#!/bin/bash -Ceuo pipefail
echo "=== Running Sentieon Alignment and QC on test_sample_1 ==="
echo "SENTIEON_LICENSE: ${SENTIEON_LICENSE:0:5}..."
echo "Downsampling to 100 reads (400 lines)"

set +o pipefail
zcat SRR7890919_WES_HCC1395BL-EA_normal_1.fastq.gz | head -n 400 | \
sentieon bwa mem \
    -R "@RG\tID:test_sample_1\tSM:test_sample_1\tPL:ILLUMINA" \
    -t 8 \
    human_g1k_v37_decoy.fasta \
    - | \
sentieon util sort \
    -r human_g1k_v37_decoy.fasta \
    -o test_sample_1_sorted.bam \
    -t 8 \
    --sam2bam -i -
set -o pipefail

sentieon driver \
    -r human_g1k_v37_decoy.fasta \
    -t 8 \
    -i test_sample_1_sorted.bam \
    --algo QualDistribution test_sample_1_qd_metrics.txt \
    --algo MeanQualityByCycle test_sample_1_mq_metrics.txt

echo "Sentieon alignment and QC completed for test_sample_1"