#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i HCC1395_tumor.md.bam \
     \
    --algo AlignmentStat HCC1395_tumor.sentieon.alignment_summary_metrics \
    --algo InsertSizeMetricAlgo HCC1395_tumor.sentieon.insert_size_metrics \
    --algo QualDistribution HCC1395_tumor.sentieon.quality_distribution_metrics \
    --algo BaseDistributionByCycle HCC1395_tumor.sentieon.base_distribution_by_cycle_metrics \
    --algo MeanQualityByCycle HCC1395_tumor.sentieon.quality_by_cycle_metrics

sentieon plot InsertSizeMetricAlgo \
    -o HCC1395_tumor.sentieon.insert_size_histogram.pdf \
    HCC1395_tumor.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