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fix(pipeline): fall back to a name-only group key on an unreadable aux offset - #880
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Included review availability: 0 reviews are currently available. Your included PR review attempts over the past 7 days set your current allowance at 1 review per hour. WalkthroughMalformed BAM records could cause out-of-bounds auxiliary-data slices. Primary and secondary/supplementary paths now validate offsets and use regression tests to verify fallback behavior without panics. ChangesBAM offset safety
Estimated code review effort: 2 (Simple) | ~10 minutes Merge Risk: ⚪ Minimal · up to The change safely falls back to a name-only group key for out-of-range auxiliary-data offsets and adds regression coverage; no actionable merge-blocking risk remains at the current head. 🚥 Pre-merge checks | ✅ 3✅ Passed checks (3 passed)
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #880 +/- ##
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- Coverage 94.56% 94.53% -0.04%
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Files 268 268
Lines 141664 141811 +147
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+ Hits 133959 134054 +95
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In `@src/lib/unified_pipeline/bam.rs`:
- Line 554: Update the auxiliary-offset handling in the surrounding BAM record
key-generation flow to inspect the raw result before clamping; when it is out of
range, return GroupKey { name_hash, ..GroupKey::default() } with None instead of
generating a position-based key. Update the regression to request
Some(*SamTag::RX) and assert the name-only key.
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src/lib/unified_pipeline/bam.rs
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…x offset
compute_group_key_from_raw derives the aux-data offset from the record's own n_cigar_op/l_seq fields, so a corrupt or truncated record can report an offset past the body — or aux_data_offset_from_record can return None for a record too short to read those fields. The original code fed that through unwrap_or(raw.len()), slicing an empty aux region and then building a *position* key from defaulted library/cell hashes. Because the position key excludes name_hash, that malformed record could group with unrelated records at the same position.
Detect the unresolvable/out-of-range offset in the primary path and return a name-only key (GroupKey { name_hash, ..default() }) plus no UMI position, matching the secondary/supplementary and i32::MAX fallbacks. A valid record with no optional fields resolves to off == raw.len() (an empty aux slice) and still takes the normal position-key path. The primary path's RG/CB resolution is unified with the secondary branch's map_or idiom.
Regression tests: an out-of-range record yields the name-only key on both the primary and secondary paths, and a valid tagless record (off == raw.len()) still yields a position key, pinning the off <= raw.len() boundary.
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compute_group_key_from_raw(src/lib/unified_pipeline/bam.rs) sliced&raw[aux_offset..]whereaux_offset = aux_data_offset_from_record(raw).unwrap_or(raw.len()). Theunwrap_orguards a missing offset (None) but not an out-of-rangeSome(offset).aux_data_offset_from_recordderives the offset from the record's ownn_cigar_op/l_seqheader fields, so a malformed or truncated record can report an offset past the record body and panic the slice while computing its group key.validate_record_for_decodedoes not reject this offset, so a corruption-controlled input reaches it.Fix
Clamp with
.min(raw.len())at both aux-slice sites — the primary path and the secondary/supplementary (tc-keyed) path — matching the empty-aux fallback thatfgumi_raw_bam's siblingaux_data_slicehelper already applies for a missing offset. An out-of-range record now yields an empty aux slice (no tags, and therefore no UMI position) and a name-only key, instead of panicking.Test
Adds
compute_group_key_from_raw_survives_out_of_range_aux_offsetwith primary and secondary#[rstest]cases. Each builds a valid raw record then inflatesl_seqsoaux_data_offset_from_recordreports an offset past the body (CIGAR/position left intact so both slice sites are reached). Without the clamp both cases panic at the slice; with it they return a name-only key.Surfaced during CodeRabbit review of #872, but the code lives on
main(it merged via #870), so it is fixed here rather than in that PR.Risk: grouping output changes for malformed records, pinned by primary and secondary regression tests;
unsafechanges: none, and theCLAUDE.mdallowlist is unchanged; memory bounds, queue capacity, and thread/backpressure policy changes: none.Clamps auxiliary-data offsets to
raw.len()in both primary and secondary paths. Malformed records now produce a name-only group key instead of panicking.Adds regression tests for out-of-range offsets.