static GtOptionParser*
gt_condenseq_compress_option_parser_new(void *tool_arguments)
{
GtCondenseqCompressArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option,
*option_fraction;
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[options] INPUTENCSEQ",
"Compresses a GtEncseq to a UniqueEncseq.");
/* -indexname */
option = gt_option_new_string("indexname",
"path and basename of files to store",
arguments->indexname, NULL);
gt_option_parser_add_option(op, option);
/* -kmersize */
option = gt_option_new_uint_min("kmersize",
"kmer-size used for the seeds, default "
"depends on alphabet size",
&arguments->kmersize, GT_UNDEF_UINT, 2U);
gt_option_parser_add_option(op, option);
/* -windowsize */
option = gt_option_new_uint("windowsize",
"Size of window in which to search for hit pairs "
"of kmers, has to be larger than kmersize" ,
&arguments->windowsize, GT_UNDEF_UINT);
gt_option_parser_add_option(op, option);
/* -initsize */
option = gt_option_new_uword("initsize",
"length of inital unique database in bases, "
"should be larger than -alignlength",
&arguments->initsize, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -alignlength */
option = gt_option_new_uword("alignlength",
"required minimal length of an xdrop-alignment, "
"should be larger than -windowsize",
&arguments->minalignlength, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, option);
/* -cutoff */
option = gt_option_new_uword("cutoff",
"if a kmer is found more often than this value "
"it will be ignored for alignment searches. "
"Setting this to 0 will disable cutoffs, "
"leaving it undefined will use a cutoff based "
"on the mean number of occurences of a k-word.",
&arguments->cutoff_value, GT_UNDEF_UWORD);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -fraction */
option_fraction = gt_option_new_uword("fraction",
"when cutoffs aren'd disabled and no specific "
"value is set the mean number of occurrences "
"of each kmer divided by -fraction will be used "
"as cutoff",
&arguments->fraction, (GtUword) 2);
gt_option_is_extended_option(option_fraction);
gt_option_exclude(option, option_fraction);
gt_option_parser_add_option(op, option_fraction);
/* -disable_prune */
option = gt_option_new_bool("disable_prune",
"when cutoffs and this option are set, "
"the database will still save every kmer, even "
"though only cutoff many kmers will be used.",
&arguments->prune, false);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -mat */
option = gt_option_new_int("mat",
"matchscore for extension-alignment, "
"requirements: mat > mis, mat > 2ins, mat > 2del",
&arguments->scores.mat, 2);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -mis */
option = gt_option_new_int("mis",
"mismatchscore for extension-alignment, ",
&arguments->scores.mis, -1);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -ins */
option = gt_option_new_int("ins",
"insertionscore for extension-alignment",
&arguments->scores.ins, -2);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -del */
option = gt_option_new_int("del",
"deletionscore for extension-alignment",
&arguments->scores.del, -2);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -xdrop */
option = gt_option_new_word("xdrop",
"xdrop score for extension-alignment",
&arguments->xdrop, (GtWord) 3);
gt_option_is_extended_option(option);
gt_option_parser_add_option(op, option);
/* -brute_force */
option = gt_option_new_bool("brute_force", "disable filtering of seeds. "
"Incompatible with -diagonals yes "
"or -full_diags yes",
&arguments->brute, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -diagonals */
option = gt_option_new_bool("diagonals", "use sparse diagonals. "
"Incompatible with -brute_force yes. "
"Disabling both diagonals will result in simple "
"filtering of seed positions.",
&arguments->diags, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -full_diags */
option = gt_option_new_bool("full_diags", "use full (time efficient "
"space inefficient) diagonals. "
"Incompatible with -brute_force yes. "
"Disabling both diagonals will result in simple "
"filtering of seed positions.",
&arguments->full_diags, false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -clean_percent */
option = gt_option_new_uint("diags_clean",
"Percentage of sparse diagonals that is allowed "
"to be marked as deletable. Sensible default is "
"set." ,
&arguments->clean_percent, GT_UNDEF_UINT);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -verbose */
option = gt_option_new_bool("verbose", "enable verbose output",
&arguments->verbose, false);
gt_option_parser_add_option(op, option);
/* -kdb*/
option = gt_option_new_bool("kdb", "prints out the kmer database (frequency "
"of each kmer), if -verbose each startposition "
"will be shown instead",
&arguments->kdb, false);
gt_option_parser_add_option(op, option);
return op;
}
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_ltrdigest_option_parser_new(void *tool_arguments)
{
GtLTRdigestOptions *arguments = tool_arguments;
GtOptionParser *op;
GtOption *o, *ot, *oto;
GtOption *oh, *oc, *oeval;
static const char *cutoffs[] = {"NONE", "GA", "TC", NULL};
static GtRange pptlen_defaults = { 8UL, 30UL},
uboxlen_defaults = { 3UL, 30UL},
pbsalilen_defaults = {11UL, 30UL},
pbsoffsetlen_defaults = { 0UL, 5UL},
pbstrnaoffsetlen_defaults = { 0UL, 5UL};
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] gff3_file",
"Identifies and annotates sequence features in LTR "
"retrotransposon candidates.");
/* Output files */
oto = gt_option_new_string("outfileprefix",
"prefix for output files (e.g. 'foo' will create "
"files called 'foo_*.csv' and 'foo_*.fas')\n"
"Omit this option for GFF3 output only.",
arguments->prefix,
NULL);
gt_option_parser_add_option(op, oto);
gt_option_hide_default(oto);
o = gt_option_new_bool("metadata",
"output metadata (run conditions) to separate file",
&arguments->print_metadata,
true);
gt_option_parser_add_option(op, o);
gt_option_imply(o, oto);
o = gt_option_new_uint("seqnamelen",
"set maximal length of sequence names in FASTA headers"
" (e.g. for clustalw or similar tools)",
&arguments->seqnamelen,
20U);
gt_option_parser_add_option(op, o);
/* PPT search options */
o = gt_option_new_range("pptlen",
"required PPT length range",
&arguments->ppt_len,
&pptlen_defaults);
gt_option_parser_add_option(op, o);
o = gt_option_new_range("uboxlen",
"required U-box length range",
&arguments->ubox_len,
&uboxlen_defaults);
gt_option_parser_add_option(op, o);
o = gt_option_new_uint("uboxdist",
"allowed U-box distance range from PPT",
&arguments->max_ubox_dist, 0);
gt_option_parser_add_option(op, o);
o = gt_option_new_uint("pptradius",
"radius around beginning of 3' LTR "
"to search for PPT",
&arguments->ppt_radius,
30U);
gt_option_parser_add_option(op, o);
o = gt_option_new_probability("pptrprob",
"purine emission probability inside PPT",
&arguments->ppt_purine_prob,
PPT_PURINE_PROB);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
o = gt_option_new_probability("pptyprob",
"pyrimidine emission probability inside PPT",
&arguments->ppt_pyrimidine_prob,
PPT_PYRIMIDINE_PROB);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
o = gt_option_new_probability("pptgprob",
"background G emission probability outside PPT",
&arguments->bkg_g_prob,
BKG_G_PROB);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
o = gt_option_new_probability("pptcprob",
"background C emission probability outside PPT",
&arguments->bkg_c_prob,
BKG_C_PROB);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
o = gt_option_new_probability("pptaprob",
"background A emission probability outside PPT",
&arguments->bkg_a_prob,
BKG_A_PROB);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
o = gt_option_new_probability("ppttprob",
"background T emission probability outside PPT",
&arguments->bkg_t_prob,
BKG_T_PROB);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
o = gt_option_new_probability("pptuprob",
"U/T emission probability inside U-box",
&arguments->ubox_u_prob,
UBOX_U_PROB);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
/* PBS search options */
ot = gt_option_new_filename("trnas",
"tRNA library in multiple FASTA format for PBS "
"detection\n"
"Omit this option to disable PBS search.",
arguments->trna_lib);
gt_option_parser_add_option(op, ot);
gt_option_hide_default(ot);
o = gt_option_new_range("pbsalilen",
"required PBS/tRNA alignment length range",
&arguments->alilen,
&pbsalilen_defaults);
gt_option_parser_add_option(op, o);
gt_option_imply(o, ot);
o = gt_option_new_range("pbsoffset",
"allowed PBS offset from LTR boundary range",
&arguments->offsetlen,
&pbsoffsetlen_defaults);
gt_option_parser_add_option(op, o);
gt_option_imply(o, ot);
o = gt_option_new_range("pbstrnaoffset",
"allowed PBS/tRNA 3' end alignment offset range",
&arguments->trnaoffsetlen,
&pbstrnaoffsetlen_defaults);
gt_option_parser_add_option(op, o);
gt_option_imply(o, ot);
o = gt_option_new_uint("pbsmaxedist",
"maximal allowed PBS/tRNA alignment unit "
"edit distance",
&arguments->max_edist,
1U);
gt_option_parser_add_option(op, o);
gt_option_imply(o, ot);
o = gt_option_new_uint("pbsradius",
"radius around end of 5' LTR "
"to search for PBS",
&arguments->pbs_radius,
30U);
gt_option_parser_add_option(op, o);
gt_option_imply(o, ot);
/* Protein domain search options */
oh = gt_option_new_filename_array("hmms",
"profile HMM models for domain detection "
"(separate by spaces, finish with --) in "
"HMMER3 format\n"
"Omit this option to disable pHMM search.",
arguments->hmm_files);
gt_option_parser_add_option(op, oh);
oeval = gt_option_new_probability("pdomevalcutoff",
"global E-value cutoff for pHMM search\n"
"default 1E-6",
&arguments->evalue_cutoff,
0.000001);
gt_option_parser_add_option(op, oeval);
gt_option_is_extended_option(oeval);
gt_option_hide_default(oeval);
gt_option_imply(oeval, oh);
oc = gt_option_new_choice("pdomcutoff", "model-specific score cutoff\n"
"choose from TC (trusted cutoff) | "
"GA (gathering cutoff) | "
"NONE (no cutoffs)",
arguments->cutoffs, cutoffs[0], cutoffs);
gt_option_parser_add_option(op, oc);
gt_option_is_extended_option(oeval);
gt_option_imply(oeval, oh);
o = gt_option_new_bool("aliout",
"output pHMM to amino acid sequence alignments",
&arguments->write_alignments,
false);
gt_option_parser_add_option(op, o);
gt_option_imply(o, oh);
gt_option_imply(o, oto);
o = gt_option_new_bool("aaout",
"output amino acid sequences for protein domain "
"hits",
&arguments->write_aaseqs,
false);
gt_option_parser_add_option(op, o);
gt_option_imply(o, oh);
gt_option_imply(o, oto);
o = gt_option_new_bool("allchains",
"output features from all chains and unchained "
"features, labeled with chain numbers",
&arguments->output_all_chains,
false);
gt_option_parser_add_option(op, o);
gt_option_imply(o, oh);
o = gt_option_new_uint("maxgaplen",
"maximal allowed gap size between fragments (in amino "
"acids) when chaining pHMM hits for a protein domain",
&arguments->chain_max_gap_length,
50U);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
gt_option_imply(o, oh);
o = gt_option_new_uword("threads",
"DEPRECATED, only included for compatibility reasons!"
" Use the -j parameter of the 'gt' call instead.",
&arguments->nthreads,
0);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
/* Extended PBS options */
o = gt_option_new_int("pbsmatchscore",
"match score for PBS/tRNA alignments",
&arguments->ali_score_match,
5);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
gt_option_imply(o, ot);
o = gt_option_new_int("pbsmismatchscore",
"mismatch score for PBS/tRNA alignments",
&arguments->ali_score_mismatch,
-10);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
gt_option_imply(o, ot);
o = gt_option_new_int("pbsinsertionscore",
"insertion score for PBS/tRNA alignments",
&arguments->ali_score_insertion,
-20);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
gt_option_imply(o, ot);
o = gt_option_new_int("pbsdeletionscore",
"deletion score for PBS/tRNA alignments",
&arguments->ali_score_deletion,
-20);
gt_option_parser_add_option(op, o);
gt_option_is_extended_option(o);
gt_option_imply(o, ot);
/* verbosity */
o = gt_option_new_verbose(&arguments->verbose);
gt_option_parser_add_option(op, o);
/* output file options */
gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp);
/* region mapping and sequence source options */
gt_seqid2file_register_options_ext(op, arguments->s2fi, false, false);
return op;
}
