P6 validated against GTCtoVCF too: zero unexplained genotype differences

- GTCtoVCF (Apache-2.0, 36 GSA samples, merged sites): 23.66 M identical calls; every difference named
  (intensity-only probes merged by the oracle, its opposite-strand indel bug EDGE-012, normalisation-based
  grouping, OUT-018 ploidy); indel representations identical, including 144 gtc2vcf cannot resolve
- validate_p6_vcf.py: rule-based categories (--bpm for [I/D]/[D/I] detection)
- docs: validation P6 complete, README status

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

scripts/validate_p6_vcf.py

@@ -49,14 +49,27 @@ def main() -> int:
     ap.add_argument("--bcftools", required=True)
     ap.add_argument("--out", required=True, type=Path)
     ap.add_argument("--name", default="oracle")
+    ap.add_argument("--bpm", type=Path, help="manifest, to recognise opposite-strand indel designs (EDGE-012)")
     a = ap.parse_args()
 
     samples = subprocess.run([a.bcftools, "query", "-l", str(a.oracle)], capture_output=True, text=True,
                              check=True).stdout.split()  # fmt: skip
     oracle: dict[str, tuple[str, str, str, str, list[str]]] = {}
+    oracle_group: dict[str, frozenset[str]] = {}
     for f in query(a.bcftools, a.fasta, a.oracle):
-        for pid in f[0].replace(";", ",").split(","):
+        ids = f[0].replace(";", ",").split(",")
+        for pid in ids:
             oracle[pid] = (f[1], f[2], f[3], f[4], f[5:])
+            oracle_group[pid] = frozenset(ids)
+    snp: dict[str, str] = {}
+    if a.bpm:
+        sys.path.insert(0, str(Path(__file__).resolve().parents[1] / "src"))
+        from simurg.formats.bpm import read_bpm
+
+        m = read_bpm(a.bpm)
+        snp = dict(zip(m.names, m.snps, strict=True))
+    first = a.ours / f"{samples[0]}.snv.vcf.gz"
+    ours_all = {pid for f in query(a.bcftools, a.fasta, first) for pid in f[0].replace(";", ",").split(",")}
     cats: Counter[str] = Counter()
     examples: dict[str, list[Any]] = defaultdict(list)
     ours_ids: set[str] = set()
@@ -71,6 +84,8 @@ def main() -> int:
             merged = len(ids) > 1
             ours_al = alleles_of(f[5], f[3], f[4])
             haploid = "/" not in f[5] and f[5] != "."
+            group = frozenset(ids)
+            mixed_indel = {snp.get(x) for x in ids} >= {"[I/D]", "[D/I]"}
             for pid in ids:
                 if si == 0:
                     ours_ids.add(pid)
@@ -88,17 +103,27 @@ def main() -> int:
                 if ours_al == theirs:
                     cats["match_called" if ours_al else "match_missing"] += 1
                     continue
-                if ours_al is None:
-                    if merged:
-                        key = "ours_missing_merged_site"
+                og = oracle_group[pid]
+                if og - ours_all:
+                    key = "oracle_site_includes_probes_we_skip"  # e.g. intensity-only CNV probes (OUT-019)
+                elif og != group and (merged or len(og) > 1):
+                    key = "grouping_differs"  # same normalised variant, different manifest positions (OUT-030)
+                elif ours_al is not None and theirs is None and mixed_indel:
+                    key = "oracle_opposite_strand_indel_bug"  # EDGE-012: [I/D] + [D/I] both het → 0/1
+                elif ours_al is None:
+                    if theirs is not None and theirs[0] != theirs[1] and f[5] == ".":
+                        key = "ours_missing_het_in_haploid"  # OUT-018
                     elif f[1] in ("Y", "chrY") and f[5] == ".":
-                        key = "ours_missing_haploid_Y"
-                    elif theirs is not None and theirs[0] != theirs[1] and (f[5] == "." or haploid):
-                        key = "ours_missing_het_in_haploid"
+                        key = "ours_missing_haploid_Y"  # OUT-018: Y of female samples
+                    elif merged:
+                        key = "ours_missing_merged_site"
                     else:
                         key = "ours_missing_UNEXPLAINED"
                 elif theirs is None:
-                    key = "oracle_missing_ours_called_merged" if merged else "oracle_missing_ours_called"
+                    if merged and haploid:
+                        key = "oracle_diploid_candidates_in_haploid_context"  # OUT-031 enumerates with the ploidy
+                    else:
+                        key = "oracle_missing_ours_called_merged" if merged else "oracle_missing_ours_called"
                 else:
                     key = "diff_merged_site" if merged else "diff_UNEXPLAINED"
                 cats[key] += 1