Remove all the haplotypes that were cached by a previous caching call and free up the memory that was allocated for future use.
Details
To achieve higher performance, kalis internally represents haplotypes in an efficient raw binary format in memory which cannot be directly viewed or manipulated in R, though you can extract a view from it using QueryCache().
In particular, this cache sits outside R's memory management and will never be garbage collected (unless R is quit or the package is unloaded).
Therefore, this function is provided to enable freeing the memory used by this cache.
References
Aslett, L.J.M. and Christ, R.R. (2024) "kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R", BMC Bioinformatics, 25(1). Available at: doi:10.1186/s12859-024-05688-8 .
See also
CacheHaplotypes() to create a haplotype cache;
QueryCache() to view the cache contents in an R matrix.
Examples
# First fill the cache with the toy data included in the package
data("SmallHaps")
CacheHaplotypes(SmallHaps)
#> Warning: haplotypes already cached ... overwriting existing cache.
# Verify it is there
CacheSummary()
#> Cache currently loaded with 300 haplotypes, each with 400 variants.
#> Memory consumed: 16 kB.
# Now clear
ClearHaplotypeCache()
# Verify it is gone
CacheSummary()
#> Cache currently empty.