Create a reusable 'sassy' searcher — sassy

A searcher stores the selected alphabet profile and reverse-complement behavior. Reuse a searcher when searching many patterns or texts with the same settings.

Usage

sassy_searcher(alphabet = "dna", rc = TRUE, alpha = NULL)

Arguments

alphabet: Alphabet profile. One of "dna", "iupac", or "ascii".
rc: If TRUE, search reverse-complement strand as well where supported.
alpha: Optional IUPAC overhang cost in [0, 1]. Use NULL to disable.

Value

An external pointer with class sassy_searcher.

Examples

searcher <- sassy_searcher("dna", rc = FALSE)
sassy_searcher_search(searcher, list("ACGT"), list("TTACGTAA"), 0)
#> <sassy_matches> 1 match
#> pattern_idx text_idx text_start text_end pattern_start pattern_end cost strand cigar
#>           0        0          2        6             0           4    0      +    4=