Create FASTA Table — rduckhts

Creates a DuckDB table from FASTA files using the DuckHTS extension.

Usage

rduckhts_fasta(
  con,
  table_name,
  path,
  region = NULL,
  index_path = NULL,
  gzi_path = NULL,
  sequence_encoding = NULL,
  scan_mode = NULL,
  overwrite = FALSE
)

Arguments

con: A DuckDB connection with DuckHTS loaded
table_name: Name for the created table
path: Path to the FASTA file
region: Optional genomic region (e.g., "chr1:1000-2000" or "chr1:1-10,chr2:5-20")
index_path: Optional explicit path to FASTA index file (.fai)
gzi_path: Optional explicit BGZF FASTA block index path (.gzi) for bgzipped FASTA inputs when the sidecar is not colocated with the FASTA.
sequence_encoding: Character. Sequence encoding for the SEQUENCE column: "string" (default) returns decoded bases as VARCHAR; "nt16" returns raw htslib nt16 4-bit codes as UTINYINT[].
scan_mode: Optional scan mode. Use "auto" (default extension behavior) or "sequential" to force full-file streaming/counting instead of index-backed count paths. Sequential mode is incompatible with region.
overwrite: Logical. If TRUE, overwrites existing table

Value

Invisible TRUE on success