solo: count intronic reads by default on 10x (closes 30 of the 32 points vs CellRanger, stacked on #182) - #184

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BenjaminDEMAILLE wants to merge 12 commits into

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BenjaminDEMAILLE:bd/solo-10x-introns

Commits on Jul 31, 2026

fix(solo): MultiGeneUMI_CR gives a tied UMI to nobody, not to everybody

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docs(changelog): record the MultiGeneUMI_CR tie fix

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feat(solo): --soloOutRawBarcodes Observed, for a CellRanger-shaped raw matrix

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fix(solo): MultiGeneUMI_CR decides ownership on corrected UMIs

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feat(solo): CellRanger behaviour by default on 10x geometry

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docs(divergence): correct the CellRanger gap figure in 1.3

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docs(divergence): restore the measured CellRanger gap in 1.3

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feat(solo): --soloOutLayout CellRanger, CellRanger's output shape

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feat(solo): metrics_summary.csv under the CellRanger layout

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docs(divergence): pin down what differs in Sequencing Saturation

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feat(solo): --soloCellFilter OrdMag, CellRanger's cell call

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feat(solo): count intronic reads by default on 10x geometry

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