#!/bin/bash -euo pipefail
AIH_TS="${PWD}/_empty_aih_blacklist.tsv"
if [[ -n 'blacklist_breakpoint_database_2026-04-27.tsv' ]] && [[ -f 'blacklist_breakpoint_database_2026-04-27.tsv' ]]; then
    AIH_TS='blacklist_breakpoint_database_2026-04-27.tsv'
else
    printf 'BREAKPOINT_ID\tblacklist_evidence_score\n' > "$AIH_TS"
fi
filter_arriba_main.py \
    --input 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.tsv \
    --filter-config arriba_filter_config.yaml \
    --aih-blacklist-breakpoints "$AIH_TS" \
    --output 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filtered.tsv \
    --summary 659_bjQ-T1-TRNA-1_B23MHV2LT4_1.arriba.fusions.filter_summary.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_RNAFUSION:RNAFUSION:ARRIBA_WORKFLOW:ARRIBA_FILTER":
    filter_arriba_main.py: "1.0"
    pandas: $(python -c "import pandas; print(pandas.__version__)" 2>/dev/null || echo "unknown")
    pyyaml: $(python -c "import yaml; print(yaml.__version__)" 2>/dev/null || echo "unknown")
END_VERSIONS