refactor(benchmark): consolidate generated artifacts under run/ directory

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 Adjust documentation and dependency tracking to match the revised layout, and remove outdated temporary artifacts.
2026-08-29 00:20:31 +02:00
parent 54e4600120
commit 26026288de
1058 changed files with 450 additions and 450 deletions
@@ -30,25 +30,7 @@ data-stress
 *.bin.idx
 *.prsb
 Betula_exilis--IGA-24-33
-benchmark/genomes
-benchmark/genomes_orig
-benchmark/simulated_data
-benchmark/specimen_index_presence
-benchmark/global_index_count_dense
-benchmark/global_index_presence
-benchmark/global_index_presence_orig
-benchmark/global_index_presence_sav
-benchmark/global_index_presence_dense
-benchmark/all_specific
-benchmark/global_index_count
-benchmark/specimen_index_count
-benchmark/stats
-benchmark/reference_index
-benchmark/reference_dist
-benchmark/obikmer_dist
-benchmark/specific_index_count
-benchmark/specific_index_presence
-benchmark/query_data
+benchmark/run/
 TNT
 phyg
 biblio