Common data structures and utilities for AGC genome compression.

This crate provides the foundational types and utilities used across the ragc project:

• Archive I/O - Reading and writing AGC archive format
• Collection metadata - Managing samples, contigs, and segment descriptors
• Variable-length integers - Space-efficient encoding/decoding
• Hash functions - MurmurHash implementations for k-mer hashing
• Stream naming - Archive version-aware stream identification

Examples

Creating and reading an archive

use ragc_common::Archive;

// Create a new archive for writing
let mut archive = Archive::new_writer();
archive.open("output.agc").expect("Failed to create archive");

// Register a stream and add data
let stream_id = archive.register_stream("my_stream");
let data = b"Hello, AGC!";
archive.add_part(stream_id, data, data.len() as u64).expect("Failed to add data");

archive.close().expect("Failed to close archive");

// Read it back
let mut archive = Archive::new_reader();
archive.open("output.agc").expect("Failed to open archive");

let stream_id = archive.get_stream_id("my_stream").expect("Stream not found");
let (data, _) = archive.get_part_by_id(stream_id, 0).expect("Failed to read data");

assert_eq!(&data, b"Hello, AGC!");

Variable-length integer encoding

use ragc_common::{write_varint, read_varint};
use std::io::Cursor;

let mut buffer = Vec::new();
write_varint(&mut buffer, 12345).expect("Failed to encode");

let mut cursor = Cursor::new(&buffer);
let (value, bytes_read) = read_varint(&mut cursor).expect("Failed to decode");

assert_eq!(value, 12345);

Using hash functions

use ragc_common::MurMur64Hash;

let kmer_value = 0x12345678u64;
let hash = MurMur64Hash::hash(kmer_value);