% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/duckhts.R
\name{rduckhts_fasta}
\alias{rduckhts_fasta}
\title{Create FASTA Table}
\usage{
rduckhts_fasta(
  con,
  table_name,
  path,
  region = NULL,
  index_path = NULL,
  gzi_path = NULL,
  sequence_encoding = NULL,
  scan_mode = NULL,
  overwrite = FALSE
)
}
\arguments{
\item{con}{A DuckDB connection with DuckHTS loaded}

\item{table_name}{Name for the created table}

\item{path}{Path to the FASTA file}

\item{region}{Optional genomic region (e.g., "chr1:1000-2000" or "chr1:1-10,chr2:5-20")}

\item{index_path}{Optional explicit path to FASTA index file (.fai)}

\item{gzi_path}{Optional explicit BGZF FASTA block index path (.gzi) for
bgzipped FASTA inputs when the sidecar is not colocated with the FASTA.}

\item{sequence_encoding}{Character. Sequence encoding for the SEQUENCE column:
\code{"string"} (default) returns decoded bases as \code{VARCHAR};
\code{"nt16"} returns raw htslib nt16 4-bit codes as \code{UTINYINT[]}.}

\item{scan_mode}{Optional scan mode. Use \code{"auto"} (default extension
behavior) or \code{"sequential"} to force full-file streaming/counting
instead of index-backed count paths. Sequential mode is incompatible with
\code{region}.}

\item{overwrite}{Logical. If TRUE, overwrites existing table}
}
\value{
Invisible TRUE on success
}
\description{
Creates a DuckDB table from FASTA files using the DuckHTS extension.
}
