#!/bin/bash -Ceuo pipefail
tabix -p bed boost_status.bed.gz
tabix -p bed region_type.bed.gz

bcftools annotate \
    -a boost_status.bed.gz \
    -h <(echo '##INFO=<ID=BOOST_STATUS,Number=1,Type=String,Description="Variant region boost status: BOOSTED or NONBOOSTED">') \
    -c CHROM,FROM,TO,BOOST_STATUS \
    positive_somatic_control_1.snv_indel.hotspot.vcf.gz \
    -Oz -o tmp.boost.vcf.gz

tabix -p vcf tmp.boost.vcf.gz

bcftools annotate \
    -a region_type.bed.gz \
    -h <(echo '##INFO=<ID=REGION_TYPE,Number=1,Type=String,Description="Region type: STANDARD, HOMOPOLYMER, GC_BIAS, or HOMOPOLYMER_AND_GC_BIAS">') \
    -c CHROM,FROM,TO,REGION_TYPE \
    tmp.boost.vcf.gz \
    -Oz -o positive_somatic_control_1.snv_indel.annotated.vcf.gz

tabix -p vcf positive_somatic_control_1.snv_indel.annotated.vcf.gz
rm -f tmp.boost.vcf.gz tmp.boost.vcf.gz.tbi

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:ANNOTATE_BED_INFO":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS