Minor changes & bug removal
find_optimised_snps
can use
BiocParallel::SnowParam()
for windows.Minor changes & testing
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
First release to CRAN.
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
.