work with .chain files in Rust
docs .
usage .
tools .
chains
cargo install --all-features chaintoolsdocker pull ghcr.io/alejandrogzi/chaintools:latestconda install -c bioconda chaintoolsAdd this to your Cargo.toml:
[dependencies]
chaintools = { version = "0.0.13", features = ["mmap", "gzip", "parallel"] }| 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 |
chaintools swap |
8.371 ± 0.163 | 8.183 | 8.475 | 1.00 |
UCSC chainSwap |
14.152 ± 0.119 | 14.021 | 14.254 | 1.69 ± 0.04 |
chaintools liftover |
4.380 ± 0.009 | 4.372 | 4.390 | 1.00 |
UCSC liftOver |
16.540 ± 0.121 | 16.424 | 16.666 | 3.78 ± 0.03 |
*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
**swap and liftover were measured on the same machine with the same methodology, on their own inputs: swap on a 344 MB chain.gz (hg38 vs HLrhiRex1, 3,049,608 chains) and liftover on a 6.5 MB .over.chain.gz (16,278 chains) lifting 244,296 BED3 intervals sampled from its aligned blocks. Both commands produced byte-identical output to their UCSC counterpart on every input tested. bed, split and convert have no equivalent UCSC tool to compare against, and score/antirepeat/convert require genome sequence, so they are not listed.