WIP BCF 2.2#1550

Draft

andersleung wants to merge 22 commits intosamtools:cn_vcf_headerfrom

ga4gh:bcf22writer

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 29, 2021

Add VCF 4.3 writing

Anders Leung
authored and
Anders Leung
committed
BCF 2.2 writing WIP

Anders Leung
authored and
Anders Leung
committed
Make scripts/install-bcftools.sh executable
Anders Leung
committed
Add installing bcftools step in github workflow
Anders Leung
committed

Commits on Nov 30, 2021

Update to bcftools 1.14, set env variable in github workflow
Anders Leung
committed
Add tests for BCF2Dictionary, refactor BCF2WriterUnitTest
Anders Leung
committed

Commits on Dec 6, 2021

Begin removing BCF 2.1, update tests files
Anders Leung
committed

Commits on Dec 7, 2021

Cleanup various TODOs, remove/fix failing tests
Anders Leung
committed
Fully remove BCF 2.1 encoder and decoder
Anders Leung
committed
Tag BCF lazy data with version, only use lazy data in BCF2Writer if versions match
Anders Leung
committed

Commits on Dec 8, 2021

Fix BCF lazy data version checking and genotype key computation
Anders Leung
committed

Commits on Dec 10, 2021

Match bcftools behavior when writing empty vectors
Anders Leung
committed
Fix spotbugs warning
Anders Leung
committed
Clean up BCF2Encoder, better error in BCF2FieldEncoder
Anders Leung
committed

Commits on Dec 14, 2021

Cleanup in BCF code
Anders Leung
committed

Commits on Dec 22, 2021

Add disabled test for missing Character and String VCF types
Anders Leung
committed

Commits on Dec 23, 2021

Change BCF2Dictionary interface to be immutable
Anders Leung
committed