NEWS.md

In minSNPs: Resolution-Optimised SNPs Searcher

minSNPs v0.1.1

• Modified how process_snp_result calculates the number of reads and proportion of search sequences found in the long read sequences to be more accurate. In the previous version, tag that also form part of other tag, e.g., CC15 and CC1, are miscalculated with those matching only CC1 are also used to match CC15. This is now fixed.

minSNPs v0.1.0

• Added method to generate search strings (generate_snp_search_string) from identified SNPs set.
• Added method to search through long read sequence (search_from_fastq_reads).

minSNPs v0.0.5

Fixed bug in find_optimised_snps where when multiple SNPs sets are looked, not all SNPs set will iterate to the next depth even if max_depth has not been reached and resolving power is not 1.

minSNPs v0.0.4

Fixed bug in find_optimised_snps when there are included SNPs.

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.

minSNPs documentation built on May 29, 2024, 2:48 a.m.