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Rename probabilistic sampling group
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Making way for other options that configure group sizes and must be
mutually exclusive with the current options in this group.
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victorlin committed May 6, 2024
1 parent 22a60b3 commit 80eb23b
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions augur/filter/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -67,9 +67,9 @@ def register_arguments(parser):
subsample_limits_group = subsample_group.add_mutually_exclusive_group()
subsample_limits_group.add_argument('--sequences-per-group', type=int, help="subsample to no more than this number of sequences per category")
subsample_limits_group.add_argument('--subsample-max-sequences', type=int, help="subsample to no more than this number of sequences; can be used without the group_by argument")
probabilistic_sampling_group = subsample_group.add_mutually_exclusive_group()
probabilistic_sampling_group.add_argument('--probabilistic-sampling', action='store_true', help="Allow probabilistic sampling during subsampling. This is useful when there are more groups than requested sequences. This option only applies when `--subsample-max-sequences` is provided.")
probabilistic_sampling_group.add_argument('--no-probabilistic-sampling', action='store_false', dest='probabilistic_sampling')
group_size_options = subsample_group.add_mutually_exclusive_group()
group_size_options.add_argument('--probabilistic-sampling', action='store_true', help="Allow probabilistic sampling during subsampling. This is useful when there are more groups than requested sequences. This option only applies when `--subsample-max-sequences` is provided.")
group_size_options.add_argument('--no-probabilistic-sampling', action='store_false', dest='probabilistic_sampling')
subsample_group.add_argument('--priority', type=str, help="""tab-delimited file with list of priority scores for strains (e.g., "<strain>\\t<priority>") and no header.
When scores are provided, Augur converts scores to floating point values, sorts strains within each subsampling group from highest to lowest priority, and selects the top N strains per group where N is the calculated or requested number of strains per group.
Higher numbers indicate higher priority.
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