Malariagen-data

Latest version: v15.0.1

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6.0.1

What's Changed
* Fix sample metadata dtype by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/261
* Prep v6.0.1 by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/262


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v6.0.0...v6.0.1

6.0.0

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 https://github.com/malariagen/malariagen-data-python/pull/258
* prep v6.0.0 [ci skip] by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/259


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v5.1.0...v6.0.0

5.1.0

**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v5.0.1...v5.1.0

5.0.1

What's Changed
* Use blank DataFrame when species calls are missing by leehart in https://github.com/malariagen/malariagen-data-python/pull/251
* Prep v5.0.1 by leehart in https://github.com/malariagen/malariagen-data-python/pull/254


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v5.0.0...v5.0.1

5.0.0

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been replaced by "intermediate_gambcolu_arabiensis" for consistency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](https://github.com/malariagen/malariagen-data-python/issues/236)).
* Add site filters tracks to IGV via `Ag3.view_alignments()`
([GH246](https://github.com/malariagen/malariagen-data-python/issues/246)).


What's Changed
* Add new and improved AIMs by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/245
* Maintenance 2022-05-31 by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/247
* Prep v5.0.0 by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/249


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v4.4.0...v5.0.0

4.4.0

Highlights
* Add `Ag3.aim_variants()` function
([GH233](https://github.com/malariagen/malariagen-data-python/issues/233)).
* Enable plotting high coverage variance samples with
`Ag3.plot_cnv_hmm_coverage()`
([GH240](https://github.com/malariagen/malariagen-data-python/issues/240)).


What's Changed
* Fix Ag3.plot_cnv_hmm_coverage() by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/241
* Implements ag3.aim_sites() by cclarkson in https://github.com/malariagen/malariagen-data-python/pull/234
* v4.4.0 prep by alimanfoo in https://github.com/malariagen/malariagen-data-python/pull/242


**Full Changelog**: https://github.com/malariagen/malariagen-data-python/compare/v4.3.1...v4.4.0

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