Add VCF 4.3 writing#1548

Draft

andersleung wants to merge 14 commits intosamtools:cn_vcf_headerfrom

ga4gh:vcf43writer

Commits on Nov 8, 2021

Commit with raw GATK SequenceDictionaryUtils and SequenceDictionaryUtilsTest.
cmnbroad
committed

Commits on Nov 9, 2021

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

Commits on Nov 15, 2021

Commits on Nov 23, 2021

Changes needed to port GATK over to htsjdk SAMSequenceDictionaryUtils.
cmnbroad
committed

Commits on Nov 30, 2021

One more code review comment fix.
cmnbroad
committed

Commits on Dec 6, 2021

Make VCFMetaDataLines public/@InternalAPI to allow consumers access for customs serialization.
cmnbroad
committed

Commits on Dec 7, 2021

Add VCF 4.3 writing

Anders Leung
authored and
Anders Leung
committed
Refactor VariantContext decoding, decode VCs with different version from header on write
Anders Leung
committed

Commits on Dec 9, 2021

Move version upgrading from codec to VCFWriter
Anders Leung
committed

Commits on Dec 10, 2021

Fix PrintVariantsExampleTest
Anders Leung
committed

Commits on Dec 17, 2021

Add javadoc
Anders Leung
committed

Commits on Dec 23, 2021

Address some review comments
Anders Leung
committed