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UML

Source: vignettes/uml.qmd
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)Dragensync_excludeinitialize(path)DragenBclrefine_files(files)parse_demux(x,tile)initialize(path,files_tbl)parse_demultiplexstats(x)parse_demultiplextilestats(x)parse_fastqlist(x)parse_runinfo(x)DragenCovinitialize(path,files_tbl)tidy_covmetrics(x)parse_finehist(x)parse_reportbed(x)tidy_reportbed(x)DragenFqcinitialize(path,files_tbl)parse_fastqc(x)tidy_fastqc(x)DragenMapinitialize(path,files_tbl)tidy_metrics(x)tidy_umi(x)tidy_gc(x)tidy_time(x)parse_fraglenhist(x)parse_replay(x)tidy_replay(x)DragenRnainitialize(path,files_tbl)DragenToolon_unmappedon_coerce_failon_unexpected_colextra_ftypes()tidy_file(x,table_name,convert_types)refine_files(files)parse_metrics(x)coerce_by_type(vec,type)region_split(x)tidy_metrics(x,table_name,normalise,on_unmapped,on_coerce_fail,on_unexpected_col,drop_constant)DragenTsosar_amet(am)sar_snv(snvs)refine_files(files)initialize(path,files_tbl)parse_smallvariants(x)parse_fusions(x)parse_sar(x)tidy_sar(x)DragenVarinitialize(path,files_tbl)tidy_vc(x)tidy_gvcf(x)tidy_cnv(x)tidy_hethom(x)tidy_ploidy(x)tidy_nuctrans(x)parse_microsat(x)parse_contamination(x)parse_ploidyvcf(x)Interoprefine_files(files)split_pm(x)split_slash(x)num(x)parse_labelled_blocks(body,id_name,id_from_label)parse_index_blocks(body)initialize(path,files_tbl)parse_summary(x)tidy_summary(x)parse_indexsummary(x)tidy_indexsummary(x)parse_imagingtable(x)tidy_imagingtable(x)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)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)