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Benchmark: query-path testing

benchmark/Makefile exercises indexing, merge, and phylo distance reconstruction against simulated bacterial genomes. It now also covers obikmer query — the read-matching path — and the sparse packed presence-matrix format (obikmer pack --sparse), previously untested by this pipeline.

Motivation

  • query had no end-to-end coverage. A regression there would not be caught by verify_presence/verify_merge_presence, which only check index content against the .npz truth, never the query API.
  • pack --sparse produces a presence-matrix format documented (see siblings.md) as faster for single-row access (query) and slower for column-oriented access (phylo --metric). global_index_presence/ built by merge_presence.sh is always packed dense (packing is a stage inside merge, not a separate pack invocation) — there was no dense/sparse regression check.

Query read source

Query reads are independent of simulated_data/ (which is folded into the index being queried): reusing those reads would test against the exact error draw the index was built from. query_data/<species>/<strain>/ holds a second, independent iss generate run against the same reference genome, via simulate_query_one.sh — unseeded, so a second draw picks up different sequencing errors than simulate_one.sh's draw for the same genome. Fixed at 100,000 read pairs per genome (not coverage-proportional like the 15x used for simulated_data/), so wall/RSS numbers stay comparable across genomes of very different sizes.

Two query-source specimens, hardcoded as QUERY_SPECIMENS in make_deps.py: Escherichia_coli--K-12_MG1655 (common, well-represented bacterium) and Saccharolobus_islandicus--M.16.4 (the only archaeon in SPECIES — distant lineage, stresses the query path differently from a close-relative match). Two is enough to catch a dense/sparse regression without duplicating the exhaustive per-specimen coverage verify_merge_presence already provides across all SPECIMENS.

Sparse global index

global_index_presence_sparse/ is built by pack_sparse.sh: copy global_index_presence/ wholesale, then obikmer pack --sparse in place. This works directly because merge's pack stage (merge.rs:252, pack_matrices(false)) keeps the per-genome column files on disk after dense-packing — pack_sparse_bit_matrix (obicompactvec/src/bitmatrix/sparse.rs:447) reads those, is idempotent, and removes matrix.pbmx once the sparse form is written, so Persistent::open falls through to the sparse format afterward. No separate merge run needed.

Query runs

query_one.sh dense|sparse SPECIMEN runs obikmer query --count-missing against global_index_presence or global_index_presence_sparse, output gzipped to query_{dense,sparse}/SPECIMEN.fasta.gz, Reporter wall/RSS captured to stats/query_{dense,sparse}/SPECIMEN.stats (same stderr-parsing convention as merge_presence.sh).

Flags: --count-missing only. --mismatch is a no-op today (query/mod.rs:212-213, prints "not yet implemented, ignored") — left off rather than tested for a feature that doesn't exist yet.

Dense/sparse regression

verify_query.py compares the two query outputs per specimen, matched by read id (not stream position — the query pipeline chunks input across worker threads and doesn't guarantee output order). Compares kmer_count, kmer_missing, and the full kmer_strict_matches map per read. Any mismatch is a real regression: dense and sparse must be content-identical, only I/O access pattern differs. .stats → stats/verify_query/, aggregated by aggregate_stats.sh query|verify_query-style cases (query_dense, query_sparse, verify_query).

Performance comparison

No dedicated script: the wall/RSS columns from the query_dense and query_sparse aggregated .stats CSVs are the dense-vs-sparse performance comparison — the expected win for query on sparse, per the pack --sparse help text.

Scope

count track excluded from the sparse branch: pack --sparse targets presence matrices only (per CLI help); pack_matrices leaves count matrices untouched regardless of the sparse flag (obikindex/src/index.rs:308).

New Makefile targets

simulate_query, pack_sparse, query_dense, query_sparse, aggregate_query_dense, aggregate_query_sparse, verify_query, aggregate_verify_query — the last three folded into all.