[Pilot invitation] Rust-Bio pairwise gap-semantics validation

[logannye]

@johanneskoester — we are piloting hcp-align, an exact solve/verify/compare tool with a Rust-Bio 4.0.1 differential adapter. The adapter accounts for Rust-Bio 4's first-gap semantics by translating rust_gap_open = hcp_gap_open + hcp_gap_extend, then normalizes clipping and operation orientation to canonical =XID records.

Would you be willing to spend 30–60 minutes reviewing that translation or trying a small pairwise-alignment corpus? We are specifically looking for API/scoring-convention mistakes, not throughput comparisons.

A pilot counts as either 100 real records, a complete smaller failure corpus, or one portable disagreement artifact. We will independently rescore and minimize every discrepancy before reporting it.

Pilot guide: https://github.com/logannye/hcp-dp/blob/main/docs/pilot-guide.md
Signed prerelease: https://github.com/logannye/hcp-dp/releases/tag/v0.2.0-alpha.2

Sequence data may stay private; minimized fixtures, digests, aggregate statuses, and scoring metadata are sufficient. This is a request for technical feedback, not an endorsement. If the timing or scope is not useful, no response is expected.

[logannye]

@johanneskoester — one brief follow-up in case a corpus run is too much. The smallest useful contribution would be confirming or correcting the Rust-Bio 4 affine-gap translation described above, especially whether gap_open + gap_extend correctly represents the first gap position. We can provide a tiny reproducible fixture and own the verification/reduction work. If this is not a fit, no reply is needed and we will not follow up again.