[adamant-pwn]

Problem

LabeledAligner segfaults after many align() calls on one aligner object. A language binding drives the aligner this way. The batched CLI is not affected, because it builds a new aligner per batch.

Reproduction:

• 24 RefSeq bacterial genomes, k=31 CANONICAL graph, column annotation.
• 1000 simulated ONT reads (400 bp, 97% identity), full-k seeds.
• One LabeledAligner, align() called once per read.
• SIGSEGV on read 981. That read aligns fine when it runs alone or with only its 20 predecessors.

Root cause, found with an assertion-enabled build: assert(val != nannot) fails at the end of AnnotationBuffer::fetch_queued_annotations.

Fixes

Two dangling-reference bugs, both in AnnotationBuffer, the aligner's per-object label cache:

1. fetch_queued_annotations, CANONICAL graphs (the crash).
   • A node whose canonical counterpart is already registered is inserted into node_to_cols_ with try_emplace.
   • The code then reads the counterpart's value through the iterator find_b.
   • When the insert reallocates the vector-backed map, find_b dangles. The node can be left unqueued and keep the "not fetched" marker.
   • LabeledAligner::filter_seeds then dereferences a null label pointer; the guarding assert is compiled out in Release.
   • Fix: copy the value before inserting.
2. Cached label sets.
   • LabeledExtender holds references from get_cached_column_set() and get_labels_and_coords() while it caches new intersected label sets in the same loop.
   • The sets lived in a vector, so caching could move them.
   • Fix: store them in a deque (VectorSet with a std::deque container), so caching never moves existing sets.
   • The same issue was noticed earlier on hm/align_nomutex (414cfb0), which re-fetched the reference per iteration; that commit never reached master.

Tests

• LabeledAlignerTest.CachedColumnSetsKeepTheirAddress: references to a cached set and to a node's labels stay valid while 10,000 new sets are cached.
• LabeledAlignerTest.FetchBothStrandsInOneBatch: on a CANONICAL graph, queueing the forward and reverse-complement paths of a 5 kbp sequence in one batch fetches labels for every node.
• Locally, with an assertion-enabled -O2 build: 14/14 test instances pass. The full suites were not run locally.
• Negative control: with the vector container restored, CachedColumnSetsKeepTheirAddress fails on 7/7 graph and annotation types.
• FetchBothStrandsInOneBatch exercises the iterator path, but it cannot catch that bug deterministically: the bug is a read after reallocation, which needs a sanitizer to detect reliably. The crash reproduction below is the evidence for that fix.

Before / after (benchmark harness, branch bench/align-harness)

Setup:

• Driver: align_bench, one aligner reused across reads.
• 21 labeled arms: CANONICAL with full-k and seed-19 seeds, BASIC with seed 19.
• Reads: 150 bp Illumina-like, plus ONT 400 bp and 1–5 kb at 3/5/10% error.
• Before and after were interleaved, 4 single-threaded arms at a time.

	before (8b77fc8f9)	after
reads crashing the process	1 (r980, SIGSEGV)	0
arms with identical output (all columns but latency)	—	20/21
the remaining arm	r980 CRASH	r980 aligned to its true genome, score 826

• Latency is unchanged within run-to-run noise. Examples, p50/p99 ms before → after:
  • CANONICAL seed 19, 400 bp 3%: 7.7/21 → 7.7/19;
  • long reads 3%: 71.9/344 → 70.1/317;
  • BASIC seed 19, long reads 5%: 31.3/172 → 32.3/182.
• Peak RSS is unchanged (0.2–0.8 GB).

Multi-threaded CLI

metagraph align -p 8, CANONICAL graph, 945 long ONT reads (3/5/10% error). Master 8b77fc8f9 vs this PR, 3 interleaved repeats each; median wall (per-repeat values), peak RSS.

config	master	this PR	peak RSS
labeled, seed 19	53.6 s (53.6/49.2/63.8)	50.1 s (50.1/47.3/58.4)	0.95–0.96 GB both
labeled, full k	29.2 s (29.2/25.2/36.5)	28.9 s (28.9/27.4/32.0)	0.82–0.90 vs 0.80–0.86 GB
unlabeled, seed 19 (control)	44.6 s	42.9 s	0.67–0.69 vs 0.65–0.71 GB

• Output checksums are identical across all 18 runs.
• No regression beyond run-to-run noise. The laptop was shared, which explains the slower third repeat on both sides.

🤖 Generated with Claude Code

[cubic-dev-ai]

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