Normalize Variant Alleles with bcftools-style Semantics — rduckhts_bcftools

Applies the DuckHTS `duckhts_bcftools_norm(...)` table macro to rows from a SQL query or table expression. Input rows must expose chromosome, 1-based position, reference allele, and alternate allele columns. Alternate alleles may be supplied either as a comma-delimited `VARCHAR` or as a `VARCHAR[]` list, matching the common DuckDB representations used by plain tables and `read_bcf(...)`.

Usage

rduckhts_bcftools_norm(
  con,
  query,
  fasta_ref,
  chrom_col = "chrom",
  pos_col = "pos",
  ref_col = "ref",
  alt_col = "alt",
  split_multiallelic = FALSE,
  end_pos_col = NULL,
  svlen_col = NULL,
  fasta_index_path = NULL,
  gzi_path = NULL
)

Arguments

con: A DuckDB connection with DuckHTS loaded
query: SQL query or table expression to normalize
fasta_ref: Path to the reference FASTA
chrom_col: Source chromosome column name
pos_col: Source 1-based position column name
ref_col: Source reference allele column name
alt_col: Source alternate allele column name (`VARCHAR` or `VARCHAR[]`)
split_multiallelic: If `TRUE`, split multiallelic sites before normalization so `alt_normed` is emitted as `VARCHAR` plus `alt_index`. If `FALSE` (default), keep sites intact and emit `alt_normed` as `VARCHAR[]`.
end_pos_col: Optional source column name containing an END-like 1-based end coordinate for symbolic deletions.
svlen_col: Optional source column name containing an SVLEN-like signed length for symbolic duplications.
fasta_index_path: Optional explicit `.fai` sidecar path.
gzi_path: Optional explicit `.gzi` sidecar path for bgzipped FASTA.

Value

A data frame with the original columns plus `pos_normed`, `end_pos_normed`, `ref_normed`, `alt_normed`, `normed`, and `norm_status`. In split mode the result additionally includes `alt_index`.