All pull requests

Pull requests

• Advance countMatMult stride once per gene, not once per dedup option (fixes #2704)

  #2705·danielsharritt opened Sep 8, 2026·

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• fix C++ compatibility issues with operator>> on char*

  #2703·satta opened Aug 19, 2026Contributor·

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• Align in-memory splice-junction records

  #2699·justinblethrow-cloud opened Jul 15, 2026·

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• Initialize optional transcriptome state

  #2698·justinblethrow-cloud opened Jul 15, 2026·

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• Avoid unaligned packed index accesses

  #2697·justinblethrow-cloud opened Jul 15, 2026·

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• Bound inserted-sequence suffix comparisons

  #2696·justinblethrow-cloud opened Jul 15, 2026·

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• feat: native ARM64 / Apple Silicon and macOS clang build support

  #2694·BenjaminDEMAILLE opened Jun 26, 2026·

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• fix(macOS): spawn readFilesCommand via shell (posix_spawnp) so gzipped input works

  #2693·BenjaminDEMAILLE opened Jun 26, 2026·

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• fix(build): avoid parallel-make (-j) race on generated parametersDefault.xxd

  #2692·BenjaminDEMAILLE opened Jun 26, 2026·

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• Improve genomeGenerate multicore index build performance

  #2687·justinblethrow-cloud opened May 20, 2026·

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• Add persistent genome insertion with delta overlay mode

  #2686·justinblethrow-cloud opened May 17, 2026·

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• Replace limitGenomeGenerateRAM parameter by required memory

  #2680·entzian opened Apr 14, 2026·

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• Fix sjA/sjFilter/sjChunks memory leaks

  #2676·lkeegan opened Mar 4, 2026·

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• Add native CRAM output support (unsorted and coordinate-sorted) via HTSlib

  #2670·BenjaminDEMAILLE opened Oct 27, 2025·

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• Adding usegalaxy.org and usegalaxy.eu badges

  #2666·nekrut opened Oct 14, 2025·

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• Bugfix: Resolve race condition with FIFO cleanup and child process termination

  #2636·robsyme opened Jun 4, 2025·

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• Allow vW:i tag for wasp in SAM output

  #2617·ASLeonard opened Apr 11, 2025·

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• Silicon chip

  #2605·senku-kz opened Mar 2, 2025·

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• remove extraenous OOB write

  #2163·eternal-flame-AD opened Jun 28, 2024·

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• When soloOutFormatFeaturesGeneField3 is +, write GeneBiotype as FeaturesGeneField3.

  #2071·galaxy001 opened Feb 24, 2024·

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• Typo in manual? (genomeTransformVCF)

  #2029·TomHarrop opened Jan 2, 2024·

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  · 2.7.12

• Support SAM vector tags

  #2011·ohad-rodeh opened Nov 29, 2023·

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  · 2.7.12

• fix small typos in STARmanual.tex

  #1926·kew24 opened Aug 16, 2023·

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• fix: build under aarch64

  #1863·starsareintherose opened May 22, 2023·

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• Unbundle htslib

  #1586·SoapGentoo opened Jun 18, 2022Contributor·

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