WIP BCF 2.2

[andersleung]

Description

WIP PR just to keep track of progress. Implements BCF 2.2 reading and writing. Not mergeable yet because of some outstanding questions about the interpretation of the spec and missing/failing tests.

Things to think about before submitting:

• Make sure your changes compile and new tests pass locally.
• Add new tests or update existing ones:
  • A bug fix should include a test that previously would have failed and passes now.
  • New features should come with new tests that exercise and validate the new functionality.
• Extended the README / documentation, if necessary
• Check your code style.
• Write a clear commit title and message
  • The commit message should describe what changed and is targeted at htsjdk developers
  • Breaking changes should be mentioned in the commit message.

[codecov-commenter]

Codecov Report

Merging #1550 (f8583e2) into cn_vcf_header (d233891) will increase coverage by 0.093%.
The diff coverage is 80.441%.

❗ Current head f8583e2 differs from pull request most recent head b54ae82. Consider uploading reports for the commit b54ae82 to get more accurate results

@@                  Coverage Diff                  @@
##             cn_vcf_header     #1550       +/-   ##
=====================================================
+ Coverage           69.927%   70.019%   +0.093%     
- Complexity            9830      9894       +64     
=====================================================
  Files                  706       710        +4     
  Lines                38120     38668      +548     
  Branches              6188      6292      +104     
=====================================================
+ Hits                 26656     27075      +419     
- Misses                8987      9094      +107     
- Partials              2477      2499       +22     

Impacted Files	Coverage Δ
...va/htsjdk/samtools/SAMSequenceDictionaryUtils.java	96.610% <ø> (ø)
...main/java/htsjdk/samtools/util/FileExtensions.java	80.000% <ø> (ø)
...n/java/htsjdk/variant/vcf/VCFFilterHeaderLine.java	90.909% <ø> (-0.395%)	⬇️
...main/java/htsjdk/variant/vcf/VCFHeaderVersion.java	79.412% <ø> (+4.412%)	⬆️
...htsjdk/variant/vcf/VCFPassThruTextTransformer.java	50.000% <0.000%> (-50.000%)	⬇️
...in/java/htsjdk/variant/vcf/VCFVersionUpgrader.java	0.000% <0.000%> (ø)
...c/main/java/htsjdk/tribble/index/IndexFactory.java	73.410% <25.000%> (-0.859%)	⬇️
src/main/java/htsjdk/variant/vcf/VCFEncoder.java	77.578% <46.667%> (-10.805%)	⬇️
.../htsjdk/variant/variantcontext/VariantContext.java	76.256% <50.000%> (-2.200%)	⬇️
...tsjdk/variant/variantcontext/writer/VCFWriter.java	77.907% <50.000%> (+0.456%)	⬆️
... and 58 more

[lindenb]

Hi all, is there anything new about this old PR ? I'm working more and more with intermediate uncompressed BCF files and I would love to handle this with htsjdk without converting the stream to VCF :-)

thanks !

[cmnbroad]

@lindenb This PR is dependent on both #1581 and #1596. I wish I could be more definitive - I still hope to get these merged somehow, but until then this PR will have to remain as draft.