v0.14.1

What's Changed

• Fix bug in applying site_mask parameter in Amin1 by @alimanfoo in #77

Full Changelog: v0.14.0...v0.14.1

v0.14.0

Highlights

• Adds the Amin1 class providing access to the Anopheles minimus
  Amin1 SNP data release.

Pull requests

• Amin1 by @alimanfoo in #75

Full Changelog: v0.12.1...v0.14.0

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