cyanea-core 0.1.0

Shared primitives, traits, and utilities for the Cyanea bioinformatics ecosystem
Documentation

cyanea-core

Shared primitives, traits, and utilities for the Cyanea bioinformatics ecosystem.

What's Inside

  • Error handling -- CyaneaError enum used by every crate in the workspace
  • Core traits -- Sequence, ContentAddressable, Compressible, Scored, Annotated, Summarizable
  • SHA-256 hashing -- in-memory and streaming file hashing
  • Compression -- zstd and gzip compress/decompress with auto-detection
  • Memory mapping -- read-only memory-mapped file access via memmap2
  • Probability types -- LogProb and PhredProb for numerically stable log-space computation
  • Rank/select bitvectors -- O(1) rank, O(log n) select with superblock index
  • Wavelet matrix -- O(log sigma) access/rank/select over integer alphabets
  • Fenwick tree -- O(log n) prefix sums and point updates

Quick Start

[dependencies]
cyanea-core = "0.1"

use cyanea_core::{sha256, LogProb};

let hash = sha256(b"ACGTACGT");

let p = LogProb::from_prob(0.001).unwrap();
let q = LogProb::from_prob(0.002).unwrap();
let combined = p.ln_add(q); // log-sum-exp

Feature Flags

Flag Default Description
std Yes Compression (zstd, flate2), memory mapping (memmap2)
wasm No WASM target marker
serde No Serialize/Deserialize derives

Modules

Module Description
error CyaneaError enum and Result<T> alias
traits Core trait definitions for the ecosystem
hash SHA-256 hashing (in-memory and file)
compress Zstd/gzip compression with auto-detection
mmap Memory-mapped file access (std only)
prob LogProb and PhredProb newtypes
bitvec RankSelectBitVec and WaveletMatrix
fenwick Generic FenwickTree<T>

See Also