2 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	bc93e00318	CLI: a closed stdout pipe exits 141 silently (was E_INTERNAL); example avoids head under pipefail ... Found by the P10 fresh-VM run: `simurg inspect … | head` raised BrokenPipeError, reported as an internal error, and stopped examples/gsa_demo.sh (set -o pipefail). run_guarded now flushes stdout inside the guard and maps BrokenPipeError to ExitCode.SIGPIPE (141) without a message. p10.sh: SKIP_DOCKER/SKIP_CONDA, clearer digest report; p10t.sh runs build+pip+tutorial only. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-28 23:14:47 +01:00
kemalandClaude Opus 5.5	4357d3deef	P1: file parsers, sample sheet, discovery, CLI inspect ... 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	2026-09-27 16:56:39 +01:00