Published July 16, 2024 | Version 2.3.0
Software Open

fulcrumgenomics/fgbio: Release 2.3.0

  • 1. @fulcrumgenomics
  • 2. Fulcrum Genomics
  • 3. @twinstrandbio
  • 4. Bio-Rad Laboratories
  • 5. @bwlang
  • 6. TwinStrand Biosciences

Description

What's Changed

  • Add a Zenodo DOI to the README by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/955
  • PileupBuilder should not report insertions when checking the final mapped base before soft-clipping by @jrm5100 in https://github.com/fulcrumgenomics/fgbio/pull/956
  • fix: ensure that the GroupReadsByUmiTests for marking duplicates are by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/962
  • fix: mapped header records should overwrite unmapped in ZipperBams by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/963
  • Fix typo in ExtractUmisFromBam.scala by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/966
  • ZipperBams to produce mate score ("ms") for samtools markdup by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/952
  • Make PileupBuilder.includeMapPositionsOutsideFrInsert intuitively correct by @clintval in https://github.com/fulcrumgenomics/fgbio/pull/981
  • doc: update description of consenus tags for duplex by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/983
  • Update UpdateGffContigNames.scala (typo in docs) by @yfarjoun in https://github.com/fulcrumgenomics/fgbio/pull/985
  • Add conda install instructions to README by @clintval in https://github.com/fulcrumgenomics/fgbio/pull/988
  • Add TemplateCoordinate sort order to the usage of SortBam by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/993
  • Create CODEOWNERS by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/999
  • feat: add --umi-prefix to CopyUmiFromReadName by @msto in https://github.com/fulcrumgenomics/fgbio/pull/958
  • Validate IO in SortBam to provide nicer exceptions by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/994
  • Improve the list of tools in the README.md by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/991
  • doc: fix duplicate "the" in sequence dictionary docstrings by @nh13 in https://github.com/fulcrumgenomics/fgbio/pull/1000

New Contributors

  • @yfarjoun made their first contribution in https://github.com/fulcrumgenomics/fgbio/pull/985
  • @msto made their first contribution in https://github.com/fulcrumgenomics/fgbio/pull/958

Full Changelog: https://github.com/fulcrumgenomics/fgbio/compare/2.2.1...2.3.0

Files

fulcrumgenomics/fgbio-2.3.0.zip

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Additional details

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