static void *gt_tyr_arguments_new(void) { GtToolbox *tyr_toolbox = gt_toolbox_new(); gt_toolbox_add_tool(tyr_toolbox, "mkindex", gt_tyr_mkindex()); gt_toolbox_add_tool(tyr_toolbox, "occratio", gt_tyr_occratio()); gt_toolbox_add_tool(tyr_toolbox, "search", gt_tyr_search()); return tyr_toolbox; }
static void* gt_condenseq_toolbox_new(void) { GtToolbox *condenseq_toolbox = gt_toolbox_new(); gt_toolbox_add_tool(condenseq_toolbox, "compress", gt_condenseq_compress()); gt_toolbox_add_tool(condenseq_toolbox, "search", gt_condenseq_search()); gt_toolbox_add_tool(condenseq_toolbox, "extract", gt_condenseq_extract()); gt_toolbox_add_tool(condenseq_toolbox, "info", gt_condenseq_info()); return condenseq_toolbox; }
static void *gt_cge_arguments_new(void) { GtToolbox *cge_toolbox = gt_toolbox_new(); gt_toolbox_add_tool(cge_toolbox, "spacedseed", gt_cge_spacedseed()); return cge_toolbox; }
GtToolbox* gtt_tools(void) { GtToolbox *tools = gt_toolbox_new(); /* add tools */ gt_toolbox_add(tools, "mgth", gt_mgth); gt_toolbox_add(tools, "mkfmindex", gt_mkfmindex); gt_toolbox_add(tools, "suffixerator", gt_suffixerator); gt_toolbox_add_hidden_tool(tools, "dev", gt_dev()); gt_toolbox_add_hidden_tool(tools, "filter", gt_select()); /* hidden "link from the mutate to the seqmutate tool for backward compatibility */ gt_toolbox_add_hidden_tool(tools, "mutate", gt_seqmutate()); gt_toolbox_add_hidden_tool(tools, "template", gt_template()); gt_toolbox_add_tool(tools, "bed_to_gff3", gt_bed_to_gff3()); gt_toolbox_add_tool(tools, "cds", gt_cds()); gt_toolbox_add_tool(tools, "chain2dim", gt_chain2dim()); gt_toolbox_add_tool(tools, "chseqids", gt_chseqids()); gt_toolbox_add_tool(tools, "clean", gt_clean()); gt_toolbox_add_tool(tools, "compreads", gt_compreads()); gt_toolbox_add_tool(tools, "condenseq", gt_condenseq()); gt_toolbox_add_tool(tools, "congruence", gt_congruence()); gt_toolbox_add_tool(tools, "convertseq", gt_convertseq()); gt_toolbox_add_tool(tools, "csa", gt_csa()); gt_toolbox_add_tool(tools, "dot", gt_dot()); gt_toolbox_add_tool(tools, "dupfeat", gt_dupfeat()); gt_toolbox_add_tool(tools, "encseq", gt_encseq()); gt_toolbox_add_tool(tools, "encseq2spm", gt_encseq2spm()); gt_toolbox_add_tool(tools, "eval", gt_eval()); gt_toolbox_add_tool(tools, "extractfeat", gt_extractfeat()); gt_toolbox_add_tool(tools, "extractseq", gt_extractseq()); gt_toolbox_add_tool(tools, "fastq_sample", gt_fastq_sample()); gt_toolbox_add_tool(tools, "fingerprint", gt_fingerprint()); gt_toolbox_add_tool(tools, "genomediff", gt_genomediff()); gt_toolbox_add_tool(tools, "gff3", gt_gff3()); gt_toolbox_add_tool(tools, "gff3_to_gtf", gt_gff3_to_gtf()); gt_toolbox_add_tool(tools, "gff3validator", gt_gff3validator()); gt_toolbox_add_tool(tools, "gtf_to_gff3", gt_gtf_to_gff3()); gt_toolbox_add_tool(tools, "hop", gt_hop()); gt_toolbox_add_tool(tools, "id_to_md5", gt_id_to_md5()); gt_toolbox_add_tool(tools, "inlineseq_split", gt_inlineseq_split()); gt_toolbox_add_tool(tools, "inlineseq_add", gt_inlineseq_add()); gt_toolbox_add_tool(tools, "interfeat", gt_interfeat()); gt_toolbox_add_tool(tools, "loccheck", gt_loccheck()); gt_toolbox_add_tool(tools, "ltrclustering", gt_ltrclustering()); gt_toolbox_add_tool(tools, "ltrdigest", gt_ltrdigest()); gt_toolbox_add_tool(tools, "ltrharvest", gt_ltrharvest()); gt_toolbox_add_tool(tools, "matchtool", gt_matchtool()); gt_toolbox_add_tool(tools, "matstat", gt_matstat()); gt_toolbox_add_tool(tools, "md5_to_id", gt_md5_to_id()); gt_toolbox_add_tool(tools, "merge", gt_merge()); gt_toolbox_add_tool(tools, "mergefeat", gt_mergefeat()); gt_toolbox_add_tool(tools, "mmapandread", gt_mmapandread()); gt_toolbox_add_tool(tools, "orffinder", gt_orffinder()); gt_toolbox_add_tool(tools, "packedindex", gt_packedindex()); gt_toolbox_add_tool(tools, "prebwt", gt_prebwt()); gt_toolbox_add_tool(tools, "readjoiner", gt_readjoiner()); gt_toolbox_add_tool(tools, "repfind", gt_repfind()); gt_toolbox_add_tool(tools, "scriptfilter", gt_script_filter()); gt_toolbox_add_tool(tools, "seed_extend", gt_seed_extend()); gt_toolbox_add_tool(tools, "select", gt_select()); gt_toolbox_add_tool(tools, "seq", gt_seq()); gt_toolbox_add_tool(tools, "seqfilter", gt_seqfilter()); gt_toolbox_add_tool(tools, "seqids", gt_seqids()); gt_toolbox_add_tool(tools, "seqmutate", gt_seqmutate()); gt_toolbox_add_tool(tools, "seqorder", gt_seqorder()); gt_toolbox_add_tool(tools, "seqstat", gt_seqstat()); gt_toolbox_add_tool(tools, "seqtransform", gt_seqtransform()); gt_toolbox_add_tool(tools, "seqtranslate", gt_seqtranslate()); gt_toolbox_add_tool(tools, "sequniq", gt_sequniq()); gt_toolbox_add_tool(tools, "shredder", gt_shredder()); gt_toolbox_add_tool(tools, "shulengthdist", gt_shulengthdist()); gt_toolbox_add_tool(tools, "simreads", gt_simreads()); gt_toolbox_add_tool(tools, "snpper", gt_snpper()); gt_toolbox_add_tool(tools, "speck", gt_speck()); gt_toolbox_add_tool(tools, "splicesiteinfo", gt_splicesiteinfo()); gt_toolbox_add_tool(tools, "splitfasta", gt_splitfasta()); gt_toolbox_add_tool(tools, "stat", gt_stat()); gt_toolbox_add_tool(tools, "tagerator", gt_tagerator()); gt_toolbox_add_tool(tools, "tallymer", gt_tallymer()); gt_toolbox_add_tool(tools, "tirvish", gt_tir()); gt_toolbox_add_tool(tools, "uniq", gt_uniq()); gt_toolbox_add_tool(tools, "uniquesub", gt_uniquesub()); gt_toolbox_add_tool(tools, "wtree", gt_wtree()); #ifndef WITHOUT_CAIRO gt_toolbox_add_tool(tools, "sketch", gt_sketch()); gt_toolbox_add_tool(tools, "sketch_page", gt_sketch_page()); #endif #if defined (HAVE_MYSQL) || defined (HAVE_SQLITE) gt_toolbox_add_tool(tools, "featureindex", gt_featureindex()); gt_toolbox_add_tool(tools, "mkfeatureindex", gt_mkfeatureindex()); #endif return tools; }
static void* gt_dev_arguments_new(void) { GtToolbox *dev_toolbox = gt_toolbox_new(); /* add development tools here with a function call like this: gt_toolbox_add(dev_toolbox, "devtool", gt_devtool); */ gt_toolbox_add(dev_toolbox, "gthbssmbuild", gt_gthbssmbuild); gt_toolbox_add(dev_toolbox, "gthbssmfileinfo", gt_gthbssmfileinfo); gt_toolbox_add(dev_toolbox, "gthbssmprint", gt_gthbssmprint); gt_toolbox_add(dev_toolbox, "gthmkbssmfiles", gt_gthmkbssmfiles); gt_toolbox_add(dev_toolbox, "guessprot", gt_guessprot); gt_toolbox_add(dev_toolbox, "mergeesa", gt_mergeesa); gt_toolbox_add(dev_toolbox, "paircmp", gt_paircmp); gt_toolbox_add(dev_toolbox, "patternmatch", gt_patternmatch); gt_toolbox_add(dev_toolbox, "regioncov", gt_regioncov); gt_toolbox_add(dev_toolbox, "trieins", gt_trieins); gt_toolbox_add_tool(dev_toolbox, "compbits", gt_compressedbits()); gt_toolbox_add_tool(dev_toolbox, "condenser", gt_condenser()); gt_toolbox_add_tool(dev_toolbox, "consensus_sa", gt_consensus_sa_tool()); gt_toolbox_add_tool(dev_toolbox, "extracttarget", gt_extracttarget()); gt_toolbox_add_tool(dev_toolbox, "gdiffcalc", gt_gdiffcalc()); gt_toolbox_add_tool(dev_toolbox, "gthbssmrmsd", gt_gthbssmrmsd()); gt_toolbox_add_tool(dev_toolbox, "gthbssmtrain", gt_gthbssmtrain()); gt_toolbox_add_tool(dev_toolbox, "idxlocali", gt_idxlocali()); gt_toolbox_add_tool(dev_toolbox, "kmer_database", gt_kmer_database()); gt_toolbox_add_tool(dev_toolbox, "linspace_align", gt_linspace_align()); gt_toolbox_add_tool(dev_toolbox, "magicmatch", gt_magicmatch()); gt_toolbox_add_tool(dev_toolbox, "parsexrf", gt_parsexrf()); gt_toolbox_add_tool(dev_toolbox, "readreads", gt_readreads()); gt_toolbox_add_tool(dev_toolbox, "sain", gt_sain()); gt_toolbox_add_tool(dev_toolbox, "sambam", gt_sam_interface()); gt_toolbox_add_tool(dev_toolbox, "seqcorrect", gt_seqcorrect()); gt_toolbox_add_tool(dev_toolbox, "seqlensort", gt_seqlensort()); gt_toolbox_add_tool(dev_toolbox, "sfxmap", gt_sfxmap()); gt_toolbox_add_tool(dev_toolbox, "skproto", gt_skproto()); gt_toolbox_add_tool(dev_toolbox, "sortbench", gt_sortbench()); return dev_toolbox; }