kemal/SimurgArray
1
0 Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
89 Commits 1 Branch 3 Tags
275398328558619ccd84348088b83da72635f2af
Commit Graph
2 Commits
Author SHA1 Message Date
kemalandClaude Opus 5.5 9f36f6443b P8 cloud task: stream NYGC VCFs through bcftools instead of downloading
ci / test (3.12) (push) Failing after 8s
Details
ci / test (3.13) (push) Failing after 10s
Details 
The download-only phase (EBI ~15 MB/s) left the CPU idle long enough for the
idle alarm to terminate the first run. Streams are now cut to the manifest
positions (±100 bp) and the 120 individuals while genotyping runs.

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-28 19:06:36 +01:00
kemalandClaude Opus 5.5 70c36446a0 P8: GSE165845 validation scripts (prepare, §16.5 metrics) and cloud task
ci / test (3.12) (push) Failing after 8s
Details
ci / test (3.13) (push) Failing after 10s
Details 
scripts/p8/prepare.py lays out the 360 GEO IDATs under their header barcode/position;
scripts/p8/validate_p8.py computes concordance, NRD, no-call rate, per-class and per-MAF
sensitivity/specificity/precision/F1 vs NYGC 30x and GIAB HG001, replicate concordance,
systematic/allele-swap site errors, per-chip batch table and duplicate detection.
Cloud userdata can skip the Omni2.5 archive (OMNI=0).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
 2026-09-28 17:43:31 +01:00