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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

Rename Variant.jl to Haplotype.jl

github.com/BioJulia/SequenceVariation.jl - 44aa41e6285ae3855f7e4495dd9baa582cef4116 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add equals functionality to Deletion

github.com/BioJulia/SequenceVariation.jl - da2cbbd5282b93b6c8399c943734057fa55d61f0 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstring for Variant

github.com/BioJulia/SequenceVariation.jl - f49220782b8c6535d864ae55815c11389c605e9f authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `mutation(::Edit)` as private API

github.com/BioJulia/SequenceVariation.jl - e8457e4241467448d449387bae6d6d0b2a50fef3 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add length method for Substitution

github.com/BioJulia/SequenceVariation.jl - f08d6eb99167f1a82185bf9626c425b701e874c8 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Refactor Edit length to use dispatch instead of type checking

github.com/BioJulia/SequenceVariation.jl - cab3029bc6cdc8821eaa08c3b5d857a0d886b079 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Declare Blue style formatting for all new documents

github.com/BioJulia/SequenceVariation.jl - a6ad47a5687b89e15de444582200d8924deadf1a authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstrings for Variant methods

github.com/BioJulia/SequenceVariation.jl - ea25ab87dcc6d8c03748af9db830c05dc485b45d authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Remove unused argument names from base getters for edits

github.com/BioJulia/SequenceVariation.jl - 22d460b15a8d366594e32a7c026ded20cfeb725c authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Move Deletion-related code to edits/Deletion.jl

github.com/BioJulia/SequenceVariation.jl - b36ab69c728bf287219e5ff9fea1926cb0cdb7ae authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Remove commented-out code

github.com/BioJulia/SequenceVariation.jl - fb5b7dfacf695a5df5540271d068690afec0e3e1 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstring for Variation

github.com/BioJulia/SequenceVariation.jl - 673481b40f98049c0d4c37f50a9e28a01c4d4965 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add export for translate and reconstruct!

github.com/BioJulia/SequenceVariation.jl - 3b2730b5c1432d41a35f835f0130ec8e737506de authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add Aqua tests

github.com/BioJulia/SequenceVariation.jl - cb53defe9adaa652af8caf5ff1709ca5566a2fd4 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `edit(::Variation)` as private function

github.com/BioJulia/SequenceVariation.jl - a573693737e2ca4edc3f11d65e652b2fd0ce0d1e authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Move Edit-related code to Edit.jl

github.com/BioJulia/SequenceVariation.jl - 3f631ace8fc1979ddf3104c143f4582760c97b4e authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Move Substitution-related code to edits/Substitution.jl

github.com/BioJulia/SequenceVariation.jl - ba9f0e8fb155b810771ea6261b6526145d8e6215 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `lendiff(::Edit)` as private API

github.com/BioJulia/SequenceVariation.jl - 2719c438f3261d6b0345e70afd3ffff6a97b7543 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `edits(::Variant)` as private API

github.com/BioJulia/SequenceVariation.jl - 386acba8ab0a17879ac4e1afb884d38fcd8be87a authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Correct package install directions in docs

github.com/BioJulia/SequenceVariation.jl - 134ee771b9963819b336655c552b70278eeab775 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Organize API docs

github.com/BioJulia/SequenceVariation.jl - 6f7110caec1894d89b5a41b4d5688d4fd8701760 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Refactor _lendiff to use multiple dispatch

github.com/BioJulia/SequenceVariation.jl - dd405c5f4b75d8d201a684165da1747eac039db0 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 3ef4a92ba268faa509547bb9774d070aba38cdd5 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Apply Blue style to tests file

github.com/BioJulia/SequenceVariation.jl - d29764d2bce83822b83e4d8581d7eceb25b43f63 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Remove Windows and Mac CI tests

There is no platform-specific code in this package, so this just slows down
CI with no benefit

github.com/BioJulia/SequenceVariation.jl - 1942090cd610108a8056d6b955b17519ab2e3bb1 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Move exports to top of file

Per Blue style, exports should be one per line, and appear immediately
after using statements. R...

github.com/BioJulia/SequenceVariation.jl - 25c63906dc60ac2efc94be67d8a273a04b7b9251 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Move Insertion-related code to edits/Insertion.jl

github.com/BioJulia/SequenceVariation.jl - 9f9d0899bdff26f936bc90e2b99ec2b395bf5071 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Replace field accession with getter function usage

github.com/BioJulia/SequenceVariation.jl - ef4460bbbf0172cf68edb65397616dba8b7fa0f0 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstring for `lendiff(::Edit)`

github.com/BioJulia/SequenceVariation.jl - f1baf27865125b6d86ff991ce2e8a62740d5eb19 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstring for `mutation(::Edit)`

github.com/BioJulia/SequenceVariation.jl - 82ba8386147f6b60d0dc58dd868f941e2d2bf4ce authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Move Variant-related code to Variant.jl

github.com/BioJulia/SequenceVariation.jl - 37965ac7eb80992a0580d86b7e4d9a67b65e752f authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Move Variation-related code to Variation.jl

github.com/BioJulia/SequenceVariation.jl - 8c2dd271f3f51c14b945fb1a3d6c8e416f8a4a27 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Apply Blue style to docs file

github.com/BioJulia/SequenceVariation.jl - fb9ab68cca925e138fd9dc1ebbccdb23c6257f89 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add linting workflow for PRs

github.com/BioJulia/SequenceVariation.jl - 8ae09aa9a1bbd0376d51483b4134d968b242863e authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Mark is_valid(::Variation) as private function

github.com/BioJulia/SequenceVariation.jl - 1f2b116518ebea297c71e69e026d25fc4efbbffc authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add tutorial-type documentation

github.com/BioJulia/SequenceVariation.jl - 6510ee3fc030992f93562c4c072b57f2b2c621c2 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add docstrings for Variation functions

github.com/BioJulia/SequenceVariation.jl - 2a7d61e43d61d8ace9cfbe7fb157a5e707683945 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update getter usage in translate function

github.com/BioJulia/SequenceVariation.jl - cb1c429610e214de017cb57726ecc539669dc24b authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Mark `is_valid(::Variant)` as private function

github.com/BioJulia/SequenceVariation.jl - 2f4f5fb5aeeeaf42d23dd740de8e6d124c7499cb authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Release v3.1.0 (#89)

github.com/BioJulia/BioAlignments.jl - ceb3fe6ce85c794adde877b0bd048905557dc1e2 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Improve precompilation

Improve precompilation by operating on files instead of IOBuffers. This is more
representative o...

github.com/BioJulia/FASTX.jl - 617e7c1ebf39896671979bf499137101804c2a28 authored almost 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #475 from kool7d/dev

Update Project.toml

github.com/BioJulia/BioMakie.jl - 747b377406393cb03f7ba1eb6c0d3f6b6ab9cd73 authored almost 2 years ago by Dan Kool <[email protected]>
Update Project.toml

github.com/BioJulia/BioMakie.jl - 85cf66fb60c6c885c6b908bc30c9c97a7b662f4f authored almost 2 years ago by Dan Kool <[email protected]>
Merge pull request #474 from kool7d/dev

update project

github.com/BioJulia/BioMakie.jl - 97a04d38fc39e1be514e3dbde4bfbda890c642b8 authored almost 2 years ago by Dan Kool <[email protected]>
Merge branch 'master' into dev

github.com/BioJulia/BioMakie.jl - ba5ae5229d8f573c3df979355eb82983d36230c0 authored almost 2 years ago by Dan Kool <[email protected]>
Merge pull request #473 from kool7d/dev

Dev

github.com/BioJulia/BioMakie.jl - 4b4dedd388d16d7ddba6cdb351feb27d461a9a4a authored almost 2 years ago by Dan Kool <[email protected]>
update project

github.com/BioJulia/BioMakie.jl - 02ccc442462436520e1e193fbb3e0462a375b232 authored almost 2 years ago by kool7d <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 73d2781ee945ebc64f6b5599ef0838f4cab585e9 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number in Project.toml

github.com/BioJulia/SequenceVariation.jl - 6ba583de4f42f0fc711085705c024e441b265d67 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for soft clips

github.com/BioJulia/SequenceVariation.jl - dd00231840f0288a30c6da2c63925a581e559204 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for ending substitutions being invalid

github.com/BioJulia/SequenceVariation.jl - f9e76d60d6d23530b449062e4e5ac7998f25a978 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 17f4cd6f395610f30ee0856f55a473b830378455 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Switch alignment validation to after edit construction

github.com/BioJulia/SequenceVariation.jl - 128a5445ad566ee4c0bf9f9d0331ec1cd1e5e41c authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add check for soft clips when construction Variants from alignment

github.com/BioJulia/SequenceVariation.jl - 5be4dce200ad3e4f9ea121c9159e5ec30d7c6eb1 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update ranges to allow end position insertions

github.com/BioJulia/SequenceVariation.jl - f9058c5cb393a2a616535843eba15a3c2ed0f3b4 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for ending insertion

github.com/BioJulia/SequenceVariation.jl - 3b61ccefb5eb783d819468680bc77bb8d198ec3d authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add Variation-level validation for Variants

Testing indicates that some Variants (particularly those with insertions
and/or clips at the sen...

github.com/BioJulia/SequenceVariation.jl - d8435be115d38d450a283f2ed4a8b212b192dce0 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add test for combined clips

github.com/BioJulia/SequenceVariation.jl - abff6692d49052e88966d40fdb92194a7290b0e9 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add equality function for Variant

github.com/BioJulia/SequenceVariation.jl - 91c3acc85ee9c9aec558b94f3b41fa38d9d84931 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Grantham's substitution matrix (#88)

Added support for R. Grantham's substitution matrix based on chemical properties from his 1974 p...

github.com/BioJulia/BioAlignments.jl - 26be95a2e9a7776031bd910fbd7b61892403ff6e authored almost 2 years ago by Kapara newbie <[email protected]>
Initial commit

github.com/BioJulia/.github - 9d9210005816907bd4b530cbf4ebd5b32f883086 authored almost 2 years ago by Sabrina Jaye Ward <[email protected]>
Fix bug in zero_offset! called when materializing seqview (#261)

When materializing a seqview, a slice of the underlying buffer is copied
directly, for efficien...

github.com/BioJulia/BioSequences.jl - 1cfea08e9f08ce8a2282a1e2abfebb1773a8fb77 authored almost 2 years ago by Jakob Nybo Nissen <[email protected]>
Bump version number in Project.toml

github.com/BioJulia/SequenceVariation.jl - 00495d4e14537454a5f0a952d5e9fc29d24e1279 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG for v0.1.3

github.com/BioJulia/SequenceVariation.jl - b45081a56e1602dc546ee0f75787611b57726418 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 3ed27f0c4e53c2662da4ddd1af224fed733de44c authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Add type parameterization to variations getter

I have encountered some cases where having a non-parameterized vector can
crash a downstream pro...

github.com/BioJulia/SequenceVariation.jl - 3b33c85d00db3437998fdc93075b37399204ff42 authored almost 2 years ago by Thomas A. Christensen II <[email protected]>
Update Documenter.yml

github.com/BioJulia/BioMakie.jl - d6372772fd16ce09e8f8550beefeb8dcc86b2a48 authored almost 2 years ago by Dan Kool <[email protected]>
Stop pirating BioSymbols (#259)

BioSequences pirated BioSymbols by overloading `gap`, `isambigous`, `isgap` and
`iscertain`. Re...

github.com/BioJulia/BioSequences.jl - db8a69293e45910e60b0aae4e7f468621cb5b21d authored almost 2 years ago by Jakob Nybo Nissen <[email protected]>
Add `gap(::Type{Char})` to prevent piracy from BioSequences. (#56)

github.com/BioJulia/BioSymbols.jl - e026408ff8ed1fbe32c3ae0051d09f7bd411862b authored almost 2 years ago by Jakob Nybo Nissen <[email protected]>
glmakie dep

github.com/BioJulia/BioMakie.jl - cc71c268e8fadd4e6daef4a03c2b62905805d19d authored almost 2 years ago by Dan Kool <[email protected]>
Update BioMakie.jl

github.com/BioJulia/BioMakie.jl - fa0fec9a84dd0d7648e44482d19212f4e49ac8fa authored almost 2 years ago by Dan Kool <[email protected]>
bugfix for delete!(genes)

github.com/BioJulia/GenomicAnnotations.jl - cb54afc2247361147c5d89ed0d776a49f8b88559 authored almost 2 years ago by Xiangting Li <[email protected]>
Update runtests.jl

github.com/BioJulia/BioMakie.jl - bc8f62469930210f348f5249ee8130ac638082bc authored almost 2 years ago by Dan Kool <[email protected]>
Update Project.toml

github.com/BioJulia/BioMakie.jl - 80af26ecda74732f927a3620cfd54ee53490fb75 authored almost 2 years ago by Dan Kool <[email protected]>
Merge pull request #468 from kool7d/compathelper/new_version/2022-10-14-02-21-12-369-00708237359

CompatHelper: bump compat for MolecularGraph to 0.12, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 99d0309bfa8cb4d537737e90fea5ace60de14780 authored almost 2 years ago by Dan Kool <[email protected]>
Merge branch 'master' into compathelper/new_version/2022-10-14-02-21-12-369-00708237359

github.com/BioJulia/BioMakie.jl - 36cd5c8acd07d811684d12134f4d26cd221c7412 authored almost 2 years ago by Dan Kool <[email protected]>
Merge pull request #467 from kool7d/compathelper/new_version/2022-10-13-02-04-00-061-00702153229

CompatHelper: add new compat entry for Makie at version 0.18, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 94a71690a2a1da17c973a223f2135eb67d7d6d3c authored almost 2 years ago by Dan Kool <[email protected]>
Update Project.toml

github.com/BioJulia/BioMakie.jl - f4a142fa63c783c1227da55112107f7b7b693f86 authored almost 2 years ago by Dan Kool <[email protected]>
Fix typo (#258)

github.com/BioJulia/BioSequences.jl - e4c89976320abff2a2c24800142296200232648c authored about 2 years ago by Jorge Fernandez-de-Cossio-Diaz <[email protected]>
Update CHANGELOG

github.com/BioJulia/XAM.jl - 50039e749f39bb7b29d28ccd808331493767eec7 authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #56 from jonathanBieler/bam_index_method

Added method for handling different bam index types.

github.com/BioJulia/XAM.jl - 8272cea71efba979b544c9f54a55cc6f26591d9e authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge branch 'master' into develop

github.com/BioJulia/XAM.jl - bda532e2ceb92e1dce80194d78cab6a25288213b authored about 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #57 from BioJulia/release/0.3.1

Release v0.3.1

github.com/BioJulia/XAM.jl - 22f939ffbe3b3b765a3b47c43fd7b795fe433b54 authored about 2 years ago by Ciarán O'Mara <[email protected]>
CompatHelper: bump compat for MolecularGraph to 0.12, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 8ce5b18b55615b44968e1e2c728e4addae22480e authored about 2 years ago by CompatHelper Julia <[email protected]>
Update CHANGELOG for v0.3.1

github.com/BioJulia/XAM.jl - fe83a749d20132b7805e611917817b91c28a00e7 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Bump version number in Project.toml to 0.3.1

github.com/BioJulia/XAM.jl - 1c57e9b0e2e8b0f87edc39387fd436ddc374a185 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #55 from MillironX/feature/bioalignments-3

github.com/BioJulia/XAM.jl - e2b22becf463acdef1fcfbfd19d2b54411f8a1f0 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
update docstring

github.com/BioJulia/XAM.jl - 286e271e9135b4379996e69deb0c6726eb4c5a01 authored about 2 years ago by Jonathan Bieler <[email protected]>
added method for handling different bam index types

github.com/BioJulia/XAM.jl - 93a6b60d26e2b0c70ea8755d5b0913c1df7bb88d authored about 2 years ago by Jonathan Bieler <[email protected]>
CompatHelper: add new compat entry for Makie at version 0.18, (keep existing compat)

github.com/BioJulia/BioMakie.jl - 2ca5eb2ecd9afa878ada1bf6b8e73b2161c961ea authored about 2 years ago by CompatHelper Julia <[email protected]>
Update CHANGELOG

github.com/BioJulia/XAM.jl - 32e3213ee8dc008084e0e3b60a51e3993f8a71dc authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update tests to use new AlignmentAnchor structure

github.com/BioJulia/XAM.jl - f7b9d9fa75ca686c6412fdecd6a012f1dfaa7fcc authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Bump BioAlignments version compat to 3

github.com/BioJulia/XAM.jl - 9720fd0fcd342c10791c7e1b620653d2362845ee authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Change alignment getter for BAM.Record to use existing cigar constructor

Rather than keep a copy of the BioAlignments cigar constructor embedded in
this function, have i...

github.com/BioJulia/XAM.jl - e6f542a368c368e85c3cc411fb4fb84fa694d441 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #52 from BioJulia/release/0.3.0

Release v0.3.0

github.com/BioJulia/XAM.jl - 946e77a7343bff28da35360820655e9960236b0f authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update .github/workflows/TagBot.yml

Co-authored-by: Ciarán O'Mara <[email protected]>

github.com/BioJulia/XAM.jl - 0c4b3f5dd00de71a96d92031db0cdf14534352ce authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update .github/workflows/CompatHelper.yml

Co-authored-by: Ciarán O'Mara <[email protected]>

github.com/BioJulia/XAM.jl - 2e739e2d8d0181b5e3fb1e1c8c6b1ecb4f2d7848 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update .github/workflows/CompatHelper.yml

Co-authored-by: Ciarán O'Mara <[email protected]>

github.com/BioJulia/XAM.jl - 8d9ccc91f2953ab82b5ceb5131776ecd0da071a2 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Update .github/workflows/Documentation.yml

Co-authored-by: Ciarán O'Mara <[email protected]>

github.com/BioJulia/XAM.jl - a7a8e53e4d211f45594213c5fbf5ef2f27286184 authored about 2 years ago by Thomas A. Christensen II <[email protected]>
Add CHANGELOG

github.com/BioJulia/XAM.jl - 46fcf71f96ef03de906ea7f7ae7fea9a1801e098 authored about 2 years ago by Thomas A. Christensen II <[email protected]>