bio2zarr 0.2.0

Feature release

on Python PyPI

Feature release: adds Zip output, (partial) support for Windows and improved Python API.

New features

• Add zip VCZ output support to CLI and Python APIs (#462).
• Add zipzarr CLI to make converting between .vcz and .vcz.zip straightforward (#470)
• Add in-memory VCZ output to Python API; convert() functions (vcf, plink, tskit) and vcf.encode() now return a zarr.Group (#462).
• Add plink2zarr Python API documentation (#462).
• Preliminary Windows support for tskit and plink conversion (#460)
• Add ancestral allele output (variant_AA) to tskit output (#469)
• vcf2zarr inspect now accepts a .vcz.zip archive in addition
  to a directory store (#471).

Breaking changes

• The stored sizes reported by vcf2zarr inspect no longer include filesystem inode overhead; they now report the compressed bytes as returned by Zarr's Array.nbytes_stored() (#471).
• Change the metadata format for distributed encode to drop the unused dimension_separator field. The metadata format version has been bumped from 0.1 to 0.2: any in-progress distributed dencode run started with an earlier version will now fail with a format-version-mismatch error at dencode-partition/dencode-finalise time and must be restarted from dencode-init. (#472)

Bug fixes

• vcf2zarr convert now accepts VCFs with zero variant records (plain, tabix-indexed, or CSI-indexed), producing a valid empty VCZ instead of crashing with an unrelated error (#478).
• Fix stdlib typing module shadowing caused by bio2zarr/typing.py, which broke the bio2zarr console script entry point (#461).
• Missing GT incorrectly marked as phased (#454)