#!/bin/bash -Ceuo pipefail
annotate_indel_entropy.py \
--mpileup HCC1395_BL.mpileup.gz \
--input-vcf HCC1395_BL.haplotyper.split.vcf.gz \
--output-vcf HCC1395_BL.entropy.vcf
bgzip HCC1395_BL.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