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/fetch_data.sh

@@ -74,6 +74,18 @@ p2)
   get "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE96nnn/GSE96909/suppl/GSE96909_RAW.tar" "$d/gse96909"
   get "https://s3.amazonaws.com/webdata.illumina.com/downloads/productfiles/global-diversity-array-pgx/GDAPGx_Demo_idats.zip" "$d/gda_pgx480"
   ;;
+p6)
+  # GRCh38 primary assembly (Ensembl release 110; contigs named 1..22, X, Y, MT like the GSA/GDA manifests)
+  d=data/p6; mkdir -p "$d"
+  ENS=https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna
+  f=Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
+  [[ -f "$d/$f" ]] || curl -sSfL -o "$d/$f" "$ENS/$f"
+  want=$(curl -sSfL "$ENS/CHECKSUMS" | awk -v f="$f" '$3==f {print $1" "$2}')
+  got=$(sum "$d/$f" | awk '{print $1" "$2}')
+  [[ "$want" == "$got" ]] || { echo "!! checksum mismatch for $f ($got vs $want)"; exit 1; }
+  [[ -f "$d/GRCh38.primary.fa" ]] || gzip -dc "$d/$f" > "$d/GRCh38.primary.fa"
+  echo "FASTA ready: $d/GRCh38.primary.fa (the .fai is built on first use)"
+  ;;
 *) echo "unknown tier $tier"; exit 2;;
 esac
 echo "checksums in $sums"