#!/bin/bash -Ceuo pipefail
annotate_indel_entropy.py \
    --mpileup Sig_18_Blood.mpileup.gz \
    --input-vcf Sig_18_Blood.haplotyper.split.vcf.gz \
    --output-vcf Sig_18_Blood.entropy.vcf

bgzip Sig_18_Blood.entropy.vcf

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:INDEL_ENTROPY_ANNOTATION":
    python: $(python --version | sed 's/Python //g')
    numpy: $(python -c "import numpy; print(numpy.__version__)")
    scipy: $(python -c "import scipy; print(scipy.__version__)")
    pysam: $(python -c "import pysam; print(pysam.__version__)")
END_VERSIONS