[adamant-pwn]

Stacked on #690. Review only the top commit, "Label seeds that match only a source dummy k-mer on BASIC graphs"; this PR will be retargeted to master after #690 merges.

Problem

On BASIC graphs, the labeled aligner misses seeds shorter than k that occur only within the first k−1 characters of an input sequence.

• Such a string S is a k-mer suffix only of a source dummy k-mer $…$T.
• With the graph unmasked, as align_to_graph does and as graphs are built by default, suffix seeding finds that dummy k-mer.
• But dummy k-mers have no annotation, so filter_seeds drops the seed.
• CANONICAL graphs recover the hit from the other strand, and PRIMARY graphs (CanonicalDBG) from the existing suffix_to_prefix pass.

Fix

In AnnotationBuffer::fetch_queued_annotations, on BASIC succinct graphs:

• For a source dummy k-mer that fetched an empty label set, walk forward through its $ count to the real k-mers that continue it. They all start with T.
• Give the dummy the union of their labels, with coordinates shifted back to the dummy k-mer's start.
• Seeds on the dummy and extensions through it then get labels like any other node: label and coordinate consistency in LabeledExtender work unchanged.
• Fan-out cap: a dummy continued by more than 16 real k-mers keeps its empty set, the same drop-the-locus rule as max_num_seeds_per_locus. For scale, on a 24-genome graph with 19-mer seeds, the forward-resolution fan-out over read windows has p50 1, p99 3 and p99.9 ≤ 14.
• Real annotated k-mers never fetch an empty set, so the extra check runs only for dummy k-mers.

Test

LabeledAlignerTest.SubkSeedLabels (BASIC, CANONICAL and PRIMARY; A = TTACGAAA, B = ACGTTGCA, k = 5, seeds ≥ 3):

• It checks ACGT → B, TACGA → A, CGTTG → B and TGCA → B, and that every reported label contains the aligned sequence on either strand.
• Without the fix it fails on BASIC for ACGT; with it, it passes. Checked locally, assertion-enabled build, filtered run only.

Before / after (benchmark harness bench/align-harness, labeled, seed 19)

Targeted set: the first 20/25/30 bp of each of the 42 contigs of a 24-genome graph, both strands (252 reads).

graph	aligned, before → after	top-1 label correct, before → after
BASIC	0.286 → 0.976	0.143 → 0.857
CANONICAL (control)	0.976 → 0.976	0.845 → 0.845

BASIC per strand: + 36 → 123 of 126, − 36 → 123 of 126.

Regression check: simulated reads (150 bp Illumina-like; ONT 400 bp and 1–5 kb at 3/5/10% error) on BASIC and CANONICAL.

• 16/16 arms have byte-identical output apart from latency. Random reads almost never start in a sequence's first k−1 bases.
• p50/p99 latency is unchanged within noise.

Multi-threaded CLI, metagraph align -p 8, labeled BASIC graph, 945 long reads, 3 interleaved repeats each (median wall, before → after):

config	wall	peak RSS
seed 19	19.14 → 18.83 s	0.71–0.73 GB both
full k	9.12 → 9.28 s (spread 8.84–9.93)	0.63–0.70 GB both
unlabeled, seed 19	24.79 → 24.65 s	0.49–0.55 GB both

Output checksums are identical in all three configurations.

🤖 Generated with Claude Code

---

Summary by cubic

Fixes the labeled aligner dropping seeds shorter than k that occur only within the first k−1 characters of an input sequence on BASIC graphs. Such seeds match only source dummy k-mers $…$T, which carry no annotations and were filtered out; CANONICAL and PRIMARY graphs recovered them through separate passes.

• On BASIC succinct graphs, the annotation buffer now resolves a source dummy k-mer with an empty label set by walking forward to the real k-mers that continue it (all start with T) and assigning their labels, with coordinates shifted to the dummy's start.
• Dummies continued by more than 16 real k-mers keep an empty label set, so the locus is dropped as if it had too many matches.
• Adds LabeledAlignerTest.SubkSeedLabels, covering BASIC, CANONICAL, and PRIMARY modes.

^{Written for commit be7c376. Summary will update on new commits.}

[cubic-dev-ai]

All reported issues were addressed across 3 files

<sub>Reply with feedback, questions, or to request a fix.

View guided diff | Turn on auto-fix | Re-trigger cubic</sub>