SimurgArray

6 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	8b1e5d8dab	P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset ci / test (3.12) (push) Failing after 8s Details ci / test (3.13) (push) Failing after 9s Details - vendor comparison (1000 Genomes Omni2.5, AutoCall 1.6.2.2): every computed field identical in 2138/2141 samples; the 3 others trace back to the single-locus raw-intensity rule (K-009); sex rule 1 matches all - AutoCall 1.6.2.x leaves GC10/GC50/#calls/#no-calls at 0 in GTC v3: new `--preset autocall-1.6.2` (1.1.2 normalization, sex rule 1, GTC v3, legacy statistics); the sample summary keeps the real statistics - NaN sign canonicalised to the x86 pattern (K-014); report P4.md Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 01:21:49 +01:00
kemalandClaude Opus 5.5	0cd7eb8aa0	P3 validated: normalization bit-identical on 2141 vendor GTCs ci / test (3.12) (push) Failing after 8s Details ci / test (3.13) (push) Failing after 9s Details Normalization 1.1.2 reproduces all 109,191 bins of the 1000 Genomes Omni2.5 GTCs (AutoCall 1.6.2.2) with 0 ULP difference, reserved fields included; 1.2.0 and 1.1.2 are bit-identical to the no-FMA gtc2vcf oracle on 36 GSA samples. AWS run: 33 min, ~$0.15, no resources left. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 23:41:43 +01:00
kemalandClaude Opus 5.5	5c93e194e0	P2 validated on 2141 vendor GTCs (1000 Genomes Omni2.5) ci / test (3.12) (push) Failing after 8s Details ci / test (3.13) (push) Failing after 10s Details Raw X/Y and controls assembled from IDATs equal the vendor GTC arrays for 2138/2141 samples x 2.45M loci; 3 single-locus differences are recorded as K-009 (probable per-channel missing rule in AutoCall 1.6.2.2). Channel order X=Red confirmed (U1). `simurg ingest` processed all 2141 samples in 19 min (I/O-bound). AWS run cost ~$0.34 and left no resources. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 22:19:28 +01:00
kemalandClaude Opus 5.5	f10c651f0f	P0: project setup (packaging, CI, licences, data/oracle scripts) - pyproject (uv/hatch, ruff, mypy strict, pytest markers), MIT LICENSE, THIRD_PARTY_NOTICES with verbatim BSD-2 (BeadArrayFiles) and MIT (gtc2vcf) - CI workflow for Gitea/GitHub Actions: lint, type check, unit tests - fetch_data.sh p0 now fetches the GSA v4 PGx demo IDATs (the GDA "Demo 36" bundle is a GenomeStudio project), unpacks archives, fixes pipefail bug - make_oracle_gtcs.sh builds bcftools + gtc2vcf and writes oracle GTCs - plan §17: corrected P0 dataset table Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 16:56:39 +01:00
kemalandClaude Opus 5.5	6449440492	Add functional specification (416 items) and link it from plan/docs SIMURGARRAY_FUNCTIONAL_SPEC.md defines externally visible behaviour: CLI, inputs, genotyping outputs, QC and report, cytogenetics CNV/LOH, targeted PGx copy number, star alleles, methylation control QC, edge-case catalogue, performance targets, open questions and a traceability table. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 16:13:40 +01:00
kemalandClaude Opus 5.5	ee4ebaaa1e	SimurgArray: master plan, repo scaffolding and data/ref fetch scripts Phase 0 deliverables: full technical specification and roadmap (SIMURGARRAY_MASTER_PLAN.md), CLAUDE.md, bootstrap script for reference open-source repos and tiered dataset fetch script with checksums. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-27 15:20:06 +01:00