Add optional per-seed match dates to include_samples - #625
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Add optional per-seed match dates to include_samples#625jeromekelleher wants to merge 2 commits into
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Each include_samples entry may now be a (strain, match_date) tuple in
addition to a bare strain ID. A non-None match_date matches the seed in
on that date instead of its actual date; it may be before the actual
date, in which case the seed node retains its actual date via a negative
("in the future") node time relative to the match-day time-zero. This
lets widely-diverged seeds (e.g. Omicron BA.1/BA.2/BA.3) be matched in on
the same early day so a rudimentary ancestry tree forms before other
tree building, instead of matching to derived samples with many
reversions.
Also detach future (negative-time) nodes when setting up match_tsinfer,
so that other samples cannot copy from a node that lies in the future
relative to the current time-zero.
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #625 +/- ##
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+ Coverage 88.13% 88.24% +0.11%
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Lines 4163 4204 +41
Branches 596 606 +10
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+ Hits 3669 3710 +41
Misses 363 363
Partials 131 131
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A seed strain in include_samples that is not present in the dataset now raises a ValueError up-front in extend() instead of being silently warned-and-skipped, so typos and bad configs fail fast. The no-alignment corner case is handled the same as for any other sample (no seed-specific path). detach_future_nodes now fully detaches negative-time nodes: in addition to removing incident edges, it drops mutations over those nodes and clears their NODE_IS_SAMPLE flag so the matcher cannot treat them as ancestors, recomputing mutation parents afterwards. Node IDs and times are preserved. Rewrite the detach_future_nodes tests with hand-drawn topologies (including recombination) following the conventions in test_tree_ops.py.
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July 28, 2026 20:40
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This should work now, and allow us to do something like this: So, the
The sample will be inserted at its real date, meaning that it is initially inserted as a "future" node (negative time). This PR also includes a function to detach future nodes so that they are not available for matching against. |
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Opening this so we can see it, but probably won't be merged.