#!/bin/bash -Ceuo pipefail
pre_filter_chip_candidates.py \
    --vcf 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.CHIP_PON.merged.vcf.gz \
    --output 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.prefiltered.vcf.gz \
    --survivors-vcf 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.survivors.vcf.gz \
    --survivors-bed 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.survivors.bed \
    --cohort-blacklist cohort_blacklist.bed.gz \
    --gene-family-blacklist gene_family_blacklist.bed.gz \
    --encode-blacklist encode_blacklist.bed.gz \
    --gene-tiers gene_tiers.tsv

tabix -p vcf 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.prefiltered.vcf.gz
tabix -p vcf 1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.survivors.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:PRE_FILTER_CHIP_CANDIDATES":
    pre_filter_chip_candidates: $(pre_filter_chip_candidates.py --version 2>&1 || echo "1.0.0")
    cyvcf2: $(python -c "import cyvcf2; print(cyvcf2.__version__)")
END_VERSIONS