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, ¶ms->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", ¶ms->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", ¶ms->maxPatLen, -1); gt_option_parser_add_option(op, option); option = gt_option_new_ulong("nsamples", "number of sequences to search for", ¶ms->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", ¶ms->progressInterval, DEFAULT_PROGRESS_INTERVAL); gt_option_parser_add_option(op, optionProgress); option = gt_option_new_bool("v", "print verbose progress information", ¶ms->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(¶ms->idx, BWTBaseFeatures); gt_option_parser_delete(op); return oprval; }
static GtOptionParser *gt_idxlocali_option_parser_new (void *tool_arguments) { IdxlocaliOptions *arguments = tool_arguments; GtOptionParser *op; GtOption *option, *optionesaindex, *optionpckindex, *optiononline, *optioncmp; gt_assert (arguments != NULL); arguments->indexname = gt_str_new (); arguments->queryfiles = gt_str_array_new (); op = gt_option_parser_new ("[options] -q query-file-names [-esa|-pck] indexname", "Find all local alignments using suffix tree."); gt_option_parser_set_mailaddress (op, "<*****@*****.**>"); option = gt_option_new_filenamearray ("q","Specify files containing the " "query sequences", arguments->queryfiles); gt_option_parser_add_option (op, option); option = gt_option_new_long ("match", "Specify match score", &arguments->matchscore, 1L); gt_option_parser_add_option (op, option); option = gt_option_new_long ("mismatch", "Specify mismatch score", &arguments->mismatchscore, -3L); gt_option_parser_add_option (op, option); option = gt_option_new_long ("gapstart", "Specify gap start score", &arguments->gapstart, -5L); gt_option_parser_add_option (op, option); option = gt_option_new_long ("gapextend", "Specify gap extension score", &arguments->gapextend, -2L); gt_option_parser_add_option (op, option); option = gt_option_new_ulong_min ("th", "Specify the threshold", &arguments->threshold, 0, 1UL); gt_option_parser_add_option (op, option); gt_option_is_mandatory (option); optionesaindex = gt_option_new_string ("esa", "Specify index " "(enhanced suffix array)", arguments->indexname, NULL); gt_option_parser_add_option (op, optionesaindex); arguments->refoptionesaindex = gt_option_ref (optionesaindex); optionpckindex = gt_option_new_string ("pck", "Specify index (packed index)", arguments->indexname, NULL); gt_option_parser_add_option (op, optionpckindex); arguments->refoptionpckindex = gt_option_ref (optionpckindex); gt_option_exclude (optionesaindex, optionpckindex); gt_option_is_mandatory_either (optionesaindex, optionpckindex); optiononline = gt_option_new_bool("online","Perform online searches", &arguments->doonline, false); gt_option_parser_add_option(op, optiononline); gt_option_is_development_option(optiononline); optioncmp = gt_option_new_bool("cmp","Compare results of offline and online " "searches", &arguments->docompare, false); gt_option_parser_add_option(op,optioncmp); gt_option_exclude(optiononline,optioncmp); option = gt_option_new_bool("s", "Show alignments", &arguments->showalignment, false); gt_option_parser_add_option (op, option); option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); return op; }