static GtOptionParser* gt_extractfeat_option_parser_new(void *tool_arguments) { GtExtractFeatArguments *arguments = tool_arguments; GtOptionParser *op; GtOption *option; gt_assert(arguments); op = gt_option_parser_new("[option ...] [GFF3_file]", "Extract features given in GFF3 file from " "sequence file."); /* -type */ option = gt_option_new_string("type", "set type of features to extract", arguments->type, NULL); gt_option_is_mandatory(option); gt_option_parser_add_option(op, option); /* -join */ option = gt_option_new_bool("join", "join feature sequences in the same " "subgraph into a single one", &arguments->join, false); gt_option_parser_add_option(op, option); /* -translate */ option = gt_option_new_bool("translate", "translate the features (of a DNA " "sequence) into protein", &arguments->translate, false); gt_option_parser_add_option(op, option); /* -seqid */ option = gt_option_new_bool("seqid", "add sequence ID of extracted features " "to FASTA descriptions", &arguments->seqid, false); gt_option_parser_add_option(op, option); /* -target */ option = gt_option_new_bool("target", "add target ID(s) of extracted " "features to FASTA descriptions", &arguments->target, false); gt_option_parser_add_option(op, option); /* -seqfile, -matchdesc, -usedesc and -regionmapping */ gt_seqid2file_register_options(op, arguments->s2fi); /* -v */ option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); /* -width */ option = gt_option_new_width(&arguments->width); gt_option_parser_add_option(op, 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); gt_option_parser_set_max_args(op, 1); return op; }
static GtOptionParser* gt_csa_option_parser_new(void *tool_arguments) { CSAArguments *arguments = tool_arguments; GtOptionParser *op; GtOption *option; gt_assert(arguments); /* init */ op = gt_option_parser_new("[option ...] [GFF3_file]", "Transform spliced alignments from GFF3 file into " "consensus spliced alignments."); /* -join-length */ option = gt_option_new_uword("join-length", "set join length for the spliced " "alignment clustering", &arguments->join_length, GT_DEFAULT_JOIN_LENGTH); gt_option_parser_add_option(op, option); /* -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); gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL); gt_option_parser_set_max_args(op, 1); return op; }
static GtOptionParser* gt_cds_option_parser_new(void *tool_arguments) { CDSArguments *arguments = tool_arguments; GtOptionParser *op; GtOption *option; gt_assert(arguments); op = gt_option_parser_new("[option ...] [GFF3_file]", "Add CDS (coding sequence) features to exon " "features given in GFF3 file."); /* -minorflen */ option = gt_option_new_uint_min("minorflen", "set the minimum length an open " "reading frame (ORF) must have to be added " "as a CDS feature (measured in amino acids)", &arguments->minorflen, 64, 1); gt_option_parser_add_option(op, option); /* -startcodon */ option = gt_option_new_bool("startcodon", "require than an ORF must begin " "with a start codon", &arguments->start_codon, false); gt_option_parser_add_option(op, option); /* -finalstopcodon */ option = gt_option_new_bool("finalstopcodon", "require that the final ORF " "must end with a stop codon", &arguments->final_stop_codon, false); gt_option_parser_add_option(op, option); /* -genericstartcodons */ option = gt_option_new_bool("genericstartcodons", "use generic start codons", &arguments->generic_start_codons, false); gt_option_is_development_option(option); gt_option_parser_add_option(op, option); /* -seqfile, -matchdesc, -usedesc and -regionmapping */ gt_seqid2file_register_options(op, arguments->s2fi); /* -v */ option = gt_option_new_verbose(&arguments->verbose); gt_option_parser_add_option(op, option); /* output file options */ gt_outputfile_register_options(op, &arguments->outfp, arguments->ofi); gt_option_parser_set_comment_func(op, gt_gtdata_show_help, NULL); gt_option_parser_set_max_args(op, 1); return op; }
static OPrval parse_options(int *parsed_args, int argc, const char **argv, GtError *err) { GtOptionParser *op; OPrval oprval; op = gt_option_parser_new("[GFF3_file ...]", "Parse GFF3 file(s) and show it as " "GTF2.2."); /* parse */ gt_option_parser_set_max_args(op, 1); oprval = gt_option_parser_parse(op, parsed_args, argc, argv, gt_versionfunc, err); gt_option_parser_delete(op); return oprval; }
static GtOPrval parse_env_options(int argc, const char **argv, GtError *err) { GtOptionParser *op; GtOption *o; GtOPrval oprval; op = gt_option_parser_new("GT_ENV_OPTIONS='[option ...]' ...", "Parse the options contained in the " "environment variable GT_ENV_OPTIONS."); o = gt_option_new_bool("spacepeak", "show space peak on stdout upon deletion", &spacepeak, false); gt_option_parser_add_option(op, o); o = gt_option_new_bool("showtime", "enable output for run-time statistics", &showtime, false); gt_option_parser_add_option(op, o); gt_option_parser_set_max_args(op, 0); oprval = gt_option_parser_parse(op, NULL, argc, argv, gt_versionfunc, err); gt_option_parser_delete(op); return oprval; }
static GtOptionParser* gt_readjoiner_cnttest_option_parser_new( void *tool_arguments) { GtReadjoinerCnttestArguments *arguments = tool_arguments; GtOptionParser *op; GtOption *option; gt_assert(arguments); /* init */ op = gt_option_parser_new("-readset [option ...]", "Test/development tool for readjoiner containments filtering."); /* -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); /* -test */ option = gt_option_new_string("test", "select among the available tests:\n" "showlist: show content of an cnt list (input: cntlist)\n" "bruteforce: memcmp reads vs all suffixes and prefixes (input: encseq)\n" "kmp: variant of Knuth-Morris-Pratt (input: encseq)\n" "esa: own esa-based algorithm (input: esa)", arguments->teststr, NULL); gt_option_parser_add_option(op, option); gt_option_is_mandatory(option); /* -singlestrand */ option = gt_option_new_bool("singlestrand", "do not use reads " "reverse complements", &arguments->singlestrand, false); gt_option_parser_add_option(op, option); /* -v */ option = gt_option_new_verbose(&arguments->verbose); 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_bed_to_gff3_option_parser_new(void *tool_arguments) { BEDToGFF3Arguments *arguments = tool_arguments; GtOptionParser *op; GtOption *o; op = gt_option_parser_new("[bed_file]", "Parse BED file and show it as GFF3."); o = gt_option_new_string("featuretype", "Set type of parsed BED features", arguments->feature_type, BED_FEATURE_TYPE); gt_option_parser_add_option(op, o); o = gt_option_new_string("thicktype", "Set type of parsed thick BED features", arguments->thick_feature_type, BED_THICK_FEATURE_TYPE); gt_option_parser_add_option(op, o); o = gt_option_new_string("blocktype", "Set type of parsed BED blocks", arguments->block_type, BED_BLOCK_TYPE); gt_option_parser_add_option(op, o); gt_option_parser_set_max_args(op, 1); 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; }