| binomial_naive_bayes | 'binomial_naive_bayes' | 
| calculate_mcc | 'calculate_mcc' | 
| calculate_mcc_multi | 'calculate_mcc_multi' | 
| calculate_percent | 'calculate_percent' | 
| calculate_simpson | 'calculate_simpson' | 
| calculate_simpson_by_group | 'calculate_simpson_by_group' | 
| calculate_state | 'calculate_state' | 
| calculate_variant_within_group | 'identify_group_variant_breakdown' | 
| cal_fn | 'cal_fn' | 
| cal_fp | 'cal_fp' | 
| cal_met_snp | 'cal_met_snp' | 
| check_fasta_meta_mapping | 'check_fasta_meta_mapping' | 
| check_meta_target | 'check_meta_target' | 
| check_multistate | 'check_multistate' | 
| check_percent | 'check_percent' | 
| coef.binomial_naive_bayes | 'coef.binomial_naive_bayes' | 
| combine_fastq_search_result | 'combine_fastq_search_result' | 
| combine_search_string_result | 'combine_search_string_result' | 
| combine_search_string_result_from_files | 'combine_search_string_result_from_files' | 
| combine_search_string_result_from_list | 'combine_search_string_result_from_list' | 
| estimate_coverage | 'estimate_coverage' | 
| extend_length | 'extend_length' | 
| find_optimised_snps | 'find_optimised_snps' | 
| full_merge | 'full_merge' | 
| full_merge_1 | 'full_merge_1' | 
| generate_kmers | 'generate_kmers' | 
| generate_kmer_search_string | 'generate_kmer_search_string' | 
| generate_pattern | 'generate_pattern' | 
| generate_prioritisation | 'generate_prioritisation' | 
| generate_snp_search_string | 'generate_snp_search_string' | 
| get_all_process_methods | 'get_all_process_methods' | 
| get_binomial_tables | 'get_binomial_tables' | 
| get_metric_fun | 'get_metric_fun' | 
| get_snps_set | 'get_snps_set' | 
| identify_overlaps | 'identify_overlaps' | 
| infer_from_combined | 'infer_from_combined' | 
| iterate_merge | 'iterate_merge' | 
| iterate_through | 'iterate_through' | 
| map_profile_to_target | 'map_profile_to_target' | 
| match_count | 'match_count' | 
| mcc_calculation | 'mcc_calculation' | 
| merge_fasta | 'merge_fasta' | 
| output_result | 'output_result' | 
| output_to_files | 'output_to_files' | 
| parse_group_mcc | 'parse_group_mcc' | 
| parse_group_mcc_multi | 'parse_group_mcc_multi' | 
| predict.binomial_naive_bayes | 'predict.binomial_naive_bayes' | 
| predict_balk | 'predict_balk' | 
| print.binomial_naive_bayes | 'print.binomial_naive_bayes' | 
| process_allele | 'process_allele' | 
| process_kmer_result | 'process_kmer_result' | 
| process_result_file | 'process_result_file' | 
| process_snp_result | 'process_snp_result' | 
| profile_to_group_result | 'profile_to_group_result' | 
| read_fasta | 'read_fasta' | 
| read_sequences_from_fastq | 'read_sequences_from_fastq' | 
| remove_snp_conflict | 'remove_snp_conflic' | 
| resolve_IUPAC_missing | 'resolve_IUPAC_missing' | 
| reverse_complement | 'reverse_complement' | 
| scramble_sequence | 'scramble_sequence' | 
| search_from_fastq_reads | 'search_from_fastq_reads' | 
| search_from_reads | 'search_from_reads' | 
| sequence_reads_match_count | 'sequence_reads_match_count' | 
| summarise_result | 'summarise_result' | 
| summary.binomial_naive_bayes | 'summary.binomial_naive_bayes' | 
| train_balk | 'train_balk' | 
| transform_snp | 'transform_snp' | 
| translate_position | 'translate_position' | 
| view_mcc | 'view_mcc' | 
| view_mcc_multi | 'view_mcc_multi' | 
| view_percent | 'view_percent' | 
| view_simpson | 'view_simpson' | 
| write_fasta | 'write_fasta' |