{
  "checker": {
    "details": {
      "argv": [
        "<host-path>",
        "score",
        "--plink",
        "<host-path>",
        "--weights",
        "<host-path>",
        "--weight-col-prefix",
        "WEIGHT",
        "--chrom-col",
        "CHROM",
        "--pos-col",
        "POS",
        "--alt-col",
        "ALT",
        "--ref-col",
        "REF",
        "--out",
        "<host-path>",
        "--center",
        "True",
        "--threads",
        "4",
        "--memory",
        "2000"
      ],
      "kind": "cli",
      "needs_browser": false,
      "needs_credentials": false,
      "returncode": 0,
      "scope": "product operation",
      "stderr": "",
      "stdout": "2026-10-18 17:41:40 [info     ] Received parameters: \ndapgen score\n  --plink=<host-path>\n  --weights=<host-path>\n  --out=<host-path>\n  --weight_col_prefix=WEIGHT\n  --freq_suffix=None\n  --center=True\n  --chrom_col=CHROM\n  --pos_col=POS\n  --ref_col=REF\n  --alt_col=ALT\n[excerpt truncated]",
      "working": true
    },
    "status": "PASS"
  },
  "deviations": [
    "README 'pip install -e .' needs a venv on this Ubuntu (PEP 668); created <host-path>",
    "unzip not installed; used python3 zipfile to extract plink2 from the CI zip.",
    "plink2 is not an install dependency of the package; installed it manually from the CI URL to <host-path> since dapgen raises 'plink2 not found in PATH' otherwise.",
    "Weights file generated with dapgen.read_pvar + numpy random (the repo's test_cli approach) because README weights path is user-supplied."
  ],
  "main_blocker": null,
  "operation": "dapgen score (README Example) on tests/test-data/plink2.merged.pgen with a generated 3-column random weight file; output written to .coldpass/probe_score.tsv and read back",
  "operation_scope": "Runs the CLI score path end to end including plink2 allele frequency calculation. Requires plink2 binary on PATH (downloaded from the CI URL in .github/workflows/workflow.yml). Not exercised: pip install from PyPI, the README's example weights (user-supplied), full pytest/flake8 suites (intentionally skipped).",
  "outcome": "working",
  "steps": [
    "sudo apt-get install python3-venv",
    "python3 -m venv <host-path>",
    "<host-path> install -U cython numpy pandas_plink pytest",
    "<host-path> install -e . (README 'git clone ... pip install -e .' path) ",
    "curl plink2 zip from CI URL, extracted with python zipfile, placed at <host-path>",
    "dapgen score --plink <test pgen> --weights .coldpass/weight.tsv ... --center True --out .coldpass/score.tsv (exit 0, 522 variants, 99 individuals scored)"
  ],
  "stuck_step": null,
  "suggested_fix": null
}