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< h1 id = "benchmark-query-path-testing" > Benchmark: query-path testing</ h1 >
< p >< code > benchmark/Makefile</ code > exercises indexing, merge, and phylo distance
reconstruction against simulated bacterial genomes. It now also covers
< code > obikmer query</ code > — the read-matching path — and the sparse packed
presence-matrix format (< code > obikmer pack --sparse</ code > ), previously untested by
this pipeline.</ p >
< h2 id = "motivation" > Motivation</ h2 >
< ul >
< li >< code > query</ code > had no end-to-end coverage. A regression there would not be caught
by < code > verify_presence</ code > /< code > verify_merge_presence</ code > , which only check index
< em > content</ em > against the < code > .npz</ code > truth, never the query API.</ li >
< li >< code > pack --sparse</ code > produces a presence-matrix format documented (see
< a href = "../../architecture/siblings/" > siblings.md</ a > ) as faster for single-row
access (query) and slower for column-oriented access (phylo < code > --metric</ code > ).
< code > global_index_presence/</ code > built by < code > merge_presence.sh</ code > is always packed
dense (packing is a stage inside < code > merge</ code > , not a separate < code > pack</ code >
invocation) — there was no dense/sparse regression check.</ li >
</ ul >
< h2 id = "query-read-source" > Query read source</ h2 >
< p > Query reads are independent of < code > simulated_data/</ code > (which is folded into the
index being queried): reusing those reads would test against the exact
error draw the index was built from. < code > query_data/< species> /< strain> /</ code > holds
a < em > second</ em > , independent < code > iss generate</ code > run against the same reference
genome, via < code > simulate_query_one.sh</ code > — unseeded, so a second draw picks up
different sequencing errors than < code > simulate_one.sh</ code > 's draw for the same
genome. Fixed at 100,000 read pairs per genome (not coverage-proportional
like the 15x used for < code > simulated_data/</ code > ), so wall/RSS numbers stay
comparable across genomes of very different sizes.</ p >
< p > Two query-source specimens, hardcoded as < code > QUERY_SPECIMENS</ code > in
< code > make_deps.py</ code > : < code > Escherichia_coli--K-12_MG1655</ code > (common, well-represented
bacterium) and < code > Saccharolobus_islandicus--M.16.4</ code > (the only archaeon in
< code > SPECIES</ code > — 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
< code > verify_merge_presence</ code > already provides across all < code > SPECIMENS</ code > .</ p >
< h2 id = "sparse-global-index" > Sparse global index</ h2 >
< p >< code > global_index_presence_sparse/</ code > is built by < code > pack_sparse.sh</ code > : copy
< code > global_index_presence/</ code > wholesale, then < code > obikmer pack --sparse</ code > in place.
This works directly because < code > merge</ code > 's pack stage (< code > merge.rs:252</ code > ,
< code > pack_matrices(false)</ code > ) keeps the per-genome column files on disk after
dense-packing — < code > pack_sparse_bit_matrix</ code > (< code > obicompactvec/src/bitmatrix/sparse.rs:447</ code > )
reads those, is idempotent, and removes < code > matrix.pbmx</ code > once the sparse form
is written, so < code > Persistent::open</ code > falls through to the sparse format
afterward. No separate merge run needed.</ p >
< h2 id = "query-runs" > Query runs</ h2 >
< p >< code > query_one.sh dense|sparse SPECIMEN</ code > runs < code > obikmer query --count-missing</ code >
against < code > global_index_presence</ code > or < code > global_index_presence_sparse</ code > , output
gzipped to < code > query_{dense,sparse}/SPECIMEN.fasta.gz</ code > , Reporter wall/RSS
captured to < code > stats/query_{dense,sparse}/SPECIMEN.stats</ code > (same
stderr-parsing convention as < code > merge_presence.sh</ code > ).</ p >
< p > Flags: < code > --count-missing</ code > only. < code > --mismatch</ code > is a no-op today
(< code > query/mod.rs:212-213</ code > , prints "not yet implemented, ignored") — left off
rather than tested for a feature that doesn't exist yet.</ p >
< h2 id = "densesparse-regression" > Dense/sparse regression</ h2 >
< p >< code > verify_query.py</ code > 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 < code > kmer_count</ code > ,
< code > kmer_missing</ code > , and the full < code > kmer_strict_matches</ code > map per read. Any
mismatch is a real regression: dense and sparse must be content-identical,
only I/O access pattern differs. < code > .stats</ code > → < code > stats/verify_query/</ code > ,
aggregated by < code > aggregate_stats.sh query|verify_query</ code > -style cases
(< code > query_dense</ code > , < code > query_sparse</ code > , < code > verify_query</ code > ).</ p >
< h2 id = "performance-comparison" > Performance comparison</ h2 >
< p > No dedicated script: the wall/RSS columns from the < code > query_dense</ code > and
< code > query_sparse</ code > aggregated < code > .stats</ code > CSVs are the dense-vs-sparse performance
comparison — the expected win for query on sparse, per the < code > pack --sparse</ code >
help text.</ p >
< h2 id = "scope" > Scope</ h2 >
< p >< code > count</ code > track excluded from the sparse branch: < code > pack --sparse</ code > targets
presence matrices only (per CLI help); < code > pack_matrices</ code > leaves count
matrices untouched regardless of the < code > sparse</ code > flag
(< code > obikindex/src/index.rs:308</ code > ).</ p >
< h2 id = "new-makefile-targets" > New Makefile targets</ h2 >
< p >< code > simulate_query</ code > , < code > pack_sparse</ code > , < code > query_dense</ code > , < code > query_sparse</ code > ,
< code > aggregate_query_dense</ code > , < code > aggregate_query_sparse</ code > , < code > verify_query</ code > ,
< code > aggregate_verify_query</ code > — the last three folded into < code > all</ code > .</ p >
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