clip: CellRanger4 3' poly-A trim - #148

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BenjaminDEMAILLE:bd/clip-cellranger4

Commits on Jul 29, 2026

feat(swalign): in-tree affine-gap aligner, and the CellRanger4 clip built on it

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feat(clip): --clipAdapterType CellRanger4 now actually clips

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docs: changelog for CellRanger4 clipping

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test(swalign): differential harness that every backend has to pass

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feat(swalign): NEON backend, checked against the scalar path on every case

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test(swalign): check every backend this machine can run, not just the detected one

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refactor(clip): drop the in-tree SW engine, keep the poly-A trim

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test(clip): end-to-end test for --clipAdapterType CellRanger4
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