Add benchmark pipeline for dense and sparse query testing

Introduces a complete query benchmark track to evaluate performance and verify consistency between dense and sparse index formats. Adds scripts to simulate fixed-size paired-end reads, pack a sparse presence index, execute queries in both modes, and capture wall time and RSS metrics. Includes a verification step that compares outputs by read ID to ensure content identity across parallel processing. Updates build configuration, documentation, and ignore patterns to support the new pipeline for two microbial specimens.

benchmark/Makefile

@@ -38,6 +38,12 @@ SPECIFIC_PRESENCE_STATS := $(SPECIES:%=stats/specific_kmer_presence/%.stats)
 SPECIFIC_COUNT_DONE     := $(SPECIES:%=specific_index_count/%/index.done)
 SPECIFIC_COUNT_STATS    := $(SPECIES:%=stats/specific_kmer_count/%.stats)
 SIMULATED_READS := $(foreach s,$(SPECIMENS),simulated_data/$(subst --,/,$s)/reads_R1.fastq.gz)
+QUERY_READS      := $(foreach s,$(QUERY_SPECIMENS),query_data/$(subst --,/,$s)/reads_R1.fastq.gz)
+QUERY_DENSE_DONE  := $(QUERY_SPECIMENS:%=query_dense/%.fasta.gz)
+QUERY_DENSE_STATS := $(QUERY_SPECIMENS:%=stats/query_dense/%.stats)
+QUERY_SPARSE_DONE  := $(QUERY_SPECIMENS:%=query_sparse/%.fasta.gz)
+QUERY_SPARSE_STATS := $(QUERY_SPECIMENS:%=stats/query_sparse/%.stats)
+VERIFY_QUERY_STATS := $(QUERY_SPECIMENS:%=stats/verify_query/%.stats)
 
 .NOTPARALLEL:
 
@@ -51,7 +57,11 @@ SIMULATED_READS := $(foreach s,$(SPECIMENS),simulated_data/$(subst --,/,$s)/read
         aggregate_verify_presence aggregate_verify_count \
         verify_merge_presence verify_merge_count \
         filter_presence filter_count \
-        aggregate_filter_presence aggregate_filter_count
+        aggregate_filter_presence aggregate_filter_count \
+        pack_sparse simulate_query \
+        query_dense query_sparse \
+        aggregate_query_dense aggregate_query_sparse \
+        verify_query aggregate_verify_query
 
 verify_merge_presence: stats/verify_merge_presence/current.csv
 verify_merge_count:    stats/verify_merge_count/current.csv
@@ -59,12 +69,13 @@ verify_merge_count:    stats/verify_merge_count/current.csv
 all: aggregate_verify_presence aggregate_verify_count \
      verify_merge_presence verify_merge_count \
      aggregate_filter_presence aggregate_filter_count \
-     dist_comparison
+     dist_comparison \
+     aggregate_query_dense aggregate_query_sparse aggregate_verify_query
 
 # ── dependency file ───────────────────────────────────────────────────────────
 
-deps.mk: $(GENOMES)
-	$(VENV_PY) make_deps.py $^ > $@
+deps.mk: $(GENOMES) make_deps.py
+	$(VENV_PY) make_deps.py $(GENOMES) > $@
 
 # ── simulation ────────────────────────────────────────────────────────────────
 # Prerequisites (genome → reads) are in deps.mk; $< is the genome file.
@@ -74,6 +85,14 @@ $(SIMULATED_READS):
 
 simulate: $(SIMULATED_READS)
 
+# ── query read simulation (fixed size, independent draw) ───────────────────────
+# Prerequisites (genome → reads) are in deps.mk; $< is the genome file.
+
+$(QUERY_READS):
+	bash simulate_query_one.sh $< $(dir $@)
+
+simulate_query: $(QUERY_READS)
+
 # ── reference kmer sets ───────────────────────────────────────────────────────
 # Prerequisites (reads → npz) are in deps.mk.
 
@@ -228,3 +247,40 @@ stats/verify_merge_presence/current.csv: $(REF_NPZS) global_index_presence/index
 
 stats/verify_merge_count/current.csv: $(REF_NPZS) global_index_count/index.done
 	bash verify_merge_count.sh
+
+# ── sparse presence index (query benchmark) ─────────────────────────────────────
+
+global_index_presence_sparse/index.done: global_index_presence/index.done $(BINARY)
+	bash pack_sparse.sh
+
+pack_sparse: global_index_presence_sparse/index.done
+
+# ── query: dense vs sparse ───────────────────────────────────────────────────────
+# Prerequisites (reads + index → output + .stats) are in deps.mk.
+
+query_dense/%.fasta.gz \
+stats/query_dense/%.stats &: $(BINARY)
+	bash query_one.sh dense $*
+
+query_sparse/%.fasta.gz \
+stats/query_sparse/%.stats &: $(BINARY)
+	bash query_one.sh sparse $*
+
+query_dense:  $(QUERY_DENSE_DONE)
+query_sparse: $(QUERY_SPARSE_DONE)
+
+aggregate_query_dense: $(QUERY_DENSE_STATS)
+	bash aggregate_stats.sh query_dense
+
+aggregate_query_sparse: $(QUERY_SPARSE_STATS)
+	bash aggregate_stats.sh query_sparse
+
+# ── query: dense/sparse regression ──────────────────────────────────────────────
+
+stats/verify_query/%.stats:
+	bash verify_query_one.sh $*
+
+verify_query: $(VERIFY_QUERY_STATS)
+
+aggregate_verify_query: $(VERIFY_QUERY_STATS)
+	bash aggregate_stats.sh verify_query