[alejandrogzi]

Stacked on #6 (v0.0.5), which is stacked on #5 (v0.0.4). Merge and tag in order; this PR then retargets to master.

Syncs the tested experimental tree (alejandrogzi/hspZ experimental @ 29e9e43) into production with the production packaging kept (file headers, clap attribute). Sources are experimental's byte-for-byte except those.

What changes

• --query-list: one reference, many queries in one process. hspz run --reference ref.fa --query-list queries.txt --output OUT builds and uploads each reference bin once for all listed queries; every query keeps its own plan, cap, seed batches, dedup scopes and -D history, so its output under OUT/000001/… is byte-identical to a standalone run. -Z gives one archive per job; OUT/queries.tsv records job → path, size, sha256, blocks, units, HSPs, completion. This release: W=1; identical reference bins required across jobs; -B 0, --kegalign-bins, --from-manifest rejected in batch mode; a failing job aborts the batch.
• hspz hits-estimate (CPU only). Exact per-work-unit seed-hit counts before any GPU work (matches the --time ledger on the whole genome, 6.12e12 hits); a planning/diagnostic tool.

Measurements (Delta L4, W=1, hg38 reference, ABBA, per-query outputs byte-identical to standalone)

query list	standalone × N (a / b)	--query-list (a / b)	aggregate wall
100 × 5 Mbp	10,400 / 11,581 s	1,899 / 1,891 s	−82%
3 × 5 Mbp	311 / 313 s	117 / 120 s	−62%
chr19 + chr18 + chr11 (61–121 Mbp)	1,042 / 1,042 s	1,014 / 1,014 s	−2.6% (GPU-bound)

Exactness: 149 unit tests; ZLUDA gate with three queries incl. several blocks, masked/N + empty output and duplicate record names, -D -Z archives and reversed list order; 100/100 jobs identical on the L4 in both reps; frozen single-query digests unchanged. Reviews: grok-4.6 PORT WITH FIXES (all applied).

Release check: Cargo.toml version 0.0.6 (release.yml asserts tag == version); CLI reference regenerated.

🤖 Generated with Claude Code

[alejandrogzi]

Superseded: rounds 83-96 are collapsed into a single v0.0.4 release (one branch, one changelog entry, one PR). Nothing here is dropped — the replacement PR carries this branch's tree plus the on-disk reference index and multi-GPU batching.