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WIP BCF 2.2 #1550

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WIP BCF 2.2 #1550

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Commits on Nov 8, 2021

  1. Commit with raw GATK SequenceDictionaryUtils and SequenceDictionaryUt… 

    …ilsTest.
    @cmnbroad
    cmnbroad committed Nov 8, 2021
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Commits on Nov 9, 2021

  1. VCFHeader and VCFHeaderLine refactoring to enable support for VCF4.3/… 

    …BCF2.2 and bug fixes.
    @cmnbroad
    cmnbroad committed Nov 9, 2021
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Commits on Nov 15, 2021

  1. Eliminate redundant modeling of VCFHeaderVersion in VCFHeader.

    @cmnbroad
    cmnbroad committed Nov 15, 2021
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  2. Eliminate redundant modeling of file format lines in VCFMetaDataLines.

    @cmnbroad
    cmnbroad committed Nov 15, 2021
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  3. More code review comments.

    @cmnbroad
    cmnbroad committed Nov 15, 2021
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Commits on Nov 29, 2021

  1. Add VCF 4.3 writing

    Anders Leung authored and Anders Leung committed Nov 29, 2021
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  2. BCF 2.2 writing WIP

    Anders Leung authored and Anders Leung committed Nov 29, 2021
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  3. Make scripts/install-bcftools.sh executable

    Anders Leung committed Nov 29, 2021
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  4. Add installing bcftools step in github workflow

    Anders Leung committed Nov 29, 2021
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Commits on Nov 30, 2021

  1. Update to bcftools 1.14, set env variable in github workflow

    Anders Leung committed Nov 30, 2021
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  2. Add tests for BCF2Dictionary, refactor BCF2WriterUnitTest

    Anders Leung committed Nov 30, 2021
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Commits on Dec 6, 2021

  1. Begin removing BCF 2.1, update tests files

    Anders Leung committed Dec 6, 2021
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Commits on Dec 7, 2021

  1. Cleanup various TODOs, remove/fix failing tests

    Anders Leung committed Dec 7, 2021
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  2. Fully remove BCF 2.1 encoder and decoder

    Anders Leung committed Dec 7, 2021
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  3. Tag BCF lazy data with version, only use lazy data in BCF2Writer if v… 

    …ersions match
    Anders Leung committed Dec 7, 2021
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Commits on Dec 8, 2021

  1. Fix BCF lazy data version checking and genotype key computation

    Anders Leung committed Dec 8, 2021
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Commits on Dec 10, 2021

  1. Match bcftools behavior when writing empty vectors

    Anders Leung committed Dec 10, 2021
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  2. Fix spotbugs warning

    Anders Leung committed Dec 10, 2021
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  3. Clean up BCF2Encoder, better error in BCF2FieldEncoder

    Anders Leung committed Dec 10, 2021
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Commits on Dec 14, 2021

  1. Cleanup in BCF code

    Anders Leung committed Dec 14, 2021
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Commits on Dec 22, 2021

  1. Add disabled test for missing Character and String VCF types

    Anders Leung committed Dec 22, 2021
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Commits on Dec 23, 2021

  1. Change BCF2Dictionary interface to be immutable

    Anders Leung committed Dec 23, 2021
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