Create GTF Table — rduckhts

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

Usage

rduckhts_gtf(
  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,
  overwrite = FALSE
)

Arguments

con: A DuckDB connection with DuckHTS loaded
table_name: Name for the created table
path: Path to the GTF 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
overwrite: Logical. If TRUE, overwrites existing table

Value

Invisible TRUE on success