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github.com/BioJulia/PopGen.jl

Population Genetics in Julia
https://github.com/BioJulia/PopGen.jl

fix get_genotype return value

e4c583c69269d249fac1ee67431a974b5ee04e2e authored over 4 years ago by Pavel Dimens <[email protected]>
fix breaking typo

741faa5665b63385cdbf6a18ebe9e0ed35a841fa authored over 4 years ago by Pavel Dimens <[email protected]>
rm loopvectorization

540e929e91715cac2d097d6e52aa9237604eecf2 authored over 4 years ago by Pavel Dimens <[email protected]>
remove LoopVectorization, fix pairwise_identical

c0fb384d7c8f0f0aeb5b231ac7fde0bc3dea6f38 authored over 4 years ago by Pavel Dimens <[email protected]>
split out get_genotype

1149c0cbf5032e4652ccd7f2b589b770f973e01e authored over 4 years ago by Pavel Dimens <[email protected]>
Merge pull request #23 from pdimens/compathelper/new_version/2020-07-15-00-22-32-536-2459766818

CompatHelper: add new compat entry for "FileIO" at version "1.3"

db7c495b462086ac40f16efd1aa3da91fdfb0c8f authored over 4 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for "FileIO" at version "1.3"

5cc15ac047a1e4b80c57ec76d344cdd2140cb36e authored over 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Update CompatHelper.yml

0685d4ffb3df4b0f96635f8de205a4daa02cc156 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update CompatHelper.yml

5b32e387872bbdec62990ebc5ec15ef8f75b7c5f authored over 4 years ago by Pavel V. Dimens <[email protected]>
update compat

4ae10e4b6ac85e719d445d981e70ae2a6f8d6c9b authored over 4 years ago by Pavel Dimens <[email protected]>
Merge pull request #22 from pdimens/compathelper/new_version/2020-07-14-00-25-20-295-1723802824

CompatHelper: add new compat entry for "FileIO" at version "1.3"

7f592479d7a9b8853b044ccdd9bfd675bf8e2531 authored over 4 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for "FileIO" at version "1.3"

f885c6194ec0910e0b6787d411fea76acbedc78c authored over 4 years ago by $(ci_cfg.username) <$(ci_cfg.email)>
new add_meta! functins

54d78a4d4618001f8378cc3937a9d1aaa7f5ab85 authored over 4 years ago by Pavel Dimens <[email protected]>
Update README.md

eec74bb855eab4a3c12870983c3591a5348cd831 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Create ci_dev.yaml

2556d9e126b7092c393ce5f5eb69abb227dbe40a authored over 4 years ago by Pavel V. Dimens <[email protected]>
Delete ci_dev.yml

6d0a364cd5e6676b122fc51c0188cba315d84dfe authored over 4 years ago by Pavel V. Dimens <[email protected]>
add workflows to gitignore

84ec9785203bd006ebf4a972a43a81224b699630 authored over 4 years ago by Pavel Dimens <[email protected]>
Update README.md

df12474d425101b9aef2ecd87a567af5d0db5e38 authored over 4 years ago by Pavel V. Dimens <[email protected]>
separate dev readme

5d5e6be8a96f68cdc232230569a38ebbd5fdf510 authored over 4 years ago by Pavel Dimens <[email protected]>
Rename ci_dev to ci_dev.yml

b670e5fafe799e98135e8580963b7e044b466f5f authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update README.md

2a1c301c73aa9762e0eda964d007116785f2be18 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update README.md

f582bed2b44e977f32789fb3b4506f869b6ccc20 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Create ci_dev

f66e5f08d120cbc7e501cc6b5e68c3e224ce32de authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update and rename ci.yml to ci_main.yml

387b14310b73038ddc6fb2cbae5e35c0235a1dde authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update ci.yml

restrict CI to main and dev branches

5a7d30a08d402540b5dc530e9dca709ef5fa3e1b authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update README.md

667cb35b1a3a9ff6bb3cc47f5c998f2fca772ccf authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update README.md

3d07e743743233b7b3d67ce8e66f5408c84efba1 authored over 4 years ago by Pavel V. Dimens <[email protected]>
change docs logo to white

d7f2bd6171f47b1e0943be0893363edd28045497 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Update ci.yml

f9810546ed058ce65b365fa538fa8e5c3c6c4a3a authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'main' of https://github.com/pdimens/PopGen.jl into main

f307419b6c6c344d4d8160baf1b04c1d32f0b0d3 authored over 4 years ago by Pavel Dimens <[email protected]>
update manipulate, trigger compat

51f029fdf40c02eb911f1c548a5cb1a8f9b38d64 authored over 4 years ago by Pavel Dimens <[email protected]>
Update CompatHelper.yml

f65a3b71cd8b634ad15d0b9d5bb8827e4e1c70f8 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Create ci.yml

4e8ed9a4cabc7ddd1543f20bf90b3e80586434b2 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'main' of https://github.com/pdimens/PopGen.jl into main

6d71dc0554fc6bf96495ccb8ef7cc8f7d5f7a7a3 authored over 4 years ago by Pavel Dimens <[email protected]>
Update CompatHelper.yml

825bee70bad26268cdf998a4d0fabe5147357274 authored over 4 years ago by Pavel V. Dimens <[email protected]>
add secret

b6d30a773423d77e71e4bf87869888a4b84f96f7 authored over 4 years ago by Pavel Dimens <[email protected]>
restore deps for compat

a57d9ba19864a10778e3bf7e96f39fff5ec80b9c authored over 4 years ago by Pavel Dimens <[email protected]>
clear project toml

6a10b8ddde6b5c480ac47b9561141c2b2afb1547 authored over 4 years ago by Pavel Dimens <[email protected]>
update readme + version info

57b053108ccaa2b66a677f378308db518de68b49 authored over 4 years ago by Pavel Dimens <[email protected]>
Create CompatHelper.yml

726fd4763bf24d19bf87d083eabe8c4baceb53f8 authored over 4 years ago by Pavel V. Dimens <[email protected]>
Create TagBot.yml

09c328f12364710ea91e7f50ff681329c89893d0 authored over 4 years ago by Pavel V. Dimens <[email protected]>
update export

e6d9c199253b277ba0891c3052f2e3ac20eab58a authored over 4 years ago by Pavel Dimens <[email protected]>
add DataExploration.jl to module

ce8cf5cfb57a6ed421bf5f3ed1693b87ca97240a authored over 4 years ago by Pavel Dimens <[email protected]>
moved missing into DataExploration, add pw_ident

0c6dd8ad3d981858c126f16be76e09732973e5ef authored over 4 years ago by Pavel Dimens <[email protected]>
change method to Base.Iterators.product

af6ad61f727bbf5842ccdcf60385b2ac0fe9429a authored over 4 years ago by Pavel Dimens <[email protected]>
updated docstrings

2cc7c910b52956f95c0992c84b3d56c715955a04 authored over 4 years ago by Pavel Dimens <[email protected]>
support for 00000 missing genotypes in write funcs

dec081180a88d9f0e5492ba0f6cf38bc4821a666 authored over 4 years ago by Pavel Dimens <[email protected]>
change exclude! to decide on fastest filt method

44bdb93dd1d4ac7bd649b12f1140ef235d19f5de authored over 4 years ago by Pavel Dimens <[email protected]>
update populations and tweak exclude

7b96de07c94c3b4066c0a3f878cc202f3748be51 authored over 4 years ago by Pavel Dimens <[email protected]>
export write_to

4cf3230786e0571d780e1e3f094aa01f1c68db86 authored over 4 years ago by Pavel Dimens <[email protected]>
fix @view usage

88c8bb8f550be5ad256b34fd4c0e850f9826d16f authored over 4 years ago by Pavel Dimens <[email protected]>
update populations! and remove DataFramesMeta dep

166406030023055e8cfa321e13b46ef8f11ef674 authored over 4 years ago by Pavel Dimens <[email protected]>
update docstring

f620f070fc815e60ab69e0b70f67b89267518075 authored over 4 years ago by Pavel Dimens <[email protected]>
update docstrings

d822bb37607c990dbdadb99fd5041c7b6752eee7 authored over 4 years ago by Pavel Dimens <[email protected]>
Delete FStats_beta.jl

cc45dd2b0f225dcd9e8391cbf1cb7e27548dce7d authored over 4 years ago by Pavel V. Dimens <[email protected]>
Delete BenchmarkPlots.jl

ae7d85f3f882cf45c256f646c130b5f7a3ece452 authored over 4 years ago by Pavel V. Dimens <[email protected]>
include Permutations.jl

b3a4e6ac0da4cea4a11e37276385e186897e08d5 authored over 4 years ago by Pavel Dimens <[email protected]>
multithreading with @spawn for Fstat permutation test

49894bd7eedc99f519bcbc12a13236bc05eea28c authored over 4 years ago by Pavel Dimens <[email protected]>
ploidy-finding feature for permute_alleles!

87f0c4210e0fc567fe0e0a10ab710ae0c2444234 authored over 4 years ago by Pavel Dimens <[email protected]>
overload Base.copy for a PopObj

26b037ff7f3193608945fab5f4133eae74c6d061 authored over 4 years ago by Pavel Dimens <[email protected]>
small fixes

2ac5fbfae1fb4e94909a19f4d08d2d2840f31947 authored over 4 years ago by Pavel Dimens <[email protected]>
move datasets.jl to io/

c7edde869bab940ed2aa70b0f555aaf0539c875e authored over 4 years ago by Pavel Dimens <[email protected]>
update fstats

c1abee357057721c8804006149bbf628696b863e authored over 4 years ago by Pavel Dimens <[email protected]>
fix up permute_alleles!

dae5e949226ae2426b7ab02252c6fcdba2a16fd3 authored over 4 years ago by Pavel Dimens <[email protected]>
write permute_alleles!

a193de7374806b21180bf31860478d2edc35c610 authored over 4 years ago by Pavel Dimens <[email protected]>
merge permute_genotypes into single function

259307c5d4275fe36caa397b8eeb211e02020ad9 authored over 4 years ago by Pavel Dimens <[email protected]>
tweak strict_shuffle!

f87d42ba4bbd14010e06524279c21674ca972daf authored over 4 years ago by Pavel Dimens <[email protected]>
move permutations to own file, create strict_shuffle methods

f7f42c05edd6da2ed88081602c18da7849f28216 authored over 4 years ago by Pavel Dimens <[email protected]>
Merge branch 'fstats' of https://github.com/pdimens/PopGen.jl into fstats

596906f6591e37652feabeea1701a3d6213e8a2a authored over 4 years ago by Pavel Dimens <[email protected]>
cleanup

76d2bb313ee74e87dd2ca9af93e22dbf7efdaf21 authored over 4 years ago by Pavel Dimens <[email protected]>
Update FStats.jl

eb9918709ae6c068f5f461a042bddf31b208f31a authored over 4 years ago by jdselwyn <[email protected]>
add early fstat permutation test

0af336372f882d1871470ae52c1ec355afdfd732 authored over 4 years ago by Pavel Dimens <[email protected]>
Update Utils.jl

f0ee4700363969d63af862bc2f607f553a3da979 authored over 4 years ago by Pavel V. Dimens <[email protected]>
touch up quickstart

a1e29d9e445032767a872377066a98d79109b879 authored over 4 years ago by Pavel Dimens <[email protected]>
fix what pavel broke

16a3689cdb8d441536aa6df1e209d4f13d58ed98 authored over 4 years ago by Pavel Dimens <[email protected]>
Update PopGen.jl

2bba9f646faf518a01271eacccf01bf74f7752e7 authored over 4 years ago by Pavel Dimens <[email protected]>
add quickstart and module docstring

ab42a925ff58ca51c90f9fe4ad59a5ce45cd7bcb authored over 4 years ago by Pavel Dimens <[email protected]>
Update CONTRIBUTING.md

55764770b30c4a0619b6a7478bd184ba909a953d authored over 4 years ago by Pavel Dimens <[email protected]>
Update Manipulate.jl

a207bb42f1a7fede2d189ac740ce1a200c62a95e authored over 4 years ago by Pavel Dimens <[email protected]>
shrink exclude to feed into exclude!

a39c320f9af9e2aad23d36e77bc9417a4159c0ea authored over 4 years ago by Pavel Dimens <[email protected]>
less verbose show()

d2b304954481b6f4192d975b30b7a72fa78dee25 authored over 4 years ago by Pavel Dimens <[email protected]>
replace exclude_ with exclude and exclude!

73a8adffe60bb00e596eafbefa4ba6ff08d75691 authored over 4 years ago by Pavel Dimens <[email protected]>
begin rewriting permutation test for fstats

761b49a62f8ca3ca057392a037da3afdb35a5268 authored over 4 years ago by Pavel Dimens <[email protected]>
add permutation methods

ae7b8a03117bbc775b81fd386c9c10a275f79641 authored over 4 years ago by Pavel Dimens <[email protected]>
comment out unused math

59fb9e5e94bd0310fd9996e1cba773982a81145c authored over 4 years ago by Pavel Dimens <[email protected]>
better using specification

a9c33fb7a26f1cf4bf41df688078b867e7a88fd9 authored over 4 years ago by Pavel Dimens <[email protected]>
fix mixed ploidy printing

eb0e8a5f7dd287506453b6cae55bcbd2138beb70 authored over 4 years ago by Pavel Dimens <[email protected]>
CSV.read => CSV.File

329aa86d17d8167f1a2a239bc9f057b4d2facfa9 authored over 4 years ago by Pavel Dimens <[email protected]>
add fstats docstring

29ffc8ed91068e7eaad637d446fa4d3392ec51cb authored over 4 years ago by Pavel Dimens <[email protected]>
add summarystats

67f3e7aea4d2495a1206fc76a9e3d96abcea51f0 authored over 4 years ago by Pavel Dimens <[email protected]>
Update AlleleFreq.jl

4a2aa7a3deda8eb2a30fe123d156666c35d181d5 authored over 4 years ago by Pavel Dimens <[email protected]>
add avg_allele_freq

this adds a function that returns a dictionary of the average allele frequencies across multuple...

97fbf356258798b05b45c2add4757c35b61d83fd authored over 4 years ago by Pavel Dimens <[email protected]>
fix float conversion

73e611272e45181e8480ed9b72293818f1588502 authored over 4 years ago by Pavel Dimens <[email protected]>
extend nei het and fix reciprocal

590bd6d7412f4040c9b68e14afa2db8f03318c01 authored over 4 years ago by Pavel Dimens <[email protected]>
add genepop ibd output

772f6d0e87a973b52899c5a33940228d79b17af6 authored over 4 years ago by Pavel Dimens <[email protected]>
update docstrings

4368180c37be6e89f078d488d4f4d75276bd0413 authored over 4 years ago by Pavel Dimens <[email protected]>
add popdata2delimited

4c3f1cdf019d44ac106536c4cad98e6ba1552a78 authored over 4 years ago by Pavel Dimens <[email protected]>
read_in => read_from

add `write_to`

40cd934b1b4dcf05435de00a0b263d5089328ee0 authored over 4 years ago by Pavel Dimens <[email protected]>
Update .gitignore

4b62bd8565fbcdcb2480ac9accd924eef7821927 authored over 4 years ago by Pavel V. Dimens <[email protected]>
create genepop wrriter

5c5ca48263436bff05a0eb96e7ae9541a7ba3a20 authored over 4 years ago by Pavel Dimens <[email protected]>