v6.0.1

What's Changed

• Fix sample metadata dtype by @alimanfoo in #261
• Prep v6.0.1 by @alimanfoo in #262

Full Changelog: v6.0.0...v6.0.1

v6.0.0

Highlights

• Add Ag3.plot_heterozygosity()
• Add Ag3.cohort_diversity_stats() and Ag3.diversity_stats() with supporting functions
• Add Ag3.plot_samples_interactive_map()
• Add Ag3.count_samples()
• Add Ag3.roh_hmm() and Ag3.plot_roh() with supporting functions

What's Changed

• Workshop 5 dev by @alimanfoo in #258
• prep v6.0.0 [ci skip] by @alimanfoo in #259

Full Changelog: v5.1.0...v6.0.0

v5.1.0

Highlights

• Upgrade the default cohorts analysis in the Ag3 class to 20220608
  (GH256).

What's Changed

• Update default cohorts analysis for ag3 to 20220608 by @leehart in #256
• v5.1.0 release prep by @leehart in #257

Full Changelog: v5.0.1...v5.1.0

v5.0.1

What's Changed

• Use blank DataFrame when species calls are missing by @leehart in #251
• Prep v5.0.1 by @leehart in #254

Full Changelog: v5.0.0...v5.0.1

v5.0.0

Highlights

• Upgrade the default species analysis in the Ag3 class to use a new
  set of improved ancestry-informative markers (AIMs). Note that this
  includes a small change to the values in the aim_species column of
  the sample metadata: the value "intermediate_arabiensis_gambiae" has
  been replaced by "intermediate_gambcolu_arabiensis" for consistency
  with AIM naming conventions used elsewhere.
• Add Ag3.aim_calls() and Ag3.plot_aim_heatmap() functions for
  accessing and plotting ancestry-informative marker (AIM) genotypes
  (GH236).
• Add site filters tracks to IGV via Ag3.view_alignments()
  (GH246).

What's Changed

• Add new and improved AIMs by @alimanfoo in #245
• Maintenance 2022-05-31 by @alimanfoo in #247
• Prep v5.0.0 by @alimanfoo in #249

Full Changelog: v4.4.0...v5.0.0

v4.4.0

Highlights

• Add Ag3.aim_variants() function
  (GH233).
• Enable plotting high coverage variance samples with
  Ag3.plot_cnv_hmm_coverage()
  (GH240).

What's Changed

• Fix Ag3.plot_cnv_hmm_coverage() by @alimanfoo in #241
• Implements ag3.aim_sites() by @cclarkson in #234
• v4.4.0 prep by @alimanfoo in #242

Full Changelog: v4.3.1...v4.4.0

v4.3.1

What's Changed

• Tweak Ag3 repr - add "client" by @alimanfoo in #230
• Fix broken igv notebook by @alimanfoo in #238
• Use blank DataFrame when cohorts metadata are missing by @leehart in #235
• Prep v4.3.1 by @alimanfoo in #239

Full Changelog: v4.3.0...v4.3.1

v4.3.0

Highlights

• Add Ag3.plot_snps() to plot segregating and non-segregating SNPs and
  visualise site filters
  (GH226).

What's Changed

• Plot SNPs and site filters by @alimanfoo in #227
• v4.3.0 release prep by @alimanfoo in #228

Full Changelog: v4.2.0...v4.3.0

v4.2.0

Highlights

• Add progress bars for longer-running computations using tqdm
  (GH217).
• Add SNP genotypes to Ag3.view_alignments()
  (GH216).

What's Changed

• Add SNP genotypes to Ag3.view_alignments by @alimanfoo in #219
• Use tqdm to show progress during longer-running computations by @alimanfoo in #218
• IGV tweaks by @alimanfoo in #220
• Simplify allele frequencies implementations vis-a-vis handling sample queries by @alimanfoo in #221
• Use debug logging by @alimanfoo in #222
• Prep v4.2.0 by @alimanfoo in #223

Full Changelog: v4.1.0...v4.2.0

v4.1.0

Highlights

• Use pypi for igv-notebook dependency
  (GH209).
• Add sample_query parameter to Ag3.haplotypes()
  (GH210).
• Add sample_query and max_coverage_variance parameters to
  Ag3.cnv_hmm() and Ag3.gene_cnv()
  (GH213).

What's Changed

• Depend on igv-notebook by @alimanfoo in #212
• Add parameters to Ag3.haplotypes() and Ag3.cnv_hmm() by @alimanfoo in #214
• Prep v4.1.0 release by @alimanfoo in #215

Full Changelog: v4.0.1...v4.1.0