binomial_naive_bayes	binomial_naive_bayes
branch_and_search	branch_and_search
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	calculate_variant_within_group
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
flag_allele	flag_allele
flag_position	flag_position
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_positions_to_search	get_positions_to_search
get_snps_set	get_snps_set
get_usual_length	get_usual_length
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_parsed	output_parsed
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_dup_isolate	remove_dup_isolate
remove_snp_conflict	remove_snp_conflict
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
select_n_set_i_depth	select_n_set_i_depth
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
