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UML

Source: vignettes/uml.qmd
Alignmentsinitialize(path,files_tbl)parse_markdup(x)Amberextra_ftypes()initialize(path,files_tbl)Bamtoolsinitialize(path,files_tbl)parse_summary(x)tidy_summary(x)parse_wgsmetrics(x)tidy_wgsmetrics(x)parse_flagstats(x)tidy_flagstats(x)tidy_genecvg(x)tidy_exoncvg(x)Chordinitialize(path,files_tbl)parse_signatures(x)tidy_signatures(x)Ciderinitialize(path,files_tbl)Cobaltextra_ftypes()initialize(path,files_tbl)parse_gcmed(x)tidy_gcmed(x)Configtablescacheschemas_rawschemas_tidyschemas_bothtoolpkgvalidate_tables()validate_outputs()collect_invalid_schema_types()format_invalid_types_msg(invalid)assert_version(x,version,versions)resolve_version(x,version,versions)read()get_field_for_table(x,key)get_field_for_all_tables(key)compute_schema_rows(columns,name,description,parent)compute_schema_one(tab,tab_name)compute_schemas()derive_schema(cache,side)cached(key,compute)get_schema_both_one(x,version)get_schema(x,version,side)initialize(tool,pkg)print(...)get_patterns()get_globs()get_ftypes()get_descriptions()get_pattern(x)get_ftype(x)get_description(x)get_tables()get_table_outputs(x)get_output_shape(x)get_outputs()get_schemas_raw()get_schemas_tidy()get_schemas_both()get_schema_raw(x,version)get_schema_tidy(x,version)get_col_map(x,version)Cuppainitialize(path,files_tbl)parse_predsum(x)tidy_predsum(x)Esveeinitialize(path,files_tbl)Isofoxextra_ftypes()initialize(path,files_tbl)Lilacinitialize(path,files_tbl)Linxextra_ftypes()refine_files(files)initialize(path,files_tbl)Neoinitialize(path,files_tbl)Peachinitialize(path,files_tbl)Purpleextra_ftypes()refine_files(files)initialize(path,files_tbl)Qseeinitialize(path,files_tbl)Sagerefine_files(files)initialize(path,files_tbl)tidy_genecvg(x)Sigsinitialize(path,files_tbl)parse_snvcounts(x)Tealinitialize(path,files_tbl)Toolis_tidiedis_writtenfilestblsfiles_tblnamepkgpathconfigwritten_filesrefine_files(files)empty_files_tbl()compute_files()prepend_id_cols(d,tidy_name,prefix,input_id,output_id,prefix_include)with_file_context(expr,step,parser,path)dispatch_parse(x,table_name)dispatch_tidy(x,table_name)check_outputs(res,table_name,outputs)check_output_shape(d,output,ctx)check_method_names()extra_ftypes()parse_by_ftype(x,table_name)parse_file(x,table_name,delim,...)tidy_file(x,table_name,convert_types)parse_file_keyvalue(x,table_name,delim,...)parse_file_nohead(x,table_name,delim,...)build_d_write(tbls_with_tidy,output_dir,input_id,output_id,prefix_include)assert_no_dup_fpfix(fpfixes)write_d_write(d_write,format,dbconn)validate_write_setup(format,output_dir,write_metadata)write_metadata_file(input_id,output_id,output_dir)initialize(name,pkg,path,files_tbl)print(...)list_files()get_globs()get_tbls()filter_files(include,exclude)tidy(keep_raw)write(output_dir,format,input_id,output_id,prefix_include,dbconn,write_metadata)get_metadata(input_id,output_id,output_dir,pkgs)run(output_dir,format,input_id,output_id,prefix_include,dbconn,write_metadata,include,exclude)Virusbreakendinitialize(path,files_tbl)parse_vcfsummary(x)Virusinterpreterinitialize(path,files_tbl)Wigitss3sync_excludeinitialize(path)Workflowis_tidiedis_writtenfiles_tbltoolsnamepathmetapkgwritten_filessync_excludevalidate_tools(x)write_metadata_file(input_id,output_id,output_dir)initialize(name,path,tools,metapkg)print(...)get_tools()get_globs()get_sync_patterns()filter_files(include,exclude)list_files()tidy(keep_raw)write(output_dir,format,input_id,output_id,prefix_include,dbconn,write_metadata)run(output_dir,format,input_id,output_id,prefix_include,dbconn,write_metadata,include,exclude)get_schemas_raw()get_schemas_tidy()get_tbls()get_metadata(input_id,output_id,output_dir,pkgs)