#!/bin/bash -euo pipefail
compare_fusions_with_adjudication.py \
    --fusion \
    --test test_harmonized_calls.tsv \
    --truth truth_harmonized_calls.tsv \
    --patient-id-list patient_id_list.txt \
    --gene-list selected_gene_list.txt \
    --output-dir . \
    --alternative-confirmation alt_truth_harmonized_calls.tsv \
     \
     \
    --test-filters 'FILTER==PASS' --truth-filters 'FILTER==PASS' --alt-confirmation-filters 'FILTER==PASS' --starfusion-filters 'F' --starfusion-filters 'U' --starfusion-filters 'S' --starfusion-filters 'I' --starfusion-filters 'O' --starfusion-filters 'N' --starfusion-filters '_' --starfusion-filters 'R' --starfusion-filters 'E' --starfusion-filters 'A' --starfusion-filters 'D' --starfusion-filters 'S' --starfusion-filters '>' --starfusion-filters '=' --starfusion-filters '8' --arriba-filters 'A' --arriba-filters 'R' --arriba-filters '_' --arriba-filters 'C' --arriba-filters 'O' --arriba-filters 'N' --arriba-filters 'F' --arriba-filters 'I' --arriba-filters 'D' --arriba-filters 'E' --arriba-filters 'N' --arriba-filters 'C' --arriba-filters 'E' --npa-fusion-catalog-from-truth

cat <<-END_VERSIONS > versions.yml
"RECALL:RUN_FUSION_PERFORMANCE":
    python: $(python --version 2>&1 | sed 's/Python //')
    compare_fusions_with_adjudication: "1.0.0"
END_VERSIONS