#!/bin/bash
# Test RNA-seq Alignment

set -e

echo "=== RNA-seq Align Test ==="

# Activate environment
source ~/miniconda3/etc/profile.d/conda.sh
conda activate rnaseq

cd /home/xia-lab/wutx/00test/bbav20311

# Setup test directories
TEST_JOB="test_align_$(date +%s)"
WORKSPACE="workspace/${TEST_JOB}"
INPUT_DIR="${WORKSPACE}/input"
FINAL_DIR="${WORKSPACE}/final"
ALIGN_DIR="${WORKSPACE}/rnaseq_align"

mkdir -p "${INPUT_DIR}" "${FINAL_DIR}" "${ALIGN_DIR}"

# Copy clean reads from previous QC test
cp workspace/job_1773836437033/final/SRR6847697_1.clean.fastq.gz "${FINAL_DIR}/"
cp workspace/job_1773836437033/final/SRR6847697_2.clean.fastq.gz "${FINAL_DIR}/"

# Create sample config
cat > "${INPUT_DIR}/samples.yaml" << EOF
samples:
  SRR6847697:
    - SRR6847697_1.clean.fastq.gz
    - SRR6847697_2.clean.fastq.gz
EOF

# HISAT2 index
HISAT2_INDEX="/home/xia-lab/wutx/00test/bbav2.0302/workspace/rnaseq_test/Ft.genome"

echo "Input files:"
ls -lh "${FINAL_DIR}/"

echo ""
echo "Running RNA-seq Align..."
python apps/cli/run_rnaseq_align.py \
    -i "${FINAL_DIR}" \
    -x "${HISAT2_INDEX}" \
    -o "${ALIGN_DIR}" \
    -j "${TEST_JOB}" \
    -p "Ft.SPL" \
    -t 4 \
    --sample-config "${INPUT_DIR}/samples.yaml"

echo ""
echo "=== Results ==="
echo "Final directory:"
ls -lh "${FINAL_DIR}/"

echo ""
echo "Align directory:"
ls -lh "${ALIGN_DIR}/"

echo ""
echo "Manifest:"
cat "${FINAL_DIR}/Ft.SPL.rnaseq_align.manifest.json" | head -50

echo ""
echo "Report:"
cat "${FINAL_DIR}/Ft.SPL.rnaseq_align_report.md"

echo ""
echo "=== Test Complete ==="