rduckhts_bcf_convert_parquet: Convert VCF/BCF reader output to Parquet with DuckHTS...

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

Convert VCF/BCF reader output to Parquet with DuckHTS metadata

Description

'rduckhts_bcf_convert_parquet()' is a thin DBI wrapper around the extension macro 'duckhts_bcf_convert_parquet_sql(...)'. The extension macro builds the 'COPY ... TO ... (FORMAT PARQUET, KV_METADATA ...)' statement, including DuckHTS write-format metadata, optional user metadata maps, selected columns, optional SQL filter text, 'tidy_format', and the VCF header under the 'vcf_header' key. The wrapper executes the generated statement.

Usage

rduckhts_bcf_convert_parquet(
  con,
  path,
  output,
  columns = NULL,
  region = NULL,
  index_path = NULL,
  tidy_format = FALSE,
  additional_csq_column_types = NULL,
  decompression_threads = 0,
  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 VCF/BCF 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.
tidy_format	Logical; request 'read_bcf(..., tidy_format := true)'.
additional_csq_column_types	Optional CSQ type override string.
decompression_threads	Integer htslib decompression worker threads.
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'.

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