Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Set probabilistic sampling as default subsampling behavior #659

Merged
merged 1 commit into from
Jan 20, 2021
Merged

Set probabilistic sampling as default subsampling behavior #659

merged 1 commit into from
Jan 20, 2021

Commits on Jan 20, 2021

  1. Use probabilistic sampling by default 

    Makes the optional flag `--probabilistic-sampling` enabled by default
and adds a `--no-probabilistic-sampling` flag to disable this default
behavior. These changes make the `--probabilistic-sampling` flag
unnecessary but maintain backwards-compatibility for workflows that
reference this flag.

We toggle probabilistic sampling through one variable. This simplifies
the downstream logic that checks for whether to use probabilistic
sampling or not. Note that with this approach we cannot define a
separate `help` string for the `--no-probabilistic-sampling` flag
because it will appear on the command line with a default value of its
destination variable (`probabilistic_sampling=True`).

This commit also disables probabilistic sampling for test builds. Test
builds sample so few sequences that probabilistic subsampling can end up
picking too few sequences for augur refine to work properly. This commit
disables probabilistic sampling for those builds.

Finally, this commit removes the redundant Zika test build implemented
with Snakemake since we already have a Cram test (`zika.t`) that does
the same thing.
    @huddlej
    huddlej committed Jan 20, 2021
    Configuration menu
    Copy the full SHA
    e1abcbb View commit details
    Browse the repository at this point in the history