README.md
June 13, 2026 · View on GitHub
chaintools
work with .chain files in Rust
docs .
usage .
tools .
chains
Installation
Binary
cargo install --all-features chaintools
Docker
docker pull ghcr.io/alejandrogzi/chaintools:latest
Conda
conda install -c bioconda chaintools
Library
Add this to your Cargo.toml:
[dependencies]
chaintools = { version = "0.0.8", features = ["mmap", "gzip", "parallel"] }
Benchmarks
| Command | Mean [s] | Min [s] | Max [s] | Relative |
|---|---|---|---|---|
chaintools filter | 7.205 ± 0.102 | 7.087 | 7.266 | 1.00 |
UCSC chainFilter | 11.778 ± 0.043 | 11.729 | 11.812 | 1.63 ± 0.02 |
chaintools sort | 12.434 ± 0.165 | 12.298 | 12.617 | 1.00 |
UCSC chainSort | 18.279 ± 0.025 | 18.254 | 18.303 | 1.47 ± 0.02 |
chaintools merge | 11.995 ± 0.045 | 11.943 | 12.024 | 1.00 |
UCSC chainMergeSort | 17.616 ± 0.071 | 17.557 | 17.696 | 1.47 ± 0.01 |
*ran using hyperfine 1.18.0 on an AMD Ryzen 7 5700X with 128 GB of RAM and 16 cores with a 262 MB chain.gz file as input