Advance countMatMult stride once per gene, not once per dedup option (fixes #2704) - #2705
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…up option Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Moves SoloFeature_collapseUMIall.cpp:530 out of the indDedup loop so each multimapping gene occupies one countMatMult group, which is the layout ParametersSolo.cpp:661-665 and SoloFeature_outputResults.cpp:151-197 already assume. With more than one --soloUMIdedup option the current code writes N records per multimapping gene to every UniqueAndMult-*.mtx, N-1 of them on feature index 1. Tested on pbmc_1k_v3: with this change the three-option run's UniqueAndMult-EM_umiDedup-1MM_Directional_UMItools.mtx is byte-identical to the single-option UniqueAndMult-EM.mtx (md5 6c89f52b389b2432b0c5571bfbf8dcf9). Full evidence, logs and reproduction in #2704. Fixes #2704.
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