Rename ByteArrayAlelle to SimpleAllele and make it public

samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

http://samtools.github.io/htsjdk/

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Rename ByteArrayAlelle to SimpleAllele and make it public #1576

Closed lbergelson closed 2 years ago

lbergelson commented 2 years ago

When we refactored Allele into an interface we made the implementation package protected.
This caused problems for downstream tools which previously subclassed allele.
Making the implementation public so that there is an equivalent class to subclass as a base for downstream implementations.

lbergelson commented 2 years ago

@cmnbroad I updated the doc with your suggestions. Do you think the name SimpleAllele is ok? ByteArrayAllele was more descriptive of the implementation but seemed a bit over prescribed.