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/pack_sparse.sh

@@ -0,0 +1,86 @@
+#!/usr/bin/env bash
+# Builds global_index_presence_sparse/ from global_index_presence/ by
+# copying the index (column files are kept in place after merge's dense
+# pack — see obikindex::KmerIndex::pack_matrices) and repacking in place
+# with --sparse.
+# Outputs:
+#   global_index_presence_sparse/index.done  (copied from source)
+#   stats/pack_sparse/current.stats          (one CSV data row, no header)
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
+SOURCE="${SCRIPT_DIR}/global_index_presence"
+OUTPUT="${SCRIPT_DIR}/global_index_presence_sparse"
+STATS_DIR="${SCRIPT_DIR}/stats/pack_sparse"
+STATS_FILE="${STATS_DIR}/current.stats"
+
+mkdir -p "${STATS_DIR}"
+
+echo "[pack_sparse] ${SOURCE} → ${OUTPUT}"
+
+rm -rf "${OUTPUT}"
+cp -r "${SOURCE}" "${OUTPUT}"
+
+STDERR_LOG=$(mktemp)
+trap 'rm -f "${STDERR_LOG}"' EXIT
+
+"${BINARY}" pack --sparse "${OUTPUT}" 2>"${STDERR_LOG}"
+
+cat "${STDERR_LOG}" >&2
+
+python3 - "${STDERR_LOG}" <<'PYEOF' >"${STATS_FILE}"
+import sys, re
+
+logfile = sys.argv[1]
+
+def strip_ansi(s):
+    return re.sub(r'\x1b\[[\x30-\x3f]*[\x20-\x2f]*[\x40-\x7e]', '', s)
+
+def parse_wall(s):
+    s = s.strip()
+    if s.endswith('ms'): return float(s[:-2]) / 1000.0
+    if s.endswith('s'):  return float(s[:-1])
+    return 0.0
+
+def parse_rss(s):
+    m = re.match(r'([\d.]+)\s*(GB|MB|KB|B)', s.strip())
+    if not m: return 0
+    return int(float(m.group(1)) * {'GB': 1<<30, 'MB': 1<<20, 'KB': 1024, 'B': 1}[m.group(2)])
+
+def is_sep(s):
+    return bool(s) and not re.search(r'[A-Za-z0-9]', s)
+
+stats = {}
+state = 'scan'
+with open(logfile, errors='replace') as fh:
+    for raw in fh:
+        line = strip_ansi(raw.rstrip('\n'))
+        s    = line.strip()
+        if state == 'scan':
+            if re.search(r'\bstage\b.*\bwall\b', line):
+                state = 'in_header'
+        elif state == 'in_header':
+            if is_sep(s): state = 'rows'
+        elif state == 'rows':
+            if is_sep(s): state = 'total'
+            elif s:
+                parts = re.split(r'  +', s)
+                if len(parts) >= 4:
+                    stats[parts[0]] = (parse_wall(parts[1]), parse_rss(parts[3]))
+        elif state == 'total':
+            if s:
+                parts = re.split(r'  +', s)
+                if len(parts) >= 3:
+                    stats['TOTAL'] = (parse_wall(parts[1]),
+                                      parse_rss(parts[3]) if len(parts) > 3 else 0)
+            break
+
+w, r = stats.get('pack', ('', ''))
+tw, tr = stats.get('TOTAL', ('', ''))
+row = [f'{w:.3f}' if isinstance(w, float) else '', str(r),
+       f'{tw:.3f}' if isinstance(tw, float) else '', str(tr)]
+print(','.join(row))
+PYEOF
+
+echo "Done → ${OUTPUT}"