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Commits on May 30, 2024

• Create gradle.yml

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  oeh77

  authored
  e9240cd

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Commits on Feb 6, 2023

• Fixed gCNV bug that breaks the inference when only 2 intervals are provided. (broadinstitute#8180)

  asmirnov239

  authored
  110f4f5

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Commits on Feb 1, 2023

• Make several Funcotator methods and fields protected so it is easiest to extend the tool (broadinstitute#8166)

  bbimber

  authored
  d1a4f94

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Commits on Jan 28, 2023

• bug in dynamic read disqualification fixed (broadinstitute#8171)

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  ilyasoifer

  authored
  a3c1d2c

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Commits on Jan 12, 2023

• Fix NPE from unintialized logger in GenotypingEngine (broadinstitute#8159)

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  lbergelson

  authored
  43e2d04

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Commits on Jan 7, 2023

• SelectVariants JEXL filter fixes and refactor (broadinstitute#8092)

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  takutosato

  authored
  9f77b1f

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Commits on Jan 5, 2023

• minor documentation fix (broadinstitute#8145)

  jamesemery

  authored
  9ced727

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Commits on Jan 3, 2023

• Recognize MEI DELs with ALT format <DEL:ME> in SVAnnotate (broadinstitute#8125)

  epiercehoffman

  authored
  3687415

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Commits on Dec 24, 2022

• Removed commented lines from somatic CNV WDL. (broadinstitute#8130)

  samuelklee

  authored
  0261d43

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• Replace File.createTempFile with IOUtils.createTempFile (broadinstitute#6780)

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  lbergelson

  authored
  ba2b5b3

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Commits on Dec 23, 2022

• Improvements to PileupDetectionArgumentCollection documentation (broadinstitute#8050)

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  Yossi Farjoun

  authored
  16fc4f1

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• removed two ancient and unused test files that are probably no-longer needed (broadinstitute#7634)

  jamesemery

  authored
  4e97a8b

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• Add GenomicsDBArgumentCollection to CreateSomaticPanelOfNormals tool (broadinstitute#6746)

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  nalinigans

  authored
  9ffd649

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• Fix asynchronous Python exception propagation in StreamingPythonExecutor/CNNScoreVariants. (broadinstitute#7402)

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  cmnbroad

  authored
  aa05918

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• Test for presence of ack result message and simplify ProcessControllerAckResult API. (broadinstitute#7816)

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  cmnbroad

  authored
  7f40444

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• fixed DirichletAlleleDepthAndFractionIntegrationTest (broadinstitute#7963)

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  jamesemery

  authored
  b203569

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• Added a slightly more helpful error message to the reads filter (broadinstitute#7947)

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  jamesemery

  authored
  640d921

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• Move to GenomicsDB 1.4.4 (broadinstitute#7978)

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  nalinigans

  authored
  6932ae5

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• Don't require python to just instantiate tool classes. (broadinstitute#8128)

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  cmnbroad

  authored
  633aa4a

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Commits on Dec 19, 2022

• Add DeprecatedFeature annotation. (broadinstitute#8100)

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  cmnbroad

  authored
  273bfa9

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Commits on Dec 16, 2022

• Made several Funcotator methods and fields protected so it is easier to extend the tool (broadinstitute#8124)

  bbimber

  authored
  564be54

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Commits on Dec 14, 2022

• Refactored JointVcfFiltering WDL and expanded tests. (broadinstitute#8074)

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  samuelklee

  authored
  757112f

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• bugfix for type of some output files (broadinstitute#6735)

  slzhao

  authored
  c5bccee

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Commits on Dec 7, 2022

• Remove hardcoded limit on max homopolymer call (broadinstitute#8088)

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  ilyasoifer

  authored
  84ade40

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Commits on Nov 29, 2022

• Update Gradle to 7.5.1 (broadinstitute#8098)

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  lbergelson

  authored
  894117c

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• Use Java 11.0.11+9 for testing, upgrade hadoop to v3.3.1. (broadinstitute#8102)

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  cmnbroad

  and

  lbergelson

  authored
  ba7678e

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Commits on Nov 10, 2022

• Update instructions for installing Java 8 in the README (broadinstitute#8089)

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  droazen

  authored
  ca33bc9

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Commits on Nov 7, 2022

• Fixing the path reported by the gatkbot when there are test failures (broadinstitute#8069)

  lbergelson

  authored
  4e17418

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Commits on Nov 3, 2022

• VariantAnnotator fails when the variant contains too many alleles (broadinstitute#8075)

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  ilyasoifer

  authored
  63c548b

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Commits on Nov 2, 2022

• Updated the carrot github action workflow to the most recent version, which supports using #carrot_pr to trigger branch vs master comparison runs (broadinstitute#8084)

  KevinCLydon

  authored
  b652c1a

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Commits on Oct 25, 2022

• Require commons-text 1.10.0 to fix vulnerability (broadinstitute#8071)

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  lbergelson

  authored
  61b817a

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Commits on Oct 24, 2022

• Adding argument to GenotypeGVCFs to keep specified raw annotations (broadinstitute#7996)

  meganshand

  authored
  90bf668

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• Fixing issue in ShiftFasta where the interval list output is never written (broadinstitute#8070)

  meganshand

  authored
  277bf00

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Commits on Oct 21, 2022

• require reference as asserted in documentation (broadinstitute#8067)

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  tmelman

  authored
  9321181

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Commits on Oct 13, 2022

• don't sort rejected reads output from AnalyzeSaturationMutagenesis (broadinstitute#8053)

  tedsharpe

  authored
  07a8278

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