feat: add benchmark pipeline, expose APIs, and enforce strict paths

Introduces a Make-based orchestration for simulating, indexing, merging, filtering, and verifying k-mer counts and presence. Exposes internal builder and iterator APIs publicly, enforces mandatory leading slashes for predicate patterns, registers the `obitaxonomy` crate, and updates tooling configurations alongside documentation.
2026-06-19 09:55:41 +02:00
parent 280ca1f5a3
commit c694e1f2b0
42 changed files with 2585 additions and 84 deletions
@@ -0,0 +1,53 @@
+#!/usr/bin/env bash
+# Usage: aggregate_stats.sh TYPE
+# TYPE = indexing_presence | indexing_count | verify_presence | verify_count
+#
+# Reads all stats/TYPE/*.stats files (one CSV data row each, no header).
+# Creates a new stats/TYPE/run_NNN.csv only if any .stats file is newer than
+# the most recent run CSV (idempotent when nothing changed).
+set -euo pipefail
+
+TYPE="$1"
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+STATS_DIR="${SCRIPT_DIR}/stats/${TYPE}"
+
+case "${TYPE}" in
+    indexing_presence|indexing_count)
+        HEADER="run,species,strain,scatter_wall_s,scatter_rss_b,dereplicate_wall_s,dereplicate_rss_b,count_kmer_wall_s,count_kmer_rss_b,index_wall_s,index_rss_b,total_wall_s,total_rss_b"
+        ;;
+    verify_presence)
+        HEADER="run,species,strain,ref_kmers,idx_kmers,false_neg,false_pos,fn_pct,fp_pct"
+        ;;
+    verify_count)
+        HEADER="run,species,strain,ref_kmers,idx_kmers,false_neg,false_pos,count_mismatch,fn_pct,fp_pct,cm_pct"
+        ;;
+    specific_kmer_presence|specific_kmer_count)
+        HEADER="run,species,rebuild_wall_s,rebuild_rss_b,pack_wall_s,pack_rss_b,filter_total_wall_s,filter_total_rss_b,select_wall_s,select_rss_b,select_total_wall_s,select_total_rss_b"
+        ;;
+    *)
+        echo "ERROR: unknown stats type '${TYPE}'" >&2
+        exit 1
+        ;;
+esac
+
+# Find most recent existing run CSV (empty string if none).
+latest_csv=$(find "${STATS_DIR}" -maxdepth 1 -name 'run_*.csv' 2>/dev/null | sort | tail -1)
+
+# Check if any .stats file is newer than the latest run CSV.
+if [[ -n "${latest_csv}" ]] && \
+   [[ -z "$(find "${STATS_DIR}" -maxdepth 1 -name '*.stats' -newer "${latest_csv}" 2>/dev/null)" ]]; then
+    echo "[${TYPE}] stats up to date (${latest_csv})"
+    exit 0
+fi
+
+run_n=$(printf '%03d' "$(find "${STATS_DIR}" -maxdepth 1 -name 'run_*.csv' 2>/dev/null | wc -l | tr -d ' ')")
+CSV="${STATS_DIR}/run_${run_n}.csv"
+
+echo "${HEADER}" >"${CSV}"
+
+# Sort .stats files by name for reproducible row order.
+while IFS= read -r stats_file; do
+    sed "s/^/${run_n},/" "${stats_file}"
+done < <(find "${STATS_DIR}" -maxdepth 1 -name '*.stats' | sort) >>"${CSV}"
+
+echo "[${TYPE}] run ${run_n} → ${CSV}"