rduckhts_bcf_multi: Read multiple VCF/BCF files into a DuckDB table
In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

rduckhts_bcf_multi

R Documentation

Read multiple VCF/BCF files into a DuckDB table

Description

Read and combine multiple VCF/BCF 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_bcf_multi(
  con,
  table_name,
  files,
  region = NULL,
  index_path = NULL,
  tidy_format = FALSE,
  additional_csq_column_types = NULL,
  scan_mode = NULL,
  decompression_threads = 0,
  .params = NULL,
  overwrite = FALSE,
  samples = NULL
)

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.
`tidy_format`	Logical; use tidy FORMAT column output.
`additional_csq_column_types`	Optional CSQ type override string.
`scan_mode`	Optional scan mode ('"auto"' or '"sequential"').
`decompression_threads`	Integer. Number of htslib decompression worker threads per file handle. Default '0'.
`.params`	Optional data.frame with per-file parameter overrides.
`overwrite`	Logical; if `TRUE`, replace an existing table.
`samples`	Optional HTSlib sample-selector string, as in [rduckhts_bcf()].