First release to CRAN. ## Changes - read_fasta will be used to read fasta file, the sequence name can contain spaces. - write_fasta will be used to write fasta file, the sequence name can contain spaces. - process_allele can be used in place of the different functions to preprocess the FASTA file. It will perform all equivalent functions in one go; the others functions are no longer exported. - calculate_simpson is used to calculate the Simpson’s index from list of pattern. - calculate_percent is used to calculate the dissimilarity index from list of pattern. - check_percent is used to check that the necessary parameter for calculate_percent is passed. - get_metric_fun is used to translate the metric to the functions, additional metric can be added by defining the functions and overriding the global MinSNPs_metrics variable. - calculate_simpson, calculate_percent, and check_percent, get_metric_fun are only as default, there is no reason to call these functions directly. - find_optimised_snps is used to find optimised SNP set(s). It can also be used to recalculate index by giving it included positions and setting max_depth to 0. - output_result is used to output results from find_optimised_snps.
Minor changes & testing ## Changes - find_optimised_snps can receive an additional argument output_progress = TRUE, such that progress can be shown in terminal when looking for multiple result. - write_fasta bug where only the first letter is written to the file is fixed. - output_result bug where residuals are not returned. - process_allele will print names of duplicated isolate, and keep only the first instance of the found isolate. - iterate_merge can be used to merge alignment matrices. - find_optimised_snps reduced memory usage. - resolve_IUPAC_missing can be used to substitute the ambiguity codes found in the sequence. - output_result updated such that it can be presented correctly in excel. - cal_fn and cal_fp can be used to calculate and identify false negatives and false postives respectively. To be called with cal_met_snp