Exemplo n.º 1
0
static int gt_index_options_check_set_out_opts(void *oip, GtError *err)
{
  int had_err = 0;
  GtIndexOptions *oi = (GtIndexOptions*) oip;
  gt_assert(oi != NULL && oi->type != GT_INDEX_OPTIONS_UNDEFINED);
  gt_error_check(err);

  if (!had_err) {
    int retval;
    retval = gt_readmode_parse(gt_str_get(oi->dir), err);
    if (retval < 0) {
      had_err = -1;
    } else {
      oi->readmode = (GtReadmode) retval;
      if (oi->type == GT_INDEX_OPTIONS_PACKED
            && (oi->readmode == GT_READMODE_COMPL
                  || oi->readmode == GT_READMODE_REVCOMPL)) {
        gt_error_set(err,"construction of packed index not possible for "
                         "complemented and for reverse complemented sequences");
        had_err = -1;
      }
    }
  }
  if (!had_err && oi->type == GT_INDEX_OPTIONS_PACKED) {
#ifndef S_SPLINT_S
    gt_computePackedIndexDefaults(&oi->bwtIdxParams, BWTBaseFeatures);
#endif
  }
  if (!had_err && gt_option_is_set(oi->optionkys)) {
    oi->outkystab = true;
    if (strcmp(gt_str_get(oi->kysargumentstring), "sort") == 0) {
      oi->outkyssort = true;
    } else {
      if (strcmp(gt_str_get(oi->kysargumentstring),"nosort") != 0) {
        gt_error_set(err,"illegal argument to option -kys: either use no "
                         "argument or argument \"sort\"");
        had_err = -1;
      }
    }
  }

  return had_err;
}
Exemplo n.º 2
0
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;
}