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github.com/BioJulia/PopGenCore.jl

Core utilities for PopGen.jl, including the PopData type and file IO
https://github.com/BioJulia/PopGenCore.jl

rm empty test

4f35b3856654e2b9c6ba79e7fc44b989d9a456f7 authored about 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

3befa49ade84cec3033cb5e426bf4d7f734261bb authored about 3 years ago by Pavel V. Dimens <[email protected]>
more standardization

aaa479738a95f55d20637648e6f4f9972b0b4128 authored about 3 years ago by Pavel Dimens <[email protected]>
fix tests

d004a61deafaf50625cdd7a164fd6b0da5a187da authored about 3 years ago by Pavel Dimens <[email protected]>
update a lot of changes

1172879fea227011b8460edb2720ccb9b89edeb4 authored about 3 years ago by Pavel Dimens <[email protected]>
remove all mid-function underscores

578f688c39e2902d925d4342336a26fd1a00f2b0 authored about 3 years ago by Pavel Dimens <[email protected]>
add wrappers

84435382831ee30e688d9d8ec8879b243df72415 authored about 3 years ago by Pavel Dimens <[email protected]>
Update downstream.yml

ff7df19dfb367d3f2a9ea65e9d9fa9868a70d2cd authored about 3 years ago by Pavel V. Dimens <[email protected]>
Create downstream.yml

e8563162af50c6e5ad89a5aec303a6958239b17d authored about 3 years ago by Pavel V. Dimens <[email protected]>
add extra fields to popdatainfo show

fee32d78ead6778084cc3e65d7180bbf60f6f794 authored about 3 years ago by Pavel Dimens <[email protected]>
change popdatainfo show method

1b2a9531c46497b624d263cf03db8006688b4377 authored about 3 years ago by Pavel Dimens <[email protected]>
undo last commit

6d2858fccfee1d7375c64dc68b5ee9e1b3b32fcd authored about 3 years ago by Pavel Dimens <[email protected]>
Update Manipulate.jl

60a5f2c8e948df1cd0b4948ca694fe5e152b1c98 authored about 3 years ago by Pavel V. Dimens <[email protected]>
update .loci ref

3dfa7c45c86ed6edd06a031b880d7b211079e632 authored about 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

56212ade82b3a2fc38ab78141df884d6515d3405 authored about 3 years ago by Pavel V. Dimens <[email protected]>
Update Project.toml

d061e79daa64e35861f49b94f216af65d14cff0e authored about 3 years ago by Pavel V. Dimens <[email protected]>
migrate advanced allelefreq tests

820e4996b9f8ba3d81fd3728af43f3b01ac078f1 authored about 3 years ago by Pavel Dimens <[email protected]>
migration of AlleleFreq into Allele/GenoFreq.jl

3840860aa361327a203300351bce06d4e8cb8e5f authored about 3 years ago by Pavel Dimens <[email protected]>
change iteration logic

a7ad9287032cf471ae541ea4e2e4255e91b07175 authored about 3 years ago by Pavel Dimens <[email protected]>
typo

86442a98b0181cce42b6ecbde9ef5aa4d95acc2a authored about 3 years ago by Pavel Dimens <[email protected]>
Update conditionals.jl

28ff66fa82f3513d2d73af02583db9df22219aea authored about 3 years ago by Pavel V. Dimens <[email protected]>
update tests, bump version

8cdb424872495feb8ef7f42ca03d82de67731ea5 authored about 3 years ago by Pavel Dimens <[email protected]>
ishom/ishet return false if missing. add _ishxx() methods

4b4f3310f9995b9b517e0f15818a6286550acb98 authored about 3 years ago by Pavel Dimens <[email protected]>
remove coordinates in show()

f5eb43cafb284a0fa3cbb92122b92da637cdc8cd authored about 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

dc2e6565ef7e0dac68ce0810106ce29620ad4b02 authored about 3 years ago by Pavel Dimens <[email protected]>
hopefully fix dep

f8d3164d3a3dc6da43b6f502c8141e4c3140b0bc authored about 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

cd9bcece14d053ba57296369a46a8360e4df433e authored about 3 years ago by Pavel V. Dimens <[email protected]>
add PopDataInfo! constructor

3950d48b86338070be427a2a438be5489293049b authored about 3 years ago by Pavel Dimens <[email protected]>
fix indexing, add tests

064395924db1e985149fee741a6413f7bd65b2d6 authored about 3 years ago by Pavel Dimens <[email protected]>
add nightly to CI

59e799701ae5847c7ff869e1986ab5d8917757c5 authored about 3 years ago by Pavel Dimens <[email protected]>
temporarily rm precompilation

54d370ce38e8eb66bdf408d0d216f85e35a3cecc authored about 3 years ago by Pavel Dimens <[email protected]>
update julia compat

cb5e45fe472a4406cf0b945a9974a8246146f611 authored about 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

635aaa8d97d6f8378ce8c2766f7da22e8c4bf592 authored about 3 years ago by Pavel V. Dimens <[email protected]>
update groupby [bugfix]

03b4fa91e284825a502fa21996c21b73b05fb45f authored about 3 years ago by Pavel Dimens <[email protected]>
population => populations in tests

32775b5d32f93499ba8af78347ae5f97eda657cf authored about 3 years ago by Pavel Dimens <[email protected]>
fix @test_throws

47bc600dc5a48b1309bd639da6f5c68e36354c23 authored over 3 years ago by Pavel Dimens <[email protected]>
update get_geno tests

4cb02efa0fab470812b018437f54d60e5fa96f25 authored over 3 years ago by Pavel Dimens <[email protected]>
update manipulation

aa7d8cd7310b12b3f1a3eae73389a670e2ea2ad4 authored over 3 years ago by Pavel Dimens <[email protected]>
update tests

160751692ea93b8f11871b923eeb09151baae8f3 authored over 3 years ago by Pavel Dimens <[email protected]>
replace add_meta!

2d22a00d9bb7ecaaaaef8219ff43464c93ef8a70 authored over 3 years ago by Pavel Dimens <[email protected]>
fixes for things unit tests discovered

9cb7104d672d45ba27149526e7086574d99083d3 authored over 3 years ago by Pavel Dimens <[email protected]>
fix typo

2675cefb9d66c3e20af24c8eb501272686803842 authored over 3 years ago by Pavel Dimens <[email protected]>
update metadata calls

0837ef4c7af806ef94dd5c9ed3e1e0ce6c0c75c1 authored over 3 years ago by Pavel Dimens <[email protected]>
prettier tests that will fail

263e5837db70d704e766dfb6b502e23f89347b83 authored over 3 years ago by Pavel Dimens <[email protected]>
downstream popdata changes

7c932a96cf41ff55eea2c023bd3e85b2b18225d9 authored over 3 years ago by Pavel Dimens <[email protected]>
downstream popdata changes

d40e9011ada82b5737df9678b8f425412535f227 authored over 3 years ago by Pavel Dimens <[email protected]>
more popdata overhaul

508e78834cf7bf834496b5b781737cbc5aac2c86 authored over 3 years ago by Pavel Dimens <[email protected]>
continued PopData overhaul

6ce1585d8c12103cfbfaf006007c4de0d6b0606e authored over 3 years ago by Pavel Dimens <[email protected]>
overhaul PopData.metadata

2c7f90ccc5cba09bd61df50cba435d5ccc6a4428 authored over 3 years ago by Pavel Dimens <[email protected]>
update bed reader

224902fbce200c55f864c6c94f376ae21547cc9f authored over 3 years ago by Pavel Dimens <[email protected]>
update bed reader with bim fields

2c0193c58849b3383c72c957c3fbc1344af6ff3a authored over 3 years ago by Pavel Dimens <[email protected]>
drop_multiallelic not converting biallelic flag

a3509866686f8d3b5fd2e57815b34baa9dbf5443 authored over 3 years ago by Pavel Dimens <[email protected]>
add plink .ped writer

b525bf54ad3aef29479704eb4736b0ae5e902b44 authored over 3 years ago by Pavel Dimens <[email protected]>
fix docstrings

7282dabc6b8f4dc84ca70f79e1a035566230be55 authored over 3 years ago by Pavel Dimens <[email protected]>
remove spaces in population names

a3f47de9c9c38e84fb9f8ddc0a9c91be795c03f6 authored over 3 years ago by Pavel Dimens <[email protected]>
add filepath truncation for info printing

90fb32aaf61142483391f8fd3b2a6d104c42c49a authored over 3 years ago by Pavel Dimens <[email protected]>
fix testing typos :(

f50f1f0466ae3995ba4432452a3e115a38d040fc authored over 3 years ago by Pavel Dimens <[email protected]>
add unit tests

3a449b3125647678c03b8a49ff967edb7ffabe46 authored over 3 years ago by Pavel Dimens <[email protected]>
add missing docstring

18b78f3fcf2675cc08b915d0c1e19de3d7780757 authored over 3 years ago by Pavel Dimens <[email protected]>
fix typos

3e0a9cda47d61242d2dbfa1e1654f226fdc8f95f authored over 3 years ago by Pavel Dimens <[email protected]>
rm deprecated

dd08c3bcdf71c1dad868adbbb64c44fe08e5dcb3 authored over 3 years ago by Pavel Dimens <[email protected]>
add utils unit tests

2fcb41c206a78fde9be11cd97a9e3951daf75eed authored over 3 years ago by Pavel Dimens <[email protected]>
add Conditionals.jl tests

3955bfa38c40327503ea78ad54ec98aa44c96c61 authored over 3 years ago by Pavel Dimens <[email protected]>
fix typo

c0ee38f80e9eb440658005ffd77ba61b8815d4d1 authored over 3 years ago by Pavel Dimens <[email protected]>
fix use case of missing lat/long fields

5334cf60d8285e39703d8055c29b3dd20c976665 authored over 3 years ago by Pavel Dimens <[email protected]>
fix add_meta! joins

ce37d8cc8b2a26d9208308c737a03b4bd1e13f5e authored over 3 years ago by Pavel Dimens <[email protected]>
replace print loops with join

cb265ba51825e607cc8ea3d38c7b38ba5772d7c4 authored over 3 years ago by Pavel Dimens <[email protected]>
compress pooledarrays

27ce15210dec92d1ac60f561a20523c1975e5ac0 authored over 3 years ago by Pavel Dimens <[email protected]>
export PopDataInfo

69a97a80c3950cba53575b9ce453e56ecaea6a01 authored over 3 years ago by Pavel Dimens <[email protected]>
little improvements

514fe58d058a38ddcc6e526cdf158d403fc7a982 authored over 3 years ago by Pavel Dimens <[email protected]>
update tests for CSV 0.9

3a63ea6c621a8f067d2d459ff034015ce515a71f authored over 3 years ago by Pavel Dimens <[email protected]>
address CSV depwarn

cdf84904ed0706f1d1737b90181bea52c87d1d54 authored over 3 years ago by Pavel Dimens <[email protected]>
address new CSV test

296efc9c1a7fddf1b0cf3e21c197c0c1ded60f89 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

8cf51a7ed41d5370b2c5a767fcb8f7f9c702793a authored over 3 years ago by Pavel Dimens <[email protected]>
fix calls

223865e7d917e9a9b44a8a81d101e04772d284c3 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #15 from BioJulia/compathelper/new_version/2021-09-09-00-53-11-732-00615836688

CompatHelper: bump compat for CSV to 0.9, (keep existing compat)

467e266c45952e8cf0d7a073c6a104001c3e7092 authored over 3 years ago by Pavel V. Dimens <[email protected]>
ploidytext improvement

53d4eb187286fce437325661eb7cd44fe564de4b authored over 3 years ago by Pavel Dimens <[email protected]>
add info field and constructors to PopData

47926a3e5639f57db0365bef808e67f7c082c347 authored over 3 years ago by Pavel Dimens <[email protected]>
fix the macros so simply

a474a39ecf45dd4e2df561711a0c2f8788f52670 authored over 3 years ago by Pavel Dimens <[email protected]>
CompatHelper: bump compat for CSV to 0.9, (keep existing compat)

d63294805ba5164a781a2e1002e9f49c660c631a authored over 3 years ago by CompatHelper Julia <[email protected]>
housekeeping

b3fb63014563e49f1d178cbb45615c6cbc2f016e authored over 3 years ago by Pavel Dimens <[email protected]>
housekeeping

869dabf2005f3a7755aeb038965e156c2f4796c2 authored over 3 years ago by Pavel Dimens <[email protected]>
fix test imports

ddedb7e5671630356b29fd8be6f22b72be7f530d authored over 3 years ago by Pavel Dimens <[email protected]>
fix tests

55311091c09bbe1f338adefb481336b614c4a0ca authored over 3 years ago by Pavel Dimens <[email protected]>
add filter and filter!, update exclude! and keep!

afc5deba1ef4af7225ae4da62e84ff622647b8f0 authored over 3 years ago by Pavel Dimens <[email protected]>
update dataset macros

d87f500516ba3d4dfbc410308504b6d47c454062 authored over 3 years ago by Pavel Dimens <[email protected]>
small logic update

61a7032289fba6e25eebd11f8574330213fc1c2c authored over 3 years ago by Pavel Dimens <[email protected]>
add name pool check to reduce redundancy

bd7ab859fb03964e3ec723845e4ca510b29390e8 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

1128e9efc97fa835526da256b4c5d1ea5d3dab54 authored over 3 years ago by Pavel Dimens <[email protected]>
add file existence checks

1d897a13bae7c962023fac066bda0064e08f5bba authored over 3 years ago by Pavel Dimens <[email protected]>
add getindex filtering of PopData

601a5b6b096470ab6250677a1084553f95e2b4ba authored over 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #13 from BioJulia/compathelper/new_version/2021-09-08-00-49-49-971-03306261622

CompatHelper: add new compat entry for CodecZlib at version 0.7, (keep existing compat)

3244a6d68142ff8f596860a2f421d8f44827345e authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #12 from BioJulia/compathelper/new_version/2021-09-08-00-49-40-818-02041722700

CompatHelper: add new compat entry for VariantCallFormat at version 0.5, (keep existing compat)

8c981ca0d4062cc732c2c02412b25fc2148f0d8f authored over 3 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: add new compat entry for CodecZlib at version 0.7, (keep existing compat)

bfe0ad1b8198cc180623bf3161a04a06a4020a46 authored over 3 years ago by CompatHelper Julia <[email protected]>
CompatHelper: add new compat entry for VariantCallFormat at version 0.5, (keep existing compat)

54e558bfb3c4e29bebde6ad61233d1d655017f48 authored over 3 years ago by CompatHelper Julia <[email protected]>
add bim/fam file checks and handling

368d1276e0bbda7195b0d0eda05f332243729802 authored over 3 years ago by Pavel Dimens <[email protected]>
update plink reader, rm sorting from PopData constructor

6459c3c22542153298ed54352b8edd4774ce3156 authored over 3 years ago by Pavel Dimens <[email protected]>
add some convenience getindex

f5757305461b0f4be9980fbec904859ea7ec7109 authored over 3 years ago by Pavel Dimens <[email protected]>
update io testing

0129ce71f7e9afc84a5dde58e57182142e719c08 authored over 3 years ago by Pavel Dimens <[email protected]>
rm accidental copy

38562179d6647f0fefc696e5f58a59be17ad11b4 authored over 3 years ago by Pavel Dimens <[email protected]>