Infer a succinct tree sequence from SARS-COV-2 variation data
This is an early alpha version not intended for production use!!
If you are interested in helping to develop sc2ts or would like to work with the inferred ARGS, please get in touch.
** TODO document local install **
Inference is intended to be run from the command-line primarily, and most likely orchestrated via a shell script or Snakemake file, etc.
The CLI is split into subcommands. Get help by running the CLI without arguments:
python3 -m sc2ts
TODO document the process of getting a Zarr dataset and using it
The code is marked as licensed under the MIT license, but because the current implementation is used the matching engine from tsinfer (which is GPL licensed) this code is therefore also GPL.
However, we plan to switch out the matching engine for an implementation provided by tskit, which is MIT licensed. This will be done before the first official release.
To run the unit tests, use
python3 -m pytest
You may need to regenerate some cached test fixtures occasionaly (particularly if getting cryptic errors when running the test suite). To do this, run
rm -fR tests/data/cache/
and rerun tests as above.