#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i 1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.bam \
     \
    --algo AlignmentStat 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics \
    --algo InsertSizeMetricAlgo 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics \
    --algo QualDistribution 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics \
    --algo BaseDistributionByCycle 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics \
    --algo MeanQualityByCycle 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics

sentieon plot InsertSizeMetricAlgo \
    -o 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_histogram.pdf \
    1047_JG-T1-TDNA-1_A23MHWWLT4_1.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