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Author SHA1 Message Date
kemalandClaude Opus 5.5 2e8478cc6a P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen
ci / test (3.12) (push) Failing after 8s
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ci / test (3.13) (push) Failing after 10s
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- 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
 2026-09-28 14:29:42 +01:00
kemalandClaude Opus 5.5 63bb40c4e5 P6 validated against GTCtoVCF too: zero unexplained genotype differences
ci / test (3.12) (push) Failing after 10s
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ci / test (3.13) (push) Failing after 11s
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- GTCtoVCF (Apache-2.0, 36 GSA samples, merged sites): 23.66 M identical calls; every difference named
  (intensity-only probes merged by the oracle, its opposite-strand indel bug EDGE-012, normalisation-based
  grouping, OUT-018 ploidy); indel representations identical, including 144 gtc2vcf cannot resolve
- validate_p6_vcf.py: rule-based categories (--bpm for [I/D]/[D/I] detection)
- docs: validation P6 complete, README status

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-28 13:20:44 +01:00
kemalandClaude Opus 5.5 b56fdebaaf 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
 2026-09-28 12:17:53 +01:00