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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

update vcf support

6abe94e61fa0f0e00e0ef3c67c6e1afeaa1aacfc authored over 3 years ago by Pavel Dimens <[email protected]>
update module init

ed979b608d93082a7ec16fbdd51bc180ce372dfb authored over 3 years ago by Pavel Dimens <[email protected]>
add VCF and Zlib as standard deps, rm requires

ccc99563b0f369cf647aeefc56305608faec400d authored over 3 years ago by Pavel Dimens <[email protected]>
more plink stuff

26b3dc0f4cceea2e214be5e4075bc563218de2bd authored over 3 years ago by Pavel Dimens <[email protected]>
begin plink io reader

fdab733136d65b07870d6ef4bf41ddfa96ea2430 authored over 3 years ago by Pavel Dimens <[email protected]>
typo fix

9a12b8082b5c65ed8a87f41433762bdb709d511e authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

5f57f9e9293516924c829063dae13a128bdf7289 authored over 3 years ago by Pavel Dimens <[email protected]>
fix module load

874504bb297287037ce48a4ef21e481c48a01516 authored over 3 years ago by Pavel Dimens <[email protected]>
Update README.md

0d7e9dfccceeda6607e4fff9e801c063fbdf929f authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

088a0a3898dc84a57d4b2c54060dc53ca60f98b1 authored over 3 years ago by Pavel Dimens <[email protected]>
various fixes

49d00f8222e7197ddddc731d1606ba5a72d41d78 authored over 3 years ago by Pavel Dimens <[email protected]>
Update README.md

ba909c83917eaf670329427c68600901662c9d7d authored over 3 years ago by Pavel V. Dimens <[email protected]>
fix io things

2ccfebaabc6b79a0c7ec76f88dfef238f766f983 authored over 3 years ago by Pavel Dimens <[email protected]>
add Random dep

f1209808b7d514ac51825f63d43b96465b47f006 authored over 3 years ago by Pavel Dimens <[email protected]>
generic-ify the function signature

5a7fb14cb8f2089efb0c9c6a0a3a832d875c9eb4 authored over 3 years ago by Pavel Dimens <[email protected]>
clarify docstring

e5526a0ab092e7f48dcdd1c6e6df8b5173b0064f authored over 3 years ago by Pavel Dimens <[email protected]>
add random

761ae7252bc56ad888efc639d7fcce29da972c36 authored over 3 years ago by Pavel Dimens <[email protected]>
reorganize repo

626f22d7e2822bb792cdd613592d0a386754b7b6 authored over 3 years ago by Pavel Dimens <[email protected]>
speed up strict_shuffle

a7006ab39fd1339b106f917c0a7626161634801c authored over 3 years ago by Pavel Dimens <[email protected]>
silly typo

2fc0663445b2b9362707afd674244a80f7f7ff8d authored over 3 years ago by Pavel Dimens <[email protected]>
add GenotypeUtils to include()

8d3e519fac089619327cd0c7dda3faf29102f83a authored over 3 years ago by Pavel Dimens <[email protected]>
move things around

97ecb3c6bcfa0502787d46b1f8f156bd84922362 authored over 3 years ago by Pavel Dimens <[email protected]>
fix metadatadata bug :(

3626083184d20c915bdb857c0d2aa936a67821e3 authored over 3 years ago by Pavel Dimens <[email protected]>
organzation and exports

babc7054c936d5f3e62f14260f0b274e05ae94bb authored over 3 years ago by Pavel Dimens <[email protected]>
migrate permutations

618c4fc12bb96d265df2dc6e2c7b56606e10aa1d authored over 3 years ago by Pavel Dimens <[email protected]>
export most functions

930ad3986e193f4e92ba96fcadb7d625dce9e810 authored over 3 years ago by Pavel Dimens <[email protected]>
improve docstring

c9aa885d8449eacbaacef4a16180a7c4a3b34b25 authored over 3 years ago by Pavel Dimens <[email protected]>
fix structure write bug

4fff347c51ed396f43e138b06fceab261d2acb79 authored over 3 years ago by Pavel Dimens <[email protected]>
Update Project.toml

1fa96548bcb6ee6595aecda3ddba567f92914025 authored over 3 years ago by Pavel V. Dimens <[email protected]>
add isbinary conditional

3a2c29ea31344429b38068c53197d6097f7b4c9e authored over 3 years ago by Pavel Dimens <[email protected]>
fix bug: returning noting

368ae25c69425810cc454256f24afd2dee4e3c7c authored over 3 years ago by Pavel Dimens <[email protected]>
purge reshape references

0c9fbdbd760e383faa6f28524baab0b238e5d28c authored over 3 years ago by Pavel Dimens <[email protected]>
workaround for https://github.com/JuliaLang/julia/issues/33143

ef21561e452a46bb67e97d89dcd30be1cb235509 authored over 3 years ago by Pavel Dimens <[email protected]>
fix/update keep tests

d91982d84340ccf24e9c3c2971e3495ea7082f4e authored over 3 years ago by Pavel Dimens <[email protected]>
update tests

b2ab61b0d67d472e79b99e3aebbc0d9522a5365b authored over 3 years ago by Pavel Dimens <[email protected]>
migrate Conditionals.jl

8695452a7bc58a2e3eff1749f3faacc78aad8394 authored over 3 years ago by Pavel Dimens <[email protected]>
update

de106a631d4658a53800aaef44c69fe588f97bdc authored over 3 years ago by Pavel Dimens <[email protected]>
add columncheck

601becef5aa6cdc651b942204acee60eaec2a52b authored over 3 years ago by Pavel Dimens <[email protected]>
force strings

b5d650c0f3d58b40484e49fce540d23c4bb7534c authored over 3 years ago by Pavel Dimens <[email protected]>
remove text

05010b1c54dd1140d39d6b7153e3d3b218f90737 authored over 3 years ago by Pavel Dimens <[email protected]>
Merge branch 'dev' of https://github.com/BioJulia/PopGenCore.jl into dev

cb5681275947bd42998f8669fead960947ddea49 authored over 3 years ago by Pavel Dimens <[email protected]>
fix if statement

b32e9a5fc8229b2d48587cbfc792d9dd1ab80d77 authored over 3 years ago by Pavel Dimens <[email protected]>
fix reader and add precompile

b83e7a88b17ba5923f802ef0e3a40461adb64f9a authored over 3 years ago by Pavel Dimens <[email protected]>
rename genotypes to genodata

584e5fdf1736c16c2319531d28b73b58d6c3580e authored over 3 years ago by Pavel Dimens <[email protected]>
Merge pull request #8 from BioJulia/compathelper/new_version/2021-08-08-00-49-42-076-654269997

CompatHelper: add new compat entry for "StaticArrays" at version "1"

cd835788d787cb7dfeeb12aef65767bded7d3cf3 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge branch 'dev' into compathelper/new_version/2021-08-08-00-49-42-076-654269997

8e82215e9e7d6516ac716b803184e34eb0363952 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Merge pull request #7 from BioJulia/compathelper/new_version/2021-08-08-00-49-38-974-4170492756

CompatHelper: add new compat entry for "StatsBase" at version "0.33"

cb6d25e4245719678068b6a3df294a67a09023f8 authored over 3 years ago by Pavel V. Dimens <[email protected]>
rewritten parser

3daffe234504aa9942cacaee0bc1ef5302be7e7e authored over 3 years ago by Pavel Dimens <[email protected]>
added _SNP and _MSat convenience methods

9229282071cfd4521af9b8862779692da269d908 authored over 3 years ago by Pavel Dimens <[email protected]>
update readers wtith try...catch

6f694d7c7049294ebece5eb562d045d591fc404d authored over 3 years ago by Pavel Dimens <[email protected]>
add SNP and MSat convenience constants

541ecdf62afd016f1b9d2ab267fff2694ba121f9 authored over 3 years ago by Pavel Dimens <[email protected]>
more robust locus phasing

9532de06249f3479258062262f35f5fb3942cea1 authored over 3 years ago by Pavel Dimens <[email protected]>
CompatHelper: add new compat entry for "StaticArrays" at version "1"

066da4aa8970e811639053774f6498d190ff2552 authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
CompatHelper: add new compat entry for "StatsBase" at version "0.33"

a8a6a5438b92c7c26fa72eb00de16cbeb53ccfda authored over 3 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
testfix

1dde094e9d5d64277d6925a56d2b32c1a9935670 authored over 3 years ago by Pavel Dimens <[email protected]>
vcf precompile path (again)

f835b87fad21b291612c9a46fff0189757718691 authored over 3 years ago by Pavel Dimens <[email protected]>
fix path

4f22da614cd45054049a37b2dc51851743762669 authored over 3 years ago by Pavel Dimens <[email protected]>
vcf fixes

56f966f6c65ce9cad90030c5ebe967c31c4a6452 authored over 3 years ago by Pavel Dimens <[email protected]>
update stuff

d60cfb96de7b98d69c8c0f6baf0a4b57e939567b authored over 3 years ago by Pavel Dimens <[email protected]>
touch up b/vcf

0c00bc7a3877a5f3361ef7e1ae56e31f793dc3ca authored over 3 years ago by Pavel Dimens <[email protected]>
fixes

c99dd1c4082e5b93d177534c5e54026e0bd2a680 authored over 3 years ago by Pavel Dimens <[email protected]>
compress all PooledArray constructors

8b4cc539392a98e4bec37a669daf735050c9de3e authored over 3 years ago by Pavel Dimens <[email protected]>
fix structure parser

78212f5d7fa8ade8101ecb22b54858d71aae8b09 authored over 3 years ago by Pavel Dimens <[email protected]>
change precomp and remove loci/samples in utils

44e871d0447f73ec716c64ecacc01381804a3f96 authored over 3 years ago by Pavel Dimens <[email protected]>
add manipulate tests

ae6a6f8122ba4754cd7305330e81abecd00bc3d9 authored over 3 years ago by Pavel Dimens <[email protected]>
update popdata fields everywhere

ab10a7a7a9d9bb5a72eb4446aaef1762f948695b authored over 3 years ago by Pavel Dimens <[email protected]>
update tests

fbc80d7ed6f0d993d4914f5d81f4ed55eb497b9c authored over 3 years ago by Pavel Dimens <[email protected]>
rename fields and add internal constructor

22f4bd758a1a5f5dc91df17ff137cb483ba5d7a9 authored over 3 years ago by Pavel Dimens <[email protected]>
update show

af77d066875cb432631e635fdd548295092f6347 authored over 3 years ago by Pavel Dimens <[email protected]>
precompile io

e0c0e357af77092ae153d59165a9b68ffd147d40 authored over 3 years ago by Pavel Dimens <[email protected]>
notes and new show method

4893a7fa2e45e824f0a6f23132f1c2e30d805068 authored over 3 years ago by Pavel Dimens <[email protected]>
pilot idea for popdata improvement

24b2d6111b5829ae62bf658d89b2f4ebd7376ab8 authored over 3 years ago by Pavel Dimens <[email protected]>
include manipulate

de64988f24c26be49130f3d5439908fb5395b015 authored over 3 years ago by Pavel Dimens <[email protected]>
migrate manipulate

1b39186e3767f3c60d07563521d840e36b72f342 authored over 3 years ago by Pavel Dimens <[email protected]>
Add files via upload

72a8213f7741281662bb4f85f3508aa1d6a65584 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update README.md

838116a1ccccc47ac372f36b12c094ad6b511d50 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Delete popgenio.png

6255e7827ae39d3bdddc1443e5e035fb31558c95 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Add files via upload

51130efd6f2fa6f417772ba99f8f2074d4885586 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update README.md

48527ac92877769c008a03ff879a24b699a122cf authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update PopGenCore.jl

ba518ce87eb234775da9fed33bcc353b8535ca8b authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update Project.toml

b3c4996257ff0577762b346aa9401a53bac16859 authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update types.jl

6c026391c772c5a3a55c69480f14c23c061e4dce authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update io.jl

c6de2e0ac184fff3749370ec736b5a7bb26a04ad authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update runtests.jl

dfc0b93735238a087be67b7f8b6189f158dc9b6b authored over 3 years ago by Pavel V. Dimens <[email protected]>
Rename PopGenIO.jl to PopGenCore.jl

c02b4a65ef4205a400659188fec8f64c7422047e authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update README.md

fa21c0ac4c0a51e2115f04632b4008408a6c72af authored over 3 years ago by Pavel V. Dimens <[email protected]>
rename to PopGenCore

62294b29dc627cb85132ffec8851f3998d72d14f authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update ci_dev.yaml

63fea2e85b07f08986ed3bc1db997e1806fa5403 authored over 3 years ago by Pavel V. Dimens <[email protected]>
add compat entries

7136057140bb7d239a945f5a1e8a48db62b6bb9f authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update README.md

1618fc7754baa57aa84df0c5ead568e39ff49e7a authored over 3 years ago by Pavel V. Dimens <[email protected]>
Update README.md

cd82144bc7689a3980b5653dd4636daa065009db authored over 3 years ago by Pavel V. Dimens <[email protected]>
attempt to update VCF

c2efd631096f2adbf2e68df7d0346c431dd230d6 authored over 3 years ago by Pavel Dimens <[email protected]>
disable vcf test (needs fixing)

7b93d1143317a6b6e4f8d1f9fab2353f1eae36fb authored over 3 years ago by Pavel Dimens <[email protected]>
rename and update branch

969bf3a403ce91598be42042260a7690f386a6ed authored over 3 years ago by Pavel Dimens <[email protected]>
fix vxf

aaece3dc43711efa723b3f6603e014b19d8a059a authored over 3 years ago by Pavel Dimens <[email protected]>
fix io tests

05e254047c5ab1ff09107d1e316d05b39d671991 authored over 3 years ago by Pavel Dimens <[email protected]>
fix datasets

9d40b8ef9bb5cbd9167915a7219371197584c2b2 authored over 3 years ago by Pavel Dimens <[email protected]>
rm precompile()

7eed7832f94c09b9ab5c9ee9b56c15a7e45549c0 authored over 3 years ago by Pavel Dimens <[email protected]>
add some precompilation

0c8bdbb6d1c6327988370976501f7971bd47ca7d authored over 3 years ago by Pavel Dimens <[email protected]>
fix datasets

32815afdf95785a92f4132038be898d50d118527 authored over 3 years ago by Pavel Dimens <[email protected]>