RuNA

RuNA is a library for aligning DNA sequences.

Docs

https://angramme.github.io/RuNA/

You can also run

cargo doc --open

This will generate and open the docs on you local machine.

Commands

run all tests

cargo test 

Performance limits of all functions:

cargo bench

Generate performance graphs for (in this example dist_2, but you can switch it to a different function)

cargo bench -- gnuplot dist_2

test memory usage of a function (for example dist_2)

cargo build --test mem_use
GENOME_DATA=? valgrind --tool=massif ???/mem_use-? dist_2

One example might be:

GENOME_DATA=./tests/genome_instances_data/ valgrind --tool=massif ./target/debug/dep
s/mem_use-67d566998f108632 dist_2

You can use all other standard cargo commands, for example to generate documentation or others. You can find all the performance tests in benches/, all the memory tests in tests/ and all the unit-tests at the bottom of the corresponding files.

Questions

overleaf

Alternatively, the pdf is attached in the project.