More flexible VCF support

• Add support for merging contig IDs across multiple VCFs (#335)

• Add support for unindexed (and uncompressed) VCFs (#337)

Bugfix release

• Fix bug in handling all-missing genotypes (#328)

Bugfix for packaging

Minor packaging bugfix release

• Fix missing dependency issue for packaging
• Support out-of-order field definitions in the VCF header (#322, @ACEnglish)

Feature release

Various bugfixes and improvements:

• Numpy >= 1.26 and 2.x support
• Change default chunk size from 10,000 variants x 1,000 samples to 1,000 variants x 10,000 samples
• Add chunk size options to mkschema

Experimental:

• Initial support for local alleles (via --local-alleles option to mkschema)
• Experimental region_index array to support range queries

Breaking:

• ICF metadata format version was bumped to ensure long-term compatility between numpy 1.26.x and numpy >= 2. Existing ICFs will need to be recreated.

Maintenance release

Maintenance release to minimise impact of upstream version changes.

• Pin numpy to < 2
• Pin Zarr to < 3

Initial stable release

This is the first stable release of bio2zarr, in which vcf2zarr and vcfpartition are considered production ready.

Bugfix

Fixes bugs in progress reporting on macs.

Bugfixes on intermediate format

Breaking changes on ICF, older files will need to be re-exploded.

Packaging bugfix

Same as 0.0.7 with packaging bugfix

Improved distributed encode

Updated distributed encode + some bug fixes