#!/bin/bash -Ceuo pipefail
compare_variants.py \
    --test-tsv test_variants.tsv \
    --truth-tsv truth_variants.tsv \
    --bed-exome xgen-exome-hyb-panel-v2-targets-hg38_short.mrg.bed \
    --bed-boosted altera_v3_targets_coding_postQC_hg38.bed \
    --bed-truth-panel TruSight_Oncology_500_Manifest_hg38.st.mrg.bed \
    --blacklist-bed pepe_blacklist_sorted_hg38.bed \
    --pon-vcf pon_tnseq_42_curated_v4.vcf.gz \
    --pot-vcf aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz \
    --reclassify-germline \
    --reclassify-somatic-normal-af 0.30 \
    --rescue-germline-normal-af 0.10 \
    --max-indel-length 25 \
    --vaf-threshold-hotspot-snv 0.025 \
    --vaf-threshold-hotspot-indel 0.05 \
    --vaf-threshold-boosted-snv 0.05 \
    --vaf-threshold-boosted-indel 0.075 \
    --vaf-threshold-nonboosted-snv 0.10 \
    --vaf-threshold-nonboosted-indel 0.15 \
    --outdir comparison

cat <<-END_VERSIONS > versions.yml
"VARIANT_COMPARISON_TSO500:COMPARE_VARIANTS":
    python: $(python --version 2>&1 | sed 's/Python //')
    pandas: $(python -c "import pandas; print(pandas.__version__)")
    matplotlib: $(python -c "import matplotlib; print(matplotlib.__version__)")
END_VERSIONS