Man pages for ludwigHoon/minSNPs
Resolution-Optimised SNPs Searcher
| 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 | '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' |
| 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_balk | 'predict_balk' |
| predict.binomial_naive_bayes | 'predict.binomial_naive_bayes' |
| 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_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' |
| 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' |
