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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

Update CHANGELOG

github.com/BioJulia/SequenceVariation.jl - 1cfe128070f55c582688abf11ce081cc7112ee52 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add VCF spec tests for reference and alternate bases

github.com/BioJulia/SequenceVariation.jl - 97e1d193a64b06f298c990076dc83aeaf3b87e44 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add public alternate base getter for Variation

github.com/BioJulia/SequenceVariation.jl - b8e44c7b815f2021fddc022822737f02a46503e3 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add public reference base getter for Variation

github.com/BioJulia/SequenceVariation.jl - cab314ec0baaa8b076cea5b8cbcfd86ce0aa71b1 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add private alternate base getter for Insertion

github.com/BioJulia/SequenceVariation.jl - ccbe6eed62ff2c96b115323d50d6faaa70655cf3 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add private reference base getter for Insertion

github.com/BioJulia/SequenceVariation.jl - 1b7c7f86d78ef68020810595e273515e018b2273 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add private alternate base getter for Deletion

github.com/BioJulia/SequenceVariation.jl - 145e9e5f8853072c47b3cd004d0a3783810c9372 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add private reference base getter for Deletion

github.com/BioJulia/SequenceVariation.jl - bc073eaf20b807cb4c4be8a36f6b5c5eda069bc0 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add private alternate base getter for Substitution

github.com/BioJulia/SequenceVariation.jl - c1f47c7b223ff789091b170b4e8ce48e7d69bbb4 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add private reference base getter for Substitution

github.com/BioJulia/SequenceVariation.jl - 73c2c2764f520e8e2b963bfae6b6371fd1c2c0fe authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Fix reference(::Variation)

`reference(::Variation)` used the wrong field name. Fix that so I can use
it downstream.

github.com/BioJulia/SequenceVariation.jl - a80ff869ce1243a2c832abebbfc26fcf6c97fc24 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add reverse translation (#20)

Add reverse translation

github.com/BioJulia/Kmers.jl - f7a1328a744e30840326943bcace9aa6590aba3c authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add Unsafe trait object (#27)

The `Unsafe` trait object allows access to unsafe methods.

github.com/BioJulia/Kmers.jl - cb76fbee736f74e5157a449745a584123042aa8e authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Remove 32-bit arches from unit testing CI workflow

32-bit is causing problems in an upstream package, and I'm not sure why, so remove it for now.

github.com/BioJulia/SequenceVariation.jl - ece50c1ee98fc0939a185acbd117ef23475d99e4 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Fix iterator error in API auto-documentation

github.com/BioJulia/SequenceVariation.jl - 467fa4d261b6a950d5aad1cf7ad10f6953ceecff authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update Documentation CI workflow to use julia-actions workflows

github.com/BioJulia/SequenceVariation.jl - 1c9511310ff2a54049d3602a89dcd47b7dce8d59 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update CI Unit Tests job name to match parameters matrix

github.com/BioJulia/SequenceVariation.jl - 9920ad25177f9983083f84c17c63cfffecdc8fbd authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update CI Unit Tests job name to match parameters matrix

github.com/BioJulia/SequenceVariation.jl - 03a4eb392dfa628ea6ea75371d7d47d2de9f8ca7 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #12 from MillironX/registration-prep

Prepare for package registration

github.com/BioJulia/SequenceVariation.jl - 976d5b3a3d503c9a2c46403f53057b07605ff54b authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add README

github.com/BioJulia/SequenceVariation.jl - 2ccc2551f57750922c279785c7f48997241aa40d authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add a changelog

github.com/BioJulia/SequenceVariation.jl - 60cf5c1b0a8c990f84b2bdde850e469750dd9f24 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add license

github.com/BioJulia/SequenceVariation.jl - e8bb2f6f8ef6d0afca38b06ab3f360b6c67279e6 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add compat section for all dependencies to Project.toml

github.com/BioJulia/SequenceVariation.jl - f7f9e3190c49da078b9d84ec83b694edf32bcad9 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add Thomas Christensen as author in Project.toml

github.com/BioJulia/SequenceVariation.jl - a461152e555b47ae378cb38e5627ed5759548bab authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update documentation

github.com/BioJulia/SequenceVariation.jl - 3d03740741310f34462707c8322a0be01a47b8eb authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Run DocumenterTools.generate()

github.com/BioJulia/SequenceVariation.jl - 4ef7ba4450082ac3013a5cdc425dce78a1b8a812 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add pull request template

github.com/BioJulia/SequenceVariation.jl - 39f3de83ad7519425a59a1b8cf935641396cc815 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add feature request template

github.com/BioJulia/SequenceVariation.jl - 15420d4f52afe332d81c40b5ba72dfda500662f5 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add bug report template

github.com/BioJulia/SequenceVariation.jl - e4300d020aa2d6801db8af4657bf9d1b0d17b416 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Install JuliaRegistrator

github.com/BioJulia/SequenceVariation.jl - 72611659f1ea549d41197bc10bdee098320ce501 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add CompatHelper workflow

github.com/BioJulia/SequenceVariation.jl - 23f75aad22978dc5297a179fa99352d05d66dbb9 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add unit testing workflow

github.com/BioJulia/SequenceVariation.jl - 6e2eab42c7a7d23fccc78bd0c9dd22dd5659c17d authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add TagBot workflow

github.com/BioJulia/SequenceVariation.jl - c5b28e282fcffaf2bf2fa99bc1774869fd63144c authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update minimum Julia version to 1.6

BioSymbols v3 requires Julia 1.6+, so update the "julia" compat entry and
remove unit testing ag...

github.com/BioJulia/XAM.jl - 03d8e5e7456da6e4149f44b299e1181a9d5c8ea8 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Correct docstring

github.com/BioJulia/XAM.jl - 675e5828b198bc997a76d60ea3a125d46897a4ba authored over 2 years ago by Ciarán O'Mara <[email protected]>
add julia 1.7

github.com/BioJulia/PopGen.jl - 115a95e2b484a3f87da88198ce1da5e0d2d85202 authored over 2 years ago by Pavel Dimens <[email protected]>
bump PopGenCore compat to 0.6.0

github.com/BioJulia/PopGen.jl - 82fa72f78ddb24da698be9048d7ec745184f1766 authored over 2 years ago by Pavel Dimens <[email protected]>
Improve hasinterface(::Type{BioSequence}) (#248)

github.com/BioJulia/BioSequences.jl - 8d015fd44ce1e27fb8dbf5ec9b0f37dcece3d0cc authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
fix vers

github.com/BioJulia/PopGenCore.jl - a93becf80f4697ab50b3fd2c3140c41f619ed3c4 authored over 2 years ago by Pavel Dimens <[email protected]>
Merge pull request #18 from BioJulia/release-0.7.0

New version: v0.7.0

github.com/BioJulia/PopGenCore.jl - 784c529d229e67ed834ede50e5f1db850be30883 authored over 2 years ago by Pavel V. Dimens <[email protected]>
Set version to v0.7.0

github.com/BioJulia/PopGenCore.jl - d015dec5c4d46fb3207c85c25fed84ec466b7a4e authored over 2 years ago by Pavel Dimens <[email protected]>
Set version to v0.7.1-DEV

github.com/BioJulia/PopGenCore.jl - 45d85c9d8fe5637d67e4ae6faf1202162768c096 authored over 2 years ago by Pavel Dimens <[email protected]>
add dev text

github.com/BioJulia/PopGenCore.jl - 335b4b65f4cf7a78d872ec7098a273f09b4ce656 authored over 2 years ago by Pavel Dimens <[email protected]>
fixes

github.com/BioJulia/PopGen.jl - b878567386e1b667e7fd119ca1e21bebb26fa0a6 authored over 2 years ago by Pavel Dimens <[email protected]>
add Baypass conversion

github.com/BioJulia/PopGenCore.jl - 474e6c9d17419c1d3ad55877a25c74813896d021 authored over 2 years ago by Pavel Dimens <[email protected]>
fix typo

github.com/BioJulia/PopGenCore.jl - 1c824eec3d30202addb3fe354c880aa23387b59e authored over 2 years ago by Pavel Dimens <[email protected]>
Update BAM.sequence to return BioSequences.LongDNA{4}

Same principles apply as updating SAM.sequence

github.com/BioJulia/XAM.jl - a7a76db3d454353af8a83434e3492ac355fe3ea7 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update SAM.sequence to return BioSequences.LongDNA{4}

BioSequences v3 changed LongDNASeq to LongDNA{N}. We can't assume that
there aren't ambiguous nu...

github.com/BioJulia/XAM.jl - 1660a24a0fe9283a1d38631e39644e51a506b7c1 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Update BioAlignments to v2.2 and BioSequences to v3

Ok, so this isn't atomic, but we can't upgrade these separately.

github.com/BioJulia/XAM.jl - e560681afa7c441584bbc26fac0cf0f04f6ef931 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Reset Julia compat to v1.5 (#245)

Commit 3c8f501 changed Julia compat to from 1.5 to 1.6, since the join method
used sum with ini...

github.com/BioJulia/BioSequences.jl - f7ccb6b0de045aa7d80945ce218918b95fd7867d authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #57 from CiaranOMara/hotfix/docs

github.com/BioJulia/IntervalTrees.jl - fa2ab8461328540b2b99c6e819d9a36da425314d authored over 2 years ago by Ciarán O'Mara <[email protected]>
Add Pkg to documentation’s package requirements

github.com/BioJulia/IntervalTrees.jl - 4e0cb968b3ad1fc0dfcf0e585bb3eda937d5d293 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Merge pull request #52 from CiaranOMara/feature/ci

- Migrates CI to GitHub workflows
- Adds downstream tests
- Updates readme
- Removes HUMANS.m...

github.com/BioJulia/IntervalTrees.jl - 2f6b054902c6dd09d69a9bc57851d9e91b6c9fb4 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Use naive hash fallback for BioSequence (#244)

Current hashing behaviour hashes equal biosequences with different encodings to
different value...

github.com/BioJulia/BioSequences.jl - 9ec17a24d50dc57315d71a2658fdddbe77175fda authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Merge pull request #52 from jakobnissen/v511

Bump version

github.com/BioJulia/BioSymbols.jl - 3311b5b6dc67a9cb71e552e41944c058196719f9 authored over 2 years ago by Kevin Bonham <[email protected]>
Bump version

github.com/BioJulia/BioSymbols.jl - 37bbae4f9c486eb96f29923e8711489d337012fb authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add documentation workflow

github.com/BioJulia/SequenceVariation.jl - 48470028cac6e2282daac6545ebf4bdaf9b99aa8 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add Julia gitignore

github.com/BioJulia/SequenceVariation.jl - a1f55d1c7078bab10d65a375f97efa4f8201af66 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Remove Manifest.toml

github.com/BioJulia/SequenceVariation.jl - d9cd1fb33fe44b89caa14629ab5f804c67f3a0ec authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #11 from MillironX/feature/variations-from-variant

github.com/BioJulia/SequenceVariation.jl - e79968c4eceea510f8c893cb310b66ff4de79676 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add tests for variations function

github.com/BioJulia/SequenceVariation.jl - 36cbd5abb9464c4d5d138eba9e6727ddb8e54565 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add function to get variations from variant

github.com/BioJulia/SequenceVariation.jl - 6d7a93604a3f1c4ab5507b5f4f89ce861d29e6b1 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add accessor functions for Variant

github.com/BioJulia/SequenceVariation.jl - dbdc575d757f1a63bc3ce8d3bcea18d5d8ff354c authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add rightposition functions

github.com/BioJulia/SequenceVariation.jl - 89cad0120f64d334f133c23c260d832fdac86034 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Optimise hashing (#51)

Default implementation of Base.hash uses objectid, which is slow.
Use a new implementation whic...

github.com/BioJulia/BioSymbols.jl - 040a11f27f480974da73203140dcbb880172196a authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Apply suggestions from code review

Update `CHANGELOG.md` to better reflect the state of the project.

Co-authored-by: Thomas A. Ch...

github.com/BioJulia/BioAlignments.jl - 7414bb4c847619aee031f9cbb0ebe9a8b5e8250c authored over 2 years ago by Ciarán O'Mara <[email protected]>
Apply suggestions from code review

Change type from `Int8` to `UInt8` for efficiency.

Co-authored-by: Jakob Nybo Nissen <jakobnyb...

github.com/BioJulia/BioAlignments.jl - 6d96e79d7a518f28a83f42de7c59b90f25f63eec authored over 2 years ago by Ciarán O'Mara <[email protected]>
CHANGELOG entries

github.com/BioJulia/BioAlignments.jl - d86d69ddba9d98eadee996805f092e58e9f07786 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add more SubstitutionMatrix operations (#60)

SubstitutionMatrix is not a subtype of AbstractArray.
This may or may not be intentional, but c...

github.com/BioJulia/BioAlignments.jl - c023a3c71a133ec688eaf09f0e758e39f9b731e4 authored over 2 years ago by Tim Holy <[email protected]>
Increment version

github.com/BioJulia/BioAlignments.jl - 2f38c3a4007c666100e7915bddbe11123f4fe920 authored over 2 years ago by Ciarán O’Mara <[email protected]>
Add more SubstitutionMatrix operations (#60)

SubstitutionMatrix is not a subtype of AbstractArray.
This may or may not be intentional, but c...

github.com/BioJulia/BioAlignments.jl - 1ea30c7b51170d95478921ea6e4a16e61d7c8b87 authored over 2 years ago by Tim Holy <[email protected]>
Merge pull request #10 from MillironX/feature/variation-equality

github.com/BioJulia/SequenceVariation.jl - 538b612fafb2f9a8f4c4b246f93a89904cc06802 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add hash function for Variation

github.com/BioJulia/SequenceVariation.jl - fe1bbcc0f37b02967e01957533a0022e9b9a3f0b authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Add equality function for Variation

github.com/BioJulia/SequenceVariation.jl - 70965732cf7b9abcadaf247bd2caab661dfd9c2c authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Merge pull request #9 from MillironX/feature/variations-parse

github.com/BioJulia/SequenceVariation.jl - 5f7d5e59a14d5a8e7ef283581f408ddf46498369 authored over 2 years ago by Thomas A. Christensen II <[email protected]>
Support HTTP.jl 1.0 (#43)

github.com/BioJulia/BioServices.jl - ec331bb3c4340573c6c4ca4f195f5e714c83990d authored over 2 years ago by Jacob Quinn <[email protected]>
CompatHelper: bump compat for Term to 1, (keep existing compat)

github.com/BioJulia/PopGen.jl - 2b8538f0a79c1d8c1affbd5b0ac9fe319f951aa6 authored over 2 years ago by CompatHelper Julia <[email protected]>
CompatHelper: bump compat for HTTP to 1, (keep existing compat)

github.com/BioJulia/BioMakie.jl - fb5aa38ff21c1ef50ff51cea40a7b96471bb7071 authored over 2 years ago by CompatHelper Julia <[email protected]>
alignment.svg: use embedded fonts

github.com/BioJulia/BioAlignments.jl - 2d3be18fef3b68925ce18f6d4d536ab0bb2db756 authored over 2 years ago by Alexey Stukalov <[email protected]>
alignment.svg: try workaround unsafe-inline secpol

github.com/BioJulia/BioAlignments.jl - 4bb08d9e9e0e08a73f0be8de0d1604e12b7dc2cf authored over 2 years ago by Alexey Stukalov <[email protected]>
docs: update the alignment figure

github.com/BioJulia/BioAlignments.jl - d5f7385cb6cb47f2a5e463bf2dce3060e755f382 authored over 2 years ago by Alexey Stukalov <[email protected]>
Remove change log

github.com/BioJulia/IntervalTrees.jl - 8185756a41faced1a97dba1e19d035db1ec08822 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Remove humans

github.com/BioJulia/IntervalTrees.jl - 87c57e7fb2e5e738d5916fba18b5110f024d5c5c authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update Project.toml

github.com/BioJulia/IntervalTrees.jl - ad59719613ab8f90052341f25409fa212fa00c61 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Add branch link

github.com/BioJulia/IntervalTrees.jl - fb234cb85f2d85c209211ee0404af56b7e8fb4f5 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update Install instructions

github.com/BioJulia/IntervalTrees.jl - 4b60196a0232409e9a5b7809b0d07859e9b6aede authored over 2 years ago by Ciarán O'Mara <[email protected]>
Add funding

github.com/BioJulia/IntervalTrees.jl - 0799de5b3ee473dd8b49d54a03d3348118e48681 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Add workflow for downstream tests

github.com/BioJulia/IntervalTrees.jl - de1170424cdfd8b62e7f838bbfa44fff5c31c6cf authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update contributing section

github.com/BioJulia/IntervalTrees.jl - 394b24a66a3aa24a37de2edc3c9c49624a78db82 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Add workflow for Tagbot

github.com/BioJulia/IntervalTrees.jl - a85c91a8bad528f9c1855f9cdad8ab1f7d91cab6 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update status badges

github.com/BioJulia/IntervalTrees.jl - 5c8dd7166b753957247bec7e05a2c5d25897bd5c authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update chat links

github.com/BioJulia/IntervalTrees.jl - 5f85bcfaaa7c4ee9417ac7a2c8824b93e460c227 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Migrate tests to GitHub workflow

github.com/BioJulia/IntervalTrees.jl - 396536bdb7c1b3fbc037a753328c3695cf8ecc09 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Migrate documentation to GitHub workflow

github.com/BioJulia/IntervalTrees.jl - b78210aace5285059cd2911b1ff43dd25819deb6 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Update Documenter

github.com/BioJulia/IntervalTrees.jl - ed412f45e4abc9cabb2737c7e478e360a3696f17 authored over 2 years ago by Ciarán O'Mara <[email protected]>
Cosmetic changes in constructors (#240)

Small fixes and simplifications

github.com/BioJulia/BioSequences.jl - 31936ce08b22d2676c04ad1ff67e8a229ec42557 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add translation of kmers (#24)

* Add translation of kmers

* Allow translation of DNA

* Support alternative_start

* Opt...

github.com/BioJulia/Kmers.jl - 320439bd99bb1304c7faa55bd11429daaaa64e40 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Resolve ambiguity error Kmer() (#26)

* Add constructors

* Kmer(nts...) should have minimum one nt

Co-authored-by: Sabrina Jaye ...

github.com/BioJulia/Kmers.jl - 619f5ad6e10ae1db4440b9923f5c54b964c3d487 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Add constructors (#25)

github.com/BioJulia/Kmers.jl - 0e5d10d477ed824d6a44bbdc5bcafb5158190410 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>
Use codeunits over unsafe_wrap (#239)

github.com/BioJulia/BioSequences.jl - 625ab2f517f7ab29ebb8402dc7ab0c14046addb0 authored over 2 years ago by Jakob Nybo Nissen <[email protected]>