P6: gtc-to-vcf (VCF/BCF + indexes), harmonisation, exports (plink, bedgraph, finalreport)

- formats/fasta: plain/BGZF FASTA, .fai/.gzi built identical to htslib, index check, build detection,
  contig aliases, mmap genome cache (IN-060..064)
- formats/bgzf, formats/bcf: pure-Python BGZF, tabix .tbi, BCF 2.2 and CSI (OUT-010, OUT-038, OUT-040)
- harmonize/sites: plus-strand mapping with audit rows, indel resolution from SourceSeq (port of GTCtoVCF,
  Apache-2.0) and left normalisation (OUT-014..021, OUT-030, OUT-042)
- harmonize/combine: OUT-031 genotype combination (ploidy-aware, Infinium I/II signal classes, OUT-037)
- pipeline/vcf: `simurg gtc-to-vcf` (per-sample VCF.gz+tbi, --merge cohort BCF+csi, audit parquet)
- pipeline/export: `simurg export bedgraph|finalreport|plink|locus-summary` (OUT-043, OUT-050..052, OUT-071)
- validation: 36 GSA samples vs gtc2vcf: 23.66 M identical calls, 0 unexplained differences; PLINK identical
  to plink2 on 637,397 variants; bcftools validates VCF/BCF and our indexes answer region queries correctly
- fetch_data.sh p6 (Ensembl GRCh38 with checksum), make_oracle_vcf.sh, validate_p6_vcf.py; K-022/K-023

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

scripts/make_oracle_vcf.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+# Oracle VCFs for phase P6 on the 36 GSA oracle GTCs (needs make_oracle_gtcs.sh and fetch_data.sh p6):
+#  * gtc2vcf (MIT) → data/p6/oracle/gsa36_gtc2vcf.vcf.gz (one multi-sample VCF, one record per probe)
+#  * optional: GTCtoVCF (Apache-2.0) — python2-era code run under python3 with two local compatibility patches,
+#    see docs/validation/P6.md; enable with GTCTOVCF=1.
+set -euo pipefail
+cd "$(dirname "$0")/.."
+B=refs/tools/bcftools-1.22
+export BCFTOOLS_PLUGINS=$B/plugins
+D=data/p0/gsa_v4_pgx
+OUT=data/p6/oracle
+mkdir -p $OUT data/p6/work
+$B/bcftools +gtc2vcf --no-version -t GT,BAF,LRR \
+  -b $D/GSA-PGx-48v4-0_20079540_E2_bpm/GSA-PGx-48v4-0_20079540_E2.bpm \
+  -c $D/GSA-PGx-48v4-0_20079540_E2_csv/GSA-PGx-48v4-0_20079540_E2.csv \
+  -e $D/GSA-PGx-48v4-0_20079540_E2_ClusterFile/GSA-PGx-48v4-0_20079540_E2_ClusterFile.egt \
+  -f data/p6/GRCh38.primary.fa -g data/p0/oracle/gsa_gt3_nofma -O u 2> $OUT/gtc2vcf.log \
+  | $B/bcftools sort -Oz -o $OUT/gsa36_gtc2vcf.vcf.gz -T data/p6/work/sorttmp
+$B/bcftools index -f -t $OUT/gsa36_gtc2vcf.vcf.gz
+echo "wrote $OUT/gsa36_gtc2vcf.vcf.gz"