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refactor(benchmark): consolidate generated artifacts under run/ directory
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Restructure the benchmark pipeline to direct all simulated data, indices, statistics, and query outputs into a unified `run/` directory. Update Makefile targets, shell scripts, and Python utilities to resolve paths relative to this new base. Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
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Eric Coissac committed 2026-08-29 00:20:31 +02:00
1 parent 54e4600120
commit 26026288de
1058 files changed
+450 -450
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benchmark/index_one_presence.sh
+4 -3
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@@ -8,14 +8,15 @@ set -euo pipefail
SPECIMEN="$1"
SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
RUN_DIR="${SCRIPT_DIR}/run"
BINARY="${SCRIPT_DIR}/../src/target/release/obikmer"
species="${SPECIMEN%%--*}"
strain="${SPECIMEN#*--}"
READS_DIR="${SCRIPT_DIR}/simulated_data/${species}/${strain}"
INDEX_PATH="${SCRIPT_DIR}/specimen_index_presence/${SPECIMEN}"
STATS_DIR="${SCRIPT_DIR}/stats/indexing_presence"
READS_DIR="${RUN_DIR}/simulated_data/${species}/${strain}"
INDEX_PATH="${RUN_DIR}/specimen_index_presence/${SPECIMEN}"
STATS_DIR="${RUN_DIR}/stats/indexing_presence"
STATS_FILE="${STATS_DIR}/${SPECIMEN}.stats"
mkdir -p "${STATS_DIR}"