% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/duckhts.R
\name{rduckhts_fastq}
\alias{rduckhts_fastq}
\title{Create FASTQ Table}
\usage{
rduckhts_fastq(
  con,
  table_name,
  path,
  mate_path = NULL,
  interleaved = FALSE,
  sequence_encoding = NULL,
  quality_representation = NULL,
  input_quality_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 FASTQ file}

\item{mate_path}{Optional path to mate file for paired reads}

\item{interleaved}{Logical indicating if file is interleaved paired reads}

\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{quality_representation}{Character. Quality representation for the QUALITY column:
\code{"string"} (default) returns canonical Phred+33 text;
\code{"phred"} returns raw Phred values as \code{UTINYINT[]}.}

\item{input_quality_encoding}{Character. Input FASTQ quality encoding:
\code{"phred33"} (default FASTQ convention), \code{"auto"}, \code{"phred64"},
or \code{"solexa64"}.}

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

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