feat: --outMultimapperOrder; deterministic default primary selection - #111
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STAR's default (--outMultimapperOrder Old_2.4) does not use the RNG for
primary selection among equal-scoring multimappers. rustar-aligner was
unconditionally shuffling the tied top-score prefix, randomising the
primary and diverging from STAR. Add --outMultimapperOrder
{Old_2.4|Random} (default Old_2.4) and gate the shuffle behind Random,
matching STAR. Dedup now preserves discovery order (removes dead
cmp_cigar).
Yeast 10k raw exact matches vs STAR: SE 8606->8789, PE 16278->16575
(+480); no regression. 455 tests pass
Psy-Fer
enabled auto-merge (squash)
July 24, 2026 04:46
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STAR's default (--outMultimapperOrder Old_2.4) does not use the RNG for primary selection among equal-scoring multimappers. rustar-aligner was unconditionally shuffling the tied top-score prefix, randomising the primary and diverging from STAR. Add --outMultimapperOrder {Old_2.4|Random} (default Old_2.4) and gate the shuffle behind Random, matching STAR. Dedup now preserves discovery order (removes dead cmp_cigar).
Yeast 10k raw exact matches vs STAR: SE 8606->8789, PE 16278->16575 (+480); no regression. 455 tests pass