All pull requests

Pull requests

• Third-party notices for ported code, in source and in what we ship

  #337·Psy-Fer opened Oct 14, 2026Collaborator·

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• chore: update to msrv 1.91

  #331·ilan-gold opened Oct 12, 2026·

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• feat(solo): reproduce cellranger count 10.0.0 outputs (--soloOutLayout CellRanger, clean-room)

  #323·BenjaminDEMAILLE opened Oct 10, 2026Contributor·

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• docs(roadmap): mark 17.2-17.6 and 17.B done

  #296·BenjaminDEMAILLE opened Oct 8, 2026Contributor·

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• perf(io): encode SAM/BAM records on the align workers (stacked on #276)

  #278·BenjaminDEMAILLE opened Sep 29, 2026Contributor·

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• perf(io): parallel order-preserving BGZF compression for BAM output

  #276·BenjaminDEMAILLE opened Sep 29, 2026Contributor·

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• feat(solo): optional CellRanger v3 .h5 count matrices via hdf5-pure

  #275·BenjaminDEMAILLE opened Sep 29, 2026Contributor·

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• feat(io): optional paraseq FASTQ backend

  #273·BenjaminDEMAILLE opened Sep 29, 2026Contributor·

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• test: yeast-tier differential in a minute, and a SAM agreement tool

  #253·BenjaminDEMAILLE opened Aug 27, 2026Contributor·

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• bench: add a divan harness and the first hot-path benchmarks

  #248·BenjaminDEMAILLE opened Aug 27, 2026Contributor·

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• docs: record dependency decisions in DEPENDENCIES.md

  #246·BenjaminDEMAILLE opened Aug 27, 2026Contributor·

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• feat(cli): parameter files, --sysShell, and a shell-run readFilesCommand

  #239·BenjaminDEMAILLE opened Aug 26, 2026Contributor·

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• feat: output anndata

  #237·ilan-gold opened Aug 25, 2026·3 of 4 tasks·

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• feat(io): optional pure-Rust parallel gzip input decoding (rapidgzip-core)

  #225·BenjaminDEMAILLE opened Aug 11, 2026Contributor·

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• feat(io): native CBQ input support

  #213·alejandrogzi opened Aug 6, 2026·

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

  #184·BenjaminDEMAILLE opened Jul 31, 2026Contributor·

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• solo: --soloCellFilter OrdMag, CellRanger's cell call (first item of #181, stacked on #180)

  #182·BenjaminDEMAILLE opened Jul 31, 2026Contributor·

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• solo: metrics_summary.csv under the CellRanger layout (stacked on #178)

  #179·BenjaminDEMAILLE opened Jul 31, 2026Contributor·

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• solo: --soloOutLayout CellRanger, CellRanger's output shape (changes output paths on 10x, stacked on #176)

  #178·BenjaminDEMAILLE opened Jul 31, 2026Contributor·

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• feat(solo): CellRanger behaviour by default on 10x geometry (changes default output, stacked on #175)

  #176·BenjaminDEMAILLE opened Jul 31, 2026Contributor·

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• feat(solo): --soloOutRawBarcodes Observed — a CellRanger-shaped raw matrix (stacked on #173)

  #174·BenjaminDEMAILLE opened Jul 31, 2026Contributor·

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• genome: --genomeType SuperTranscriptome

  #161·BenjaminDEMAILLE opened Jul 29, 2026Contributor·

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• genome: --genomeTransformOutput SAM reports original coordinates

  #160·BenjaminDEMAILLE opened Jul 29, 2026Contributor·

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• feat: STARlong binary + long-read window-coverage filter

  #116·BenjaminDEMAILLE opened Jul 24, 2026Contributor·

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• genomeGenerate: libsais suffix-array builder, selected by --limitGenomeGenerateRAM

  #109·BenjaminDEMAILLE opened Jul 23, 2026Contributor·

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