% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/duckhts.R
\name{rduckhts_samtools_idxstats}
\alias{rduckhts_samtools_idxstats}
\title{samtools idxstats-Compatible Alignment Summary}
\usage{
rduckhts_samtools_idxstats(
  con,
  path,
  output = NULL,
  index_path = NULL,
  threads = 0,
  overwrite = FALSE
)
}
\arguments{
\item{con}{A DuckDB connection with DuckHTS loaded}

\item{path}{Path to the input alignment file}

\item{output}{Optional output path for the written idxstats text file}

\item{index_path}{Optional explicit BAM/CRAM index path}

\item{threads}{htslib decompression thread count for scan fallback}

\item{overwrite}{Overwrite an existing output file}
}
\value{
A data frame with `success`, `path`, `output_path`,
  `used_index_fast_path`, and `error_message`
}
\description{
Writes samtools idxstats-compatible alignment summary output for BAM, CRAM,
or SAM input.
}
