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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

Bump version number to 0.3.0 in Project.toml

github.com/BioJulia/XAM.jl - 5cbf9dfb1cec668f6dcaefdef8a4d9d58736743a authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update project version number to 3.0.0

github.com/BioJulia/BioAlignments.jl - 91a6d1e0301655aa5970fb46c6c3153012de7064 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update changelog for v3.0.0

github.com/BioJulia/BioAlignments.jl - 9a6a37defeef5176ae82332b67007a4f1ab8784d authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove docs workflow

github.com/BioJulia/BioFetch.jl - 61c5de4bd529702809beff5d1dce3e4a75c0832f authored about 2 years ago by Nicholas Bauer <[email protected]>
Bump Julia versions

github.com/BioJulia/BioFetch.jl - 0fb90f0ad2dbf5797d271b25f6a62e0b97144915 authored about 2 years ago by Nicholas Bauer <[email protected]>
Bump compat, fix test, bump version to v0.2.1

github.com/BioJulia/BioFetch.jl - 6dcf7d00190770ddae18b47ead2311e62e18490e authored about 2 years ago by Nicholas Bauer <[email protected]>
Update project version number to v0.1.2

github.com/BioJulia/SequenceVariation.jl - 4de936cc83abfdcd037c2eb9874f885bd8db9df1 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.1.2

github.com/BioJulia/SequenceVariation.jl - 752b482a0b7ba9374ec43032b7499b65ab721762 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add ranged dependency compats

github.com/BioJulia/SequenceVariation.jl - b20d603f95e624aed55e1c2698f043eadc0d2da4 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 780a5add8a01b0b0db1467ff8ce1639deba6c983 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove unused AminoAcidSeq reference

github.com/BioJulia/SequenceVariation.jl - f7278bd7d7345aafe399c0a7622027de12bc800a authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #64 from MillironX/operations-fix

github.com/BioJulia/BioAlignments.jl - c7bb5a849a270d4b84d306282c862e4a5f8d0718 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add clarification comments to soft clip anchor checking

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 96f8ee7f99bbfe3fd2ff0d47e40326845b4faeed authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Make conditional non-empty

Co-authored-by: Kevin Bonham <[email protected]>

github.com/BioJulia/BioAlignments.jl - b99bada025798d49731e04f63a7aa4fda2b294e9 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for padded alignments

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 118ad0ec78fb78cb272e16599992bf3031ec4ff3 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add meta-operation support to PairwiseAlignment iterator

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - bc19366d48c2e4a366f2d3766015736e9a09b773 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Revert count_aligned function to 0156de451254 ("alignment position support")

The `count_aligned` function was updated by @alyst to use the new `alnpos`
field in cc8237c48ad1...

github.com/BioJulia/BioAlignments.jl - f63ee256f68bb568224db27301d71b8d9e14688f authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - b60800927ad7fef8586446af57a8e7acaa019686 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for soft clip as second-to-last operation

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 6bb6df5b8744a75c089a0088de1368a1ce89bda8 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for clips at end of alignment

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 1d7ac42c180ed87f6bc16a4bc7d968cb2c5d706d authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add soft clips back into the alignment simulator

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - b067303968dd1929ad11a63d3ba96ced9555d753 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add hard clips back into the alignment simulator

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 0832146eee33ed4db6e7bb79dabe7c9828405e8c authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove never-reached code from random alignment generator

The test suite included logic for treating ends of alignment differently,
but due to the loop co...

github.com/BioJulia/BioAlignments.jl - f89415d951490d46b13fb31edcbe39996ae3be39 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add support to meta operations to test suite

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - cf400cc9a4f5a39188f6ae9955b7874e0e6b437a authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Correct variable name typo in random alignment generation

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 43541f81145db2c53eadf2dc75a54c34f25cb00f authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove SOFT_CLIP from insertion operations in random alignment generation

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 28bd1d44b529b14c9e6147926f2426c5ae3768b2 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add check for valid OP_SOFT_CLIP location

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - c6a531b93efe1402ea47076b45026b0825f35d71 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add check for invalid location of OP_HARD_CLIP

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 0d6b90af886558bfb39e4de5acdb7554e3ca6563 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Switch to using alnpos to determine CIGAR numbers

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - be9f93aa0141ae0974a5fdfa099aabfe2e922eeb authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove HARD_CLIP from insert operation list in test suite

According to the SAM spec, "H can only be present as the first and/or last
operation." In additi...

github.com/BioJulia/BioAlignments.jl - 0f3090c7058208b1685fefd1cb7cc7bcf52c1587 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add export for ismetaop function

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 4a4e722ba13239f9f1446320aeef09ef2c733844 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add update on OP_PAD to docs

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 268c69617a26e409d8464420700481afceda68f4 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Indicate that OP_PAD is now supported

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 7fb5a46492d18a328847824796009b038b57b560 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove unused assignments from cigar function

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - d7c3179ccbe9106925ba955eac41e499716fac53 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add skip for printing meta operations in cigar strings

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 30478c486fe347422b7c76cee4715f50f0fe4763 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add meta operations into alignment building from CIGAR strings

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - f48c9c63f88e9d9076aeb4edd970d21ec98bcb6c authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Remove OP_HARD_CLIP from isinsertop trait

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 11ec678f5260142d8ff4f302c87c6a24312c97f0 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add new trait for operations, `ismetaop`

Signed-off-by: Thomas A. Christensen II <[email protected]>

github.com/BioJulia/BioAlignments.jl - 3850382fe7f2cee449656f1c6804c7ba0fd24aea authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #62 from alyst/agn_figs

github.com/BioJulia/BioAlignments.jl - f0b768945a3ae38eabbd0f6951ce005abde4098d authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #85 from BioJulia/release/v2.3.0

Downstream tests are failing because the breaking change from
#44 was merged here.

github.com/BioJulia/BioAlignments.jl - b92ccf3e9ed8976496880c3a521f4622ffeffeda authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Merge branch 'master' into release/v2.3.0

github.com/BioJulia/BioAlignments.jl - eceafe684719a8490196440b5396999cf17c2fdf authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v2.3.0

github.com/BioJulia/BioAlignments.jl - 53f975cd1f8581242ac9c349444b53c0a4448b62 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number in Project.toml

github.com/BioJulia/BioAlignments.jl - 898beae1fb8888b8171a7cf2897d87373fe4f566 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Merge branch 'MillironX/feature/getter-methods'

This merge is basically merging a PR on top of the v2.2.0 tag, because
GitHub doesn't appreciate...

github.com/BioJulia/BioAlignments.jl - 33477483e0474ce586cb7a5f84b1d0b69e9cb560 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add iterate method for Alphabets (#233)

* Add iterate method for Alphabets

* fixup

* fixup

github.com/BioJulia/BioSequences.jl - da14bd9809c657508028215c46fe0290549a955a authored about 2 years ago by Sabrina Jaye Ward <[email protected]>
Improve type stability slightly

github.com/BioJulia/FASTX.jl - 29f386d2d82969ec14bccde5a47aff79692d0198 authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
rm makie import

github.com/BioJulia/BioMakie.jl - 5fda574da77ec6b3faf0ffd4e4e2b9e20bd936bd authored about 2 years ago by kool7d <[email protected]>
add glmakie

github.com/BioJulia/BioMakie.jl - 141f1dc5bae538f52d71cab30fec81be134264c5 authored about 2 years ago by kool7d <[email protected]>
notransduce

github.com/BioJulia/BioMakie.jl - 609a42488bda2012b42d6494509e68fa8f676a35 authored about 2 years ago by kool7d <[email protected]>
Merge pull request #464 from kool7d/dev

revive

github.com/BioJulia/BioMakie.jl - df1aaf03d61097baf82ed8f599df1cdc2f45b9ad authored about 2 years ago by Dan Kool <[email protected]>
Merge branch 'master' into dev

github.com/BioJulia/BioMakie.jl - fe56f51e1c935b00697e08ef592d9d6645037fd0 authored about 2 years ago by Dan Kool <[email protected]>
cleanup1

github.com/BioJulia/BioMakie.jl - cfeb3d3f4fdd382310c25a1b09edd000492725ea authored about 2 years ago by kool7d <[email protected]>
Merge pull request #458 from kool7d/compathelper/new_version/2022-05-15-01-48-12-919-02592511390

CompatHelper: add new compat entry for Transducers at version 0.4, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 4357f5a66e4d54e0a21606fb74e127b7d0a9885c authored about 2 years ago by Dan Kool <[email protected]>
Merge pull request #463 from kool7d/compathelper/new_version/2022-08-25-01-58-44-549-03720471237

CompatHelper: bump compat for Meshes to 0.24, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 4a49a5b6e3c9b9f506504655675a4f3b6495ab4f authored about 2 years ago by Dan Kool <[email protected]>
Merge pull request #462 from kool7d/compathelper/new_version/2022-08-18-01-59-16-523-02627684957

CompatHelper: bump compat for FASTX to 2, (keep existing compat)

github.com/BioJulia/BioMakie.jl - a8744dbcf7fc346d30f1c959bedcffee5687df19 authored about 2 years ago by Dan Kool <[email protected]>
Merge pull request #460 from kool7d/compathelper/new_version/2022-06-20-01-41-58-923-01690078014

CompatHelper: bump compat for HTTP to 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 560964a8ccf757d96f796d89d3cdc165ee3dfbcf authored about 2 years ago by Dan Kool <[email protected]>
revive

github.com/BioJulia/BioMakie.jl - c665a9021b7891735eb7a2add456ad6f59fec043 authored about 2 years ago by kool7d <[email protected]>
require Julia 1.6

github.com/BioJulia/MMTF.jl - 25a3cfaba07a936b03b7d75d69da6c767da0e22d authored about 2 years ago by Joe Greener <[email protected]>
Add SnoopPrecompile

The small dependency SnoopPrecompile allows more efficient precompile statements
in packages. He...

github.com/BioJulia/FASTX.jl - f59007a884bc6ae4b4b2a57a9eb6ce494cbe8554 authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Add SnoopPrecompile (#257)

Add the SnoopPrecompile dependency to improve precompilation. While BioSequences
is already eff...

github.com/BioJulia/BioSequences.jl - 3627b63681dede3bba41daaba2b8c1f4d44cf9bf authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Add SnoopPrecompile (#54)

Add SnoopPrecompile

github.com/BioJulia/BioSymbols.jl - 2ea9143a9605e0a249efd9a6299cc57b5233f37b authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
CompatHelper: bump compat for Meshes to 0.24, (keep existing compat)

github.com/BioJulia/BioMakie.jl - e51736560f1877892bd777a4292143445a5fc27f authored about 2 years ago by CompatHelper Julia <[email protected]>
Merge pull request #86 from BioJulia/docs-preview

Try to get preview build to work

github.com/BioJulia/FASTX.jl - ac28dbbd4f2767c1e1db30b4ce541acb6dd66a8a authored about 2 years ago by Kevin Bonham <[email protected]>
try to get preview build

github.com/BioJulia/FASTX.jl - f1681919342c71b58945650bec755c8efed5b234 authored about 2 years ago by Kevin Bonham <[email protected]>
add newline

github.com/BioJulia/FASTX.jl - 9dae22f30767937778973c959f6088e2cc9d9943 authored about 2 years ago by Kevin Bonham <[email protected]>
CompatHelper: bump compat for FASTX to 2, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 936d00dee907eb2d2ea021ed60361829b3c05cc3 authored about 2 years ago by CompatHelper Julia <[email protected]>
Fix printing of Records

github.com/BioJulia/FASTX.jl - 76bdf567bb7f41ea109261778ae577c99832a20d authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Rename seqlen to seqsize and export it

github.com/BioJulia/FASTX.jl - 7bd3183f65feec35dd1f39dd93873ed36c026c85 authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Update README

* Remove reference to OpenCollective
* Remove reference to Gitter

github.com/BioJulia/FASTX.jl - 8da41e7b1a06d4d711f60bbfd77f392947fd21db authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
compress gulfsharks source file

github.com/BioJulia/PopGenCore.jl - ecc4b3d274749ba55587338a38e095e7f2cb6bf7 authored about 2 years ago by pdimens <[email protected]>
change pairwise FST api for dispatch

github.com/BioJulia/PopGen.jl - c99741eac529a0e4c02880844bcffca453b09f44 authored about 2 years ago by pdimens <[email protected]>
Use ReTest (#84)

Use ReTest testing framework

github.com/BioJulia/FASTX.jl - 5250a27bd7480225dca3f90d07f0881b78206050 authored about 2 years ago by Kevin Bonham <[email protected]>
Rewrite for v2 (#68)

Complete rewrite for v2.
See the changelog for more details.

github.com/BioJulia/FASTX.jl - f44c49832b5f736adf52a5fcffecfaa9118e63ae authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Add messages to assertions

github.com/BioJulia/XAM.jl - 5da017052b32433ecbd41042600271e7e0c4a387 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

# Conflicts:
# Project.toml
# test/runtests.jl

github.com/BioJulia/XAM.jl - 8424757cc21cf46e2cec58d9aa501b17931125f7 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'hotfix/issue-31'

github.com/BioJulia/XAM.jl - 4490e7c890bb32ba9068c4e06e8a3f731f023454 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #48 from MillironX/feature/BioAlignmentsv2.2

Upgrade BioAlignments to v2.2 & BioSequences to v3

github.com/BioJulia/XAM.jl - d37e9a04d8b7b1f2b67ffa6202336c19500163eb authored about 2 years ago by Ciarán O'Mara <[email protected]>
Increment BGZFStreams compatibility

github.com/BioJulia/XAM.jl - 0cc0405ca02a7087c7b157665570152eda6562fe authored about 2 years ago by Ciarán O'Mara <[email protected]>
Add tests for issue #31

Test for expected results as described in https://github.com/BioJulia/XAM.jl/issues/31.

github.com/BioJulia/XAM.jl - 99aa013c2b6687ab466a92a694a5e13cd1ff7dd9 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Increment version

github.com/BioJulia/XAM.jl - 7609f6e24dedfcdb573bfab462ec7ffeed381bf3 authored about 2 years ago by Ciarán O'Mara <[email protected]>
make pairwisefst method text consistent in print

github.com/BioJulia/PopGen.jl - e8252df4bc7c0402535e0b9a3560daaf76b05d79 authored about 2 years ago by pdimens <[email protected]>
prettier printing

github.com/BioJulia/PopGen.jl - e52042f87fc4862f150f2a924703bed22d487277 authored about 2 years ago by pdimens <[email protected]>
add initial AMOVA

github.com/BioJulia/PopGen.jl - 3b2b9750e6728a94ea49d4f42867961bc0f17f35 authored about 2 years ago by pdimens <[email protected]>
add Printf import statement

github.com/BioJulia/PopGen.jl - 88f4129c69b0bcaba9a70a66c86e56b231c9a0e2 authored about 2 years ago by pdimens <[email protected]>
add

github.com/BioJulia/PopGen.jl - 897cc765b38c6686c5d86e0bac162d65eada6066 authored about 2 years ago by pdimens <[email protected]>
add AMOVA fst and make it default

github.com/BioJulia/PopGen.jl - a70a4214a459bac10acfadb831f80a96c7ae3969 authored about 2 years ago by pdimens <[email protected]>
fix progressbar

github.com/BioJulia/PopGen.jl - 019265b8a43e6380aad5b85551722a8d2201e13d authored about 2 years ago by pdimens <[email protected]>
some fixes

github.com/BioJulia/PopGen.jl - 1bd9ab4ecd348ab49a89e5ad0e1d66091ddd7fe2 authored about 2 years ago by pdimens <[email protected]>
update compat

github.com/BioJulia/PopGen.jl - 5fd5bba17f2b1778474c03f77c293f9a08c3c3a2 authored about 2 years ago by pdimens <[email protected]>
Merge pull request #108 from BioJulia/compathelper/new_version/2022-08-07-02-12-29-900-03575162840

CompatHelper: bump compat for MultivariateStats to 0.10, (keep existing compat)

github.com/BioJulia/PopGen.jl - 88ec014ae840c54258d8efcf13b256ddde31f2d4 authored about 2 years ago by Pavel V. Dimens <[email protected]>
CompatHelper: bump compat for MultivariateStats to 0.10, (keep existing compat)

github.com/BioJulia/PopGen.jl - 0bd2f7eaf5a7f4690c111fa5a3c02f1d7dc78ee0 authored about 2 years ago by CompatHelper Julia <[email protected]>
interface changes

github.com/BioJulia/PopGen.jl - 6ce957c9d79876e98a0978ad25fc81a484d894ba authored about 2 years ago by pdimens <[email protected]>
formatting change for missing filter

github.com/BioJulia/PopGen.jl - 0da75eb78743fd32613d591e054e48cb9ead8509 authored about 2 years ago by pdimens <[email protected]>
Update README.md

github.com/BioJulia/PopGen.jl - 18e981f054fab6b855a116cb2d09249a81996894 authored about 2 years ago by Pavel V. Dimens <[email protected]>
begin writing AMOVA

github.com/BioJulia/PopGen.jl - fb533246bd3fbfd2ab2f1d34fedc149dfb71e0db authored about 2 years ago by pdimens <[email protected]>
remove tsne

github.com/BioJulia/PopGen.jl - c35cadf30454a9ad783c14846c3206202f558dfc authored about 2 years ago by pdimens <[email protected]>
add percent column

github.com/BioJulia/PopGen.jl - 07aa75e683cb12edf31b0ede6f50d7de1ebfe5eb authored about 2 years ago by pdimens <[email protected]>
Remove unused files

github.com/BioJulia/Automa.jl - 8dd2672fd838430f673294b2c0c9c011ab9f469e authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Better error on compiling null regex

It is possible for users to construct a regex that matches the null set, i.e.
no strings, not ev...

github.com/BioJulia/Automa.jl - 82238fbd723b1f6608e332ceb9fcf01912cdf47c authored about 2 years ago by Jakob Nybo Nissen <[email protected]>
Remove StableSet and StableDict

These two data types were originally added to prevent nondeterminism when
compiling regex.
Inste...

github.com/BioJulia/Automa.jl - 3a06e84b400646707a95eba48c9e463bdd58aa30 authored about 2 years ago by Jakob Nybo Nissen <[email protected]>