Add cached cd hit est reference collapse step to pathoscope#188
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- run cd-hit-est per segment with bounded concurrency - keep each cd-hit-est process single-threaded so proc controls segment-level parallelism
- allow isolates to omit schema segments during reference collapse - permit empty segment sentinels for unsegmented OTUs
ReeceHoffmann
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June 12, 2026 21:32
igboyes
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Jun 29, 2026
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utils.py is turning into a pig and should be modularized.
…into reecehoffmann/vir-2534-add-cached-cd-hit-est-reference-collapse-step-to-pathoscope # Conflicts: # tests/test_workflow.py
- move reference collapse helpers out of general workflow utilities - stop persisting collapse stats as a cache manifest
- preserve OTUs that cannot be safely collapsed and report per-outcome counts - build explicit OTU fixtures for validation and mixed-result coverage
igboyes
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Jul 15, 2026
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Summary
Adds a cached preprocessing step that collapses redundant reference isolates with
cd-hit-estbefore Pathoscope builds its mapping indexes.cd-hit-estat 99% identity for each OTU segment, with concurrency limited by the workflow processor count.cd-hit-estversion, and collapse identity.cd-hit-est4.8.1 to the workflow image.reference.pymodule.Collapse behavior
For eligible OTUs, sequences are clustered independently by segment. The collapsed reference:
OTUs with a single isolate are left unchanged. OTUs whose structure cannot be collapsed safely—such as invalid segment names, duplicate segments, or ambiguous unsegmented isolates are unchanged