cyanea-core

Overview

cyanea-core provides the shared foundation that every other crate in the ecosystem depends on. It defines the core type system — biological alphabets (DNA, RNA, amino acid), genomic coordinate types, strand enums, and a common error hierarchy — so that data flows cleanly between crates without conversion overhead.

Beyond types, it bundles essential utilities: SHA-256 hashing for data integrity, zstd compression for efficient storage and transfer, and memory-efficient bit-packed collections for working with large biological datasets.

Key Concepts

Alphabets and Encoding

Biological sequences are ultimately strings over small alphabets. cyanea-core defines Alphabet variants for DNA (A, C, G, T), RNA (A, C, G, U), amino acids (20 standard residues plus stop), and IUPAC ambiguity codes. These alphabets power validation, encoding, and 2-bit packing throughout the stack.

Coordinate Systems

Genomic intervals are represented as zero-based, half-open (chrom, start, end, strand) tuples — the BED convention. This eliminates off-by-one errors when crates exchange interval data.

Hashing and Compression

sha256 provides fast, deterministic content hashing — useful for deduplication, caching, and verifying file integrity. compress / decompress wrap the zstd codec, giving 3–5x compression on typical bioinformatics text formats at interactive speeds.

Code Examples

Rust

use cyanea_core::{sha256, compress, decompress, Alphabet};

let hash = sha256(b"ATCGATCG");
let packed = compress(b"ATCGATCG...");
let original = decompress(&packed);
assert!(Alphabet::Dna.is_valid(b"ATCGATCG"));

Python

import cyanea

h = cyanea.sha256("ATCGATCG")
compressed = cyanea.compress("ATCGATCG" * 1000)
original = cyanea.decompress(compressed)

JavaScript (WASM)

import { sha256, compress, decompress } from '/wasm/cyanea_wasm.js';

const hash = sha256("ATCGATCG");
const packed = compress("ATCGATCG".repeat(1000));
const original = decompress(packed);

Use Cases

• Data integrity — Hash FASTA/VCF files before and after transfer to verify nothing was corrupted.
• Compact storage — Compress intermediate analysis results for browser-side caching.
• Type safety — Use shared alphabet types to catch invalid sequences at parse time rather than deep inside an analysis pipeline.