#!/bin/bash -Ceuo pipefail
gt_correction.py \
    --input-vcf HCC1395_BL.haplotyper_rf.rf_filtered.vcf.gz \
    --output-vcf HCC1395_BL.haplotyper_rf.gt_corrected.vcf.gz \
    --gt-model gt_correction_model_v2.joblib \
    --repeatmasker-bed rf_repeatmasker.bed.gz \
    --threshold 0.5 \


tabix -p vcf HCC1395_BL.haplotyper_rf.gt_corrected.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION":
    python: $(python --version | sed 's/Python //g')
    cyvcf2: $(python -c "import cyvcf2; print(cyvcf2.__version__)")
    lightgbm: $(python -c "import lightgbm; print(lightgbm.__version__)")
    bedtools: $(bedtools --version | sed 's/bedtools v//')
END_VERSIONS