setup_hts_env: Setup HTSlib Environment

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

Setup HTSlib Environment

Description

Sets the 'HTS_PATH' environment variable to point to the bundled htslib plugins directory. This enables remote file access via libcurl plugins (e.g., s3://, gs://, http://) when plugins are available.

Usage

setup_hts_env(plugins_dir = NULL)

Arguments

plugins_dir

Optional path to the htslib plugins directory. When NULL, uses the bundled plugins directory if available.

Details

Call this before the process opens its first HTS file. htslib discovers dynamic plugins on first file access and does not rescan 'HTS_PATH' later.

Value

Invisibly returns the previous value of 'HTS_PATH' (or 'NA' if unset).

Examples

## Not run: 
setup_hts_env()

plugins_path <- tempfile("hts_plugins_")
dir.create(plugins_path)
setup_hts_env(plugins_dir = plugins_path)
unlink(plugins_path, recursive = TRUE)

## End(Not run)

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