| Title: | Approximate String Matching for 'DuckDB' |
|---|---|
| Description: | Builds and loads the 'ducksassy' extension for 'DuckDB', providing approximate DNA, IUPAC and ASCII string matching through the 'Sassy' SIMD kernels. Search scalar values, pattern panels and CRISPR guide targets from SQL. The matching method is described by Beeloo and Groot Koerkamp (2026) <doi:10.1093/bioinformatics/btag244>. |
| Authors: | Sounkou Mahamane Toure [aut, cre], Rick Beeloo [ctb, cph] (Sassy, bundled under the MIT license), Ragnar Groot Koerkamp [ctb, cph] (Sassy, bundled under the MIT license), DuckDB Foundation [cph] (DuckDB headers and metadata tool, bundled under the MIT license) |
| Maintainer: | Sounkou Mahamane Toure <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 0.1.0 |
| Built: | 2026-10-07 08:22:15 UTC |
| Source: | https://github.com/RGenomicsETL/ducksassy |
Creates an isolated DuckDB database handle, opens a DBI connection, and loads the extension bundled with Rducksassy. The database handle permits unsigned extensions because locally built DuckDB extensions are not signed.
rducksassy_connect(dbdir = ":memory:", read_only = FALSE, config = list(), ...)rducksassy_connect(dbdir = ":memory:", read_only = FALSE, config = list(), ...)
dbdir |
Database file path or |
read_only |
Open an existing database without write access. |
config |
Named DuckDB configuration values. |
... |
Additional arguments passed to |
A live DuckDB DBI connection. Disconnect it with
DBI::dbDisconnect(con, shutdown = TRUE).
con <- rducksassy_connect() DBI::dbGetQuery(con, "SELECT sassy_contains('ACGT', 'TTACGT', 0)") DBI::dbDisconnect(con, shutdown = TRUE)con <- rducksassy_connect() DBI::dbGetQuery(con, "SELECT sassy_contains('ACGT', 'TTACGT', 0)") DBI::dbDisconnect(con, shutdown = TRUE)
Loads the extension bundled with Rducksassy into an existing compatible DuckDB DBI connection.
rducksassy_load(con)rducksassy_load(con)
con |
A DuckDB DBI connection. |
con, invisibly.
driver <- duckdb::duckdb( config = list(allow_unsigned_extensions = "true"), shared_home = FALSE ) con <- DBI::dbConnect(driver) rducksassy_load(con) DBI::dbDisconnect(con, shutdown = TRUE)driver <- duckdb::duckdb( config = list(allow_unsigned_extensions = "true"), shared_home = FALSE ) con <- DBI::dbConnect(driver) rducksassy_load(con) DBI::dbDisconnect(con, shutdown = TRUE)