Files in minSNPs

Resolution-Optimised SNPs Searcher

NEWS.md README.md R/search.R R/output.R R/search_string_generation.R R/addn_search.R R/merge.R R/balk_helper.r R/process.R R/search_from_reads.R R/guided_helpers.r R/utility.R R/balk.r R/zzz.R inst/doc/MinSNPs_Workflow.R inst/doc/MinSNPs_Workflow.Rmd tests/testthat.R tests/testthat/test-process.R tests/testthat/test-search.R vignettes/MinSNPs_Workflow.Rmd man/summary.binomial_naive_bayes.Rd man/combine_search_string_result_from_files.Rd man/resolve_IUPAC_missing.Rd man/view_mcc_multi.Rd man/read_fasta.Rd man/remove_dup_isolate.Rd man/output_result.Rd man/generate_kmer_search_string.Rd man/view_percent.Rd man/read_sequences_from_fastq.Rd man/flag_allele.Rd man/predict_balk.Rd man/check_fasta_meta_mapping.Rd man/calculate_simpson.Rd man/iterate_merge.Rd man/view_simpson.Rd man/search_from_fastq_reads.Rd man/calculate_simpson_by_group.Rd man/write_fasta.Rd man/get_all_process_methods.Rd man/select_n_set_i_depth.Rd man/train_balk.Rd man/get_snps_set.Rd man/calculate_percent.Rd man/sequence_reads_match_count.Rd man/scramble_sequence.Rd man/combine_search_string_result_from_list.Rd man/full_merge.Rd man/combine_fastq_search_result.Rd man/reverse_complement.Rd man/identify_overlaps.Rd man/get_positions_to_search.Rd man/map_profile_to_target.Rd man/binomial_naive_bayes.Rd man/process_result_file.Rd man/get_usual_length.Rd man/check_percent.Rd man/profile_to_group_result.Rd man/branch_and_search.Rd man/estimate_coverage.Rd man/print.binomial_naive_bayes.Rd man/cal_met_snp.Rd man/generate_kmers.Rd man/find_optimised_snps.Rd man/full_merge_1.Rd man/extend_length.Rd man/combine_search_string_result.Rd man/infer_from_combined.Rd man/cal_fn.Rd man/search_from_reads.Rd man/cal_fp.Rd man/generate_pattern.Rd man/calculate_variant_within_group.Rd man/flag_position.Rd man/transform_snp.Rd man/remove_snp_conflict.Rd man/get_binomial_tables.Rd man/calculate_mcc.Rd man/summarise_result.Rd man/process_kmer_result.Rd man/generate_snp_search_string.Rd man/iterate_through.Rd man/calculate_mcc_multi.Rd man/mcc_calculation.Rd man/get_metric_fun.Rd man/output_to_files.Rd man/process_allele.Rd man/match_count.Rd man/predict.binomial_naive_bayes.Rd man/merge_fasta.Rd man/view_mcc.Rd man/check_multistate.Rd man/generate_prioritisation.Rd man/coef.binomial_naive_bayes.Rd man/parse_group_mcc.Rd man/calculate_state.Rd man/parse_group_mcc_multi.Rd man/translate_position.Rd man/process_snp_result.Rd man/output_parsed.Rd man/check_meta_target.Rd