fix(duplex): reconcile single-strand rejections with --stats and --rejects - #758
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Included review availability: 0 reviews are currently available. Based on recent review activity, included reviews refill at 1 per hour. WalkthroughDuplex consensus now tracks group outcomes, preserves alignment-filtered raw records in input order, merges single-strand rejection statistics for kept groups, and prevents duplicate whole-group rejects. Tests cover single-threaded and threaded execution. ChangesDuplex rejection accounting
Estimated code review effort: 4 (Complex) | ~45 minutes Merge Risk: ⚪ Minimal · up to The change reconciles single-strand rejected records with rejection statistics while preserving input order; no actionable merge-blocking risk remains after normal checks and review. Sequence Diagram(s)sequenceDiagram
participant DuplexConsensusCaller
participant VanillaUmiConsensusCaller
participant RejectsBAM
participant ConsensusCallingStats
DuplexConsensusCaller->>VanillaUmiConsensusCaller: Filter alignment sources
DuplexConsensusCaller->>VanillaUmiConsensusCaller: Record rejected raw records
DuplexConsensusCaller->>VanillaUmiConsensusCaller: Take single-strand statistics
DuplexConsensusCaller->>ConsensusCallingStats: Merge counts for kept groups
DuplexConsensusCaller->>RejectsBAM: Write whole-group rejects once
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In `@crates/fgumi-consensus/src/duplex_caller.rs`:
- Around line 2017-2023: Update the X/Y rejection flow around
filter_by_alignment and record_ss_rejects to preserve each input group’s
original ordinal through partitioning, merge rejected raw records by that
ordinal, then append them in input order rather than draining X before Y. Add a
/B minority test that compares the serialized reject sequence with the original
input sequence.
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crates/fgumi-consensus/src/duplex_caller.rscrates/fgumi-consensus/src/vanilla_caller.rstests/integration/test_duplex_command.rs
…jects `DuplexConsensusCaller` drives a composed `VanillaUmiConsensusCaller` for single-strand consensus, and that sub-caller keeps its own counters and rejects buffer. Nothing merged either one back, so a read the single-strand layer dropped from a molecule that still produced a duplex consensus reached neither `--stats` nor `--rejects`: `raw_reads_rejected` under-reported and the rejects BAM was missing records it plainly should have held. `filter_by_alignment` returns the indices it rejected rather than the records, because the duplex caller owns those bytes; hand them back so they land in the sub-caller's rejects buffer, and take its statistics per molecule so the delta folds into the duplex caller's own. The fold is conditional, and must be: a whole-group duplex rejection counts and emits every raw input record, so the single-strand subset is already covered and adding it on top would report more rejected reads than the rejects BAM holds. That is signalled by an explicit `DuplexGroupOutcome` rather than by an empty reject payload, which is also empty whenever tracking is off — inferring it that way would double-count every run made without `--rejects`. `log_statistics` no longer logs the sub-caller separately: its counters are now drained per molecule, so the block would print zeroes and imply the drops went uncounted.
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The duplex path built its X/Y SourceRead vectors with a bare filter_map, silently discarding every read create_source_read rejected (a read that quality-trims to zero, or has absent qualities). Those reads reached neither --stats nor --rejects, so raw_reads_rejected under-counted. Capture the dropped raw records and hand them to the single-strand sub-caller via a new record_zero_length_after_trimming, so #758's existing per-molecule drain folds them into the duplex statistics and rejects buffer symmetrically. This matches fgbio, whose base toSourceRead rejects a zero-length read as ZeroPostAfterTrimming on the duplex caller's own writer and counter (UmiConsensusCaller.toSourceRead). Closes #792
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The duplex path built its X/Y SourceRead vectors with a bare filter_map, silently discarding every read create_source_read rejected (a read that quality-trims to zero, or has absent qualities). Those reads reached neither --stats nor --rejects, so raw_reads_rejected under-counted. Capture the dropped raw records and hand them to the single-strand sub-caller via a new record_zero_length_after_trimming, so #758's existing per-molecule drain folds them into the duplex statistics and rejects buffer symmetrically. This matches fgbio, whose base toSourceRead rejects a zero-length read as ZeroPostAfterTrimming on the duplex caller's own writer and counter (UmiConsensusCaller.toSourceRead). Closes #792
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The duplex path built its X/Y SourceRead vectors with a bare filter_map, silently discarding every read create_source_read rejected (a read that quality-trims to zero, or has absent qualities). Those reads reached neither --stats nor --rejects, so raw_reads_rejected under-counted. Capture the dropped raw records and hand them to the single-strand sub-caller via a new record_zero_length_after_trimming, so #758's existing per-molecule drain folds them into the duplex statistics and rejects buffer symmetrically. This matches fgbio, whose base toSourceRead rejects a zero-length read as ZeroPostAfterTrimming on the duplex caller's own writer and counter (UmiConsensusCaller.toSourceRead). Closes #792
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The duplex path built its X/Y SourceRead vectors with a bare filter_map, silently discarding every read create_source_read rejected (a read that quality-trims to zero, or has absent qualities). Those reads reached neither --stats nor --rejects, so raw_reads_rejected under-counted. Capture the dropped raw records and hand them to the single-strand sub-caller via a new record_zero_length_after_trimming, so #758's existing per-molecule drain folds them into the duplex statistics and rejects buffer symmetrically. This matches fgbio, whose base toSourceRead rejects a zero-length read as ZeroPostAfterTrimming on the duplex caller's own writer and counter (UmiConsensusCaller.toSourceRead). Closes #792
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Aug 18, 2026
The duplex path built its X/Y SourceRead vectors with a bare filter_map, silently discarding every read create_source_read rejected (a read that quality-trims to zero, or has absent qualities). Those reads reached neither --stats nor --rejects, so raw_reads_rejected under-counted. Capture the dropped raw records and hand them to the single-strand sub-caller via a new record_zero_length_after_trimming, so #758's existing per-molecule drain folds them into the duplex statistics and rejects buffer symmetrically. This matches fgbio, whose base toSourceRead rejects a zero-length read as ZeroPostAfterTrimming on the duplex caller's own writer and counter (UmiConsensusCaller.toSourceRead). Closes #792
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Aug 19, 2026
The duplex path built its X/Y SourceRead vectors with a bare filter_map, silently discarding every read create_source_read rejected (a read that quality-trims to zero, or has absent qualities). Those reads reached neither --stats nor --rejects, so raw_reads_rejected under-counted. Capture the dropped raw records and hand them to the single-strand sub-caller via a new record_zero_length_after_trimming, so #758's existing per-molecule drain folds them into the duplex statistics and rejects buffer symmetrically. This matches fgbio, whose base toSourceRead rejects a zero-length read as ZeroPostAfterTrimming on the duplex caller's own writer and counter (UmiConsensusCaller.toSourceRead). Closes #792
nh13
added a commit
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Aug 19, 2026
The duplex path built its X/Y SourceRead vectors with a bare filter_map, silently discarding every read create_source_read rejected (a read that quality-trims to zero, or has absent qualities). Those reads reached neither --stats nor --rejects, so raw_reads_rejected under-counted. Capture the dropped raw records and hand them to the single-strand sub-caller via a new record_zero_length_after_trimming, so #758's existing per-molecule drain folds them into the duplex statistics and rejects buffer symmetrically. This matches fgbio, whose base toSourceRead rejects a zero-length read as ZeroPostAfterTrimming on the duplex caller's own writer and counter (UmiConsensusCaller.toSourceRead). Closes #792
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* fix(duplex): count and route reads that trim to zero length The duplex path built its X/Y SourceRead vectors with a bare filter_map, silently discarding every read create_source_read rejected (a read that quality-trims to zero, or has absent qualities). Those reads reached neither --stats nor --rejects, so raw_reads_rejected under-counted. Capture the dropped raw records and hand them to the single-strand sub-caller via a new record_zero_length_after_trimming, so #758's existing per-molecule drain folds them into the duplex statistics and rejects buffer symmetrically. This matches fgbio, whose base toSourceRead rejects a zero-length read as ZeroPostAfterTrimming on the duplex caller's own writer and counter (UmiConsensusCaller.toSourceRead). Closes #792 * fix(duplex): split whole-group rejection reasons first-writer-wins (#795) On a whole-group rejection downstream of the single-strand filter, reads already rejected as MinorityAlignment were re-attributed entirely to the duplex whole-group reason. fgbio keeps the single-strand reason on those records (first-writer-wins) and applies the whole-group reason only to the survivors; the reject total agreed but the --stats per-reason split did not. The rejects BAM carries no per-record reason (records are byte-for-byte with input), so this is a --stats attribution fix at the drain site. New reattribute_single_strand_rejections moves the single-strand-rejected reads out of the whole-group reason bucket and into their own, a reason move that leaves the reject total unchanged so --rejects still reconciles with raw_reads_rejected. Closes #791 * fix(consensus)!: error on reads with absent base qualities (#796) A mapped read that reaches a quality-weighted consensus caller with no base qualities (BAM QUAL of '*', encoded as 0xFF per base) is structurally invalid input, not a biological filter: it cannot be weighted by the model. fgumi dropped such reads silently, folding them under ZeroLengthAfterTrimming, which can quietly degrade a molecule's depth when an upstream tool strips QUAL — with no signal to the user. create_source_read now returns Result<Option<SourceRead>>: Err on absent or length-mismatched qualities (the run aborts, naming the read), Ok(None) on the legitimate zero-length-after-trimming path, Ok(Some) otherwise. The vanilla and duplex production callers propagate the error; codec builds source reads through its own path and is unaffected. This matches fgbio, whose toSourceRead throws on missing base qualities. BREAKING CHANGE: inputs containing mapped reads with absent base qualities now abort consensus calling instead of silently dropping those reads. Closes #794
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Closes #757.
Where the issue was wrong
The issue says the records "are routed correctly" and reach
--rejectswhile only the counts are stranded. They do not.DuplexConsensusCallerreaches the single-strand caller throughfilter_by_alignment, which counts what it dropped onss_caller.statsbut returns the rejected indices rather than the records — the raw bytes belong to the duplex caller, and the duplex caller discarded the indices (let (filtered_xs, _) = ...). The vanilla caller populatesrejected_readsonly insideprocess_subgroup, which the duplex path never enters, soss_caller.take_rejected_reads()at the drain site always returned an empty vec.So the single-strand drops reached neither output, not just
--stats.raw_reads_rejectedunder-reported and the rejects BAM was missing records — which is what #756's own "Not changed here" section said ("they appear in neither output"), and is the stronger claim.The issue is also wrong that the numbers were "visible in the run log".
log_statistics()has no callers anywhere in the repo — the commands log throughlog_consensus_summary(&metrics), derived fromstatistics(). The counts were invisible everywhere.Everything else holds:
statistics()returned onlyself.stats, nothing merged the sub-caller's, the reasons involved are recorded atvanilla_caller.rs's alignment filter, and record-count-equals-raw_reads_rejectedis the right invariant to pin.The fix
Two halves, both required for the invariant:
filter_by_alignment's rejected indices are mapped back to their raw records and handed to the sub-caller via a newrecord_rejected_raw, in input order (iterating the record slice, not theHashSet). They then drain through the existingtake_rejected_readspath.take_statisticsdrains the sub-caller's counters per molecule, andconsensus_readsfolds that delta into its own.Avoiding the double count
A whole-group duplex rejection counts and emits every raw input record, so the single-strand layer's rejections are a subset already covered; adding them on top reports more rejected reads than the rejects BAM holds. The fold therefore runs on exactly one of the two paths.
The discriminator is the load-bearing detail. The pre-existing code used
duplex_rejected_raw.is_empty(), which works only because it ran underif track_rejects— the payload is also empty whenever tracking is off, so reusing it to gate a statistics decision would double-count every run made without--rejects, i.e. the common case for--stats.process_groupnow returns an explicitDuplexGroupOutcome::{Kept, RejectedWholeGroup(records)}instead, and the enum's doc says why the payload cannot stand in for it.Both hazards are pinned by tests that were confirmed to fail against the naive fix, not merely written alongside the right one:
test_single_strand_rejections_are_not_double_counted_on_whole_group_rejectionreport 20 rejected reads against 16 input records;Keptwhen tracking is off makestest_whole_group_rejection_counts_are_independent_of_rejects_trackingreport 16 tracked vs 20 untracked.Which reasons can collide was worked out rather than assumed. The sub-caller records exactly two reasons on this path —
Unmapped(fromdrop_unmapped_if_any_mapped) andMinorityAlignment— and they are disjoint by construction, since the unmapped reads are removed before the minority pass counts what is left. Itsrecord_input/record_consensussites are inprocess_groupandconsensus_reads, which the duplex path does not call, sototal_readsandconsensus_readsare structurally zero in the delta; both are asserted to stay at the duplex layer's own values rather than left to trust.Tests
TDD; all four failed before the fix.
test_single_strand_rejections_reach_the_duplex_statistics— a molecule that survives with one minority-alignment template on/A. Pins the two counters, thattotal_reads/consensus_readsare not inflated by the fold, and that the retained bytes are exactly that template's two records — byte-for-byte, in input order — not merely the right count.test_single_strand_rejections_are_not_double_counted_on_whole_group_rejection—min_reads = 4is met before single-strand filtering and missed after it, the only way to reach a whole-group rejection downstream of that layer. A control run pins the fixture is not vacuous: four clean templates per strand clear the same threshold, so the rejection is caused by the single-strand drops rather than by the raw depth.test_whole_group_rejection_counts_are_independent_of_rejects_tracking— the same molecule with and without tracking must report identical counters and per-reason breakdown.test_duplex_rejects_bam_reconciles_with_stats(integration, single-threaded and--threads 2) — the end-to-end invariant: rejects BAM record count equalsraw_reads_rejectedfor an input where one molecule both emits a consensus and drops reads, with each reject compared byte-for-byte against the record it came from.test_duplex_command_rejects_contain_no_duplicates's doc claimed to cover the single-strand source; every molecule in it rejects at the duplex layer, so it never could. Reworded to say what it actually pins and to point at the new test for the other half.log_statisticsno longer logs the sub-caller separately — its counters are drained per molecule now, so the block would print zeroes and imply the drops went uncounted.Parity with fgbio
This moves the surviving-molecule path onto fgbio's behavior exactly.
DuplexConsensusCaller.scala:321-322calls the inheritedfilterToMostCommonAlignment, sorejectRecords(..., MinorityAlignment)lands on the duplex caller's own counter and its own rejects writer — one layer, both outputs.Not changed here
rejectRecordsis first-writer-wins (recs.filterNot(_.contains(RejectReasonTag))), so a record already rejected asMinorityAlignmentkeeps that reason and the whole-group reason applies only to the survivors —DuplexConsensusCaller.scala:359-362says so in a comment. fgumi attributes the entire raw group to the duplex reason instead. The totals agree either way (one record, one count), which is what this issue is about; the split does not, and fixing it means touching all five whole-group sites and their reject payloads. It belongs with the rejection-attribution work in codec rejection reasons are attributed differently from fgbio, making the stats files non-comparable #749.create_source_readreturningNone(zero length after trimming, absent qualities). The duplex path drops them silently viafilter_map, whereprocess_subgroupcounts them asZeroLengthAfterTrimmingand writes them. They are missing from both outputs symmetrically, so they do not break reconciliation — a separate under-count, not this one.codec— audited, no equivalent defect. Its composed single-strand caller is reached only throughconsensus_call, which records no statistics and touches no rejects buffer; codec does its own alignment filtering and counts it on its own stats. Nothing is stranded there.Memory
Bounded by one molecule's rejected records, and only when
--rejectsis set: the bytes are copied into the sub-caller's buffer and moved into the duplex caller's on the same call. Worth noting separately that single-threadedduplexnever drains its rejects buffer inside the group loop the waysimplexandcodecdo (simplex.rs:467,codec.rs:513), so that buffer holds every rejected record until the loop ends; this change adds to what accumulates there. That is a pre-existing shape, not introduced here, and the--threadspath drains per batch.Gate
cargo ci-fmt,cargo ci-lint,cargo ci-test(7499 passed, 30 skipped) andcargo ci-doctestall clean.Risk: output changes affect
--statsand--rejectsonly, pinned by raw-record order, deduplication, and reconciliation tests; grouping, consensus, sort order, and corrected UMIs: none;unsafe: none; memory bounds, queue capacity, and thread/backpressure policy: none.Fixes duplex rejection accounting. Single-strand rejected records now use the rejects buffer in raw-record order. Single-strand statistics now merge into duplex statistics without double counting whole-group rejections. Post-filter read thresholds prevent invalid single-strand consensus output.
Adds regression coverage for statistics, reject records, deduplication, tracking modes, alignment filtering, and single- versus multi-threaded execution.