P4 (WIP): GenCall-equivalent calling, BAF/LRR, sex, GTC v5, simurg genotype

- genotype/clusters.py: EGT aligned to manifest order (float32 mean R)
- genotype/gencall.py: flair, six-case likelihood, priors/posteriors,
  fuzzy sub-scores and score map, vectorised with the reference's
  float/double evaluation order and libm transcendentals
- genotype/baf_lrr.py, sex.py (rules v1/v2), sample.py (IDAT -> Gtc)
- pipeline/inputs.py shared by ingest and genotype
- pipeline/genotype.py + CLI: GTC per sample, sample_summary.tsv/json
  (OUT-060..063), run manifest
- GTCs from IDATs are byte-identical to the oracle for 36 GSA samples x
  2 normalization versions (NaN sign canonicalised to the x86 pattern)

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

src/simurg/pipeline/inputs.py

@@ -0,0 +1,87 @@
+"""Shared sample-set resolution for IDAT-based commands (spec CLI-006, IN-001 … IN-022, IN-010/IN-012)."""
+
+from __future__ import annotations
+
+from dataclasses import dataclass
+from pathlib import Path
+from typing import Any
+
+from simurg.core.errors import SimurgError
+from simurg.core.log import Reporter
+from simurg.core.provenance import RunManifest
+from simurg.formats.discovery import ResolvedSample, discover_idats, resolve_input_folder, resolve_samples
+from simurg.formats.idat import read_idat
+from simurg.formats.samplesheet import SampleSheet, output_stem, parse_samplesheet
+
+
+@dataclass
+class SampleSet:
+    folder: Path
+    sheet: SampleSheet | None
+    samples: list[ResolvedSample]
+    stems: dict[str, str]  # sample_id -> output stem
+
+
+def check_paths(pairs: list[tuple[Path | None, str]]) -> None:
+    for p, what in pairs:
+        if p is not None and not Path(p).exists():
+            raise SimurgError("E_FILE_NOT_FOUND", f"{what} not found: {p}", path=str(p))
+
+
+def resolve_sample_set(
+    idats: Path | None, sheet_path: Path | None, on_duplicate_idat: str, rep: Reporter, rm: RunManifest
+) -> SampleSet:
+    sheet = parse_samplesheet(sheet_path) if sheet_path else None
+    if sheet:
+        rm.sheet_header = sheet.header
+        for code, msg in sheet.warnings:
+            rep.warn(code, msg)
+    folder, notes = resolve_input_folder(idats, sheet)
+    for code, msg in notes:
+        rep.warn(code, msg) if code.startswith("W_") else rep.info(msg, code)
+    disc = discover_idats(folder, on_duplicate=on_duplicate_idat)
+    for code, msg in disc.warnings:
+        rep.warn(code, msg)
+    samples, notes = resolve_samples(disc, sheet)
+    for code, msg in notes:
+        rep.info(msg, code)
+    if not samples:
+        raise SimurgError("E_NO_INPUT", f"no IDAT pairs found under {folder}")
+
+    use_idat_names = sheet is None or not sheet.has_sample_name
+    stems: dict[str, str] = {}
+    taken: dict[str, str] = {}
+    for s in samples:
+        if use_idat_names and s.pair is not None and s.pair.grn is not None:
+            # IN-010: sheet Sample_Name > IDAT sample name (field 406) > sample_id
+            try:
+                idat_name = read_idat(s.pair.grn, load_arrays=False).sample_id.strip()
+            except SimurgError:
+                idat_name = ""
+            if idat_name:
+                s.sample_name = idat_name
+        stem = output_stem(s.sample_name)
+        if stem in taken and taken[stem] != s.sample_id:
+            if not use_idat_names:  # IN-012: sheet names that sanitise to the same stem
+                raise SimurgError(
+                    "E_SHEET_NAME_COLLISION",
+                    f"samples {taken[stem]} and {s.sample_id} both map to output name {stem!r}",
+                )
+            rep.info(f"{s.sample_id}: IDAT sample name {s.sample_name!r} is not unique; using the sample ID")
+            s.sample_name = s.sample_id
+            stem = output_stem(s.sample_id)
+        taken[stem] = s.sample_id
+        stems[s.sample_id] = stem
+    return SampleSet(folder=folder, sheet=sheet, samples=samples, stems=stems)
+
+
+def sample_dir(out: Path, stem: str, layout: str) -> Path:
+    return out / "samples" / stem if layout == "nested" else out
+
+
+def sheet_values(s: ResolvedSample, sheet: SampleSheet | None) -> dict[str, Any]:
+    """Pass-through sheet columns for summaries (IN-013)."""
+    if sheet is None or s.sheet_row is None:
+        return {}
+    row = s.sheet_row
+    return {c: row.values.get(c, "") for c in sheet.passthrough_columns()}  # type: ignore[attr-defined]