rduckhts_gff: Create GFF3 Table

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

Create GFF3 Table

Description

Creates a DuckDB table from GFF3 files using the DuckHTS extension.

Usage

rduckhts_gff(
  con,
  table_name,
  path,
  region = NULL,
  index_path = NULL,
  header = NULL,
  header_names = NULL,
  auto_detect = NULL,
  column_types = NULL,
  scan_mode = NULL,
  attributes_map = FALSE,
  attributes_list = FALSE,
  attributes_pairs = FALSE,
  strict = FALSE,
  overwrite = FALSE,
  attributes = NULL
)

Arguments

con	A DuckDB connection with DuckHTS loaded
table_name	Name for the created table
path	Path to the GFF3 file
region	Optional genomic region (e.g., "chr1:1000-2000")
index_path	Optional explicit path to index file (.tbi/.csi)
header	Logical. If TRUE, use first non-meta line as column names
header_names	Character vector to override column names
auto_detect	Logical. If TRUE, infer basic numeric column types
column_types	Character vector of column types (e.g. "BIGINT", "VARCHAR")
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.
attributes_map	Logical. If TRUE, returns raw attributes as a scalar MAP column
attributes_list	Logical. If TRUE, returns attributes as MAP(VARCHAR, VARCHAR[])
attributes_pairs	Logical. If TRUE, returns attributes as a LIST of key/value/index structs
strict	Logical. If TRUE, enforce GFF3 structural validation while scanning
overwrite	Logical. If TRUE, overwrites existing table
attributes	Character vector of attribute keys to expose as VARCHAR columns. Key matching is case-sensitive: "id" does not match ID, and an unmatched key gives a column of NA

Value

Invisible TRUE on success

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