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

docs/known_unknowns.md

@@ -4,7 +4,7 @@ Plan §20 lists the open questions; this file records what the implementation ha
 
 | ID | Date | Topic | Finding | Status |
 |---|---|---|---|---|
-| K-023 | 2026-09-28 | P6 options not yet implemented | `--auxiliary-loci` (OUT-035), `--info-fields`/`--extra-format` (OUT-012; GENTRAIN/CLUSTER_SEP would also need the EGT), `--merge-snv-indel` (OUT-021), PLINK 2 `.pgen`. Everything else of CLI-022/CLI-023 works. | open |
+| K-023 | 2026-09-28 | P6 optional outputs | Implemented and validated the same day: `--info-fields` (with `--egt`), `--extra-format`, `--merge-snv-indel`, `--auxiliary-loci`, PLINK 2 `.pgen`. Two decisions: OUT-035 rule (d) uses the MNV's last plus-strand base for minus-strand designs (spec amended); `--extra-format` writes NORMX/NORMY missing where the raw intensities are both 0, and THETA/R missing where both normalized intensities are 0 (148 values on 3 GSA samples; gtc2vcf writes 0). | resolved |
 | K-022 | 2026-09-28 | VCF oracles' limits (GSA v4 PGx, GRCh38) | gtc2vcf leaves 144 indel probes unresolved (`REF=I`/`D`) that SimurgArray resolves from `SourceSeq`; both leave 49 indels unresolved. GTCtoVCF (python-2.7 era) runs under Python 3 only with two local patches (pyvcf3 `Format` field; skip instead of crash on 3 CYP2D6 indels whose `SourceSeq` has the dash on the right, `[ALLELE/-]`, which SimurgArray handles), and needs the alt-contig loci filtered when the FASTA has no alts. Neither oracle applies ploidy (males' X/Y/MT hets stay diploid). | documented |
 | K-021 | 2026-09-28 | Control metrics on legacy Omni2.5 IDATs | (1) The Omni2.5 manifest lists two bead addresses per control (e.g. 27630314 and 127630314, two bead-pool versions); only one is on a given chip. Absent addresses were NaN and poisoned the bead mean → 1794/2141 samples falsely flagged on both staining metrics. Absent addresses are now skipped. (2) 1290 samples have Biotin (Bgnd) green = 0 exactly (background-subtracted), so staining green is signal/0; QC-008 now defines that as +Inf (pass) and only 0/0 as NaN (flag). | resolved (spec QC-008 amended) |
 | K-020 | 2026-09-28 | QC report scope (P5b) | Implemented: views A–E, linked selection, thresholds modal (apply/download/upload YAML), chip/plate heatmaps, trend table and Tukey box plots, PCA card, xlsx/csv table, privacy options, `--split-by dataset`. Not yet: client-side xlsx export (CSV only), density mode for > 12 000 points (WebGL scatter is used), `--split-by plate|run`, X/Y median R for the sex card (the summary does not carry them; the card shows the sex check instead), methylation datasets (v2). | open (deviations listed) |