Setup DuckDB connection with bcf_reader extension loaded

Creates a DuckDB connection and loads the bcf_reader extension for VCF/BCF queries.

Usage

vcf_duckdb_connect(
  extension_path,
  dbdir = ":memory:",
  read_only = FALSE,
  config = list()
)

Arguments

extension_path

Path to the bcf_reader.duckdb_extension file. Must be explicitly provided.

dbdir

Database directory. Default ":memory:" for in-memory database.

read_only

Logical, whether to open in read-only mode. Default FALSE.

config

Named list of DuckDB configuration options.

Value

A DuckDB connection object with bcf_reader extension loaded

Examples

if (FALSE) { # \dontrun{
# First build the extension
ext_path <- bcf_reader_build(tempdir())

# Then connect
con <- vcf_duckdb_connect(ext_path)
DBI::dbGetQuery(con, "SELECT * FROM bcf_read('variants.vcf.gz') LIMIT 10")
DBI::dbDisconnect(con)
} # }