feat: add batched int group stats API and expand benchmark variants

Introduces a `batch_int_group_stats` API for computing presence counts, sums, minimums, and maximums across sparse and dense matrix representations. The selection layer now utilizes this batched approach to optimize aggregation semantics for boolean and numeric operations. Additionally, reorganizes the benchmarking infrastructure to support querying across presence and count index variants in both dense and sparse formats, including new packing scripts and updated statistics aggregation.

benchmark/query_one.sh

@@ -1,20 +1,29 @@
 #!/usr/bin/env bash
-# Usage: query_one.sh MODE SPECIMEN
-# MODE = dense | sparse
+# Usage: query_one.sh KIND MODE SPECIMEN
+# KIND = presence | count
+# MODE = dense | sparse — `merge` packs sparse by default (2026-08-28), so
+#        "sparse" is global_index_KIND itself, unmodified; "dense" is the
+#        explicitly repacked global_index_KIND_dense (see pack_dense.sh).
 # SPECIMEN = "species--strain" (Make pattern stem), reads from query_data/
 # Outputs:
-#   query_MODE/SPECIMEN.fasta.gz     (obikmer query output, --count-missing)
-#   stats/query_MODE/SPECIMEN.stats  (one CSV data row, no header)
+#   query_KIND_MODE/SPECIMEN.fasta.gz     (obikmer query output, --count-missing)
+#   stats/query_KIND_MODE/SPECIMEN.stats  (one CSV data row, no header)
 set -euo pipefail
 
-MODE="$1"
-SPECIMEN="$2"
+KIND="$1"
+MODE="$2"
+SPECIMEN="$3"
 SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
 
+case "${KIND}" in
+    presence|count) ;;
+    *) echo "ERROR: unknown kind '${KIND}' (expected presence|count)" >&2; exit 1 ;;
+esac
+
 case "${MODE}" in
-    dense)  INDEX="${SCRIPT_DIR}/global_index_presence" ;;
-    sparse) INDEX="${SCRIPT_DIR}/global_index_presence_sparse" ;;
+    sparse) INDEX="${SCRIPT_DIR}/global_index_${KIND}" ;;
+    dense)  INDEX="${SCRIPT_DIR}/global_index_${KIND}_dense" ;;
     *) echo "ERROR: unknown mode '${MODE}' (expected dense|sparse)" >&2; exit 1 ;;
 esac
 
@@ -22,8 +31,8 @@ species="${SPECIMEN%%--*}"
 strain="${SPECIMEN#*--}"
 
 READS_DIR="${SCRIPT_DIR}/query_data/${species}/${strain}"
-OUT_DIR="${SCRIPT_DIR}/query_${MODE}"
-STATS_DIR="${SCRIPT_DIR}/stats/query_${MODE}"
+OUT_DIR="${SCRIPT_DIR}/query_${KIND}_${MODE}"
+STATS_DIR="${SCRIPT_DIR}/stats/query_${KIND}_${MODE}"
 OUT_FILE="${OUT_DIR}/${SPECIMEN}.fasta.gz"
 STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
 
@@ -36,7 +45,7 @@ if [[ ! -f "${r1}" || ! -f "${r2}" ]]; then
     exit 1
 fi
 
-echo "[${SPECIMEN}] query (${MODE}) → ${OUT_FILE}"
+echo "[${SPECIMEN}] query (${KIND}/${MODE}) → ${OUT_FILE}"
 
 STDERR_LOG=$(mktemp)
 trap 'rm -f "${STDERR_LOG}"' EXIT