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Search approximate matches with 'sassy'

Source: R/search.R
sassy_search.Rd

Convenience wrapper that creates a searcher, searches, and returns a sassy_matches data frame. Coordinates are 0-based and half-open.

Usage

sassy_search(
  pattern,
  text,
  k,
  alphabet = "dna",
  rc = TRUE,
  alpha = NULL,
  all = FALSE,
  threads = 1L,
  strategy = "pairwise",
  pattern_id = NULL,
  text_id = NULL,
  match_region = FALSE,
  sam = FALSE
)

Arguments

pattern

List of raw vectors or non-missing character scalars.

text

List of raw vectors or non-missing character scalars.

k

Maximum edit distance.

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.

all

If FALSE, return the usual local-minimum matches. If TRUE, return every end position with score <= k; this can include overlapping and nested candidate alignments and requires strategy = "pairwise".

threads

Number of worker threads to request for bulk searches.

strategy

Search strategy. "pairwise" searches each pattern/text pair independently and is the general default. "batch_texts" uses one text per SIMD lane. "batch_patterns" and "encoded_patterns" (alias "v2") use Sassy's multi-pattern encoding, which in sassy 0.2.1 is implemented for alphabet = "iupac" and equal byte-length patterns.

pattern_id

Optional pattern identifiers. If supplied, must be a non-missing character vector with one entry per pattern and adds/replaces a pattern_id column. Names on pattern are not inspected.

text_id

Optional text identifiers. If supplied, must be a non-missing character vector with one entry per text and adds/replaces a text_id column. Names on text are not inspected.

match_region

If TRUE, include a match_region column. Reverse-strand regions are reverse-complemented so the region and CIGAR are in the input pattern direction.

sam

If TRUE, format reverse-strand match_region and cigar in the text direction used by SAM and by the upstream sassy --sam output.

Value

A data frame with 0-based indices and coordinates: pattern_idx, text_idx, text_start, text_end, pattern_start, pattern_end, cost, strand, and cigar. If pattern_id or text_id are supplied, mapped identifier columns are included. If requested, also includes match_region. Rows are ordered by input text, then text start/end coordinate, then pattern index.

Examples

sassy_search(list("ACGT"), list("TTACGTAA"), 0, alphabet = "dna", rc = FALSE)
#> <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=