v0.5.0

Highlights

• Ag3: Add snp_allele_frequencies().

• Ag3: Add snp_effects().

• Ag3: Add cnv_hmm(), cnv_coverage_calls() and
  cnv_discordant_read_calls().

• Speed up test suite via caching.

• Add configuration for pre-commit hooks.

What's Changed

• Variant effects prototyping by @alimanfoo in #6
• Ag3 snp effects updates by @cclarkson in #26
• ag3.snp_allele_frequencies() by @cclarkson in #28
• Setup pre-commit by @alimanfoo in #29
• Ag3 CNV methods by @alimanfoo in #31
• Optimise snp effects by @cclarkson in #32
• Prep v0.5.0 release by @alimanfoo in #34

Full Changelog: v0.4.3...v0.5.0

v0.4.0

Highlights

• Ag3: Make public the open_genome(), open_snp_sites(), open_site_filters() and open_snp_genotypes() methods.

• Ag3: Add the cross_metadata() method.

• Ag3: Add site_annotations() and open_site_annotations() methods.

• Ag3: Add the snp_calls() method.

• Improve unit tests.

• Improve memory usage.

What's Changed

• Ag3 by @alimanfoo in #1
• s/cohort/sample_sets/ by @alimanfoo in #2
• Rename seq_id to contig by @alimanfoo in #3
• Fix path for fsspec changes by @alimanfoo in #7
• Misc enhancements by @alimanfoo in #11
• Add CI via github action by @alimanfoo in #18
• Ag3 SNP xarray dataset enhancements by @alimanfoo in #17
• Improve memory; support inline_array by @alimanfoo in #20

Full Changelog: https://github.com/malariagen/malariagen-data-python/commits/v0.4.0