#!/usr/bin/env bash
# Shallow-clone reference open-source repositories into refs/ (git-ignored).
# GPL repos are for use as external oracles only — do not copy their code into SimurgArray.
set -euo pipefail
cd "$(dirname "$0")/.."
mkdir -p refs
repos=(
  "Illumina/BeadArrayFiles"        # BSD-2
  "Illumina/GTCtoVCF"              # Apache-2.0
  "freeseek/gtc2vcf"               # MIT
  "freeseek/mocha"                 # MIT
  "broadinstitute/picard"          # MIT (see src/main/java/picard/arrays)
  "WGLab/PennCNV"                  # Unlicense
  "sbslee/pypgx"                   # MIT
  "PharmGKB/PharmCAT"              # MPL-2.0 (oracle)
  "HenrikBengtsson/illuminaio"     # GPL-2 (oracle only)
  "gjun/verifyIDintensity"         # GPL-3 (oracle only)
)
for r in "${repos[@]}"; do
  d="refs/${r#*/}"
  if [[ -d "$d/.git" ]]; then echo "skip $d"; continue; fi
  git clone --depth 1 "https://github.com/$r.git" "$d"
done
echo "done: $(ls refs | wc -l) repos in refs/"