A Rust port of the Orthograph reporter from: https://github.com/mptrsen/Orthograph/
The analyzer component has not yet been ported over to Rust, but the reporter component has been fully ported with the modifications that headers are no longer concatenated, plus additional env and hmm overlap checks.
First, modify the config.ini file as desired. This file very closely resembles the orthograph.conf file with various additional settings, mainly for the env and hmm overlap functionality.
Next, if you have Rust installed on an Ubuntu / Debian machine, you may run the command:
cargo run -p reporter
Otherwise, you can use the binary located within the /bin/ directory of this repository.
Another package is contained within this repository called biodb, which converts a SQLite database generated by the Orthograph analyzer to RocksDB. This has proven to save a great deal of hard disk space as it utilizes Snappy compression via RocksDB.
This package also uses the settings contained within the config.ini file. If you have Rust installed on a Ubuntu / Debiam machine, you can run biodb with the command:
cargo run -p biodb
Otherwise, you may simple run the /bin/biodb binary that's included with this repository.
Any questions, issues or requests please feel free to reach out via e-mail at [email protected]. Always looking for new work, especially within the bioinformatics space.