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P1: file parsers, sample sheet, discovery, CLI inspect
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Readers for IDAT v3, BPM (locus entries v4-v8), CSV manifest, EGT
(data blocks 5-9) and GTC v3-v5 (plus a layout-preserving GTC writer);
sample-sheet validation (IN-001..IN-014), IDAT discovery and pairing
(IN-020..IN-022), message catalogue and exit codes (CLI-014/016),
JSON Lines logging (CLI-007/008), atomic writes (CLI-011), run manifest,
and `simurg inspect`.

Validation (docs/validation/P1.md): GTC, BPM and EGT readers agree
exactly with Illumina BeadArrayFiles on GSA v4 / GDA v1 files; GTCs
round-trip byte-identically; BPM and CSV manifests are consistent.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
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kemalandClaude Opus 5.5 committed 2026-09-27 16:56:39 +01:00
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docs/known_unknowns.md
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# Known unknowns and findings log
Plan §20 lists the open questions; this file records what the implementation has learned. Newest first.
| ID | Date | Topic | Finding | Status |
|---|---|---|---|---|
| K-007 | 2026-09-27 | Demo data | The "GDA v1 Demo 36" download is a GenomeStudio project (`.bsc` + `Data/*.bin`), not IDATs. The GSA v4 PGx demo (`idats_Demo_36.zip`) is used as the P0 IDAT fixture instead. Bioconductor `hapmap370k` is no longer in the current release. | resolved (plan §17 updated) |
| K-006 | 2026-09-27 | Sample sheet | Recognised input columns (`Sample_ID`, `Sample_Name`, …) collide case-insensitively with output columns `sample_id`/`sample_name` (IN-005). Recognised columns are exempt from the reserved-name check and are passed through verbatim. | decision, revisit in P4 (OUT-060 pass-through) |
| K-005 | 2026-09-27 | Sample sheet | Illumina's GSA v4 template sheet has an empty `Sample_Name` column → `E_SHEET_NAME_EMPTY` (IN-010 behaviour as specified). | as specified |
| K-004 | 2026-09-27 | GTC scanner data | PMT gains are 4 bytes read as int32 by BeadArrayFiles and written as float by gtc2vcf. We keep the raw 4 bytes (byte-exact round-trip) and expose the int32 view. | resolved |
| K-003 | 2026-09-27 | Assay type from sequences | gtc2vcf's rule for inferring Infinium I colour from probe/source sequences (needed only for BPM locus entries < v6) agrees with the explicit BPM value for 99.71 % of GSA v4 Infinium I loci. The BPM is authoritative whenever it carries the assay type. | documented; test threshold 99.5 % |
| K-002 | 2026-09-27 | EGT data block (plan U3) | GSA v4 and GDA v1 EGTs are data-block v9 with 15 extra floats per record; the first extra float is the intensity threshold (non-zero for 16 015 GDA loci). The reader tries candidate record sizes and accepts the one whose trailing cluster counts match. dbv 7/8 files still untested. | partly resolved |
| K-001 | 2026-09-27 | IDAT MidBlock (plan U2) | In GSA v4 (BeadChip 48x4), HumanCNV370 (2x12) and 450k (12x8) IDATs the MidBlock count equals N and the section is 4 bytes per entry (int32, as in illuminaio). gtc2vcf reads uint8 but never uses the values. We infer the element size from the section length. | resolved for these chips |