Syncmers Library in Rust

Syncmers as defined by Dutta et al. 2022, https://www.biorxiv.org/content/10.1101/2022.01.10.475696v2.full Esp Fig 1b / Algorithm 1. Planning to implement other methods soon.

Definition

Using the parameterized syncmer scheme, a syncmer is a kmer whose smallest smer is at a given target position (t).

Extract Syncmers from &[u8]

rust let sequence = b"CCAGTGTTTACGG"; let syncmers = find_syncmers(5, 2, &[2], None, sequence); assert!(syncmers == vec![b"CCAGT", b"TTACG"]); println!("{:?}", syncmers);

Extract Syncmers from &[u8], downsampling to 20%

rust let sequence = b"CCAGTGTTTACGG"; let syncmers = find_syncmers(5, 2, &[2], Some(0.2), sequence); assert!(syncmers == vec![b"CCAGT", b"TTACG"]); println!("{:?}", syncmers);

Extract Syncmers from &[u8], keeping 80%

rust let sequence = b"CCAGTGTTTACGG"; let syncmers = find_syncmers(5, 2, &[2], Some(0.8), sequence); assert!(syncmers == vec![b"CCAGT", b"TTACG"]); println!("{:?}", syncmers);

Find positions of Syncmers

rust let sequence = b"CCAGTGTTTACGG"; let syncmer_positions = find_syncmers_pos(5, 2, &[2], None, sequence); println!("{:?}", syncmer_positions); assert!(syncmer_positions == vec![0, 7]);

Changelog

0.1.4: Added downsampling support