All pull requests

Pull requests

• chore(docs): bump the docs-minor-patch group in /docs with 2 updates

  dependenciesjavascript
  #351·dependabot[bot] opened Nov 1, 2026Bot·

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• chore(ci): bump the github-actions group with 5 updates

  dependenciesgithub_actions
  #350·dependabot[bot] opened Nov 1, 2026Bot·

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• chore(deps): bump memmap2 from 0.9.11 to 0.9.12 in the cargo-minor-patch group

  dependenciesrust
  #349·dependabot[bot] opened Nov 1, 2026Bot·

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• Transcriptome alignments as a RAD file for salmon (--quantTranscriptomeRAD)

  #348·BenjaminDEMAILLE opened Oct 30, 2026Contributor·

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• AS tag in the transcriptome BAM, on request (--quantTranscriptomeBAMattrAS)

  #347·BenjaminDEMAILLE opened Oct 30, 2026Contributor·

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• Aligner hot paths: backtracking stitcher, buffered junction scan (−22 to −38 % instructions, identical output)

  #346·BenjaminDEMAILLE opened Oct 30, 2026Contributor·

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• Fix the two STARsolo residuals of DIVERGENCE.md §5

  #345·BenjaminDEMAILLE opened Oct 29, 2026Contributor·

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• Fix the four alignment residuals of DIVERGENCE.md §5

  #344·BenjaminDEMAILLE opened Oct 29, 2026Contributor·

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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)

  sensitive license
  #323·BenjaminDEMAILLE opened Oct 10, 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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• 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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• 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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• 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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