static GtOptionParser* gt_encseq_bitextract_option_parser_new(void
*tool_arguments)
{
GtEncseqBitextractArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] [indexname]",
"Extracts internal data from encoded sequences.");
option = gt_option_new_bool("mirrored", "mirror sequence",
&arguments->mirror, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong("stoppos", "output stop positions",
&arguments->stoppos, GT_UNDEF_ULONG);
gt_option_parser_add_option(op, option);
option = gt_option_new_bool("specialranges", "output special ranges",
&arguments->specialranges, false);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong("bitpos", "extract and display "
"two bit encoding for position",
&arguments->bitpos, GT_UNDEF_ULONG);
gt_option_parser_add_option(op, option);
gt_encseq_options_add_readmode_option(op, arguments->readmode);
gt_option_parser_set_min_args(op, 1U);
return op;
}
static GtOptionParser* gt_encseq_decode_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *option,
*optionsep,
*optionseq,
*optionseqrange,
*optionmode;
GtEncseqDecodeArguments *arguments =
(GtEncseqDecodeArguments*) tool_arguments;
static const char *modes[] = {"fasta", "concat", NULL};
/* init */
op = gt_option_parser_new("(sequence_file|indexname)",
"Decode/extract encoded sequences.");
/* encseq options */
arguments->eopts = gt_encseq_options_register_loading(op, NULL);
gt_encseq_options_add_readmode_option(op, arguments->dir);
/* -singlechars */
option = gt_option_new_bool("singlechars",
"do not use a GtEncseqReader but access each "
"sequence character separately",
&arguments->singlechars,
false);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -seq */
optionseq = gt_option_new_uword("seq",
"extract sequence identified by its number",
&arguments->seq,
GT_UNDEF_UWORD);
gt_option_parser_add_option(op, optionseq);
/* -seqrange */
optionseqrange = gt_option_new_range("seqrange",
"extract multiple consecutive sequences",
&arguments->seqrng,
NULL);
gt_option_parser_add_option(op, optionseqrange);
gt_option_exclude(optionseqrange, optionseq);
/* -output */
optionmode = gt_option_new_choice("output",
"specify output format "
"(choose from fasta|concat)",
arguments->mode,
modes[0],
modes);
gt_option_parser_add_option(op, optionmode);
/* -range */
option = gt_option_new_range("range",
"concatenated range to extract "
"(implies '-output concat')",
&arguments->rng,
NULL);
gt_option_parser_add_option(op, option);
gt_option_imply(option, optionmode);
/* -sepchar */
optionsep = gt_option_new_string("sepchar",
"specify character to print as SEPARATOR",
arguments->sepchar, "|");
gt_option_parser_add_option(op, optionsep);
gt_option_imply(optionsep, optionmode);
gt_option_parser_set_min_max_args(op, 1, 1);
return op;
}
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;
}
