P2 (WIP): raw X/Y assembly, canonical Parquet model, simurg ingest

- signal/raw_xy.py: vectorised Infinium I/II raw X/Y and control assembly
  (plan §7.1) with a per-chip address-map cache; IN-027 coverage gate
- core/schemas.py: Arrow schemas (loci, sample_intensity, controls),
  deterministic atomic Parquet writing
- pipeline/ingest.py + CLI: discovery, sheet, IN-010 naming, overwrite
  check before any work, spawn-based workers, per-sample isolation,
  --resume by input hashes, run manifest, exit codes 0/3/4
- matches gtc2vcf raw X/Y and controls exactly on 18 GSA samples;
  outputs byte-identical across thread counts and layouts

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

src/simurg/core/errors.py

@@ -72,6 +72,9 @@ CATALOGUE: dict[str, MessageDef] = dict(
         _m("E_IDAT_ENCRYPTED", "error", "Encrypted (version 1) IDATs are not supported", "IN-023"),
         _m("E_IDAT_PAIR_MISMATCH", "error", "Red and Grn IDATs of a sample do not match", "IN-023"),
         _m("W_IDAT_NAME_MISMATCH", "warning", "IDAT barcode/position disagrees with its file name", "IN-023"),
+        _m("E_IDAT_MANIFEST_MISMATCH", "error", "IDATs and manifest belong to different products", "IN-027"),
+        _m("W_IDAT_LOW_ADDRESS_COVERAGE", "warning", "Some manifest addresses are absent from the IDAT", "IN-027"),
+        _m("W_IDAT_MANIFEST_NAME", "warning", "IDAT names a different manifest than the BPM", "IN-027"),
         _m("W_IDAT_NO_SCAN_TIME", "warning", "IDAT has no scan entry in its run info", "IN-024"),
         _m("I_UNLISTED_IDATS", "info", "IDAT pairs not listed in the sample sheet are ignored", "IN-016"),
         _m("E_DUP_GTC", "error", "Several GTC files resolve to the same sample", "IN-030"),

src/simurg/core/schemas.py

@@ -0,0 +1,142 @@
+"""Canonical columnar data model (plan §5) as Apache Arrow schemas, stored as Parquet.
+
+Schemas carry a ``simurg.schema`` metadata key with a version, so readers can refuse incompatible files.
+Parquet files are written without timestamps so identical inputs give byte-identical files (plan §15).
+"""
+
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from typing import Any
+
+import numpy as np
+import pyarrow as pa
+import pyarrow.parquet as pq
+
+from simurg.core.atomic import atomic_open
+from simurg.formats.bpm import Manifest
+
+LOCI_SCHEMA_ID = "simurg.loci/1"
+INTENSITY_SCHEMA_ID = "simurg.sample_intensity/1"
+CONTROLS_SCHEMA_ID = "simurg.sample_controls/1"
+
+LOCI_SCHEMA = pa.schema(
+    [
+        ("locus_idx", pa.int32()),
+        ("name", pa.string()),
+        ("ilmn_id", pa.string()),
+        ("chrom", pa.string()),
+        ("pos", pa.int64()),
+        ("snp", pa.string()),
+        ("ilmn_strand", pa.string()),
+        ("source_strand", pa.string()),
+        ("ref_strand", pa.string()),
+        ("address_a", pa.int32()),
+        ("address_b", pa.int32()),
+        ("assay_type", pa.uint8()),
+        ("norm_id", pa.uint8()),
+        ("norm_bin_id", pa.uint8()),
+        ("norm_lookup", pa.int32()),
+        ("exp_clusters", pa.int8()),
+        ("intensity_only", pa.bool_()),
+        ("ploidy", pa.string()),
+        ("genome_build", pa.string()),
+    ],
+    metadata={"simurg.schema": LOCI_SCHEMA_ID},
+)
+
+INTENSITY_SCHEMA = pa.schema(
+    [("raw_x", pa.uint16()), ("raw_y", pa.uint16()), ("missing", pa.bool_())],
+    metadata={"simurg.schema": INTENSITY_SCHEMA_ID},
+)
+
+CONTROLS_SCHEMA = pa.schema(
+    [("address", pa.int32()), ("red", pa.uint16()), ("green", pa.uint16())],
+    metadata={"simurg.schema": CONTROLS_SCHEMA_ID},
+)
+
+_WRITE_OPTS: dict[str, Any] = {"compression": "zstd", "use_dictionary": True, "write_statistics": True}
+
+
+def _dict_cols(values: list[str]) -> pa.Array:
+    return pa.array(values, type=pa.string())
+
+
+def loci_table(m: Manifest) -> pa.Table:
+    n = m.num_loci
+    cols = {
+        "locus_idx": pa.array(np.arange(n, dtype=np.int32)),
+        "name": _dict_cols(m.names),
+        "ilmn_id": _dict_cols(m.ilmn_ids),
+        "chrom": _dict_cols(m.chroms),
+        "pos": pa.array(m.map_infos.astype(np.int64)),
+        "snp": _dict_cols(m.snps),
+        "ilmn_strand": _dict_cols(m.ilmn_strands),
+        "source_strand": _dict_cols(m.source_strands),
+        "ref_strand": _dict_cols(m.ref_strands),
+        "address_a": pa.array(m.address_a.astype(np.int32)),
+        "address_b": pa.array(m.address_b.astype(np.int32)),
+        "assay_type": pa.array(m.assay_types.astype(np.uint8)),
+        "norm_id": pa.array(m.norm_ids.astype(np.uint8)),
+        "norm_bin_id": pa.array(m.norm_bin_ids()),
+        "norm_lookup": pa.array(m.normalization_lookups().astype(np.int32)),
+        "exp_clusters": pa.array(m.exp_clusters.astype(np.int8)),
+        "intensity_only": pa.array(m.intensity_only.astype(np.bool_)),
+        "ploidy": _dict_cols(m.ploidies),
+        "genome_build": _dict_cols(m.genome_builds),
+    }
+    meta = {"simurg.schema": LOCI_SCHEMA_ID, "manifest_name": m.manifest_name, "manifest_format": m.format}
+    return pa.table(cols, schema=LOCI_SCHEMA.with_metadata(meta))
+
+
+def with_metadata(table: pa.Table, extra: dict[str, Any]) -> pa.Table:
+    meta = dict(table.schema.metadata or {})
+    meta.update(
+        {k.encode(): (v if isinstance(v, str) else json.dumps(v, sort_keys=True)).encode() for k, v in extra.items()}
+    )
+    return table.replace_schema_metadata(meta)
+
+
+def intensity_table(raw_x: np.ndarray, raw_y: np.ndarray, missing: np.ndarray, meta: dict[str, Any]) -> pa.Table:
+    t = pa.table(
+        {
+            "raw_x": pa.array(raw_x.astype(np.uint16)),
+            "raw_y": pa.array(raw_y.astype(np.uint16)),
+            "missing": pa.array(missing.astype(np.bool_)),
+        },
+        schema=INTENSITY_SCHEMA,
+    )
+    return with_metadata(t, meta)
+
+
+def controls_table(addresses: np.ndarray, red: np.ndarray, green: np.ndarray, meta: dict[str, Any]) -> pa.Table:
+    t = pa.table(
+        {
+            "address": pa.array(addresses.astype(np.int32)),
+            "red": pa.array(red.astype(np.uint16)),
+            "green": pa.array(green.astype(np.uint16)),
+        },
+        schema=CONTROLS_SCHEMA,
+    )
+    return with_metadata(t, meta)
+
+
+def write_parquet(table: pa.Table, path: Path) -> None:
+    """Atomic, deterministic Parquet write."""
+    with atomic_open(Path(path), "wb") as fh:
+        pq.write_table(table, fh, **_WRITE_OPTS)
+
+
+def read_metadata(path: Path) -> dict[str, str]:
+    md = pq.read_schema(path).metadata or {}
+    return {k.decode(): v.decode() for k, v in md.items()}
+
+
+def read_table(path: Path, expect_schema: str | None = None) -> pa.Table:
+    t = pq.read_table(path)
+    if expect_schema is not None:
+        got = (t.schema.metadata or {}).get(b"simurg.schema", b"").decode()
+        if got != expect_schema:
+            raise ValueError(f"{path}: schema {got!r}, expected {expect_schema!r}")
+    return t