static GtOptionParser* gt_genomediff_option_parser_new(void *tool_arguments)
{
GtGenomediffArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *option_unitfile;
static const char *indextypes[] = { "esa", "pck", "encseq", NULL };
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] "
"(INDEX | -indexname NAME SEQFILE SEQFILE [...]) ",
"Calculates Kr: pairwise distances between genomes.");
/* options */
option = gt_option_new_choice("indextype", "specify type of index, one of: "
"esa|pck|encseq. Where encseq is an encoded "
"sequence and an enhanced suffix array will be "
"constructed only in memory.",
arguments->indextype, indextypes[2],
indextypes);
gt_option_parser_add_option(op, option);
option = gt_option_new_string("indexname", "Basename of encseq to construct.",
arguments->indexname, NULL);
gt_option_parser_add_option(op, option);
/*-unitfile*/
option_unitfile =
gt_option_new_filename("unitfile",
"specifies genomic units, "
"see below for description.",
arguments->unitfile);
gt_option_parser_add_option(op, option_unitfile);
arguments->ref_unitfile = gt_option_ref(option_unitfile);
/* encseq options */
arguments->loadopts =
gt_encseq_options_register_loading(op, arguments->indexname);
gt_option_is_development_option(
gt_encseq_options_lossless_option(arguments->loadopts));
/* esa options */
arguments->idxopts =
gt_index_options_register_esa_noout(op);
gt_option_is_development_option(
gt_index_options_spmopt_option(arguments->idxopts));
/* scan */
option = gt_option_new_bool("scan", "do not load esa index but scan "
"it sequentially.", &arguments->scanfile, true);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* dev options */
/* -max_n */
option = gt_option_new_uword("max_n", "Number of precalculated values "
"for ln(n!) and pmax(x).",
&arguments->max_ln_n_fac, 1000UL);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -maxdepth */
option = gt_option_new_int("maxdepth", "max depth of .pbi-file, use with "
"-indextype pck.",
&arguments->user_max_depth, -1);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* thresholds */
/* divergence error */
option = gt_option_new_double("thr",
"Threshold for difference (du, dl) in "
"divergence calculation.\n"
"default: 1e-9",
&arguments->divergence_threshold,
1e-9);
gt_option_is_extended_option(option);
gt_option_hide_default(option);
gt_option_parser_add_option(op, option);
/* expected shulen error */
option = gt_option_new_double("abs_err",
"absolute error for expected shulen "
"calculation.\n"
"default: 1e-5",
&arguments->divergence_abs_err,
1e-5);
gt_option_is_extended_option(option);
gt_option_hide_default(option);
gt_option_parser_add_option(op, option);
/* relative expected shulen error */
option = gt_option_new_double("rel_err",
"relative error for expected shulen "
"calculation.\n"
"default: 1e-3",
&arguments->divergence_rel_err,
1e-3);
gt_option_is_extended_option(option);
gt_option_hide_default(option);
gt_option_parser_add_option(op, option);
/* M */
option = gt_option_new_double("M",
"threshold for minimum logarithm.\n"
"default: DBL_MIN",
&arguments->divergence_m,
DBL_MIN);
gt_option_is_extended_option(option);
gt_option_hide_default(option);
gt_option_parser_add_option(op, option);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
/* mail */
gt_option_parser_set_mail_address(op, "<*****@*****.**>");
/* doc */
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
return op;
}
static GtOptionParser* gt_readjoiner_assembly_option_parser_new(
void *tool_arguments)
{
GtReadjoinerAssemblyArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *errors_option, *deadend_option, *v_option,
*q_option, *bubble_option, *deadend_depth_option;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...]",
"Construct string graph and output contigs.");
/* -readset */
option = gt_option_new_string("readset", "specify the readset name",
arguments->readset, NULL);
gt_option_parser_add_option(op, option);
gt_option_is_mandatory(option);
/* -spmfiles */
option = gt_option_new_uint_min("spmfiles", "number of SPM files to read\n"
"this must be equal to the value of -j for the overlap phase",
&arguments->nspmfiles, 1U, 1U);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -l */
option = gt_option_new_uint_min("l", "specify the minimum SPM length",
&arguments->minmatchlength, 0, 2U);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -depthcutoff */
option = gt_option_new_uint_min("depthcutoff", "specify the minimal "
"number of nodes in a contig",
&arguments->depthcutoff, 3U, 1U);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -lengthcutoff */
option = gt_option_new_uint_min("lengthcutoff", "specify the minimal "
"length of a contig",
&arguments->lengthcutoff, 100U, 1U);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -redtrans */
option = gt_option_new_bool("redtrans", "reduce transitive edges",
&arguments->redtrans, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -errors */
errors_option = gt_option_new_bool("errors", "search graph features which "
"may originate from sequencing errors and remove them",
&arguments->errors, false);
gt_option_is_extended_option(errors_option);
gt_option_parser_add_option(op, errors_option);
/* -bubble */
bubble_option = gt_option_new_uint("bubble", "number of rounds of p-bubble "
"removal to perform", &arguments->bubble, 3U);
gt_option_is_extended_option(bubble_option);
gt_option_imply(bubble_option, errors_option);
gt_option_parser_add_option(op, bubble_option);
/* -deadend */
deadend_option = gt_option_new_uint("deadend", "number of rounds of "
"dead end removal to perform a dead end",
&arguments->deadend, 10U);
gt_option_is_extended_option(deadend_option);
gt_option_imply(deadend_option, errors_option);
gt_option_parser_add_option(op, deadend_option);
/* -deadend-depth */
deadend_depth_option = gt_option_new_uint_min("deadend-depth", "specify the "
"maximal depth of a path to an end-vertex by which the path shall be "
"considered a dead end",
&arguments->deadend_depth, 10U, 1U);
gt_option_is_extended_option(deadend_depth_option);
gt_option_imply(deadend_depth_option, errors_option);
gt_option_parser_add_option(op, deadend_depth_option);
/* -paths2seq */
option = gt_option_new_bool("paths2seq", "read <indexname>"
GT_READJOINER_SUFFIX_CONTIG_PATHS " and write "
"<indexname>" GT_READJOINER_SUFFIX_CONTIGS,
&arguments->paths2seq, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -buffersize */
option = gt_option_new_string("buffersize", "specify size for read buffer"
" of paths2seq phase (in bytes, the keywords 'MB' and 'GB' are allowed)",
arguments->buffersizearg, NULL);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
arguments->refoptionbuffersize = gt_option_ref(option);
/* -vd */
option = gt_option_new_bool("vd", "use verbose descriptions for contigs",
&arguments->vd, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -astat */
option = gt_option_new_bool("astat", "calculate A-statistics for each contig",
&arguments->astat, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -cov */
option = gt_option_new_double("cov", "average coverage value to use for the "
"A-statistics calculation", &arguments->coverage, (double)0);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -copynum */
option = gt_option_new_bool("copynum", "load reads copy numbers list from "
"file for the A-statistics calculation",
&arguments->copynum, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -v */
v_option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, v_option);
/* -q */
q_option = gt_option_new_bool("q", "suppress standard output messages",
&arguments->quiet, false);
gt_option_parser_add_option(op, q_option);
gt_option_exclude(q_option, v_option);
/* -load */
option = gt_option_new_bool("load", "save the string graph from file",
&arguments->load, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -save */
option = gt_option_new_bool("save", "save the string graph to file",
&arguments->save, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -show_contigs_info */
option = gt_option_new_bool("cinfo", "output additional files required "
"for contigs graph construction (eqlen only)",
&arguments->show_contigs_info, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
gt_option_parser_set_version_func(op, gt_readjoiner_show_version);
gt_option_parser_set_max_args(op, 0);
return op;
}
static GtOptionParser* gt_sketch_page_option_parser_new(void *tool_arguments)
{
SketchPageArguments *arguments = tool_arguments;
GtOptionParser *op;
static const char *formats[] = {
#ifdef CAIRO_HAS_PDF_SURFACE
"pdf",
#endif
#ifdef CAIRO_HAS_PS_SURFACE
"ps",
#endif
NULL
};
GtOption *o;
op = gt_option_parser_new("outfile annotationfile",
"Draw a multi-page PDF/PS representation of "
"an annotation file.");
o = gt_option_new_string("seqid", "sequence region to draw\n"
"default: first in file",
arguments->seqid, NULL);
gt_option_parser_add_option(op, o);
gt_option_hide_default(o);
o = gt_option_new_string("text", "text to show in header\n"
"default: file name",
arguments->text, NULL);
gt_option_parser_add_option(op, o);
gt_option_hide_default(o);
o = gt_option_new_double("fontsize", "header and footer font size "
"(in points)",
&arguments->theight, 10.0);
gt_option_parser_add_option(op, o);
o = gt_option_new_range("range", "range to draw (e.g. 100 10000)\n"
"default: full range",
&arguments->range, NULL);
gt_option_parser_add_option(op, o);
gt_option_hide_default(o);
o = gt_option_new_ulong_min("linewidth", "base width of a single "
"repeated unit",
&arguments->width, 2000, 1000);
gt_option_is_mandatory(o);
gt_option_parser_add_option(op, o);
o = gt_option_new_double("width", "page width in millimeters "
"(default: DIN A4)",
&arguments->pwidth, 210.0);
gt_option_parser_add_option(op, o);
o = gt_option_new_double("height", "page height in millimeters "
"(default: DIN A4)",
&arguments->pheight, 297.0);
gt_option_parser_add_option(op, o);
o = gt_option_new_choice("format", "output format\n"
"choose from: "
#ifdef CAIRO_HAS_PDF_SURFACE
"pdf"
#ifdef CAIRO_HAS_PS_SURFACE
"|"
#endif
#endif
#ifdef CAIRO_HAS_PS_SURFACE
"ps"
#endif
"",
arguments->format, formats[0], formats );
gt_option_parser_add_option(op, o);
o = gt_option_new_string("style", "style file to use\n"
"default: gtdata/sketch/default.style",
arguments->stylefile,
gt_str_get(arguments->stylefile));
gt_option_parser_add_option(op, o);
gt_option_hide_default(o);
o = gt_option_new_filename("seqfile", "sequence file for GC content view",
arguments->seqfile);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
gt_option_parser_set_min_max_args(op, 2, 2);
return op;
}
static GtOptionParser* gt_gdiffcalc_option_parser_new(void *tool_arguments)
{
GtGenomediffArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *option_unitfile;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] "
"-indexname NAME AVGSHULEN) ",
"Calculates Kr: pairwise distances between genomes.");
/* options */
option = gt_option_new_string("indexname", "Basename of encseq to construct.",
arguments->indexname, NULL);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/*-unitfile*/
option_unitfile =
gt_option_new_filename("unitfile",
"specifies genomic units, see below for description",
arguments->unitfile);
gt_option_parser_add_option(op, option_unitfile);
arguments->ref_unitfile = gt_option_ref(option_unitfile);
/* encseq options */
arguments->loadopts =
gt_encseq_options_register_loading(op, arguments->indexname);
gt_option_is_development_option(
gt_encseq_options_lossless_option(arguments->loadopts));
/* dev options */
/* -max_n */
option = gt_option_new_uword("max_n", "Number of precalculated values "
"for ln(n!) and pmax(x)",
&arguments->max_ln_n_fac, 1000UL);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* thresholds */
/* divergence error */
option = gt_option_new_double("thr",
"Threshold for difference (du, dl) in "
"divergence calculation.\n"
"default: 1e-9",
&arguments->divergence_threshold,
1e-9);
gt_option_is_extended_option(option);
gt_option_hide_default(option);
gt_option_parser_add_option(op, option);
/* expected shulen error */
option = gt_option_new_double("abs_err",
"absolute error for expected shulen "
"calculation.\n"
"default: 1e-5",
&arguments->divergence_abs_err,
1e-5);
gt_option_is_extended_option(option);
gt_option_hide_default(option);
gt_option_parser_add_option(op, option);
/* relative expected shulen error */
option = gt_option_new_double("rel_err",
"relative error for expected shulen "
"calculation.\n"
"default: 1e-3",
&arguments->divergence_rel_err,
1e-3);
gt_option_is_extended_option(option);
gt_option_hide_default(option);
gt_option_parser_add_option(op, option);
/* M */
option = gt_option_new_double("M",
"threshold for minimum logarithm.\n"
"default: DBL_MIN",
&arguments->divergence_m,
DBL_MIN);
gt_option_is_extended_option(option);
gt_option_hide_default(option);
gt_option_parser_add_option(op, option);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
/* mail */
gt_option_parser_set_mail_address(op, "<*****@*****.**>");
/* doc */
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
return op;
}
static GtOptionParser* gt_condenser_search_option_parser_new
(void *tool_arguments)
{
GtCondenserSearchArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *score_opt, *ceval_opt, *feval_opt, *blastp_opt,
*blastn_opt;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...]",
"Perform a BLAST or "
"HMMSEARCH on the given compressed database.");
/* -blastn */
blastn_opt = gt_option_new_bool("blastn", "perform blastn search",
&arguments->blastn, false);
/* -blastp */
blastp_opt = gt_option_new_bool("blastp", "perform blastp search",
&arguments->blastp, false);
gt_option_exclude(blastn_opt, blastp_opt);
gt_option_parser_add_option(op, blastn_opt);
gt_option_parser_add_option(op, blastp_opt);
/* -score */
score_opt = gt_option_new_uword("score", "bitscore threshold for BLAST(p) "
"evalue calculation",
&arguments->bitscore, (GtUword) 30);
gt_option_parser_add_option(op, score_opt);
/* -ce */
ceval_opt = gt_option_new_double("ce",
"coarse e value for coarse blast search",
&arguments->ceval, 5.0);
gt_option_parser_add_option(op, ceval_opt);
/* -fe */
feval_opt = gt_option_new_double("fe", "fine e value for fine blast search, "
"defaults to calculated evalue from the "
"given score",
&arguments->feval, GT_UNDEF_DOUBLE);
gt_option_hide_default(feval_opt);
gt_option_parser_add_option(op, feval_opt);
gt_option_exclude(score_opt, ceval_opt);
gt_option_exclude(score_opt, feval_opt);
/* -db */
option = gt_option_new_filename("db", "path of (compressed) fasta database",
arguments->dbpath);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/* -query */
option = gt_option_new_filename("query", "path of fasta query file",
arguments->querypath);
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/* -verbose */
option = gt_option_new_bool("verbose", "verbose output", &arguments->verbose,
false);
gt_option_parser_add_option(op, option);
/* -blastthreads */
option = gt_option_new_int_min("blastthreads", "how many threads for blast "
"to use", &arguments->blthreads, 8, 1);
gt_option_imply_either_2(option, blastn_opt, blastp_opt);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
return op;
}
static GtOptionParser* gt_select_option_parser_new(void *tool_arguments)
{
SelectArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *contain_option, *overlap_option, *minaveragessp_option,
*singleintron_option, *optiondroppedfile;
gt_assert(arguments);
static const char *filter_logic[] = {
"AND",
"OR",
NULL
};
/* init */
op = gt_option_parser_new("[option ...] [GFF3_file ...]",
"Select certain features (specified by the used "
"options) from given GFF3 file(s).");
/* -seqid */
option = gt_option_new_string("seqid", "select feature with the given "
"sequence ID (all comments are selected). ",
arguments->seqid, NULL);
gt_option_parser_add_option(op, option);
/* -source */
option = gt_option_new_string("source", "select feature with the given "
"source (the source is column 2 in regular "
"GFF3 lines)" , arguments->source, NULL);
gt_option_parser_add_option(op, option);
/* -contain */
contain_option = gt_option_new_range("contain", "select all features which "
"are contained in the given range",
&arguments->contain_range, NULL);
gt_option_parser_add_option(op, contain_option);
/* -overlap */
overlap_option = gt_option_new_range("overlap", "select all features which "
"do overlap with the given range",
&arguments->overlap_range, NULL);
gt_option_parser_add_option(op, overlap_option);
/* -strand */
option = gt_option_new_string(GT_STRAND_OPT, "select all top-level features"
"(i.e., features without parents) whose strand "
"equals the given one (must be one of '"
GT_STRAND_CHARS"')", arguments->gt_strand_char,
NULL);
gt_option_parser_add_option(op, option);
/* -targetstrand */
option = gt_option_new_string(TARGETGT_STRAND_OPT, "select all top-level "
"features (i.e., features without parents) "
"which have exactly one target attribute whose "
"strand equals the given one (must be one of '"
GT_STRAND_CHARS"')",
arguments->targetgt_strand_char, NULL);
gt_option_parser_add_option(op, option);
/* -targetbest */
option = gt_option_new_bool("targetbest", "if multiple top-level features "
"(i.e., features without parents) with exactly "
"one target attribute have the same target_id, "
"keep only the feature with the best score. If "
"-"TARGETGT_STRAND_OPT" is used at the same time, "
"this option is applied after "
"-"TARGETGT_STRAND_OPT".\n"
"Memory consumption is proportional to the input "
"file size(s).", &arguments->targetbest, false);
gt_option_parser_add_option(op, option);
/* -hascds */
option = gt_option_new_bool("hascds", "select all top-level features which "
"do have a CDS child", &arguments->has_CDS,
false);
gt_option_parser_add_option(op, option);
/* -maxgenelength */
option = gt_option_new_uword_min("maxgenelength", "select genes up to the "
"given maximum length",
&arguments->max_gene_length, GT_UNDEF_UWORD,
1);
gt_option_parser_add_option(op, option);
/* -maxgenenum */
option = gt_option_new_uword("maxgenenum", "select the first genes up to the "
"given maximum number", &arguments->max_gene_num,
GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -mingenescore */
option = gt_option_new_double("mingenescore", "select genes with the given "
"minimum score", &arguments->min_gene_score,
GT_UNDEF_DOUBLE);
gt_option_parser_add_option(op, option);
/* -maxgenescore */
option = gt_option_new_double("maxgenescore", "select genes with the given "
"maximum score", &arguments->max_gene_score,
GT_UNDEF_DOUBLE);
gt_option_parser_add_option(op, option);
/* -minaveragessp */
minaveragessp_option =
gt_option_new_probability("minaveragessp",
"set the minimum average splice site probability",
&arguments->min_average_splice_site_prob,
GT_UNDEF_DOUBLE);
gt_option_parser_add_option(op, minaveragessp_option);
/* -singleintronfactor */
singleintron_option =
gt_option_new_double_min("singleintronfactor",
"factor to multiplicate the average splice site "
"probability with for single introns before "
"comparing it to the minimum average splice site "
"probability", &arguments->single_intron_factor,
1.0, 1.0);
gt_option_is_development_option(singleintron_option);
gt_option_parser_add_option(op, singleintron_option);
/* -featurenum */
option = gt_option_new_uword_min("featurenum",
"select feature tree occurring "
"at given position in input",
&arguments->feature_num, GT_UNDEF_UWORD, 1);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -filter_files */
option = gt_option_new_filename_array("rule_files",
"specify Lua files to be used "
"for selection",
arguments->filter_files);
gt_option_parser_add_option(op, option);
/* -filter_logic */
option = gt_option_new_choice("rule_logic", "select how multiple Lua "
"files should be combined\nchoose from AND|OR",
arguments->filter_logic, filter_logic[0],
filter_logic);
gt_option_parser_add_option(op, option);
/* -nh_file */
optiondroppedfile = gt_option_new_filename("dropped_file",
"save non-selected features to "
"file",
arguments->dropped_file);
gt_option_parser_add_option(op, optiondroppedfile);
/* -v */
option = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, option);
/* option exclusions */
gt_option_exclude(contain_option, overlap_option);
/* option implications */
gt_option_imply(singleintron_option, minaveragessp_option);
/* output file options */
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL);
return op;
}
