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github.com/BioJulia/GeneticVariation.jl

Datastructures and algorithms for working with genetic variation
https://github.com/BioJulia/GeneticVariation.jl

Update `makedocs` and `deploydocs`

2000f5947384b13272d86ee8b7c9600146eddfa9 authored over 1 year ago by Ciarán O’Mara <[email protected]>
Migrate to GitHub workflows

- Remove appveyor and Travis.
- Add UnitTests workflow.
- Add Documentation workflow.
- Add TagB...

945c53290177db81c153fa17e7dea0f5ac594ab2 authored over 1 year ago by Ciarán O’Mara <[email protected]>
Update contact information

9f3d1c1e0bfe6aff608011fd88f2040584b61be0 authored over 1 year ago by Ciarán O’Mara <[email protected]>
Merge pull request #31 from rasmushenningsson/ProjectTOMLSquashed

Adds a Project.toml, and includes fixes for deprecation warnings and compatibility.

b4789a12f5cf95a3f8463bccd51ddf0c16ae7567 authored over 1 year ago by Ciarán O'Mara <[email protected]>
Compat fixes

06cf1001642be35e8e05a7831de33893390e6803 authored over 4 years ago by Rasmus Henningsson <[email protected]>
Add Project.toml

Also fixed deprecation warnings.

7b7fa346fd94d9cfced5d55f06786a355a940315 authored over 4 years ago by Rasmus Henningsson <[email protected]>
Update changelog

f61b9dbcb1a11ea91181c8793ea22ec60c826419 authored about 6 years ago by Ben J. Ward <[email protected]>
Update changelog

4571d5796beba7f493565a272039b1b499ebecae authored about 6 years ago by Ben J. Ward <[email protected]>
Test on 0.7

7c98ce5b0286e0b6f4181a157efdfa438c7d20a4 authored about 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #21 from JuliaDocsForks/juliadocs/cap-documenter

Cap Documenter.jl to 0.19 on Travis

704300a1cd55b7b9661534449ad8cd2d984847ff authored about 6 years ago by Ben J. Ward <[email protected]>
Cap Documenter.jl to 0.19 on Travis

Documenter 0.20 will introduce breaking changes that will invalidate
existing make.jl setups. Th...

736e18942c13852969de88f85c64072176a85d55 authored about 6 years ago by Morten Piibeleht <[email protected]>
Merge branch 'master'

7cbacaf5cb4aed428f0c420f7161f0e7c36eba42 authored about 6 years ago by Ben J. Ward <[email protected]>
Update diversity manpage to use BioSequences

064e9e11fc6d0ebc8642509f52a46d9e459c828a authored about 6 years ago by Ben J. Ward <[email protected]>
Fix reading VCF files and support julia v1.0

7db502164d7c81119f6b882c67c2c1f9de9734d5 authored about 6 years ago by Ben J. Ward <[email protected]>
Minor readme update

a5dbe06c4b6e0683a312b73ddc1d872dbd14b1c1 authored about 6 years ago by Ben J. Ward <[email protected]>
Added lines to the Unreleased changelog section

ba51781e2e992488d2f50ef06f2c791db1afcd92 authored about 6 years ago by Ben J. Ward <[email protected]>
Drop x86 support on windows

8e752f774b4e521a0b9c062c6aca40e53f42a0ca authored about 6 years ago by Ben J. Ward <[email protected]>
Allow period characters in metainfo tags

This fixes issue #18

51f0748da661409af77db761fb7f04cb5dd1183e authored about 6 years ago by Ben J. Ward <[email protected]>
Make code refactors for julia v1.0 compatibility

This fixes issue #20

8bea5d8b1aee4102d096088df21a575ba69c5d0b authored about 6 years ago by Ben J. Ward <[email protected]>
Update travis and appveyor settings

6ae6b9b2f8b0867996d3a6311df94d910470c110 authored over 6 years ago by Ben J. Ward <[email protected]>
Remove NEWS file

255572700b3dcf1087c6afc79fb88769dba84183 authored over 6 years ago by Ben J. Ward <[email protected]>
Update doc files

8997176dcdcec554456a5b2f5f274f0bfa9bbb06 authored over 6 years ago by Ben J. Ward <[email protected]>
Update project files

a709b36570632532f8804a28ad96b65da21b6d66 authored over 6 years ago by Ben J. Ward <[email protected]>
Update CI files

50bc0d590a831287d99625bb18456b4f74967be4 authored over 6 years ago by Ben J. Ward <[email protected]>
Merge pull request #16 from BioJulia/nsamples

Fix n_samples method for BCF records

dee5f670270a151e43ef4174ebeceab91abaf93b authored over 6 years ago by Ben J. Ward <[email protected]>
Fix readme and add sticker

98d95aad2eb05081994dc9d814e092df2afb2589 authored over 6 years ago by Ben J. Ward <[email protected]>
Add CHANGELOG.md file

cc0d29efa3e1e504720d6da5ca82ffbd2a54615a authored over 6 years ago by Ben J. Ward <[email protected]>
Added HUMANS.md project file

a880c0ad2c649e78db393832582730cf1b83893c authored over 6 years ago by Ben J. Ward <[email protected]>
Updated README.md project file

eaff72b5b1af7d25414c27887ff420e09680d1b4 authored over 6 years ago by Ben J. Ward <[email protected]>
Fix n_samples method for BCF records

29b60ac5626084f7119e36b72d64eb899e1443ad authored over 6 years ago by Ben J. Ward <[email protected]>
Fix deprecations (#15)

850ac09e08f99ffcb903efa7d164c537d34665f2 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>
Contributing files rollout (#14)

* Rollout file CONTRIBUTING.md

* Rollout file CODE_OF_CONDUCT.md

* Rollout file .github/PU...

2051113f808255d5f707885451425aefcf3f5480 authored over 6 years ago by Ben J. Ward <[email protected]>
Update the news.md file

b7899bc231bb3ee47b3ee439fe41966486f90885 authored about 7 years ago by Ben J. Ward <[email protected]>
Add avg_mut (#13)

* Add avg_mut

* added docstring

* fix test

65169ef8ceacaaf4d931d5cc63844a3b073de065 authored about 7 years ago by Ben J. Ward <[email protected]>
Minor documentation fix

4ad828442cc3c6e8f1fe3ab3b69ce5877e882fb2 authored about 7 years ago by Ben J. Ward <[email protected]>
Compute the number of segregating sites in a set of DNA sequences.

1477f922ad33e85531e0e6328bedba1462a7cac7 authored about 7 years ago by Ben J. Ward <[email protected]>
Docs system update

2c2d9fa2ac9c840641d5e489373e54f9e1157672 authored over 7 years ago by Ben J. Ward <[email protected]>
Add allele frequency and nucleotide diversity methods (#11)

* add nuc div file

* Added a method that computes allele frequencies for a set of sequences
...

5b9b0ac8df5a742a4bb4b3a258e8f3b65796296d authored over 7 years ago by Ben J. Ward <[email protected]>
dnds api (#10)

fix

fix

pairwise fix

fix

import fix

pairwise dnds

Edit some 0.5 sy...

b1cf2f2f78941d774e205fd0e170829dff4d114d authored over 7 years ago by Ben J. Ward <[email protected]>
Drop julia 0.5 syntax and support (#9)

* Drop julia 0.5 syntax and support

* fix a takebuf_array use

* depreceate more takebuf_ar...

3a7c88f04aad3ed9446731a241af22701309541c authored over 7 years ago by Ben J. Ward <[email protected]>
NG86 methods (#5)

* Added first draft of ng86 distance methods

* Finished draft of dnds NG86 method

* Added ...

fbbdb08a6a284120119c7169913642f5401836c2 authored over 7 years ago by Ben J. Ward <[email protected]>
Add the proportion distance (#4)

* Added abstract types

* Modified evodistances.jl

* Draft proportion distance method

* ...

db632df094982cfd46082147364dadabc6190266 authored over 7 years ago by Ben J. Ward <[email protected]>
Merge branch 'release-0.1'

f412345132d19a0e86a6412e2202ac6dc3513938 authored over 7 years ago by Ben J. Ward <[email protected]>
Use get_bio_fmt_specimens from BioCore.Testing.

a6b5301ac5bf42c3f9208e9acbdc3216c72af9ac authored over 7 years ago by Ben J. Ward <[email protected]>
Overload BioSequences.diag_val

3abd0f3d0def2dc59261a98bdf81f16de4244a30 authored over 7 years ago by Ben J. Ward <[email protected]>
Changed REQUIREd Compat version

06c5638da0a43dfb80dea1d56e1368983d2ed902 authored over 7 years ago by Ben J. Ward <[email protected]>
MASH Distances (#3)

* Added MASH distances for MinHashes

* Added tests for MASH

* export tweak

* Added docu...

74c9d1aa01f5400f0d665c2fc926ed57eeca431b authored over 7 years ago by Ben J. Ward <[email protected]>
Minor import edit

e647a86b28019e09a8fd58e6b183938dbb328acf authored over 7 years ago by Ben J. Ward <[email protected]>
Added documentation files

77e975a3f0fd33e6bec1ef8dcb57badef303cd72 authored over 7 years ago by Ben J. Ward <[email protected]>
Edited readme

cf068cd2bb48ad36b320f74cd3f1e1b835871aa7 authored over 7 years ago by Ben J. Ward <[email protected]>
Site counting (#2)

* Added site counting methods

* testing

* conserved and mutated testing

* include site_...

d7ceedd0e14099c902904885575833c7bebdfb29 authored over 7 years ago by Ben J. Ward <[email protected]>
BCF IO

* Added BCF code

* Added tests

* import GeneticVariation.VCF to BCF

* Bio -> BioCore

...

d6fb3aa9cad3b2059b754b92b249e7f20ce4f395 authored over 7 years ago by Ben J. Ward <[email protected]>
VCF Submodule

62aae80022f064ac36a18eeb1f6c4ff84602ffea authored over 7 years ago by Ben J. Ward <[email protected]>
Initial commit

9d8f1e3cccd81f053104a64d6ab1bd3f8285092e authored over 7 years ago by Ben J. Ward <[email protected]>