install cargo and rust here: https://www.rust-lang.org/tools/install
bash
$ cargo install crussmap
View chain files in tsv/csv format of block pair representation:
```bash
crussmap view --input data/test.chain --output out_file
crussmap view --input data/test.chain --output out_file --csv ```
Convert BED file from one assembly to another:
```bash
crussmap bed --bed data/test.bed --input data/test.chain
crussmap bed --bed data/test.bed --input data/test.chain --output outputbed --unmap unmapbed ```
Some popular bio-formats should be supported, but I don't have enough time to do it. If you are interested in this project, just contribute to it:)
environment: 1.4 GHz 4-core Intel Core i5;16 GB 2133 MHz DDR3;macOS 13.2 (22D49)
```bash
wc -l long.bed 10013 long.bed wc -l v2v3.chain 253064 v2v3.chain time release/crussmap bed -b long.bed -i v2v3.chain -o test.out -u test.unmap
Executed in 253.78 millis fish external usr time 197.93 millis 0.16 millis 197.77 millis sys time 51.45 millis 1.02 millis 50.43 millis
```
Use nom to parse chain file, which is a fast and easy-to-use parser combinator library for Rust.
Utilize csv and serde to deserialize bed file.
A fast interval tree library: rust-lapper was used to build interval tree and query.
Licensed under the MIT license.