v0.6.3

PopGen v0.6.3

Diff since v0.6.2

Merged pull requests:

• move conditionals to Conditionals.jl (#67) (@pdimens)

v0.6.2

PopGen v0.6.2

Diff since v0.6.1

Merged pull requests:

• fix hudson fst calls (#66) (@pdimens)

v0.6.1

PopGen v0.6.1

Bugs fixed

• tiny but tragic typo in pairwise FST using the Hudson method

Diff since v0.6.0

Merged pull requests:

• Update FstMethods.jl (#65) (@pdimens)

v0.6.0

PopGen v0.6.0

✨✨ New Features

• Hudson pairwise FST & Permutation
  • adds the Hudson et al. 1992 method
• isbiallelic
  • adds boolean test if a PopData object has only biallelic loci
  • adds boolean test if a GenoArray is biallelic
• drop_multiallelic
  • mutating and non-mutating methods to remove non-biallelic loci from a PopData object

⚡⚡ Improvements

• drop_monomorphic now uses the same logic as drop_multiallelic, which should make it faster and leaner

🐛🐛 Bug fixes

• vcf and bcf kwarg rename_loci now consistent in functions and docstrings
• generate_meta now uses a comprehension rather than deprecated map(fn, groupeddataframe) method

Breaking Changes

• none

Diff since v0.5.2

Merged pull requests:

• v0.6.0 (#64) (@pdimens)

v0.5.2

PopGen v0.5.2

❗❗ Breaking changes

• none

⚡⚡ Improvements

• a rewrite of nei and weir-cockerham fst methods to be matrix-based (faster!)

✨✨ New Features

• fully implements permutation testing for both pairwise fst methods
• adds method for avg_allele_freq to accommodate new pairwise_nei
• extends pairwise_fst to include iterations keyword to activate permutation testing

Diff since v0.5.1

Merged pull requests:

• v0.5.2 release (#63) (@pdimens)

v0.5.1

PopGen v0.5.1

New features ⚡

• Pairwise FST (Nei 1987 and Weir-Cockerham)
• API: added skipinf, skipnan, and skipinfnan

Diff since v0.5.0

Merged pull requests:

• push 0.5.1 release (#62) (@pdimens)

v0.5.0

PopGen v0.5.0

❗❗ Breaking Changes

• Dropped JLD2.jl support (it's unstable between major versions, very little gain for extra deps)
• populations() by default now returns a list of the unique populations in the PopData in order of appearance in the meta
• populations() keyword argument changed from listall::Bool to counts::Bool
  • counts now returns what populations() previously returned by default
• _nancycats() and _gulfsharks() removed in favor of consistent dataset(::String) syntax (macro now works in dev environment!)
• motivational_quote() removed. It was only just barely fun while it lasted.

✨✨ New Features

• Some under the hood stuff prepping for pairwise FST calculations (in the next release)
• keep function has been added as an opposite to exclude, where you keep only a handful of something and remove everything else

🦟🦟 Bug fixes

• fixed import functions (delimited, structure, genepop) incorrectly returning nothing when dropping monomorphic
• filtering mechanics of exclude have been changed to be consistent and not cause spurious results

Diff since v0.4.5

Merged pull requests:

• CompatHelper: bump compat for "JLD2" to "0.4" (#60) (@github-actions[bot])
• fix file import functions (breaking) (#61) (@pdimens)

v0.4.5

PopGen v0.4.5

non-breaking changes

• split out VariantCall.jl to have stripped down vcf and bcf methods in the namespace before importing GeneticVariation.jl. This was done so the docstrings for the functions will be available even if the necessary packages aren't imported yet. Running either vcf or bcf before importing GeneticVariation.jl will return an error informing you that those packages must be loaded in first.

Diff since v0.4.4

Merged pull requests:

• pull 0.4.5 into release (#58) (@pdimens)

v0.4.4

PopGen v0.4.4

Diff since v0.4.3

• lazy-loading of vcf parser now more flexible to not require GZip.jl if your file(s) aren't compressed.
• docs updated

v0.4.3

PopGen v0.4.3

Diff since v0.4.0

Closed issues:

• TagBot trigger issue (#40)
• docs pages not loading (#41)
• Replace rand() and sample() use of MT (#49)
• consolidate file io APIs to use multiple dispatch (#52)

Merged pull requests:

• CompatHelper: bump compat for "CSV" to "0.8" (#42) (@github-actions[bot])
• CompatHelper: bump compat for "DataFrames" to "0.22" (#43) (@github-actions[bot])
• CompatHelper: bump compat for "JLD2" to "0.3" (#44) (@github-actions[bot])
• bump to 0.4.2 (#48) (@pdimens)
• CompatHelper: bump compat for "StaticArrays" to "1.0" (#50) (@github-actions[bot])
• CompatHelper: add new compat entry for "RandomNumbers" at version "1.4" (#51) (@github-actions[bot])
• CompatHelper: bump compat for "PooledArrays" to "1.1" (#55) (@github-actions[bot])
• bugfixes for 0.4.3 (#56) (@pdimens)