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_seqtranslate_option_parser_new(void *tool_arguments)
{
GtTranslateArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [files]",
"Translates a nucleotide sequence into a protein "
"sequence.");
option = gt_option_new_bool("reverse", "also translate reverse complements",
&arguments->reverse, true);
gt_option_parser_add_option(op, option);
option = gt_option_new_uword("fastawidth", "width of the FASTA output",
&arguments->fasta_width, 60);
gt_option_parser_add_option(op, option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_encseq_check_option_parser_new(void *tool_arguments)
{
GtEncseqCheckArguments *arguments = tool_arguments;
GtOptionParser *op;
GT_UNUSED GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [file]",
"Check the consistency of an encoded "
"sequence file.");
option = gt_option_new_ulong("scantrials", "specify number of scan trials",
&arguments->scantrials, 0);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong("multicharcmptrials",
"specify number of multicharacter trials",
&arguments->multicharcmptrials, 0);
gt_option_parser_add_option(op, option);
option = gt_option_new_ulong_min_max("prefixlength",
"prefix length",
&arguments->prefixlength, 0,
0, MAXPREFIXLENGTH);
gt_option_parser_add_option(op, option);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_script_filter_option_parser_new(void *tool_arguments)
{
GtScriptFilterArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] [script file(s)]",
"Get info about and validate Lua script filters.");
/* -showinfo */
option = gt_option_new_bool("showinfo", "show information about filter",
&arguments->showinfo, true);
gt_option_parser_add_option(op, option);
/* -validate */
option = gt_option_new_bool("validate", "validate filter function",
&arguments->validate, true);
gt_option_parser_add_option(op, option);
/* -oneline */
option = gt_option_new_bool("oneline", "show compact information on one line",
&arguments->oneline, false);
gt_option_parser_add_option(op, option);
/* -scriptname */
option = gt_option_new_bool("scriptname", "show script name",
&arguments->scriptname, true);
gt_option_parser_add_option(op, option);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_dev_option_parser_new(void *tool_arguments)
{
GtToolbox *dev_toolbox = tool_arguments;
GtOptionParser *op;
gt_assert(dev_toolbox);
op = gt_option_parser_new("[option ...] dev_tool_name [argument ...]",
"Call development tool with name dev_tool_name and "
"pass argument(s) to it.");
gt_option_parser_set_comment_func(op, gt_toolbox_show, dev_toolbox);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_packedindex_option_parser_new(void *tool_arguments)
{
GtToolbox *index_toolbox = tool_arguments;
GtOptionParser *op;
gt_assert(index_toolbox);
op = gt_option_parser_new("[option ...] index_tool [argument ...]",
"Call apacked index subtool and pass argument(s) to "
"it.");
gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
gt_option_parser_set_min_args(op, 1);
gt_option_parser_refer_to_manual(op);
return op;
}
static GtOptionParser* gt_cge_option_parser_new(void *tool_arguments)
{
GtToolbox *index_toolbox = tool_arguments;
GtOptionParser *op;
gt_assert(index_toolbox != NULL);
op = gt_option_parser_new(
"[option ...] congruence_tool [argument ...]",
"Call a congruence subtool and pass argument(s) to it.");
gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
gt_option_parser_set_min_args(op, 1U);
gt_option_parser_refer_to_manual(op);
return op;
}
static GtOptionParser* gt_sequniq_option_parser_new(void *tool_arguments)
{
GtSequniqArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *seqit_option, *verbose_option, *width_option, *rev_option,
*nofseqs_option;
gt_assert(arguments);
op = gt_option_parser_new("[option ...] sequence_file [...] ",
"Filter out repeated sequences in given "
"sequence files.");
/* -seqit */
seqit_option = gt_option_new_bool("seqit", "use sequence iterator",
&arguments->seqit, false);
gt_option_is_development_option(seqit_option);
gt_option_parser_add_option(op, seqit_option);
/* -nofseqs */
nofseqs_option = gt_option_new_uword("nofseqs", "number of sequences "
"(improves efficiency)\ndefault: unspecified",
&arguments->nofseqs, 0);
gt_option_is_development_option(nofseqs_option);
gt_option_hide_default(nofseqs_option);
gt_option_parser_add_option(op, nofseqs_option);
/* -rev */
rev_option = gt_option_new_bool("rev", "also filter out sequences whose "
"reverse complement is identical to a sequence already output",
&arguments->rev, false);
gt_option_parser_add_option(op, rev_option);
/* -v */
verbose_option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, verbose_option);
/* -width */
width_option = gt_option_new_width(&arguments->width);
gt_option_parser_add_option(op, width_option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
/* option implications */
gt_option_imply(verbose_option, seqit_option);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
gt_option_parser_set_min_args(op, 1U);
return op;
}
static GtOPrval parse_options(int *parsed_args, int argc, const char **argv,
GtError *err)
{
GtOptionParser *op;
GtOPrval oprval;
gt_error_check(err);
op = gt_option_parser_new("file [...]",
"Map the supplied files into memory and "
"read them once.");
gt_option_parser_set_min_args(op, 1);
oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc,
err);
gt_option_parser_delete(op);
return oprval;
}
static GtOptionParser* gt_condenser_option_parser_new(void *tool_arguments)
{
GtToolbox *condenser_toolbox = tool_arguments;
GtOptionParser *op;
gt_assert(condenser_toolbox);
/* init */
op = gt_option_parser_new("[option ...] [file]",
"Call one of the CONDENSER tools to prepare "
"or manipulate redundancie compressed genomic data."
);
gt_option_parser_set_comment_func(op, gt_toolbox_show, condenser_toolbox);
gt_option_parser_set_min_args(op, 1U);
return op;
}
static GtOptionParser* gt_tyr_option_parser_new(void *tool_arguments)
{
GtToolbox *index_toolbox = tool_arguments;
GtOptionParser *op;
gt_assert(index_toolbox != NULL);
op = gt_option_parser_new(
"[option ...] tallymer_tool [argument ...]",
"Call tallymer tool with name tallymer_tool and pass "
"argument(s) to it.");
gt_option_parser_set_comment_func(op, gt_toolbox_show, index_toolbox);
gt_option_parser_set_min_args(op, 1U);
gt_option_parser_refer_to_manual(op);
return op;
}
static GtOptionParser* gt_convertseq_option_parser_new(void *tool_arguments)
{
GtConvertseqArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *o;
gt_assert(arguments);
op = gt_option_parser_new("[options] file [...]",
"Parse and convert sequence file formats "
"(FASTA/FASTQ, GenBank, EMBL).");
o = gt_option_new_bool("v","be verbose", &arguments->verbose, false);
gt_option_parser_add_option(op, o);
o = gt_option_new_bool("r","reverse complement sequences",
&arguments->revcomp, false);
gt_option_parser_add_option(op, o);
o = gt_option_new_bool("showfilelengthvalues","show filelengths",
&arguments->showflv, false);
gt_option_parser_add_option(op, o);
o = gt_option_new_bool("noseq","do not show sequences",
&arguments->showseq, false);
gt_option_parser_add_option(op, o);
o = gt_option_new_uword("fastawidth",
"FASTA output line width, 0 for unlimited",
&arguments->fastawidth, 60UL);
gt_option_parser_add_option(op, o);
o = gt_option_new_bool("contractdnawc", "replace stretches of DNA wildcards "
"with a single 'N'",
&arguments->reduce_wc_dna, false);
gt_option_parser_add_option(op, o);
o = gt_option_new_bool("contractproteinwc", "replace stretches of protein "
"wildcards with a single 'X'",
&arguments->reduce_wc_prot, false);
gt_option_parser_add_option(op, o);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
gt_option_parser_set_min_args(op, 1U);
return op;
}
static GtOptionParser* gt_encseq_encode_option_parser_new(void *tool_arguments)
{
GtOptionParser *op;
GtOption *option;
GtEncseqEncodeArguments *arguments =
(GtEncseqEncodeArguments*) tool_arguments;
/* init */
op = gt_option_parser_new("sequence_file [sequence_file "
"[sequence_file ...]]",
"Encode sequence files (FASTA/FASTQ, GenBank, "
"EMBL) efficiently.");
/* -showstats */
option = gt_option_new_bool("showstats",
"show compression results",
&arguments->showstats,
false);
gt_option_parser_add_option(op, option);
/* -no_esq_header */
option = gt_option_new_bool("no_esq_header",
"omit the header in the .esq file",
&arguments->no_esq_header,
false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* encoded sequence options */
arguments->eopts = gt_encseq_options_register_encoding(op,
arguments->indexname,
NULL);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
gt_option_parser_set_min_args(op, 1);
return op;
}
static GtOptionParser* gt_sketch_option_parser_new(void *tool_arguments)
{
GtSketchArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *option2;
static const char *formats[] = { "png",
#ifdef CAIRO_HAS_PDF_SURFACE
"pdf",
#endif
#ifdef CAIRO_HAS_SVG_SURFACE
"svg",
#endif
#ifdef CAIRO_HAS_PS_SURFACE
"ps",
#endif
NULL
};
static const char *inputs[] = {
"gff",
"bed",
"gtf",
NULL
};
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] image_file [GFF3_file ...]",
"Create graphical representation of GFF3 "
"annotation files.");
/* -pipe */
option = gt_option_new_bool("pipe", "use pipe mode (i.e., show all gff3 "
"features on stdout)", &arguments->pipe, false);
gt_option_parser_add_option(op, option);
/* -flattenfiles */
option = gt_option_new_bool("flattenfiles", "do not group tracks by source "
"file name and remove file names from track "
"description", &arguments->flattenfiles, false);
gt_option_parser_add_option(op, option);
/* -seqid */
option = gt_option_new_string("seqid", "sequence region identifier\n"
"default: first one in file",
arguments->seqid, NULL);
gt_option_parser_add_option(op, option);
gt_option_hide_default(option);
/* -start */
option = gt_option_new_uword_min("start", "start position\n"
"default: first region start",
&arguments->start, GT_UNDEF_UWORD, 1);
gt_option_parser_add_option(op, option);
gt_option_hide_default(option);
/* -end */
option2 = gt_option_new_uword("end", "end position\ndefault: last region end",
&arguments->end, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option2);
/* -start and -end must be given together */
gt_option_imply(option, option2);
gt_option_imply(option2, option);
gt_option_hide_default(option2);
/* -width */
option = gt_option_new_uint_min("width", "target image width (in pixel)",
&arguments->width,
800, 1);
gt_option_parser_add_option(op, option);
/* -style */
option = gt_option_new_string("style", "style file to use",
arguments->stylefile,
gt_str_get(arguments->stylefile));
gt_option_parser_add_option(op, option);
/* -format */
option = gt_option_new_choice("format", "output graphics format\n"
"choose from png"
#ifdef CAIRO_HAS_PDF_SURFACE
"|pdf"
#endif
#ifdef CAIRO_HAS_SVG_SURFACE
"|svg"
#endif
#ifdef CAIRO_HAS_PS_SURFACE
"|ps"
#endif
"",
arguments->format, formats[0], formats);
gt_option_parser_add_option(op, option);
/* -input */
option = gt_option_new_choice("input", "input data format\n"
"choose from gff|bed|gtf",
arguments->input, inputs[0], inputs);
gt_option_parser_add_option(op, option);
/* -addintrons */
option = gt_option_new_bool("addintrons", "add intron features between "
"existing exon features (before drawing)",
&arguments->addintrons, false);
gt_option_parser_add_option(op, option);
/* -unsafe */
option = gt_option_new_bool("unsafe", "enable unsafe mode for style file",
&arguments->unsafe, false);
gt_option_parser_add_option(op, option);
/* -showrecmaps */
option = gt_option_new_bool("showrecmaps",
"show RecMaps after image creation",
&arguments->showrecmaps, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -streams */
option = gt_option_new_bool("streams", "use streams to write data to file",
&arguments->use_streams, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
/* -force */
option = gt_option_new_bool(GT_FORCE_OPT_CSTR, "force writing to output file",
&arguments->force, false);
gt_option_parser_add_option(op, option);
gt_option_parser_set_min_args(op, 1);
return op;
}
