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Clamp n_pcs so default H5 pipeline does not panic - #7
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pbmc_1k_v3 at --max-pct-mt 5 kept 21 cells; PCA asked for 50 PCs and indexed OOB.
jwg054000
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Sep 2, 2026
src/#7 published sha256:c1d9cc75…. Do not float 0.3.0. Docs-only; does not rebuild.
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H5 smoke on pin `sha256:0f7164c5…` with default flags panicked in `pca.rs` (21 cells after `max_pct_mt=5`, 50 PCs). PACKET.md outputs exist if you pass `--max-pct-mt 20`.
This clamps PCs to `min(n_pcs, n_cells-1, n_genes-1)` and fail-closes if fewer than 2 cells remain.
Does not change default 5% MT. Does not add Cell Ranger. Does not touch prairie-rna-stream. 115 tests green locally.
After merge, GHCR will mint a new digest (src/ change). Pin that; do not float `0.3.0`. Until then the old pin still needs `--max-pct-mt 20` for this H5.