#!/bin/bash -Ceuo pipefail
rf_variant_filter.py \
    --input-vcf HCC1395_BL.entropy.vcf.gz \
    --output-vcf HCC1395_BL.haplotyper_rf.rf_filtered.vcf.gz \
    --snv-model snv_rf_model_v4.joblib \
    --indel-model indel_rf_model_v7.joblib \
    --snv-fp-bed snv_fp_regions.bed.gz \
    --indel-fp-bed indel_fp_regions.bed.gz \
    --indel-fp-rates-tsv indel_locus_fp_rates.tsv \
    --boosted-bed rf_boosted_exons.bed.gz \
    --blacklist-bed rf_blacklist.bed.gz \
    --low-depth-bed rf_low_depth.bed.gz \
    --repeatmasker-bed rf_repeatmasker.bed.gz \
    --snv-threshold 0.55 \
    --indel-threshold 0.5 \


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

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER":
    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