Change local alleles default to false

[Will-Tyler]

Overview

vcf2zarr explode has a CLI option to create local-allele fields during the explode process. Currently, the CLI option's default value is true. This pull request changes the default value to false.

The default value should be false because the local alleles option is in an experimental stage of development. The current implementation does not save as much storage as hoped for and does not yet prevent the larger, global (non-local-allele) fields from being converted as well. See #277.

Testing

There are unit tests that test the default value of the local alleles option. I update those unit tests in this pull request.

References

• VCF v4.5 specification
  • The specification defines what the local-allele fields are.

• 277

  • This issue outlines the shortcomings of the current local alleles implementation.

[coveralls]

coverage: 98.91% (-0.001%) from 98.911% when pulling 4e0efca3db4a13fc8f5a8a538f592cd2b337e458 on Will-Tyler:local-alleles-default into 7c78a14f86cc27059de6c431369f97b4a13ae6fb on sgkit-dev:main.