#!/usr/bin/env bash
# Oracle outputs for phase P5 (QC) on the P0 GSA demo data:
#  * BeadArrayFiles (BSD-2) examples/locus_summary.py over the 36 oracle GTCs, run in a separate venv with
#    scipy/pandas (oracle-only dependencies; never needed by SimurgArray itself);
#  * the gtc2vcf BAFregress plugin (MIT) is built by scripts/make_oracle_gtcs.sh and run by the tests directly.
set -euo pipefail
cd "$(dirname "$0")/.."
V=refs/tools/oracle-venv
[[ -x $V/bin/python ]] || { uv venv -q $V && uv pip install -q --python $V/bin/python numpy scipy pandas; }
SHIM=refs/tools/shim
mkdir -p $SHIM && ln -sfn "$PWD/refs/BeadArrayFiles/module" $SHIM/IlluminaBeadArrayFiles
D=data/p0/gsa_v4_pgx
OUT=data/p0/oracle/locus_summary
mkdir -p $OUT
PYTHONPATH=$SHIM $V/bin/python refs/BeadArrayFiles/examples/locus_summary.py data/p0/oracle/gsa_gt3_nofma \
  $D/GSA-PGx-48v4-0_20079540_E2_bpm/GSA-PGx-48v4-0_20079540_E2.bpm \
  $D/GSA-PGx-48v4-0_20079540_E2_ClusterFile/GSA-PGx-48v4-0_20079540_E2_ClusterFile.egt \
  $OUT/gsa36_beadarrayfiles.csv
echo "wrote $OUT/gsa36_beadarrayfiles.csv"