#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i Sig_18_Blood.md.bam \
     \
    --algo AlignmentStat Sig_18_Blood.sentieon.alignment_summary_metrics \
    --algo InsertSizeMetricAlgo Sig_18_Blood.sentieon.insert_size_metrics \
    --algo QualDistribution Sig_18_Blood.sentieon.quality_distribution_metrics \
    --algo BaseDistributionByCycle Sig_18_Blood.sentieon.base_distribution_by_cycle_metrics \
    --algo MeanQualityByCycle Sig_18_Blood.sentieon.quality_by_cycle_metrics

sentieon plot InsertSizeMetricAlgo \
    -o Sig_18_Blood.sentieon.insert_size_histogram.pdf \
    Sig_18_Blood.sentieon.insert_size_metrics

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