feat(qc): add combined recombination detection strategies B+C+D+F#1742
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ivan-aksamentov wants to merge 7 commits into
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feat(qc): add combined recombination detection strategies B+C+D+F#1742ivan-aksamentov wants to merge 7 commits into
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Closes #1699 Combines four recombination detection strategies: - B: Spatial uniformity (PR #1737) - C: Cluster gaps (PR #1738) - D: Reversion clustering (PR #1739) - F: Label switching (PR #1741) Test dataset in this PR: `./data/recomb/enpen/enterovirus/ev-d68/` Preview: https://nextstrain--nextclade--pr-1742.previews.neherlab.click Preview with test dataset: https://nextstrain--nextclade--pr-1742.previews.neherlab.click?dataset-url=gh:nextstrain/nextclade@feat/qc-recomb-strategy-combined@/data/recomb/enpen/enterovirus/ev-d68/&input-fasta=example CLI test: ``` nextclade run \ --input-dataset data/recomb/enpen/enterovirus/ev-d68/ \ --output-all output/ \ data/recomb/enpen/enterovirus/ev-d68/sequences.fasta ``` Note: The current weighted score aggregation (simple sum of strategy scores) is a temporary solution. The scoring mechanism needs further discussion to determine optimal combination approach.
All four recombinant detection strategies now apply their weight consistently: base_score × weight. Previously clusterGaps was missing this final weight multiplication. - Add `weight` field to `QcRecombConfigClusterGaps` (default: 50.0) - Remove unused `QcRecombConfigWeightedThreshold` strategy - Remove `mutations_threshold` and `weighted_threshold` config fields
- Use sorted_by_key() instead of sort_by() for float sorting - Make strategy_label_switching consistent with other strategies - Simplify score summation with array-based iteration
Remove weightGapSize and weightPerGap, leaving only weight (default 1250) to match other strategies. Gap size beyond threshold was negligible and two weights were mathematically redundant for linear scoring.
Show one decimal place for score display, matching CV precision.
The previous implementation counted distinct labels minus one based on centroids. Now counts actual position-based label transitions along the genome, correctly detecting recombination breakpoints.
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Relevant piece of QC config in pathogen.json nextclade/data/recomb/enpen/enterovirus/ev-d68/pathogen.json Lines 68 to 94 in 30d267e |
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Closes #1699
Combines four recombination detection strategies:
Test dataset in this PR:
./data/recomb/enpen/enterovirus/ev-d68/Preview: https://nextstrain--nextclade--pr-1742.previews.neherlab.click
Preview with test dataset: https://nextstrain--nextclade--pr-1742.previews.neherlab.click?dataset-url=gh:nextstrain/nextclade@feat/qc-recomb-strategy-combined@/data/recomb/enpen/enterovirus/ev-d68/&input-fasta=example
CLI test:
Note: The current weighted score aggregation (simple sum of strategy scores) is a temporary solution. The scoring mechanism needs further discussion to determine optimal combination approach.