DNA Compression in Pure Rust

This project provides a Rust implementation of a compact, reversible DNA compression format using 4-bit encoding. It supports all 15 IUPAC nucleotide codes, base-pair complement generation, and efficient serialization. The tool is intended for developers working with large-scale biological data or exploring performance-efficient data representations.

Features

• 4-bit encoding of nucleotides (2× size reduction compared to plain text)
• Full IUPAC code support
• Bitwise base-pair complement generation
• Fast decompression with padding-aware decoding
• CLI interface with support for compression, decompression, complement, and benchmarking

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Installation

Clone the repository and build the tool using Cargo.

Usage

Compress a DNA sequence

cargo run . -- input.txt

This will read input.txt (a plain-text DNA sequence) and write a compressed binary file to output.txt.

Generate base-pair complements during compression

cargo run . -- input.txt --compliment

This applies a bitwise complement to the sequence prior to compression.

Run performance benchmarks

cargo run . -- input.txt --benchmark

Runs a performance comparison between bitwise rotation and match-based complement logic. Benchmark output is written to speed_test.csv.

Decompress a binary-encoded DNA file

cargo run . -- output.txt --decode

Reads output.txt (binary) and reconstructs the original DNA sequence in decoded.txt.