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VCF 4.3 writing.#1596

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cmnbroad wants to merge 24 commits intomastersamtools/htsjdk:masterfrom cn_vcf43_writersamtools/htsjdk:cn_vcf43_writerCopy head branch name to clipboard

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Commits on Mar 13, 2023

• Commit with raw GATK SequenceDictionaryUtils and SequenceDictionaryUtilsTest.

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• VCFHeader and VCFHeaderLine refactoring to enable support for VCF4.3/BCF2.2 and bug fixes.

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• Eliminate redundant modeling of VCFHeaderVersion in VCFHeader.

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• Eliminate redundant modeling of file format lines in VCFMetaDataLines.

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• More code review comments.

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• Changes needed to port GATK over to htsjdk SAMSequenceDictionaryUtils.

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• One more code review comment fix.

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• Make VCFMetaDataLines public/@internalapi to allow consumers access for customs serialization.

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• Versioned header line validation framework.

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• Remove obsolete variable.

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Commits on Jun 27, 2023

• Properly handle info fields with embedded spaces by VCF version.

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• Remove unnecessary null test.

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• Properly handle info fields with embedded spaces by VCF version.

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• Add VCF 4.3 writing

  

  Anders Leung

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• Refactor VariantContext decoding, decode VCs with different version from header on write

  

  Anders Leung

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• Move version upgrading from codec to VCFWriter

  

  Anders Leung

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• Fix PrintVariantsExampleTest

  

  Anders Leung

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• Add javadoc

  

  Anders Leung

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• Address some review comments

  

  Anders Leung

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• Add an encoder and write support for the VCF4.3 HtsCodec.

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• Remove obsolete VCFHeaderVersion method.

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• Unify validation failure framework.

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• Fix spotbugs issue.

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• Preserve more context for header mergers that fail due to version validation.

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