fix(codec): read out-of-range overlap boundaries the way fgbio does - #755
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`fgumi codec --stats` and fgbio's `CallCodecConsensusReads --stats` reject essentially the same reads but banked a large slice of them under different reasons, so the two stats files were not comparable. On a ~502M-read CODEC dataset `clip_overlap_failed` was 192,140 in fgbio against 40,344 in fgumi while `indel_error_between_strands` moved by nearly the same amount the other way. The two tools evaluate the checks in the same order; the divergence is in the phase check's predicate. The overlap window is `[negative.start, positive.end]`, and in a family with more than one template the longest R1 and the longest R2 come from different templates, so a boundary can fall outside one of the two reads. fgbio reads those boundaries with htsjdk's `getReadPositionAtReferencePosition`, which returns 0 -- a value, not "undefined" -- for a position outside the alignment, and then does arithmetic on that 0. fgumi failed closed instead and reported the family as an indel error. Substitute the same 0 rather than failing closed. This cannot change a verdict: when the window *end* is outside the negative read the check still fails, since passing would require the positive read's query position to decrease between the window start and end; and when the window *start* is outside the positive read, passing forces a consensus length strictly below the negative strand's single-strand consensus, so the family is rejected at the `ClipOverlapFailed` site -- which is the reason fgbio gives it. `check_overlap_phase_raw`'s doc comment carries the argument in full. Measured on 4M CODEC records grouped into multi-template families, against fgbio 4.0.1: `clip_overlap_failed` moves from 9,240 to 9,737 against fgbio's 9,755 and `indel_error_between_strands` from 1,034,226 to 1,033,729 against fgbio's 1,033,740, while the emitted consensus BAM stays byte-identical and `raw_reads_used`, `raw_reads_rejected`, `consensus_reads_emitted`, `r1_r2_overlap_too_short` and `minority_alignment` are all unchanged. The remaining ~18-read residue is the separate `SamRecordClipper` disagreement tracked in fgbio#1090 and is out of scope here. Both new pipeline tests pin the invariant as well as the reason: the family is rejected exactly once, emits no consensus, and contributes every record to the filtered total, so only the bucket moves. Closes #749
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WalkthroughOut-of-range overlap starts now use fgbio’s ChangesOverlap rejection attribution
Estimated code review effort: 3 (Moderate) | ~20 minutes Merge Risk: 🟡 Moderate · up to The change targets rejection attribution without changing emitted consensus output, but the new regression tests use incorrect per-reason counts after alignment filtering and need correction before merge. Possibly related PRs
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In `@crates/fgumi-consensus/src/codec_caller.rs`:
- Around line 3187-3234: Update the expectations in the tests using
cross_template_overlap_fixture and the corresponding alignment-filtering cases
so phase rejection counts two records, with the two filtered records asserted
separately as MinorityAlignment; retain the existing whole-family accounting
assertion and adjust ClipOverlapFailed and IndelErrorBetweenStrands expectations
accordingly.
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Closes #749.
What the divergence actually is
The issue framed this as an evaluation-order difference. It is not — I read fgbio's order off the source and fgumi already matches it check for check:
CodecConsensusCaller.scala)codec_caller.rs)NonPairedReadsFragmentReadNotPrimaryFrPairclipExtendingPastMateEndsnum_bases_extending_past_mate_vs_mate_rawfilterToMostCommonAlignment→MinorityAlignmentfilter_to_most_common_alignment_raw→ sameminReadsPerStrand→InsufficientSupportInsufficientReadsoverlapLength < minDuplexLength→R1R2OverlapTooShortInsufficientOverlap:221-231) →IndelErrorBetweenStrandscheck_overlap_phase_raw→ samecomputeConsensusLength == -1(:241-243) →IndelErrorBetweenStrandscompute_consensus_length_raw→None→ samen < r1Consensus.length || n < r2Consensus.length(:245-247) →ClipOverlapFailedHighDuplexDisagreementWhat differs is the predicate at step 7. The overlap window is
[negative.start, positive.end], and in a family with more than one template the longest R1 and the longest R2 come from different templates — per-template overlap clipping constrains how a read lines up against its own mate, and says nothing about how two different templates line up against each other. So a window boundary can fall outside one of the two reads. fgbio reads those boundaries with htsjdk'sSAMRecord.getReadPositionAtReferencePosition, which returns0— a value, not "undefined" — for a reference position outside the alignment, and then does arithmetic on that0. fgumi'sread_pos_at_ref_pos_rawreturnsOption, and the phase check failed closed onNone.That is why the issue's numbers were near-mirror images: the families in question pass fgbio's phase check and are then rejected at
ClipOverlapFailed, while fgumi rejected them one step earlier asIndelErrorBetweenStrands.The fix substitutes the same
0instead of failing closed.Why this cannot change a verdict
Write
p_s/p_efor the positive read's query positions at the window start and end,n_s/n_efor the negative read's. The window start is the negative read's own start and the window end is the positive read's own end, so onlyp_sandn_ecan be out of range; read position is non-decreasing in reference position, son_s <= n_e,p_s <= p_e, andn_s >= 1.n_eout of range ⟹n_e = 0, and passing would needp_e - p_s = -n_s <= -1, contradictingp_s <= p_e. The check still fails, so those families stay inIndelErrorBetweenStrands— including whenp_sis out of range as well.p_sout of range alone ⟹p_s = 0, and the check passes only whenn_e = p_e + n_s.compute_consensus_length_rawthen yieldsp_e + neg_len - n_e = neg_len - n_s <= neg_len - 1, which is strictly below the negative strand's single-strand consensus length, so the family is rejected at theClipOverlapFailedsite — the reason fgbio gives it.No family that newly passes the phase check goes on to emit a consensus. The argument is carried in full in
check_overlap_phase_raw's doc comment.Measurement
4M records from a real CODEC dataset, MI-grouped into multi-template families (mean 12 reads/family), run through fgbio 4.0.1
CallCodecConsensusReadsandfgumi codecbefore and after:raw_reads_rejected_for_clip_overlap_failedraw_reads_rejected_for_indel_error_between_strandsraw_reads_rejected_for_r1_r2_overlap_too_shortraw_reads_rejected_for_minority_alignmentraw_reads_usedraw_reads_rejectedconsensus_reads_emitted96.5% of the
ClipOverlapFailedgap closes and the emitted consensus BAM is byte-identical before and after (samtools view | md5matches), which is the strongest available statement that this is attribution only.Two things deliberately left alone:
SamRecordClipperdisagreement tracked in fgbio#1090, which is an acknowledged defect there; matching it would mean copying a bug. Out of scope, per the issue.raw_reads_considered/not_primary_fr_pairdiffer by ~10.6k, which is the expected fix(consensus)!: apply fgbio pre-group filter to simplex/codec, add --allow-unmapped #509 consequence of filtering secondary/supplementary records before counting rather than rejecting them after. Also not part of this issue.Tests
Three added, all built programmatically with
create_fr_pair/SamBuilder:test_clip_overlap_failed_attribution_matches_fgbio— a two-template family whose window opens one base before the longest R1 (tA: R1200 50M/ R2200 50M;tB: R1199 40M/ R2199 102M). Reaches theClipOverlapFailedsite through the whole pipeline, which the existing CODEC3-08 comment had claimed was impractical to construct; that comment is corrected.test_window_end_past_r2_stays_indel_error— the mirror case, pinning the half of the predicate that must not change. Without it the fix could be loosened into passing that case too, and those families would change verdict rather than bucket.test_check_overlap_phase_out_of_range_start_uses_fgbio_sentinel— the predicate on its own.Both pipeline tests assert the invariant, not just the reason, via a shared
assert_rejected_whole_family: the family is rejected exactly once, emits no consensus, and contributes every record to the filtered total. That is what makes them a regression guard on "attribution only" rather than on the bucket alone.Local gate:
cargo ci-fmt,cargo ci-lint(clippy pedantic, all targets),cargo ci-test(7497 tests),cargo ci-doctest— all pass.Risk: consensus BAM output remains byte-identical;
unsafechanges are none; memory bounds, queue capacity, and thread/backpressure policy changes are none.Fix: Treat out-of-range read positions as phase
0, matching fgbio and htsjdk. This changes rejection-reason attribution without changing acceptance decisions.IndelErrorBetweenStrandstoClipOverlapFailed.raw_reads_usedandconsensus_reads_emitted.