minSNPs v0.0.3

Minor changes & bug removal

Changes

• find_optimised_snps can use BiocParallel::SnowParam() for windows.

minSNPs v0.0.2

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

minSNPs v0.0.1

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.