Skalomerge

[jhellewell14]

• I moved the code from https://github.com/rderelle/skalo/tree/main into two files: skalo.rs which contains the larger functions used lib.rs and skalo_utils that contains utility functions (some of which are quite similar to other utility functions already in the code.
• I added a new command to the CLI: indel that can either accept a .skf file and run the skalo model or take a list of .fasta files and run ska build before passing the ska array internally to the skalo model.
• The skalo code remains mostly unchanged apart from where I have integrated it into the ska.rust code and fixed a few easy clippy warnings

[rderelle]

Hi Joel, I'm afraid this isn't the right version of skalo. Sorry about this. I'll upload it tonight and let you know.

[johnlees]

@rderelle If you are also able to provide us with a good example input file and expected output that would also be very helpful

[rderelle]

skalo has been updated (v1.0.0) and this new version is Clippy-compliant.

I put a skf file on my google drive (20 simulated samples and k=21) - 250 SNPs are expected with default parameters.
https://drive.google.com/drive/folders/1OWEQtq0UdnzZMPEIi-X0O_wxqEPn1mOo?usp=sharing

[jhellewell14]

New PR with latest skalo version here: #86