static GtOptionParser* gt_seed_extend_option_parser_new(void *tool_arguments)
{
GtSeedExtendArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *option, *op_gre, *op_xdr, *op_cam, *op_his, *op_dif, *op_pmh,
*op_len, *op_err, *op_xbe, *op_sup, *op_frq, *op_mem, *op_ali, *op_bia;
gt_assert(arguments != NULL);
/* init */
op = gt_option_parser_new("[option ...] encseq_basename [encseq_basename]",
"Calculate local alignments using the seed and "
"extend algorithm.");
/* DIAGBANDSEED OPTIONS */
/* -ii */
option = gt_option_new_string("ii",
"Input index for encseq encoded sequences",
arguments->dbs_indexname,
"");
gt_option_is_mandatory(option);
gt_option_parser_add_option(op, option);
/* -qii */
option = gt_option_new_string("qii",
"Query input index (encseq)",
arguments->dbs_queryname,
"");
gt_option_parser_add_option(op, option);
/* -seedlength */
op_len = gt_option_new_uint_min_max("seedlength",
"Minimum length of a seed",
&arguments->dbs_seedlength,
14UL, 1UL, 32UL);
gt_option_parser_add_option(op, op_len);
/* -diagbandwidth */
option = gt_option_new_uword("diagbandwidth",
"Logarithm of diagonal band width (for filter)",
&arguments->dbs_logdiagbandwidth,
6UL);
gt_option_parser_add_option(op, option);
/* -mincoverage */
option = gt_option_new_uword("mincoverage",
"Minimum coverage in two neighbouring diagonal "
"bands (for filter)",
&arguments->dbs_mincoverage,
35UL);
gt_option_parser_add_option(op, option);
/* -maxfreq */
op_frq = gt_option_new_uword_min("maxfreq",
"Maximum frequency of a k-mer (for filter)",
&arguments->dbs_maxfreq,
GT_UWORD_MAX, 1UL);
gt_option_parser_add_option(op, op_frq);
/* -t */
op_sup = gt_option_new_uword_min("t",
"Suppress k-mers occurring at least t times "
"(for filter)",
&arguments->dbs_suppress,
GT_UWORD_MAX, 2UL);
gt_option_exclude(op_sup, op_frq);
gt_option_is_development_option(op_sup);
gt_option_parser_add_option(op, op_sup);
/* -memlimit */
op_mem = gt_option_new_string("memlimit",
"Maximum memory usage to determine the maximum "
"frequency of a k-mer (for filter)",
arguments->dbs_memlimit_str,
"");
gt_option_parser_add_option(op, op_mem);
/* -debug-kmer */
option = gt_option_new_bool("debug-kmer",
"Output KmerPos lists",
&arguments->dbs_debug_kmer,
false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -debug-seedpair */
option = gt_option_new_bool("debug-seedpair",
"Output SeedPair lists",
&arguments->dbs_debug_seedpair,
false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -verify */
option = gt_option_new_bool("verify",
"Check that k-mer seeds occur in the sequences",
&arguments->dbs_verify,
false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* SEED EXTENSION OPTIONS */
/* -extendxdrop */
op_xdr = gt_option_new_uword_min_max("extendxdrop",
"Extend seed to both sides using xdrop "
"algorithm, optional parameter "
"specifies sensitivity",
&arguments->se_extendxdrop,
97UL, 90UL, 100UL);
gt_option_argument_is_optional(op_xdr);
gt_option_parser_add_option(op, op_xdr);
arguments->se_option_xdrop = gt_option_ref(op_xdr);
/* -xdropbelow */
op_xbe = gt_option_new_word("xdropbelow",
"Specify xdrop cutoff score (0 means "
"automatically defined depending on minidentity)",
&arguments->se_xdropbelowscore,
0L);
gt_option_imply(op_xbe, op_xdr);
gt_option_parser_add_option(op, op_xbe);
/* -extendgreedy */
op_gre = gt_option_new_uword_min_max("extendgreedy",
"Extend seed to both sides using greedy "
"algorithm, optional parameter "
"specifies sensitivity",
&arguments->se_extendgreedy,
97UL, 90UL, 100UL);
gt_option_argument_is_optional(op_gre);
gt_option_exclude(op_gre, op_xdr);
gt_option_parser_add_option(op, op_gre);
arguments->se_option_greedy = gt_option_ref(op_gre);
/* -history */
op_his = gt_option_new_uword_min_max("history",
"Size of (mis)match history in range [1"
"..64] (trimming for greedy extension)",
&arguments->se_historysize,
60UL, 1UL, 64UL);
gt_option_imply(op_his, op_gre);
gt_option_parser_add_option(op, op_his);
/* -maxalilendiff */
op_dif = gt_option_new_uword("maxalilendiff",
"Maximum difference of alignment length "
"(trimming for greedy extension)",
&arguments->se_maxalilendiff, 0UL);
gt_option_imply(op_dif, op_gre);
gt_option_is_development_option(op_dif);
gt_option_parser_add_option(op, op_dif);
/* -percmathistory */
op_pmh = gt_option_new_uword_min_max("percmathistory",
"percentage of matches required in "
"history (for greedy extension)",
&arguments->se_perc_match_hist,
0UL, 1UL, 100UL);
gt_option_imply(op_pmh, op_gre);
gt_option_is_development_option(op_pmh);
gt_option_parser_add_option(op, op_pmh);
/* -bias-parameters */
op_bia = gt_option_new_bool("bias-parameters",
"Use -maxalilendiff 30 and let percmathistory "
"depend on minidentiy and DNA base distribution",
&arguments->bias_parameters,
false);
gt_option_imply(op_bia, op_gre);
gt_option_exclude(op_bia, op_pmh);
gt_option_exclude(op_bia, op_dif);
gt_option_is_development_option(op_bia);
gt_option_parser_add_option(op, op_bia);
/* -cam */
op_cam = gt_option_new_string("cam",
gt_cam_extendgreedy_comment(),
arguments->se_char_access_mode,
"");
gt_option_is_development_option(op_cam);
gt_option_parser_add_option(op, op_cam);
/* -l */
op_len = gt_option_new_uword_min("l",
"Minimum alignment length "
"(for seed extension)",
&arguments->se_alignlength,
20UL, 1UL);
gt_option_imply_either_2(op_len, op_xdr, op_gre);
gt_option_parser_add_option(op, op_len);
/* -minidentity */
op_err = gt_option_new_uword_min_max("minidentity",
"Minimum identity of matches "
"(for seed extension)",
&arguments->se_minidentity,
80UL, GT_EXTEND_MIN_IDENTITY_PERCENTAGE,
99UL);
gt_option_imply_either_2(op_err, op_xdr, op_gre);
gt_option_parser_add_option(op, op_err);
/* -a */
op_ali = gt_option_new_uword_min("a",
"show alignments/sequences (optional "
"argument is number of columns per line)",
&arguments->se_alignmentwidth,
70, 20);
gt_option_argument_is_optional(op_ali);
gt_option_parser_add_option(op, op_ali);
arguments->se_option_withali = gt_option_ref(op_ali);
/* -mirror */
option = gt_option_new_bool("mirror",
"Add reverse complement reads",
&arguments->mirror,
false);
gt_option_parser_add_option(op, option);
/* -overlappingseeds */
option = gt_option_new_bool("overlappingseeds",
"Allow overlapping SeedPairs",
&arguments->overlappingseeds,
false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -benchmark */
option = gt_option_new_bool("benchmark",
"Measure total running time and be silent",
&arguments->benchmark,
false);
gt_option_is_development_option(option);
gt_option_parser_add_option(op, option);
/* -seed-display */
option = gt_option_new_bool("seed-display",
"Display seeds in #-line",
&arguments->seed_display,
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);
return op;
}
static GtOptionParser* gt_tir_option_parser_new(void *tool_arguments)
{
GtTirArguments *arguments = tool_arguments;
GtOptionParser *op;
GtOption *optionindex, /* index */
*optionseed, /* minseedlength */
*optionminlentir, /* minimal length of TIR */
*optionmaxlentir, /* maximal length of TIR */
*optionmindisttir, /* minimal distance of TIRs */
*optionmaxdisttir, /* maximal distance of TIRs */
*optionmat, /* arbitrary scores */
*optionmis,
*optionins,
*optiondel,
*optionxdrop, /* xdropbelowscore for extension alignment */
*optionsimilar, /* similarity threshold */
*optionoverlaps, /* for overlaps */
*optionmintsd, /* minimal length for Target Site Duplication */
*optionmaxtsd, /* maximal length for Target Site Duplication */
*optionvicinity, /* vicinity around TIRs to be searched for TSDs */
*optionhmms,
*optionevalcutoff,
*optionpdomcutoff,
*optionmaxgap;
static const char *overlaps[] = {
"best", /* default */
"no",
"all",
NULL
};
static const char *cutoffs[] = {
"NONE",
"GA",
"TC",
NULL
};
gt_assert(arguments);
/* init */
op = gt_option_parser_new("[option ...] -index INDEXNAME",
"Identify Terminal Inverted Repeat (TIR) elements,"
"such as DNA transposons.");
/* -index */
optionindex = gt_option_new_string("index",
"specify the name of the enhanced suffix "
"array index (mandatory)",
arguments->str_indexname, NULL);
gt_option_is_mandatory(optionindex);
gt_option_parser_add_option(op, optionindex);
/* -seed */
optionseed = gt_option_new_uword_min("seed",
"specify minimum seed length for "
"exact repeats",
&arguments->min_seed_length, 20UL, 2UL);
gt_option_parser_add_option(op, optionseed);
/* -minlentir */
optionminlentir = gt_option_new_uword_min_max("mintirlen",
"specify minimum length for "
"each TIR",
&arguments->min_TIR_length,
27UL, 1UL, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, optionminlentir);
/* -maxlentir */
optionmaxlentir = gt_option_new_uword_min_max("maxtirlen",
"specify maximum length for "
"each TIR",
&arguments->max_TIR_length,
1000UL, 1UL, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, optionmaxlentir);
/* -mindisttir */
optionmindisttir = gt_option_new_uword_min_max("mintirdist",
"specify minimum distance of "
"TIRs",
&arguments->min_TIR_distance,
100UL, 1UL, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, optionmindisttir);
/* -maxdisttir */
optionmaxdisttir = gt_option_new_uword_min_max("maxtirdist",
"specify maximum distance of "
"TIRs",
&arguments->max_TIR_distance,
10000UL, 1UL, GT_UNDEF_UWORD);
gt_option_parser_add_option(op, optionmaxdisttir);
optionmat = gt_option_new_int_min("mat",
"specify matchscore for "
"extension-alignment",
&arguments->arbit_scores.mat, 2, 1);
gt_option_parser_add_option(op, optionmat);
/* -mis */
optionmis = gt_option_new_int_max("mis",
"specify mismatchscore for "
"extension-alignment",
&arguments->arbit_scores.mis, -2, -1);
gt_option_parser_add_option(op, optionmis);
/* -ins */
optionins = gt_option_new_int_max("ins",
"specify insertionscore for "
"extension-alignment",
&arguments->arbit_scores.ins, -3, -1);
gt_option_parser_add_option(op, optionins);
/* -del */
optiondel = gt_option_new_int_max("del",
"specify deletionscore for "
"extension-alignment",
&arguments->arbit_scores.del, -3, -1);
gt_option_parser_add_option(op, optiondel);
/* -xdrop */
optionxdrop = gt_option_new_int_min("xdrop",
"specify xdropbelowscore for "
"extension-alignment",
&arguments->xdrop_belowscore, (int) 5,
(int) 0);
gt_option_parser_add_option(op, optionxdrop);
/* -similar */
optionsimilar = gt_option_new_double_min_max("similar",
"specify similaritythreshold in "
"range [1..100%]",
&arguments->similarity_threshold,
(double) 85.0, (double) 0.0,
100.0);
gt_option_parser_add_option(op, optionsimilar);
/* -overlaps */
optionoverlaps = gt_option_new_choice("overlaps", "specify no|best|all",
arguments->str_overlaps,
overlaps[0], overlaps);
gt_option_parser_add_option(op, optionoverlaps);
arguments->optionoverlaps = gt_option_ref(optionoverlaps);
/* -mintsd */
optionmintsd = gt_option_new_uword_min_max("mintsd",
"specify minimum length for each "
"TSD",
&arguments->min_TSD_length,
2U, 0, GT_UNDEF_UINT);
gt_option_parser_add_option(op, optionmintsd);
/* -maxtsd */
optionmaxtsd = gt_option_new_uword_min_max("maxtsd",
"specify maximum length for each "
"TSD",
&arguments->max_TSD_length,
11U, 0, GT_UNDEF_UINT);
gt_option_parser_add_option(op, optionmaxtsd);
gt_option_imply(optionmaxtsd, optionmintsd);
/* -vicinity */
optionvicinity = gt_option_new_uword_min_max("vic",
"specify the number of "
"nucleotides (to the left and "
"to the right) that will be "
"searched for TSDs around 5' "
"and 3' boundary of predicted "
"TIRs",
&arguments->vicinity,
60U, 1U, 500U);
gt_option_parser_add_option(op, optionvicinity);
optionhmms = 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, optionhmms);
optionevalcutoff = 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, optionevalcutoff);
gt_option_hide_default(optionevalcutoff);
gt_option_imply(optionevalcutoff, optionhmms);
optionpdomcutoff = gt_option_new_choice("pdomcutoff",
"model-specific score cutoff\n"
"choose from TC (trusted cutoff) | "
"GA (gathering cutoff) | "
"NONE (no cutoffs)",
arguments->cutoffs, cutoffs[1], cutoffs);
gt_option_parser_add_option(op, optionpdomcutoff);
gt_option_imply(optionpdomcutoff, optionhmms);
/* XXX: make -pdomcutoff and -pdomevalcutoff mutually exclusive */
optionmaxgap = 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, optionmaxgap);
gt_option_is_extended_option(optionmaxgap);
gt_option_imply(optionmaxgap, optionhmms);
return op;
}
