rduckhts_gff_multi: Read multiple GFF files into a DuckDB table

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

Read multiple GFF files into a DuckDB table

Description

Read and combine multiple GFF3 files via UNION ALL BY NAME, materialising the result as a DuckDB table. Each row includes a filename column identifying its source file.

Usage

rduckhts_gff_multi(
  con,
  table_name,
  files,
  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,
  .params = NULL,
  overwrite = FALSE
)

Arguments

con	A DBI connection to DuckDB with the duckhts extension loaded.
table_name	Name of the DuckDB table to create.
files	Character vector of file paths or glob patterns.
region	Optional region string.
index_path	Optional index file path.
header	Logical or NULL; whether the file has a header line.
header_names	Character vector of column names.
auto_detect	Logical or NULL; enable type auto-detection.
column_types	Character vector of column type names.
scan_mode	Optional scan mode ("auto" or "sequential").
attributes_map	Logical; return raw attributes as a scalar MAP.
attributes_list	Logical; return attributes as MAP(VARCHAR, VARCHAR[]).
attributes_pairs	Logical; return attributes as a LIST of key/value/index structs.
strict	Logical; enforce GFF3 structural validation while scanning.
.params	Optional data.frame with per-file parameter overrides.
overwrite	Logical; if TRUE, replace an existing table.

Value

Invisible TRUE on success.

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