binomial_naive_bayes    'binomial_naive_bayes'
cal_fn                  'cal_fn'
cal_fp                  'cal_fp'
cal_met_snp             'cal_met_snp'
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'
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_kmer_search_string
                        'generate_kmer_search_string'
generate_kmers          'generate_kmers'
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'
