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Java 17 and Spark 3.3.0.#8035

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lbergelson merged 36 commits intomasterbroadinstitute/gatk:masterfrom cn_java_17broadinstitute/gatk:cn_java_17Copy head branch name to clipboardMar 2, 2023

+1,531-1,579

Commits

Commits on Feb 28, 2023

• Java 17/Spark 3.3.0.

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• Move the --add-opens directives to the jar file.

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• Fix bad dependency picked up in rebase.

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• Repair README.md.

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• changing non-Docker from 17 to 17.0.1+12

  

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• Update ModelSegments expected results for Java 17.0.1+12.

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• Update scala to fix DirectBuffer access issue.

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• Fix scala dependencies.

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• Update Spark version.

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• Repair manifest syntax.

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• Clean up build aand test files.

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• Java 17 doclets.

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• Port gatkWDLGen doclet to Java 17.

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• Update to Barclay 5.0.0.

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• Rebase, resolve, clean up.

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• Upgrade to Picard 3.0.0.

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• Fix ClassFinder references.

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• Remove javadoc command from WDLGen and TabCompletion test, since its no longer needed in v17.

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• Now on htsjdk 3.0.5.

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• Remove obsolete jitpack.

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• Remove obsolete (and unnecessary/problematic) langauge directive.

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• Align java version.

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• Revert "Update ModelSegments expected results for Java 17.0.1+12."

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• Capture documentation generation integration test output.

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• Remove google cloud apt-key update.

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• Code review comments, plus capture doc gen test output.

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• Restore kryo version change.

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• Make docgen smoke tests non-docker only.

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• Remove unused scala version variable.

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• Revert unnecessary debugging change to IntegrationTestSpec.

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• Revert transient modifier from CachingIndexedFastaSequenceFile.

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• One more -add-opens.

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• And one more --add-opens.

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• Revert "And one more --add-opens."

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• Revert "One more -add-opens."

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• Revert "Revert transient modifier from CachingIndexedFastaSequenceFile."

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