#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i 659_bR4-T1-TDNA-1_A23MHWWLT4_1.md.bam \
    --read_filter QualCalFilter,table=659_bR4-T1-TDNA-1_A23MHWWLT4_1.table,indel=false \
    --algo QualCal \
     \
    -k dbsnp_146.hg38.vcf.gz -k Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -k Homo_sapiens_assembly38.known_indels.vcf.gz \
    659_bR4-T1-TDNA-1_A23MHWWLT4_1.table.post \
    --algo ReadWriter 659_bR4-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam

# Sentieon ReadWriter doesn't create index - use samtools
samtools index 659_bR4-T1-TDNA-1_A23MHWWLT4_1.recalibrated.bam

sentieon driver \
    -t 31 \
    --algo QualCal \
    --plot \
    --before 659_bR4-T1-TDNA-1_A23MHWWLT4_1.table \
    --after 659_bR4-T1-TDNA-1_A23MHWWLT4_1.table.post \
     \
    659_bR4-T1-TDNA-1_A23MHWWLT4_1.csv

sentieon plot QualCal -o 659_bR4-T1-TDNA-1_A23MHWWLT4_1.pdf 659_bR4-T1-TDNA-1_A23MHWWLT4_1.csv

cat <<-END_VERSIONS > versions.yml
"DAQ:SENTIEON_BQSR:QUALCAL_APPLY":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS