Get VCF/BCF schema using DuckDB — vcf_schema_duckdb • RBCFTools

Returns the column names and types for a VCF/BCF file as seen by DuckDB.

Usage

vcf_schema_duckdb(file, extension_path = NULL, tidy_format = FALSE, con = NULL)

Arguments

file: Path to VCF, VCF.GZ, or BCF file
extension_path: Path to the bcf_reader.duckdb_extension file.
tidy_format: Logical, if TRUE returns schema for tidy format. Default FALSE.
con: Optional existing DuckDB connection (with extension loaded).

Value

A data.frame with column_name and column_type

Examples

if (FALSE) { # \dontrun{
ext_path <- bcf_reader_build(tempdir())
vcf_schema_duckdb("variants.vcf.gz", ext_path)

# Compare wide vs tidy schemas
vcf_schema_duckdb("cohort.vcf.gz", ext_path) # FORMAT_GT_Sample1, FORMAT_GT_Sample2...
vcf_schema_duckdb("cohort.vcf.gz", ext_path, tidy_format = TRUE) # SAMPLE_ID, FORMAT_GT
} # }