v7.0.5

What's Changed

• Fix WGS data catalogs for Ag3.0 release to use Sanger S3 by @alimanfoo in #303

Full Changelog: v7.0.4...v7.0.5

v7.0.4

What's Changed

• Avoid broken ipinfo by @alimanfoo in #300
• Try Python 3.10 by @alimanfoo in #301

Full Changelog: v7.0.3...v7.0.4

v7.0.3

What's Changed

• Fix haplotype network grey pie segments for countries with a space in the name by @alimanfoo in #298

Full Changelog: v7.0.2...v7.0.3

v7.0.2

Fix version metadata.

Full Changelog: v7.0.1...v7.0.2

v7.0.1

What's Changed

• adds title to plot_haplotype_clustering function by @sanjaynagi in #296
• Add release notes for Pv4 and Pf7 by @kathryn1995 in #297

Full Changelog: v7.0.0...v7.0.1

v7.0.0

Highlights

• Adds H1X statistics for detecting shared selective sweeps, via Ag3.h1x_gwss() and Ag3.plot_h1x_gwss() functions.
• Adds Ag3.plot_haplotype_clustering() to visualise hierarchical clustering of haplotypes from a given genome region.
• Adds Ag3.plot_haplotype_network() to visualise a median-joining network of haplotypes from a given genome region.
• Adds the Pv4 and Pf7 classes for accessing data in the Plasmodium releases.
• Add Pv4.sample_metadata() and Pf7.sample_metadata() functions for accessing metadata.
• Add Pv4.variant_calls() and Pf7.variant_calls() functions for accessing variant calls.
• Add Pv4.genome_features() and Pf7.genome_features() functions for accessing the genome feature annotations.
• Add Pv4.genome_sequence() and Pf7.genome_sequence() functions for accessing the reference genome sequence.

What's Changed

• Implement H1X statistic for detecting shared selective sweeps by @alimanfoo in #283
• Implement interactive haplotype cluster plot by @sanjaynagi in #285
• Haplotype median-joining networks implementation by @alimanfoo in #287
• Af1.0 by @leehart in #289
• v7.0.0 release prep by @leehart in #292

New Contributors

• @sanjaynagi made their first contribution in #285

Full Changelog: v6.1.1...v7.0.0

v6.1.1

Updates client location message, adds haplotype progress bar and makes sample_sets/sample_query parameters optional in H12 functions.

v6.1.0

Highlights

• Adds cohort_size parameter to Ag3.haplotypes() function.
• Adds Ag3.h12_calibration() and Ag3.plot_h12_calibration() functions to generate and plot h12 calibration data for different window sizes.
• Adds Ag3.h12_gwss(), Ag3.plot_h12_gwss_track() and Ag3.plot_h12_gwss() to generate and plot h12 analyses.
  (GH272)
• Fixes bug where in Google Colab notebooks, debug logging couldn't be turned off.
  (GH274)

What's Changed

• GWSS method by @cclarkson in #272
• Misc Ag3 tweaks by @alimanfoo in #267
• Fixes DEBUG bug by @cclarkson in #274
• 6.1.0 update by @cclarkson in #275

Full Changelog: v6.0.1...v6.1.0

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