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STARsolo UMI dedup: look up 1-mismatch neighbours instead of comparing all pairs (200k UMIs: 44-109 s to 62-208 ms) #362

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STARsolo UMI dedup: look up 1-mismatch neighbours instead of comparing all pairs (200k UMIs: 44-109 s to 62-208 ms) #362

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6a63d19
STARsolo UMI dedup: look up 1-mismatch neighbours above 224 UMIs
BenjaminDEMAILLE Nov 2, 2026
26cf746
1MM_All: break equal-count ties by raw UMI when half-swaps collide
BenjaminDEMAILLE Nov 3, 2026
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,11 @@ Sections commonly used: Features, Bug fixes, Other changes.

### Other changes

- STARsolo UMI collapsing (`1MM_All`, `1MM_Directional`,
`1MM_Directional_UMItools`, `1MM_CR`) no longer compares all pairs of a large
`(cell, gene)` UMI set: above 224 UMIs it looks up each UMI's `3 * umi_len`
single-base variants instead. Results are unchanged.

- Third-party notices completed. `LICENSES/` gains the licences of code
ported from DegNorm (MIT) and David Elworthy's `sgt.h` via STAR (BSD
2-clause), and of libc++ (Apache 2.0 with LLVM Exceptions), whose random
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