gtars-bbcache

A Rust implementation of bbcache: a caching system for BED files from BEDbase.org.

Overview

gtars-bbcache provides an efficient local caching layer for BED files and BED sets retrieved from the BEDbase API. It handles downloading, storage, and retrieval of genomic region data.

Features

• Smart Caching: Automatically downloads and caches BED files from BEDbase API on first access
• BEDset Support: Manages collections of related BED files as coherent sets
• Local File Import: Add local BED files to the cache for unified access
• Efficient Storage: Organizes cached files in a hierarchical directory structure
• SQLite Tracking: Uses biocache for fast lookups and resource management
• Configurable: Customize cache location and API endpoints via environment variables

Quick Start

use gtars_bbcache::client::BBClient;
use std::path::PathBuf;

// Create a client with default settings
let mut client = BBClient::builder().finish()?;

// Load a BED file from BEDbase (downloads and caches if not present)
let region_set = client.load_bed("6b2e163a1d4319d99bd465c6c78a9741")?;

// Add a local BED file to the cache
let bed_id = client.add_local_bed_to_cache(
    PathBuf::from("path/to/file.bed.gz"),
    None
)?;

// Check if a file exists in cache
let cached_path = client.seek(&bed_id)?;

Configuration

The cache behavior can be configured through environment variables:

• BBCLIENT_CACHE: Custom cache directory (default: ~/.bbcache/)
• BEDBASE_API: Custom BEDbase API endpoint (default: https://api.bedbase.org)

Or programmatically via the builder:

use gtars_bbcache::client::BBClient;
use std::path::PathBuf;

let client = BBClient::builder()
    .with_cache_folder(PathBuf::from("/custom/cache/path"))
    .with_bedbase_api("https://api.bedbase.org".to_string())
    .finish()?;