Miscellaneous

Logging

fastDFE uses the standard Python logging module for logging. By default, fastDFE logs to the console at the INFO level. You can change the logging level, to for example DEBUG as follows:

import fastdfe as fd

fd.logger.setLevel("DEBUG")

You can also disable the progress bar like this:

fd.Settings.disable_pbar = True

Debugging

If you encounter an unexpected error, you might want to disable parallelization to obtain a more descriptive stack trace (see parallelize in BaseInference, JointInference, etc.).

Seeding

fastDFE is seeded by default to ensure reproducibility (see seed in BaseInference, Parser, etc.). Randomness is required for various computational tasks, such as bootstrapping, choosing initial values for different optimization runs, and taking subsamples during VCF parsing.