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Commits on Sep 9, 2024

• Ensure --min-reads is a hard filter in CallDuplexConsensusReads (#1010)

  clintval

  authored
  ba61d26

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Commits on Jul 31, 2024

• feat: raise exception if CollectDuplexSeqMetrics run on consensus BAM (#1003)

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  znorgaard

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  6ca7733

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• Fix snapshot releases (#1004)

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  nh13

  authored
  ba11bfe

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Commits on Jul 16, 2024

• feat: SequenceMetadata can have name and length looked up by key (#1002)

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  nh13

  authored
  9a4b01d

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• Updated version to 2.3.1 Snapshot

  nh13

  committed
  c4e4bb6

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• Bumped version to 2.3.0

  nh13

  committed
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Commits on Jul 15, 2024

• doc: fix duplicate "the" in sequence dictionary docstrings (#1000)

  nh13

  authored
  fee6f52

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• Improve the list of tools in the README.md (#991)

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  nh13

  authored
  4331e0d

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• Validate IO in SortBam to provide nicer exceptions (#994)

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  nh13

  authored
  f228b32

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• feat: handle reverse-complemented UMIs in CopyUmiFromReadName (#958)

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  3 peopleauthored
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Commits on Jul 14, 2024

• Create CODEOWNERS (#999)

  nh13

  authored
  fc8e1c6

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Commits on May 30, 2024

• Add TemplateCoordinate sort order to the usage of SortBam (#993)

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  nh13

  authored
  8d31cf3

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Commits on May 21, 2024

• Add conda install instructions to README (#988)

  clintval

  authored
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Commits on May 16, 2024

• Merge pull request #985 from fulcrumgenomics/yfarjoun-typo-in-update-gff-contig-name

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  yfarjoun

  authored
  ba0788e

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Commits on May 15, 2024

• Update UpdateGffContigNames.scala (typo in docs)

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  yfarjoun

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  0cb7121

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Commits on Apr 30, 2024

• doc: update description of consenus tags for duplex (#983)

  nh13

  authored
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Commits on Apr 25, 2024

• Make PileupBuilder.includeMapPositionsOutsideFrInsert intuitively correct (#981)

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  clintval

  and

  nh13

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  a82cfe0

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Commits on Feb 9, 2024

• ZipperBams to produce mate score ("ms") for samtools markdup (#952)

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  nh13

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  3a74fd2

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Commits on Feb 1, 2024

• Fix typo in ExtractUmisFromBam.scala (#966)

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  nh13

  authored
  0a03aa9

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Commits on Jan 31, 2024

• fix: mapped header records should overwrite unmapped in ZipperBams (#963)

  nh13

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  371db03

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Commits on Jan 30, 2024

• fix: ensure that the GroupReadsByUmiTests for marking duplicates are (#962)

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  nh13

  authored
  d85efb9

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Commits on Jan 17, 2024

• PileupBuilder should not report insertions when checking the final mapped base before soft-clipping (#956)

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  jrm5100

  and

  clintval

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Commits on Jan 3, 2024

• Add a Zenodo DOI to the README (#955)

  nh13

  authored
  abb741b

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• Updated version to 2.2.2 Snapshot.

  nh13

  committed
  8b6f61f

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• Bumped version to 2.2.1

  nh13

  committed
  7a2ed42

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• Allow the PairedAssigner to use UMI pairs where one is absent (#954)

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  clintval

  authored
  97a9e06

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Commits on Dec 8, 2023

• Updated version to 2.2.1 Snapshot.

  tfenne

  committed
  9c475fd

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• Bumped version to 2.2.0

  tfenne

  committed
  c668e81

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• Addition of threading in GroupReadsByUmi and some other performance optimizations. (#950)

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  tfenne

  authored
  9bb97ed

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Commits on Oct 31, 2023

• Restore consensus calling for pairs with only one mapped read.

  tfenne

  committed
  ff1ca67

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Commits on Oct 26, 2023

• Alternative PR to add duplicate marking to GroupReadsByUmi (#940)

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  3 peopleauthored
  6fa1fde

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Commits on Oct 23, 2023

• Fix reference to transient MI tag in DuplexConsensusCaller (#946)

  clintval

  authored
  2363908

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Commits on Sep 26, 2023

• Suggest fqtk in DemuxFastqs (#939)

  nh13

  authored
  d748c76

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Commits on Sep 25, 2023

• Fix link in DemuxFastqs.scala (#938)

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  PeteHaitch

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  4c1917b

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Commits on Sep 11, 2023

• adds a barcode option to FastqToBam (#936)

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  bwlang

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  2af51ac

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