Add max_pango_lineages retro group filter. - #622
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Reject retrospective groups spanning more than max_pango_lineages distinct pango lineages, defaulting to 10. A group is a set of samples sharing an HMM path, so one spanning many lineages suggests the grouping is spurious rather than a real cluster. The check uses the existing SampleGroup.pango_count and runs before tree inference, so rejected groups skip that work. It defaults to np.inf in add_matching_results, which keeps it retro-only since the close phase passes no quality thresholds. Also document min_different_dates in the example config, which was missing.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #622 +/- ##
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+ Coverage 88.11% 88.13% +0.01%
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Files 12 12
Lines 4149 4155 +6
Branches 592 594 +2
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+ Hits 3656 3662 +6
Misses 363 363
Partials 130 130
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Reject retrospective groups spanning more than max_pango_lineages distinct pango lineages, defaulting to 10. A group is a set of samples sharing an HMM path, so one spanning many lineages suggests the grouping is spurious rather than a real cluster.
The check uses the existing SampleGroup.pango_count and runs before tree inference, so rejected groups skip that work. It defaults to np.inf in add_matching_results, which keeps it retro-only since the close phase passes no quality thresholds.
Also document min_different_dates in the example config, which was missing.