For now HTSJDK does not support BCF2.2 but sometimes you just want to only get the VCF header in a BCF file while you don't care about the variants . e.g:
search all the vcfs in your filesystem with given dictionary and for given sample(s)).
So this PR, overrides BCF2Codec.validateVersionCompatibility in VCFheaderReader so the validation is just ignored.
VCFheaderReader is then used in SamSequenceDictionaryExtractor instead of VCFReader so we can extract a dictionary from a BCF2.2 file
I added tests.
Things to think about before submitting:
[X] Make sure your changes compile and new tests pass locally.
[X] 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.
[X] Extended the README / documentation, if necessary
[X] Check your code style.
[X] 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.
Description
For now HTSJDK does not support BCF2.2 but sometimes you just want to only get the VCF header in a BCF file while you don't care about the variants . e.g:
So this PR, overrides
BCF2Codec.validateVersionCompatibilityin VCFheaderReader so the validation is just ignored.VCFheaderReader is then used in SamSequenceDictionaryExtractor instead of VCFReader so we can extract a dictionary from a BCF2.2 file
I added tests.
Things to think about before submitting: