#!/bin/bash
# Phase P1/P2 validation on the 1000 Genomes Omni2.5 set + `simurg ingest` at scale.
# Args: <data dir with bpm/egt/csv and data/>  <results dir>
set -uo pipefail
D=$1; OUT=$2
.venv/bin/python scripts/validate_p1_large.py --root $D/data --bpm $D/HumanOmni2.5-4v1-Multi_B.bpm \
  --egt $D/HumanOmni2.5-4v1-Multi_B.egt --csv $D/HumanOmni2.5-4v1_B.csv --out $OUT/summary.json \
  --workers "$(nproc)" || echo "validation reported differences (see summary.json)"
/usr/bin/time -v .venv/bin/simurg ingest --bpm $D/HumanOmni2.5-4v1-Multi_B.bpm --idats $D/data \
  --out /work/ingest --threads "$(nproc)" --quiet 2> $OUT/ingest_time.txt || echo "ingest exit code $?"
cp /work/ingest/ingest_summary.tsv $OUT/ingest_summary.tsv 2>/dev/null || true
cp /work/ingest/run_manifest.json $OUT/ingest_run_manifest.json 2>/dev/null || true