULL;
    idxo->sfxstrategy.spmopt_minlength = 0;
#ifndef S_SPLINT_S
    gt_registerPackedIndexOptions(op,
                                  &idxo->bwtIdxParams,
                                  BWTDEFOPT_CONSTRUCTION,
                                  idxo->indexname);
#endif
  }

  gt_option_parser_register_hook(op, gt_index_options_check_set_out_opts, idxo);

  return idxo;
}

예제 #2

파일: gt_packedindex_chk_search.c 프로젝트: simongog/genometools

static GtOPrval
parseChkBWTOptions(int *parsed_args, int argc, const char **argv,
                   struct chkSearchOptions *params, const GtStr *projectName,
                   GtError *err)
{
  GtOptionParser *op;
  GtOPrval oprval;
  GtOption *option, *optionProgress;
  bool checkSuffixArrayValues, tryContextRetrieve, tryFullRegen;

  gt_error_check(err);
  op = gt_option_parser_new("indexname",
                         "Load (or build if necessary) BWT index for project"
                         " <indexname> and perform verification of search"
                         " results.");

  gt_registerPackedIndexOptions(op, &params->idx, BWTDEFOPT_MULTI_QUERY,
                             projectName);

  option = gt_option_new_long("minpatlen",
                           "minimum length of patterns searched for, -1 "
                           "implies automatic choice based on index "
                           "properties", &params->minPatLen, -1);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_long("maxpatlen",
                           "maximum length of patterns searched for, -1 "
                           "implies automatic choice based on index "
                           "properties", &params->maxPatLen, -1);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_ulong("nsamples",
                            "number of sequences to search for",
                            &params->numOfSamples, 1000);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("chksfxarray",
                           "verify integrity of stored suffix array positions",
                           &checkSuffixArrayValues, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("full-lfmap",
                           "verify complete backwards regeneration of "
                           "original sequence", &tryFullRegen, false);
  gt_option_parser_add_option(op, option);

  option = gt_option_new_bool("chkcontext",
                           "verify integrity of regenerated sequence context",
                           &tryContextRetrieve, false);
  gt_option_parser_add_option(op, option);

  optionProgress = gt_option_new_ulong("ticks",
                                    "print dot after this many symbols "
                                    "tested okay", &params->progressInterval,
                                    DEFAULT_PROGRESS_INTERVAL);
  gt_option_parser_add_option(op, optionProgress);

  option = gt_option_new_bool("v",
                           "print verbose progress information",
                           &params->verboseOutput,
                           false);
  gt_option_parser_add_option(op, option);

  gt_option_parser_set_min_max_args(op, 1, 1);
  oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
                                  err);

  /* condense boolean options to flags field */
  params->flags = (checkSuffixArrayValues?VERIFY_BWTSEQ_SUFVAL:0)
    | (tryFullRegen?VERIFY_BWTSEQ_LFMAPWALK:0)
    | (tryContextRetrieve?VERIFY_BWTSEQ_CONTEXT:0);
  /* compute parameters currently not set from command-line or
   * determined indirectly */
  gt_computePackedIndexDefaults(&params->idx, BWTBaseFeatures);

  gt_option_parser_delete(op);

  return oprval;
}