% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/duckhts.R
\name{rduckhts_fastq_multi}
\alias{rduckhts_fastq_multi}
\title{Read multiple FASTQ files into a DuckDB table}
\usage{
rduckhts_fastq_multi(
  con,
  table_name,
  files,
  mate_path = NULL,
  interleaved = FALSE,
  sequence_encoding = NULL,
  quality_representation = NULL,
  input_quality_encoding = NULL,
  scan_mode = NULL,
  .params = NULL,
  overwrite = FALSE
)
}
\arguments{
\item{con}{A DBI connection to DuckDB with the duckhts extension loaded.}

\item{table_name}{Name of the DuckDB table to create.}

\item{files}{Character vector of file paths or glob patterns.}

\item{mate_path}{Optional mate file path (for paired-end).}

\item{interleaved}{Logical; TRUE if file contains interleaved paired reads.}

\item{sequence_encoding}{Optional sequence encoding.}

\item{quality_representation}{Optional quality representation.}

\item{input_quality_encoding}{Optional input quality encoding override.}

\item{scan_mode}{Optional scan mode (\code{"auto"} or \code{"sequential"}).}

\item{.params}{Optional data.frame with per-file parameter overrides.}

\item{overwrite}{Logical; if \code{TRUE}, replace an existing table.}
}
\value{
Invisible \code{TRUE} on success.
}
\description{
Read and combine multiple FASTQ files via UNION ALL BY NAME,
materialising the result as a DuckDB table.
Each row includes a \code{filename} column identifying its source file.
}
