#!/bin/bash -Ceuo pipefail
bcftools norm \
    -a -m -both \
    -f Homo_sapiens_assembly38.fasta \
    HCC1395_BL.tumor_genotyped.vcf.gz \
    -Oz -o tumor_norm.vcf.gz

bcftools index -t tumor_norm.vcf.gz

transfer_caller_ad.py \
    --vcf HCC1395_BL.prefiltered.vcf.gz \
    --tumor-vcf tumor_norm.vcf.gz \
    --output HCC1395_BL.readcount_annotated.vcf.gz

tabix -p vcf HCC1395_BL.readcount_annotated.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:TRANSFER_CALLER_AD":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*//')
    cyvcf2: $(python -c "import cyvcf2; print(cyvcf2.__version__)")
END_VERSIONS