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Commits on Jan 12, 2023

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

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Commits on Dec 24, 2022

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

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Commits on Nov 29, 2022

• Update Gradle to 7.5.1 (broadinstitute#8098)

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Commits on Nov 7, 2022

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

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Commits on Oct 25, 2022

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

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Commits on Oct 12, 2022

• Upgrade htsjdk to v3.0.1 and picard to 2.27.5 (broadinstitute#8025)

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Commits on Oct 11, 2022

• Updating gsalib version to 2.2.1 (broadinstitute#8048)

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Commits on Sep 27, 2022

• Update protobuf to 3.21.6 (broadinstitute#8036)

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Commits on Apr 27, 2022

• fix initial 0 downloads bug (broadinstitute#7794)

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Commits on Apr 7, 2022

• Fix Google Cloud requester pays access harder. broadinstitute#7716 (broadinstitute#7730)

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Commits on Mar 17, 2022

• Docker build only lfs pulls main/src/resources/large (broadinstitute#7727)

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Commits on Feb 17, 2022

• install lfs with --force (broadinstitute#7682)

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Commits on Feb 7, 2022

• Adding back jcenter repository resolver (broadinstitute#7665)

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Commits on Jan 4, 2022

• Update log4j to 2.17.1 (broadinstitute#7624)

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Commits on Dec 21, 2021

• Upgrade log4j to 2.17.0 to mitigate another newly discovered issue (broadinstitute#7615)

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Commits on Dec 8, 2021

• Remove file causing git lfs error (broadinstitute#7594)

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• Remove outdated javadoc line in AssemblyBasedCallerUtils (broadinstitute#7554)

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Commits on Oct 29, 2021

• Adding comment to .travis.yml about the checkout depth (broadinstitute#7421)

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Commits on Oct 27, 2021

• Set gcloud config directory in travis (broadinstitute#7525)

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• Rotating travis secrets part 1 and 2 (broadinstitute#7521)

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Commits on Oct 26, 2021

• Update sqllite library to support M1 Macs (broadinstitute#7519)

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Commits on Jul 28, 2021

• Improve error message in GenomicsDBImport (broadinstitute#7375)

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Commits on May 14, 2021

• Always login to docker on travis instead of qualifying it (broadinstitute#7256)

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Commits on Apr 20, 2021

• Updating to the new artifactory key. (broadinstitute#7208)

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Commits on Apr 15, 2021

• Authenticating to dockerhub in travis build (broadinstitute#7204)

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Commits on Mar 29, 2021

• Update htsjdk to 2.24.1 (broadinstitute#7149)

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Commits on Feb 10, 2021

• Update Picard to 2.25.0 (broadinstitute#7075)

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Commits on Feb 9, 2021

• Update htsjdk to 2.24.0 (broadinstitute#7073)

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Commits on Sep 3, 2020

• Improving exception messages in AssemblyRegion for contigs not in reference dictionary (broadinstitute#6781)

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Commits on Sep 1, 2020

• Improve error message in GATKRead.setMatePosition (broadinstitute#6779)

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Commits on Aug 26, 2020

• Fix CountBasesSpark crash when using -L (broadinstitute#6767)

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Commits on Aug 6, 2020

• Fix a performance regression in SelectVariants (broadinstitute#6729)

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Commits on Jul 17, 2020

• Update htsjdk to 2.23.0 (broadinstitute#6702)

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Commits on Jun 29, 2020

• Removing doc reference to gatk3 annotation that not longer exists (broadinstitute#6679)

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Commits on Jun 24, 2020

• Fix crash in BQSR R script (broadinstitute#6677)

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