API and Coordinates • Rsassy

Functions

sassy_search() searches once.
sassy_searcher() creates a reusable searcher.
sassy_searcher_search() searches with that object.
sassy_features() prints backend/build information.
sassy_set_backend() selects a backend before first use.
sassy_fastx_iter() opens a chunked FASTA/FASTQ iterator.
sassy_fastx_next() returns the next record-count-bounded batch.

Coordinates

Coordinates are 0-based and half-open.

text_start, text_end: interval in the text.
pattern_start, pattern_end: interval in the pattern.
pattern_idx, text_idx: input index for vector/list inputs.

matches <- sassy_search(list("ACGT"), list("TTACGTAA"), k = 0, alphabet = "dna", rc = FALSE)
matches[, c("text_start", "text_end", "pattern_start", "pattern_end", "cigar")]
#> <sassy_matches> 1 match
#> text_start text_end pattern_start pattern_end cigar
#>          2        6             0           4    4=

Inputs

pattern and text are lists of sequence elements. Each element may be a raw vector or a non-missing character scalar. This keeps one raw vector as one sequence of bytes and lets callers mix raw bytes, ordinary strings, and ALTREP-backed raw elements in the same input list.

sassy_search(list(charToRaw("ACGT")), list(charToRaw("TTACGTAA")), k = 0, alphabet = "dna")
#> <sassy_matches> 2 matches
#> pattern_idx text_idx text_start text_end pattern_start pattern_end cost strand cigar
#>           0        0          2        6             0           4    0      +    4=
#>           0        0          2        6             0           4    0      -    4=

The FASTA/FASTQ iterator returns batches already shaped for this API: batch$seq is a list of raw ALTREP sequence elements and batch$id is an ALTREP character vector suitable for text_id.

fq <- tempfile(fileext = ".fastq")
writeLines(c("@r1", "ACGT", "+", "!!!!"), fq, useBytes = TRUE)
batch <- sassy_fastx_next(sassy_fastx_iter(fq, batch_records = 1))
sassy_search(list("ACG"), batch$seq, k = 0, alphabet = "dna", rc = FALSE, text_id = batch$id)
#> <sassy_matches> 1 match
#> pattern_idx text_idx text_id text_start text_end pattern_start pattern_end cost strand cigar
#>           0        0      r1          0        3             0           3    0      +    3=

Match regions

match_region = TRUE adds the matched text interval. Reverse-strand regions are reverse-complemented to match the pattern direction.

sassy_search(
  list("ATCGATCG"),
  list("GGGGATCGATCGTTTT"),
  k = 1,
  alphabet = "dna",
  match_region = TRUE
)
#> <sassy_matches> 3 matches
#> pattern_idx text_idx text_start text_end pattern_start pattern_end cost strand  cigar match_region
#>           0        0          2       10             0           8    1      -   7=1X     ATCGATCC
#>           0        0          4       12             0           8    0      +     8=     ATCGATCG
#>           0        0          6       14             0           8    1      - 1=1X6=     AACGATCG

Search strategies

The default strategy = "pairwise" searches each pattern/text pair independently. This is the general path and works with mixed pattern lengths and all alphabets. Other strategies are performance-oriented paths that call different Sassy kernels:

batch_texts: one pattern, multiple texts per batch.
batch_patterns: multiple equal-length patterns per batch.
encoded_patterns / v2: Sassy encoded-pattern path.

batch_patterns and encoded_patterns use Sassy’s multi-pattern encoding. In sassy 0.2.1 that encoding is implemented for the IUPAC profile and equal byte-length patterns.