Convert GFF3 reader output to Parquet with DuckHTS metadata — rduckhts_gff_convert

Thin DBI wrapper around extension macro `duckhts_gff_convert_parquet_sql(...)`.

Usage

rduckhts_gff_convert_parquet(
  con,
  path,
  output,
  columns = NULL,
  region = NULL,
  index_path = NULL,
  header = NULL,
  header_names = NULL,
  auto_detect = NULL,
  column_types = NULL,
  attributes_map = FALSE,
  attributes_list = FALSE,
  attributes_pairs = FALSE,
  strict = FALSE,
  where = NULL,
  compression = "zstd",
  row_group_size = 100000L,
  partition_by = NULL,
  include_metadata = TRUE,
  header_text = NULL,
  metadata = NULL,
  metadata_json_file = NULL,
  write_format_version = "1",
  overwrite = FALSE
)

Arguments

con: A DuckDB connection with DuckHTS loaded.
path: Path or URI to the input GFF3 file.
output: Path to the output Parquet file or partitioned directory.
columns: Optional character vector of columns to include. Defaults to all columns.
region: Optional genomic region string for indexed inputs.
index_path: Optional explicit index path.
header: Logical; pass `header := true/false` to `read_gff(...)`.
header_names: Optional character vector of column names.
auto_detect: Logical; request type auto-detection.
column_types: Optional character vector of DuckDB column types.
attributes_map: Logical; expose GFF attributes as `MAP(VARCHAR, VARCHAR)`.
attributes_list: Logical; expose attributes as `MAP(VARCHAR, VARCHAR[])`.
attributes_pairs: Logical; expose attributes as key/value/index structs.
strict: Logical; enable strict GFF validation while scanning.
where: Optional SQL predicate applied to the reader output before conversion.
compression: Parquet compression, default `"zstd"`.
row_group_size: Parquet row group size.
partition_by: Optional character vector of output partition columns.
include_metadata: Logical; include DuckHTS Parquet KV metadata.
header_text: Optional corrected header text to store instead of the source header.
metadata: Optional named list/vector of extra metadata. This is the primary CRAN/offline-safe path for arbitrary metadata; values with the same names as DuckHTS defaults override the default values.
metadata_json_file: Optional path to a JSON file containing a top-level object of extra metadata. This requires DuckDB's `json` extension to be available when the conversion SQL is generated; otherwise DuckDB will report its normal missing-extension error. Use `metadata` for offline-safe metadata.
write_format_version: DuckHTS Parquet write-format version string.
overwrite: Logical; replace an existing output path. The wrapper checks existence through DuckDB `glob(...)` where possible and passes the same flag to DuckDB `COPY` for partitioned-output overwrite handling.

Value

Invisibly returns `output`.