static GtOptionParser *gt_tyr_mkindex_option_parser_new(void *tool_arguments) { GtOptionParser *op; GtOption *option, *optionminocc, *optionmaxocc, *optionpl, *optionstoreindex, *optionstorecounts, *optionscan, *optionesa; Tyr_mkindex_options *arguments = tool_arguments; op = gt_option_parser_new("[options] -esa suffixerator-index [options]", "Count and index k-mers in the given enhanced " "suffix array for a fixed value of k."); gt_option_parser_set_mailaddress(op,"<*****@*****.**>"); optionesa = gt_option_new_string("esa","specify suffixerator-index\n" "(mandatory option)", arguments->str_inputindex, NULL); gt_option_is_mandatory(optionesa); gt_option_parser_add_option(op, optionesa); option = gt_option_new_ulong("mersize", "Specify the mer size.", &arguments->mersize, 20UL); gt_option_parser_add_option(op, option); optionminocc = gt_option_new_ulong("minocc", "Specify the minimum occurrence number for " "the mers to output/index", &arguments->userdefinedminocc, 0); gt_option_parser_add_option(op, optionminocc); optionmaxocc = gt_option_new_ulong("maxocc", "Specify the maximum occurrence number for " "the mers to output/index", &arguments->userdefinedmaxocc, 0); gt_option_parser_add_option(op, optionmaxocc); optionpl = gt_option_new_uint_min("pl", "specify prefix length for bucket boundary construction\n" "recommendation: use without argument;\n" "then a reasonable prefix length is automatically determined", &arguments->userdefinedprefixlength, 0, 1U); gt_option_argument_is_optional(optionpl); gt_option_parser_add_option(op, optionpl); arguments->refoptionpl = gt_option_ref(optionpl); optionstoreindex = gt_option_new_string("indexname", "store the mers specified by options " "-maxocc and -minocc in an index", arguments->str_storeindex, NULL); gt_option_parser_add_option(op, optionstoreindex); optionstorecounts = gt_option_new_bool("counts", "store counts of the mers", &arguments->storecounts,false); gt_option_parser_add_option(op, optionstorecounts); option = gt_option_new_bool("test", "perform tests to verify program " "correctness", &arguments->performtest, false); gt_option_is_development_option(option); gt_option_parser_add_option(op, option); optionscan = gt_option_new_bool("scan", "read enhanced suffix array sequentially " "instead of mapping it to memory", &arguments->scanfile, false); gt_option_parser_add_option(op, optionscan); option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); gt_option_imply(optionpl, optionstoreindex); gt_option_imply(optionstorecounts, optionstoreindex); gt_option_imply_either_2(optionstoreindex,optionminocc,optionmaxocc); 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->scan, 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_tyr_occratio_option_parser_new(void *tool_arguments) { GtOptionParser *op; GtOption *optionmersizes, *optionesa, *optionminmersize, *optionmaxmersize, *optionstep, *optionoutput, *option; Tyr_occratio_options *arguments = tool_arguments; op = gt_option_parser_new("[options] -esa suffixerator-index [options]", "Compute occurrence ratio for a set of sequences " "represented by an enhanced suffix array."); gt_option_parser_set_mailaddress(op,"<*****@*****.**>"); optionesa = gt_option_new_string("esa","specify suffixerator-index\n" "(mandatory option)", arguments->str_inputindex, NULL); gt_option_is_mandatory(optionesa); gt_option_parser_add_option(op, optionesa); optionminmersize = gt_option_new_ulong_min("minmersize", "specify minimum mer size for which " "to compute the occurrence distribution", &arguments->minmersize,0,1UL); gt_option_parser_add_option(op, optionminmersize); optionmaxmersize = gt_option_new_ulong_min("maxmersize", "specify maximum mer size for which " "to compute the occurrence distribution", &arguments->maxmersize,0,1UL); gt_option_parser_add_option(op, optionmaxmersize); optionstep = gt_option_new_ulong_min("step", "specify step size when specifying mer sizes", &arguments->stepmersize,1UL,1UL); gt_option_parser_add_option(op, optionstep); optionmersizes = gt_option_new_stringarray( "mersizes", "specify mer sizes as non-empty sequence of " "non decreasing positive integers", arguments->mersizesstrings); arguments->refoptionmersizes = gt_option_ref(optionmersizes); gt_option_parser_add_option(op, optionmersizes); optionoutput = gt_option_new_stringarray( "output", "use combination of the following keywords: " "unique nonunique nonuniquemulti relative total " "to specify kind of output", arguments->outputspec); gt_option_parser_add_option(op, optionoutput); option = gt_option_new_bool("scan", "read suffixerator-index sequentially " "instead of mapping it to memory", &arguments->scanfile, false); gt_option_parser_add_option(op, option); option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); gt_option_exclude(optionmersizes,optionminmersize); gt_option_exclude(optionmersizes,optionmaxmersize); gt_option_exclude(optionmersizes,optionstep); 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* gtr_option_parser_new(GtR *gtr) { GtOptionParser *op; GtOption *o, *only_option, *debug_option, *debugfp_option; gt_assert(gtr); op = gt_option_parser_new("[option ...] [tool | script] [argument ...]", "The GenomeTools genome analysis system."); gt_option_parser_set_comment_func(op, show_gtr_help, gtr->tools); o = gt_option_new_bool("i", "enter interactive mode after executing 'tool' or " "'script'", >r->interactive, false); gt_option_hide_default(o); gt_option_parser_add_option(op, o); o = gt_option_new_bool("q", "suppress warnings", >r->quiet, false); gt_option_hide_default(o); gt_option_parser_add_option(op, o); o = gt_option_new_uint_min("j", "set number of parallel threads used at once", >_jobs, 1, 1); gt_option_is_development_option(o); gt_option_parser_add_option(op, o); o = gt_option_new_bool("test", "perform unit tests and exit", >r->test, false); gt_option_hide_default(o); gt_option_parser_add_option(op, o); only_option = gt_option_new_string("only", "perform single unit test " "(requires -test)", gtr->test_only, ""); gt_option_imply(only_option, o); gt_option_is_development_option(only_option); gt_option_hide_default(only_option); gt_option_parser_add_option(op, only_option); debug_option = gt_option_new_debug(>r->debug); gt_option_parser_add_option(op, debug_option); debugfp_option = gt_option_new_string("debugfp", "set file pointer for debugging output\n" "use ``stdout'' for standard output\n" "use ``stderr'' for standard error\n" "or any other string to use the " "corresponding file (will be overwritten " "without warning!)", gtr->debugfp, "stderr"); gt_option_is_development_option(debugfp_option); gt_option_parser_add_option(op, debugfp_option); gt_option_imply(debugfp_option, debug_option); o = gt_option_new_uint("seed", "set seed for random number generator manually.\n" "0 generates a seed from current time and process id", >r->seed, gtr->seed); gt_option_hide_default(o); gt_option_parser_add_option(op, o); o = gt_option_new_bool("64bit", "exit with code 0 if this is a 64bit binary, " "with 1 otherwise", >r->check64bit, false); gt_option_is_development_option(o); gt_option_parser_add_option(op, o); o = gt_option_new_bool("list", "list all tools and exit", >r->list, false); gt_option_is_development_option(o); gt_option_hide_default(o); gt_option_parser_add_option(op, o); o = gt_option_new_filename("testspacepeak", "alloc 64 MB and mmap the given " "file", gtr->testspacepeak); gt_option_is_development_option(o); gt_option_parser_add_option(op, o); o = gt_option_new_string("createman", "create man page sources in directory", gtr->manoutdir, ""); gt_option_is_development_option(o); gt_option_parser_add_option(op, o); return op; }
static GtOptionParser* gt_show_seedext_option_parser_new(void *tool_arguments) { GtShowSeedextArguments *arguments = tool_arguments; GtOptionParser *op; GtOption *option, *op_ali, *option_filename, *op_relax_polish, *op_seed_extend, *op_sortmatches, *op_showeoplist; gt_assert(arguments); /* init */ op = gt_option_parser_new("[options] -f <matchfilename>", "Parse output of a seed extension and show/verify " "the alignment."); /* -a */ op_ali = gt_option_new_bool("a", "show alignment", &arguments->show_alignment, false); gt_option_parser_add_option(op, op_ali); /* -seed-display */ option = gt_option_new_bool("seed-display", "Display seeds in #-line and by " "character + (instead of |) in middle " "row of alignment column", &arguments->seed_display, false); gt_option_parser_add_option(op, option); /* -seed-extend */ op_seed_extend = gt_option_new_bool("seed-extend", "read the seeds from the # seed: -lines and " "extend them; match lines are ignored; " "match coordindates are displayed", &arguments->seed_extend, false); gt_option_parser_add_option(op, op_seed_extend); /* -relax-polish */ op_relax_polish = gt_option_new_bool("relax-polish", "do not force alignments to have " "polished ends", &arguments->relax_polish,false); gt_option_parser_add_option(op, op_relax_polish); gt_option_is_development_option(op_relax_polish); gt_option_imply(op_relax_polish, op_ali); /* -sort */ op_sortmatches = gt_option_new_bool("sort","sort matches in ascending order " "of their end positon on the " "query", &arguments->sortmatches,false); gt_option_parser_add_option(op, op_sortmatches); /* -e */ op_showeoplist = gt_option_new_bool("e","show list of edit operations", &arguments->showeoplist,false); gt_option_parser_add_option(op, op_showeoplist); /* -f */ option_filename = gt_option_new_filename("f", "path to file with match coordinates", arguments->matchfilename); gt_option_is_mandatory(option_filename); gt_option_parser_add_option(op, option_filename); gt_option_exclude(op_seed_extend, op_sortmatches); gt_option_exclude(op_relax_polish, op_seed_extend); 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; }
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_ulong("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; }
static GtOptionParser *gt_idxlocali_option_parser_new(void *tool_arguments) { IdxlocaliOptions *arguments = tool_arguments; GtOptionParser *op; GtOption *option, *optionesaindex, *optionpckindex, *optiononline, *optioncmp; gt_assert(arguments != NULL); arguments->indexname = gt_str_new (); arguments->queryfiles = gt_str_array_new (); op = gt_option_parser_new ("[options] -q query-file-names [-esa|-pck] indexname", "Find all local alignments using suffix tree."); gt_option_parser_set_mail_address(op, "<*****@*****.**>"); option = gt_option_new_filename_array("q","Specify files containing the " "query sequences", arguments->queryfiles); gt_option_parser_add_option (op, option); option = gt_option_new_word("match", "Specify match score", &arguments->matchscore, 1L); gt_option_parser_add_option(op, option); option = gt_option_new_word("mismatch", "Specify mismatch score", &arguments->mismatchscore, -3L); gt_option_parser_add_option(op, option); option = gt_option_new_word("gapstart", "Specify gap start score", &arguments->gapstart, -5L); gt_option_parser_add_option(op, option); option = gt_option_new_word("gapextend", "Specify gap extension score", &arguments->gapextend, -2L); gt_option_parser_add_option(op, option); option = gt_option_new_uword_min("th", "Specify the threshold", &arguments->threshold, 0, 1UL); gt_option_parser_add_option(op, option); gt_option_is_mandatory(option); optionesaindex = gt_option_new_string("esa", "Specify index " "(enhanced suffix array)", arguments->indexname, NULL); gt_option_parser_add_option(op, optionesaindex); arguments->refoptionesaindex = gt_option_ref(optionesaindex); optionpckindex = gt_option_new_string("pck", "Specify index (packed index)", arguments->indexname, NULL); gt_option_parser_add_option(op, optionpckindex); arguments->refoptionpckindex = gt_option_ref (optionpckindex); gt_option_exclude (optionesaindex, optionpckindex); gt_option_is_mandatory_either(optionesaindex, optionpckindex); optiononline = gt_option_new_bool("online","Perform online searches", &arguments->doonline, false); gt_option_parser_add_option(op, optiononline); gt_option_is_development_option(optiononline); optioncmp = gt_option_new_bool("cmp","Compare results of offline and online " "searches", &arguments->docompare, false); gt_option_parser_add_option(op,optioncmp); gt_option_exclude(optiononline,optioncmp); option = gt_option_new_bool("s", "Show alignments", &arguments->showalignment, false); gt_option_parser_add_option(op, option); option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); return op; }
static GtOptionParser* gt_eval_option_parser_new(void *tool_arguments) { EvalArguments *arguments = tool_arguments; GtOptionParser *op; GtOption *option, *ltroption, *ltrdeltaoption; gt_assert(arguments); op = gt_option_parser_new("reference_file prediction_file ", "Compare annotation files and show " "accuracy measures (prediction vs. reference)."); /* -exondiff */ option = gt_option_new_bool("exondiff", "show a diff for the exons", &arguments->exondiff, false); gt_option_is_development_option(option); gt_option_parser_add_option(op, option); /* -exondiffcollapsed */ option = gt_option_new_bool("exondiffcollapsed", "show a diff for the " "collapsed exons", &arguments->exondiffcollapsed, false); gt_option_is_development_option(option); gt_option_parser_add_option(op, option); /* -nuc */ option = gt_option_new_bool("nuc", "evaluate nucleotide level (memory consumption " "is proportional to the input file sizes)", &arguments->nuceval, true); gt_option_parser_add_option(op, option); /* -ltr */ ltroption = gt_option_new_bool("ltr", "evaluate a LTR retrotransposon " "prediction instead of a gene prediction\n" "(all LTR_retrotransposon elements are " "considered to have an undetermined strand)", &arguments->evalLTR, false); gt_option_parser_add_option(op, ltroption); /* -ltrdelta */ ltrdeltaoption = gt_option_new_uword("ltrdelta", "set allowed delta for LTR " "borders to be considered equal", &arguments->LTRdelta, 20); gt_option_parser_add_option(op, ltrdeltaoption); /* -v */ option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); /* output file options */ gt_output_file_info_register_options(arguments->ofi, op, &arguments->outfp); /* option implications */ gt_option_imply(ltrdeltaoption, ltroption); /* set comment function */ gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL); /* set minimum and maximum number of arguments */ gt_option_parser_set_min_max_args(op, 2, 2); return op; }