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fix(downsample): group by molecule by default, add --per-strand opt-out (#904) - #906
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ChangesDuplex downsampling
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: ⚪ Minimal · up to Downsampling now keeps duplex strands together by default while retaining an explicit per-strand option. The covered grouping, simplex, integer-MI, and duplex atomicity behavior is ready to merge. Sequence Diagram(s)sequenceDiagram
participant CLI
participant Downsample
participant FamilyIterator
participant BAM
CLI->>Downsample: select default or --per-strand sampling
Downsample->>FamilyIterator: pass sampling mode
FamilyIterator->>BAM: read adjacent MI-tagged records
FamilyIterator-->>Downsample: return raw-MI or molecule-level family
Downsample-->>CLI: write retained family records
🚥 Pre-merge checks | ✅ 2 | ❌ 1❌ Failed checks (1 warning)
✅ Passed checks (2 passed)
Full details: Linked Issues checkExplanation The implementation addresses duplex grouping, but it conflicts with issue
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #906 +/- ##
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- Coverage 93.55% 93.55% -0.01%
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Files 301 301
Lines 150624 150721 +97
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+ Hits 140918 141002 +84
- Misses 9706 9719 +13 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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In `@src/lib/commands/downsample.rs`:
- Around line 466-467: Restrict molecule normalization to exact trailing /A or
/B duplex suffixes: update both affected paths in src/lib/commands/downsample.rs
at lines 466-467 and 486-489 to strip the suffix only when duplex_suffix_present
is true, otherwise compare and retain the raw MI so simplex values such as /C or
/D are not merged. Update tests/integration/test_downsample_command.rs at lines
479-483 to mirror this rule and cover non-/A-/B cases.
- Line 254: Add a command-level test that invokes Downsample::execute with
multiple duplex-suffixed families and by_molecule disabled, captures log output,
and asserts the suffix warning is emitted exactly once; retain
test_duplex_suffix_present for predicate coverage.
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In `@tests/integration/test_downsample_command.rs`:
- Line 507: Extend the integration test around the simplex family entry in the
--by-molecule downsample coverage to add a deterministic f=1.0 assertion,
verifying that all four records retain MI 999; validate the records’ contents
rather than only their shape.
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Inline comments:
In `@tests/integration/test_downsample_command.rs`:
- Around line 556-560: Strengthen the assertions in
tests/integration/test_downsample_command.rs at lines 556-560 and 598-602 to
verify source-record identity, not just MI values or record counts: for each
surviving duplex molecule, compare its output read-name set with the five
expected input names, and for the simplex family assert that read_0 through
read_3 are present alongside MI 999.
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Inline comments:
In `@src/lib/commands/downsample.rs`:
- Around line 187-191: Update the sampling-mode logging around the
self.per_strand condition to add an else branch for the default path, logging
that the sampling unit is molecule-level while preserving the existing
strand-level message.
In `@tests/integration/test_downsample_command.rs`:
- Around line 686-691: Strengthen the `--per-strand` assertions around
`strands_by_base` to validate complete raw-MI family identity, not merely the
presence of a single-strand suffix: collect retained read names by raw MI and
verify each retained `/A` family contains all three source reads while each
retained `/B` family contains both source reads. Preserve the existing survival
assertion and use the test’s established expected read-name data where
available.
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…ut (#904) downsample keeps or drops whole UMI families atomically to model "fewer input molecules captured." For duplex data the `paired` grouping strategy tags a molecule's two strands `<base>/A` and `<base>/B` as distinct MI values, so each strand got an independent keep/reject draw and a duplex molecule survived as a duplex only with probability fraction^2 — low fractions silently gutted duplex structure. Group by the molecule base by default: each MI is reduced to its base via the canonical `extract_mi_base` (the same last-`/` truncation `group`, `duplex`, and `duplex_metrics` use), so both strands share one draw and are kept or dropped together. This is a no-op for simplex/integer MIs (no `/` to strip), so the only outputs that change are the duplex ones that were previously wrong. Add `--per-strand` to opt back into the legacy raw-MI behavior for deliberate strand-level sampling. This supersedes the earlier `--by-molecule` opt-in (never released): the correct behavior is the default rather than something a user must know to ask for, which also removes the need for the duplex-suffix detection and one-time warning. Note that family-size histograms now count both strands of a molecule as one family, consistent with the sampling unit.
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Fixes #904.
Problem
downsamplekeeps or drops whole UMI families atomically, to model "fewer input molecules captured." For duplex data, thepairedgrouping strategy tags a molecule's two strands<base>/Aand<base>/Bas distinct MI values. So each strand gets an independent keep/reject draw, and a duplex molecule survives as a duplex only when both draws hit — probabilityfraction². At low fractions duplex families collapse, and a duplex dataset downsampled withdownsampleis silently depleted of exactly the thing that makes it duplex.Fix
Group by the molecule base by default. Each MI is reduced to its base via the canonical
extract_mi_base(the same last-/truncationgroup,duplex, andduplex_metricsalready use to collapse strands to their source molecule), so both strands of a molecule form one family sharing a single keep/reject draw and are kept or dropped together. Duplex families then survive at the intendedfraction.This is a no-op for simplex and integer MIs (no
/to strip), so the only outputs that change are the duplex ones that were previously wrong. Molecule-atomic is also the semantically correct sampling unit for a family-atomic downsampler, and it matches how the rest of the pipeline defines a molecule.Add
--per-strand(off by default) to opt back into the legacy behavior of sampling each raw MI tag independently — for deliberate strand-level sampling.Notes
--by-moleculeopt-in from this same PR (never released). Making the correct behavior the default — rather than something a user must know to ask for — also removes the need for the previous duplex-suffix detection and the one-time "you're probably holding it wrong" warning, so the change is a net simplification: the detection predicate, the warning, and the mode-threading boolean are gone; grouping is always keyed onextract_mi_baseunless--per-strandis set.extract_mi_baserather than a local strip, so downsample's grouping rule cannot drift fromgroup/duplex. The canonical rule strips at the last/(any suffix), not only/A,/B; validpairedoutput only ever uses<int>/Aand<int>/B, and simplex assigners emit bare integer MIs, so this is exactly right for grouped input and consistent with the rest of the pipeline.--histogram-kept/--histogram-rejected) now count both strands of a duplex molecule as one family, consistent with the sampling unit — a second observable output change beyond the BAM records themselves.Testing
FamilyIteratorcollapsesN/A+N/Binto one family by default and splits them under--per-strand;family_key/family_key_equalsparity across both modes and Z/integer MIs; a pin that the default key uses the canonical any-suffix strip (not a narrowed/A,/B-only strip) and preserves a leading-/empty base.test_downsample_default_keeps_duplex_strands_together: seed-independent atomicity invariant — every surviving molecule base keeps exactly its own five reads and both/Aand/Bstrands, exercising both the kept and dropped branches atf=0.5.test_downsample_default_preserves_simplex_family: deterministicf=1.0— exactly the four input reads survive, each retaining MI999.test_downsample_per_strand_splits_duplex_strands: the opt-out inverse — under--per-strand, at least one molecule survives with only one of its two strands.cargo nextest run -p fgumi(46 downsample tests pass),cargo ci-lint(clippy-D warnings), andcargo fmt --checkall clean.Risk:
downsampleoutput changes because canonicalextract_mi_basemakes duplex strands share one decision; unsafe changes: none, and CLAUDE.md needs no update; memory, queue, and backpressure changes: none.Adds molecule-level duplex sampling by default. Adds
--per-strandfor independent raw-MI sampling. Preserves simplex and integer-MI behavior.Adds unit and integration tests for grouping keys, duplex atomicity, source-record identity, simplex preservation, and per-strand sampling.