P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen

- gtc-to-vcf --info-fields ASSAY_TYPE,NORM_BIN,GENTRAIN,CLUSTER_SEP,ILMN_STRAND,PROBE_IDS (--egt) and
  --extra-format X,Y,NORMX,NORMY,THETA,R, in per-sample VCFs and the --merge BCF (OUT-012, plan §8.3);
  equal to gtc2vcf's values (THETA/R missing where both normalized intensities are 0, K-023)
- --merge-snv-indel (OUT-021, EDGE-013): alleles extended to the longest REF; SNV probes read the base at POS
- --auxiliary-loci (OUT-035, EDGE-015): rules (a)-(e), E_AUX_INVALID; rule (d) uses the last plus-strand base
  for minus-strand designs (spec amended, as GTCtoVCF)
- export plink --format bed|pgen|both: PLINK 2 fixed-width .pgen/.pvar/.psam; plink2 reads it back to a .bed
  byte-identical to ours
- cohort store keeps raw/normalized intensities for the BCF path; tests (unit + gtc2vcf oracle); docs

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

src/simurg/harmonize/combine.py

@@ -22,13 +22,16 @@ CALL_TEXT = {NC: "NC", AA: "AA", AB: "AB", BB: "BB"}
 def signal_class(p: ProbeSite, allele: str) -> str | None:
     """OUT-031 step 1."""
     a, b = p.alleles
-    if p.kind == "snv" and p.infinium == 2 and len(allele) == 1:
-        grp = RED if allele in RED else GREEN
-        if a in grp:
-            return "A"
-        if b in grp:
-            return "B"
-        return None
+    if p.kind == "snv":  # SNV probes read the single base at POS; alleles may be extended by --merge-snv-indel
+        z, a0, b0 = allele[:1], a[:1], b[:1]
+        if p.infinium == 2:
+            grp = RED if z in RED else GREEN
+            if a0 in grp:
+                return "A"
+            if b0 in grp:
+                return "B"
+            return None
+        return "A" if z == a0 else "B" if z == b0 else None
     if allele == a:
         return "A"
     if allele == b: