rduckhts_bed: Create BED Table

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Create BED Table

Description

Creates a DuckDB table from a BED file using the DuckHTS extension.

Usage

rduckhts_bed(
  con,
  table_name,
  path,
  region = NULL,
  index_path = NULL,
  scan_mode = NULL,
  overwrite = FALSE,
  error_policy = NULL
)

Arguments

con	A DuckDB connection with DuckHTS loaded
table_name	Name for the created table
path	Path to the BED file
region	Optional genomic region for tabix-backed BED queries
index_path	Optional explicit path to a BED tabix index
scan_mode	Optional scan mode. Use "auto" (default extension behavior) or "sequential" to force full-file streaming/counting instead of index-backed count paths. Sequential mode is incompatible with region.
overwrite	Logical. If TRUE, overwrites an existing table
error_policy	Optional short-line policy: "error" (default), "skip", or "report". Report adds diagnostic columns and requires a full-file scan rather than a region query.

Value

Invisible TRUE on success

Examples

con <- rduckhts_connect()

# Intervals are 0-based and half-open, like BED: keep BED starts as they are.
DBI::dbExecute(con, 'CREATE TABLE tiles AS SELECT * FROM (VALUES
  (\'CHROMOSOME_I\', 0, 10), (\'CHROMOSOME_I\', 10, 20)) t(chrom, start, "end")')
DBI::dbGetQuery(con, "SELECT * FROM duckhts_cgranges_from_table(
  'tiles_idx', 'tiles', 'chrom', 'start', 'end')")

# end is a reserved SQL word: quote the column as "end" in the select list and
# pass that column, not the string 'end', to the scalar functions.
rduckhts_bed(con, "targets", system.file("extdata", "targets.bed", package = "Rduckhts"))
DBI::dbGetQuery(con, 'SELECT chrom, start, "end",
  duckhts_cgranges_count_overlaps(\'tiles_idx\', chrom, start, "end") AS tiles
  FROM targets')

DBI::dbDisconnect(con, shutdown = TRUE)

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.