# 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`.