rduckhts_samtools_idxstats: samtools idxstats-Compatible Alignment Summary

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

samtools idxstats-Compatible Alignment Summary

Description

Writes samtools idxstats-compatible alignment summary output for BAM, CRAM, or SAM input.

Usage

rduckhts_samtools_idxstats(
  con,
  path,
  output = NULL,
  index_path = NULL,
  threads = 0,
  overwrite = FALSE
)

Arguments

con	A DuckDB connection with DuckHTS loaded
path	Path to the input alignment file
output	Optional output path for the written idxstats text file
index_path	Optional explicit BAM/CRAM index path
threads	htslib decompression thread count for scan fallback
overwrite	Overwrite an existing output file

Value

A data frame with 'success', 'path', 'output_path', 'used_index_fast_path', and 'error_message'

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.