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

src/simurg/formats/bcf.py

@@ -71,17 +71,21 @@ def encode_record(
     filter_id: int,
     n_sample: int,
     fmt: Sequence[tuple[int, bytes, bytes]],
+    info: Sequence[tuple[int, bytes]] = (),
 ) -> bytes:
-    """``fmt``: (format dictionary index, type-descriptor bytes, per-sample payload) in FORMAT order."""
+    """``fmt``: (format dictionary index, type-descriptor bytes, per-sample payload) in FORMAT order;
+    ``info``: (dictionary index, typed value) pairs."""
     shared = bytearray()
     shared += struct.pack("<iii", contig_id, pos0, rlen)
     shared += FLOAT_MISSING  # QUAL
-    shared += struct.pack("<I", (len(alleles) << 16) | 0)  # n_allele << 16 | n_info
+    shared += struct.pack("<I", (len(alleles) << 16) | len(info))  # n_allele << 16 | n_info
     shared += struct.pack("<I", (len(fmt) << 24) | n_sample)
     shared += typed_string(vid if vid else ".")
     for a in alleles:
         shared += typed_string(a)
     shared += typed_ints([filter_id])
+    for key, value in info:
+        shared += typed_ints([key]) + value
     indiv = bytearray()
     for key, desc, payload in fmt:
         indiv += typed_ints([key]) + desc + payload
@@ -154,3 +158,7 @@ def header_dictionaries(header_text: str) -> tuple[dict[str, int], dict[str, int
             name = line[13:].split(",", 1)[0].split(">", 1)[0]
             contigs.setdefault(name, len(contigs))
     return strings, contigs
+
+
+def typed_floats(values: Sequence[float]) -> bytes:
+    return _type_byte(len(values), FLOAT) + float_bytes(values)