static GtOptionParser *gt_tyr_search_option_parser_new(void *tool_arguments) { GtOptionParser *op; GtOption *option, *optiontyr, *optionqueries; Tyr_search_options *arguments = tool_arguments; op = gt_option_parser_new("[options] -tyr tallymer-index -q queryfile0 " "[queryfile1..] [options]", "Search a set of k-mers in an index constructed " "by \"gt tyr mkindex\"."); gt_option_parser_set_mailaddress(op,"<*****@*****.**>"); optiontyr = gt_option_new_string("tyr","specify tallymer-index", arguments->str_inputindex, NULL); gt_option_is_mandatory(optiontyr); gt_option_parser_add_option(op, optiontyr); optionqueries = gt_option_new_filenamearray("q","specify query file names", arguments->queryfilenames); gt_option_is_mandatory(optionqueries); gt_option_parser_add_option(op, optionqueries); option = gt_option_new_string("strand", "specify the strand to be searched: " "use f (for forward strand) or " "p (for reverse complemented strand) or " "fp (for both); default is f", arguments->strandspec, "f"); gt_option_parser_add_option(op, option); option = gt_option_new_stringarray("output", "specify output flags " "(qseqnum, qpos, counts, sequence)", arguments->showmodespec); gt_option_parser_add_option(op, option); 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); option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); return op; }
static GtOptionParser *gt_cge_spacedseed_option_parser_new(void *tool_arguments) { GtOptionParser *op; GtOption *option, *optionesaindex, *optionpckindex; Cge_spacedseed_options *arguments = tool_arguments; op = gt_option_parser_new("[options]", "Match spaced seeds."); gt_option_parser_set_mailaddress(op,"<*****@*****.**>"); optionesaindex = gt_option_new_string("esa", "Specify index (enhanced suffix array)", arguments->str_inputindex, 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->str_inputindex, 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); option = gt_option_new_filenamearray("q", "Specify files containing the " "query sequences", arguments->queryfilenames); gt_option_parser_add_option(op, option); gt_option_is_mandatory(option); option = gt_option_new_bool("cmp","compare results of offline and online " "searches",&arguments->docompare,false); gt_option_parser_add_option(op, option); gt_option_is_development_option(option); option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); 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_mailaddress (op, "<*****@*****.**>"); option = gt_option_new_filenamearray ("q","Specify files containing the " "query sequences", arguments->queryfiles); gt_option_parser_add_option (op, option); option = gt_option_new_long ("match", "Specify match score", &arguments->matchscore, 1L); gt_option_parser_add_option (op, option); option = gt_option_new_long ("mismatch", "Specify mismatch score", &arguments->mismatchscore, -3L); gt_option_parser_add_option (op, option); option = gt_option_new_long ("gapstart", "Specify gap start score", &arguments->gapstart, -5L); gt_option_parser_add_option (op, option); option = gt_option_new_long ("gapextend", "Specify gap extension score", &arguments->gapextend, -2L); gt_option_parser_add_option (op, option); option = gt_option_new_ulong_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_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_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; }