v0.12.1

Bug fix to Ag3.sample_cohorts()

sample_sets parameter can now be a list of sample sets.

v0.12.0

Updates cohort parameters to latest analysis.

What's Changed

• gene_cnv_frequencies - fixes pandas fragment warning by @cclarkson in #68
• Upgrade cohorts_analysis to 20210927 by @cclarkson in #66
• updates docs for 0.12.0 release by @cclarkson in #71

Full Changelog: v0.11.0...v0.12.0

v0.11.0

Highlights

• Ag3: Add support for standard cohorts in the functions
  snp_allele_frequencies() and gene_cnv_frequencies().

What's Changed

• Adds cohort access to SNP and CNV frequency methods by @cclarkson in #61
• 0.11.0 release prep by @cclarkson in #63

Full Changelog: v0.10.0...v0.11.0

v0.10.0

Highlights

• Adds ag3.sample_cohorts()

What's Changed

• Cohort access by @cclarkson in #58
• 0.10.0 release prep by @cclarkson in #60

Full Changelog: v0.9.0...v0.10.0

v0.9.0

Highlights

• Ag3: Add haplotypes() and supporting functions open_haplotypes() and open_haplotype_sites().

What's Changed

• Reverse expected/actual in tests by @cclarkson in #53
• Raise error if zero samples selected for allele frequency calculations by @cclarkson in #52
• Add Ag3.haplotypes() implementation and tests by @alimanfoo in #54

Full Changelog: v0.8.0...v0.9.0

v0.8.0

Highlights

• Ag3: Add site filter columns to dataframes returned by snp_effects() and snp_allele_frequencies().

What's Changed

• Add site filter columns to SNP dataframes by @alimanfoo in #48

Full Changelog: v0.7.0...v0.8.0

v0.7.0

Highlights

• Ag3: Rename parameter "populations" to "cohorts" to be consistent with sgkit terminology.

What's Changed

• Rename populations to cohorts by @alimanfoo in #47

Full Changelog: v0.6.0...v0.7.0

v0.6.0

Highlights

• Ag3: Add gene_cnv() and gene_cnv_frequencies().
• Ag3: Improvements and maintenance to snp_effects() and snp_allele_frequencies().

What's Changed

• Maintenance on SNP effects and allele frequencies functions by @alimanfoo in #45
• Add methods for computing copy number variation by gene by @alimanfoo in #38

Full Changelog: v0.5.0...v0.6.0

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