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#all_metrics Transrate::Transrater
#allowed_deps Transrate::Cmdline
#analyse_assembly Transrate::Cmdline
#analyse_bam Transrate::ReadMetrics
#analyse_expression Transrate::ReadMetrics
#analyse_read_mappings Transrate::ReadMetrics
#argument_parser Transrate::Cmdline
#assembly Transrate::Assembly
#assembly Transrate::Transrater
#assembly_metrics Transrate::Transrater
#assembly_optimal_score Transrate::Transrater
#assembly_result_path Transrate::Cmdline
#assembly_result_paths Transrate::Cmdline
#assembly_score Transrate::Transrater
#assembly_score Transrate::Cmdline
#assign_and_quantify Transrate::ReadMetrics
#at_skew Transrate::Contig
#at_skew Transrate::ContigMetrics
#bad Transrate::ReadMetrics
#bam Transrate::Snap
#base_composition Transrate::Contig
#base_count Transrate::Contig
#bases_a Transrate::Contig
#bases_c Transrate::Contig
#bases_g Transrate::Contig
#bases_gc Transrate::Contig
#bases_n Transrate::ContigMetrics
#bases_n Transrate::Contig
#bases_t Transrate::Contig
#basic_bin_stats Transrate::Assembly
#basic_metrics Transrate::Contig
#basic_stats Transrate::Assembly
#build_command Transrate::Salmon
#build_index Transrate::Snap
#build_paired_cmd Transrate::Snap
#calculate Transrate::ContigMetrics
#calculate_reference_coverage Transrate::ComparativeMetrics
#check_arguments Transrate::Cmdline
#check_assembly Transrate::Cmdline
#check_dependencies Transrate::Cmdline
#check_install_command Transrate::Cmdline
#check_loglevel Transrate::Cmdline
#check_reads Transrate::Cmdline
#check_reference Transrate::Cmdline
#classification Transrate::Contig
#classify Transrate::Contig
#classify_contigs Transrate::Assembly
#cmd Transrate::Cmd
#common_directory_path Transrate::Cmdline
#comp_stats Transrate::ComparativeMetrics
#comparative_metrics Transrate::Cmdline
#comparative_metrics Transrate::Transrater
#comparative_metrics Transrate::Contig
#composition Transrate::Contig
#concatenate_assemblies Transrate::Cmdline
#contig_metrics Transrate::Cmdline
#contig_metrics Transrate::Assembly
#coverage Transrate::Contig
#cpg_count Transrate::Contig
#cpg_ratio Transrate::Contig
#cpg_ratio Transrate::ContigMetrics
#dibase_composition Transrate::Contig
#dibase_count Transrate::Contig
#each Transrate::Contig
#eff_count Transrate::Contig
#eff_length Transrate::Contig
#file Transrate::Assembly
#fragments Transrate::ReadMetrics
#fragments_mapping Transrate::ReadMetrics
#gc_prop Transrate::ContigMetrics
#gc_skew Transrate::Contig
#gc_skew Transrate::ContigMetrics
#geomean Transrate::ScoreOptimiser
#get_bin_path Transrate::ReadMetrics
#get_read_length Transrate::ReadMetrics
#get_reference_hits Transrate::ComparativeMetrics
#good Transrate::Contig
#good Transrate::ReadMetrics
#good_contigs Transrate::Assembly
#good_contigs Transrate::Transrater
#has_crb Transrate::Contig
#has_run Transrate::ComparativeMetrics
#has_run Transrate::ReadMetrics
#has_run Transrate::ContigMetrics
#has_run Transrate::Assembly
#help_message Transrate::Cmdline
#hits Transrate::Contig
#in_bridges Transrate::Contig
#index_name Transrate::Snap
#initial_values Transrate::ReadMetrics
#initial_values Transrate::ContigMetrics
#initialize Transrate::Salmon
#initialize Transrate::Assembly
#initialize Transrate::Contig
#initialize Transrate::ReadMetrics
#initialize Transrate::ComparativeMetrics
#initialize Transrate::Snap
#initialize Transrate::ContigMetrics
#initialize Transrate::Transrater
#initialize Transrate::Cmd
#initialize Transrate::ScoreOptimiser
#initialize Transrate::Cmdline
#install_missing_dependencies Transrate::Cmdline
#kmer_count Transrate::Contig
#linguistic_complexity Transrate::Contig
#linguistic_complexity Transrate::ContigMetrics
#load_executables Transrate::ReadMetrics
#load_expression Transrate::Salmon
#load_readcount Transrate::Snap
#longest_orf Transrate::Contig
#low_uniqueness_bases Transrate::Contig
#map_reads Transrate::Snap
#n50 Transrate::Assembly
#n_bases Transrate::Assembly
#name Transrate::Contig
#optimal_score Transrate::ScoreOptimiser
#orf_length Transrate::Contig
#orss_ublast_db Transrate::Assembly
#p_bases_covered Transrate::Contig
#p_good Transrate::Contig
#p_good_mapping Transrate::ReadMetrics
#p_not_segmented Transrate::Contig
#p_seq_true Transrate::Contig
#p_uncovered_bases Transrate::Contig
#parse_arguments Transrate::Cmdline
#per_query_contig_reference_coverage Transrate::ComparativeMetrics
#per_target_contig_reference_coverage Transrate::ComparativeMetrics
#populate_contig_data Transrate::ReadMetrics
#pretty_print_hash Transrate::Cmdline
#print_examples Transrate::Cmdline
#print_missing_dependencies Transrate::Cmdline
#prop_a Transrate::Contig
#prop_c Transrate::Contig
#prop_g Transrate::Contig
#prop_gc Transrate::Contig
#prop_n Transrate::Contig
#prop_t Transrate::Contig
#proportion_n Transrate::ContigMetrics
#raw_score Transrate::ScoreOptimiser
#rbh_per_contig Transrate::ComparativeMetrics
#rbh_per_reference Transrate::ComparativeMetrics
#read_count Transrate::Snap
#read_length Transrate::ReadMetrics
#read_metrics Transrate::Cmdline
#read_metrics Transrate::Contig
#read_metrics Transrate::Transrater
#read_stats Transrate::ReadMetrics
#reciprocal_hits Transrate::ComparativeMetrics
#reference_coverage Transrate::ComparativeMetrics
#reference_coverage Transrate::Contig
#remap_reads Transrate::Snap
#results Transrate::ContigMetrics
#run Transrate::Cmdline
#run Transrate::ComparativeMetrics
#run Transrate::ContigMetrics
#run Transrate::Cmd
#run Transrate::Salmon
#run Transrate::Assembly
#run Transrate::ReadMetrics
#run Transrate::Transrater
#run_crb_blast Transrate::ComparativeMetrics
#save_logs Transrate::Snap
#save_readcount Transrate::Snap
#score Transrate::Contig
#seq Transrate::Contig
#shannon Transrate::ContigMetrics
#status Transrate::Cmd
#stderr Transrate::Cmd
#stdout Transrate::Cmd
#supported_bridges Transrate::ReadMetrics
#terminal_columns Transrate::Cmdline
#to_fasta Transrate::Contig
#to_s Transrate::Cmd
#tpm Transrate::Contig
#transrate_banner Transrate::Cmdline
#ublast_db Transrate::Assembly
#uncovered_bases Transrate::Contig
#update_proportions Transrate::ReadMetrics
#wootton_federhen Transrate::ContigMetrics
write Transrate::Writer
#write_assembly_csv Transrate::Cmdline
#write_contig_csv Transrate::Cmdline
#zlib_comp Transrate::ContigMetrics