BioJulia commits | Ecosyste.ms: OpenCollective

Amendments

Base.bytesavailable is provided by CodecBGZF.
Add compat entry for CodecBGZF.
Keep using Transco...

github.com/BioJulia/Indexes.jl - 4883728c0c3d5aac432bbc8f2df12cdcfc7ee458 authored over 3 years ago by Ciarán O’Mara <[email protected]>

Merge pull request #5 from jakobnissen/codecbgzf

Switch to CodecBGZF

github.com/BioJulia/Indexes.jl - ef426b133820d78ef5b4822e6641e5833e33be77 authored over 3 years ago by Ciarán O'Mara <[email protected]>

add isbiallelic methods

github.com/BioJulia/PopGen.jl - 17b0390ee804b5363605dc2cd05a2826e693db4a authored over 3 years ago by Pavel Dimens <[email protected]>

Updated docs URL

github.com/BioJulia/GenomicAnnotations.jl - e1638935cc033a67f8f3e17c4885485f59f2c68d authored over 3 years ago by Karl Dyrhage <[email protected]>

Increment version

github.com/BioJulia/XAM.jl - aaf3710fbed304f7c8bb843ca6151bcdf8d12b84 authored over 3 years ago by Ciarán O’Mara <[email protected]>

Bump minor version

github.com/BioJulia/Automa.jl - 8eb8a89148a7fef057c9051ca42817a0bf616b48 authored over 3 years ago by Kevin Bonham <[email protected]>

Merge pull request #76 from jakobnissen/fixbreak

Disable breaking change: check for ambiguity

github.com/BioJulia/Automa.jl - 7f855e2fd925b08ad99701824302b6a27e5fd75b authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Disable breaking change: check for ambiguity

github.com/BioJulia/Automa.jl - b13175040508bfa63bab52e0d9befdff0c887d2e authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Updated version number

github.com/BioJulia/GenomicAnnotations.jl - 8426c5d39622ca3123c05a476f48d91e4273fb47 authored over 3 years ago by Karl Dyrhage <[email protected]>

Updated version number

github.com/BioJulia/GenomicAnnotations.jl - b1b738e2e20db50d51e854cd8114fca776445d6e authored over 3 years ago by Karl Dyrhage <[email protected]>

Removed old files

github.com/BioJulia/GenomicAnnotations.jl - 3e151335719bdbf576a558e42536975e7add0b38 authored over 3 years ago by Karl Dyrhage <[email protected]>

Removed old files

github.com/BioJulia/GenomicAnnotations.jl - 704f08d123af2976e42d37e3bfd7a1f90681a715 authored over 3 years ago by Karl Dyrhage <[email protected]>

Updated TagBot

github.com/BioJulia/GenomicAnnotations.jl - fb2589d6a59b55eb95902504766853bdd19c6cad authored over 3 years ago by Karl Dyrhage <[email protected]>

Merge branch 'master' of https://github.com/kdyrhage/GenomicAnnotations.jl

github.com/BioJulia/GenomicAnnotations.jl - bb5dfdb06b51bd8edf0ef8b92af15dbf7275acd3 authored over 3 years ago by Karl Dyrhage <[email protected]>

Updated README

github.com/BioJulia/GenomicAnnotations.jl - 0733e62fce51eecd92d12c62fddceee70590162a authored over 3 years ago by Karl Dyrhage <[email protected]>

Merge pull request #6 from kdyrhage/interface

Changing the read/write interface to mirror other BioJulia packages.

github.com/BioJulia/GenomicAnnotations.jl - 88843e21ebb19c942bf31e70b452514c3c2ac682 authored over 3 years ago by kdyrhage <[email protected]>

Updated docs

github.com/BioJulia/GenomicAnnotations.jl - 7f2ae009a9478277481a8c575be33342c4a0bc73 authored over 3 years ago by Karl Dyrhage <[email protected]>

Moved readgbk/readgff to parent module

github.com/BioJulia/GenomicAnnotations.jl - 9125b33cc3f4e647e0be9ad06b3181d4f5da7e1a authored over 3 years ago by Karl Dyrhage <[email protected]>

Changed julia versions for travis

github.com/BioJulia/GenomicAnnotations.jl - 7ffd9f145764d64799f203f5535fb0487eea10e0 authored over 3 years ago by Karl Dyrhage <>

Updated CodecZlib version

github.com/BioJulia/GenomicAnnotations.jl - 5cfa3a1e9a37c34a8d974d7e3933af87a920c457 authored over 3 years ago by Karl Dyrhage <>

More code cleaning

github.com/BioJulia/GenomicAnnotations.jl - d01071ba6a8ef640e169d21ab178f9e6e158c6c2 authored over 3 years ago by Karl Dyrhage <>

Removed GZip

github.com/BioJulia/GenomicAnnotations.jl - a98e67b4370ea3f8c2a92732ba85eb32401e3fa0 authored over 3 years ago by Karl Dyrhage <>

Cleaned up code

github.com/BioJulia/GenomicAnnotations.jl - 1e8f840e7afd3eb3dcd86136442e9ff4450e88c4 authored over 3 years ago by Karl Dyrhage <>

Cleaned up code

github.com/BioJulia/GenomicAnnotations.jl - 8a4a4cf6a790ec9ceb91c2f21f4454790f451b97 authored over 3 years ago by Karl Dyrhage <>

Removed broadcastable

github.com/BioJulia/GenomicAnnotations.jl - 91a33dccb7df4852d967d121073b6685f2f30ce4 authored over 3 years ago by Karl Dyrhage <[email protected]>

Updated tests

github.com/BioJulia/GenomicAnnotations.jl - 8ddbe56165af24a973b3f48e9b0798038f0df068 authored over 3 years ago by Karl Dyrhage <[email protected]>

Updated version and dependencies

github.com/BioJulia/GenomicAnnotations.jl - 4498ea090b0cca911811978b1cc9cd0ffcc2c989 authored over 3 years ago by Karl Dyrhage <[email protected]>

Switched to Reader/Writer interface

github.com/BioJulia/GenomicAnnotations.jl - b3882b0166cafed3ff12f187d63f8582b87b8e7e authored over 3 years ago by Karl Dyrhage <[email protected]>

add tagbot (#74)

* add tagbot

* fix automerge blockers

github.com/BioJulia/Automa.jl - 14e055cf78f2f6b4d0bac0723bac542fd43c95fc authored over 3 years ago by Kevin Bonham <[email protected]>

Merge pull request #44 from BioTurboNick/patch-2

FASTQ example added

github.com/BioJulia/FASTX.jl - be4082269bff2a797afe54dd3cd94051ca6affce authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

bump version (#73)

github.com/BioJulia/Automa.jl - f7ec42c2df160c05e17e1d35c4e14631f2894bef authored over 3 years ago by Kevin Bonham <[email protected]>

add nei87 fst permutations

github.com/BioJulia/PopGen.jl - a64ea3da1b99969cd226ad162cfecbc7d024f639 authored over 3 years ago by Pavel Dimens <[email protected]>

Merge branch 'master' into patch-2

github.com/BioJulia/FASTX.jl - e9f59467b08c0f5074319c6f5b0893f1c774b7ca authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #43 from BioTurboNick/patch-1

Model good behavior with do block syntax

github.com/BioJulia/FASTX.jl - 364c75c26eb7790ab870395dbae50e2503065b4e authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Added database option and documentation

github.com/BioJulia/BioFetch.jl - 7cea269ae213eb1bfa52add36bb6e6ff5e26d5f7 authored over 3 years ago by Nicholas Bauer <[email protected]>

Fixed fasta format

github.com/BioJulia/BioFetch.jl - 65e9d1ec4ee6cdbe11fbb9b421d778410dff1496 authored over 3 years ago by Nicholas Bauer <[email protected]>

Added a format argument and support for GenBank

github.com/BioJulia/BioFetch.jl - a3bbcb38a1a1ad32b017015f657c101fd488e1af authored over 3 years ago by Nicholas Bauer <[email protected]>

Switch to rely on BioServices

github.com/BioJulia/BioFetch.jl - a70044b79ddb0b8d3037e6712cca2946c6a29a6d authored over 3 years ago by Nicholas Bauer <[email protected]>

Added example

github.com/BioJulia/FASTX.jl - bc07e72779dc16dd176d34e7b0b6727ddd10b8b7 authored over 3 years ago by Nicholas Bauer <[email protected]>

Model good behavior

github.com/BioJulia/FASTX.jl - 3f84b0fc3f7c2548d8c3809f16176470f95cb811 authored over 3 years ago by Nicholas Bauer <[email protected]>

fix

github.com/BioJulia/FASTX.jl - dfcfd801bc5b773120bcbc73f4f0c89fa0beb802 authored over 3 years ago by Nicholas Bauer <[email protected]>

Model good behavior

github.com/BioJulia/FASTX.jl - 53a4735542f7dd0ceacd0ab0cb6fb0a4882327d0 authored over 3 years ago by Nicholas Bauer <[email protected]>

Merge pull request #72 from BioJulia/docs

Work on deploying docs via github actions

github.com/BioJulia/Automa.jl - 9c8691d68024f4aa368b6a30648886d1b3caf351 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

spaces in compat

github.com/BioJulia/Automa.jl - ec81f5e14ce213cec46de06b5757cdd7ab1facaf authored over 3 years ago by Kevin Bonham <[email protected]>

fix documenter project compat

github.com/BioJulia/Automa.jl - 30c2fc4f49a07db6f4c8d9c4fdb55413de20ef49 authored over 3 years ago by Kevin Bonham <[email protected]>

update docs make and github action

github.com/BioJulia/Automa.jl - fb36cc0db960bd690fb34afa75736bc2ac47d09e authored over 3 years ago by Kevin Bonham <[email protected]>

Initial commit

github.com/BioJulia/BioFetch.jl - 04358df82e975e506ea250a4a17ac845aa3b3b90 authored over 3 years ago by Nicholas Bauer <[email protected]>

add WC permutation methods

github.com/BioJulia/PopGen.jl - fe9462403fe56b54dead4afc5faea17a4b7a83a1 authored over 3 years ago by Pavel Dimens <[email protected]>

update permuations

github.com/BioJulia/PopGen.jl - a05abfb49311a8c99fa8c4965cd4f4956c8c468f authored over 3 years ago by Pavel Dimens <[email protected]>

optimize and prep for significance testing

github.com/BioJulia/PopGen.jl - e4d4323bc9bef654987b3390f8ad3a8a36acde89 authored over 3 years ago by Pavel Dimens <[email protected]>

residue selectors before expanding disorder

github.com/BioJulia/BioStructures.jl - 1a1274c49ae7ed0460c9970989ad2cfc2079d4c3 authored over 3 years ago by Joe Greener <[email protected]>

Remove financial backing and Gitter from README

github.com/BioJulia/BioSequences.jl - d51a551ad6478c7f3596b1cc8825315f6996357c authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #43 from jakobnissen/removeiter

Remove iteration of BioSymbol

github.com/BioJulia/BioSymbols.jl - 6f0180fa1bb839b87e9828ed190865e198251ce6 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Add broadcasting

github.com/BioJulia/BioSymbols.jl - 698855b0374d1f38b2ca7a3ba2fa1f6bcc43fb51 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove iteration of BioSymbol

Also removed `length(::BioSymbol)`

github.com/BioJulia/BioSymbols.jl - 63c1d325b8384a40e5f6db9ee1d0fdaf7669cb85 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #38 from jakobnissen/intconvert

Remove integer conversion and arithmetic

github.com/BioJulia/BioSymbols.jl - 4d11c1eac43c3fd48e1ad85f68b1529c08d32be8 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

bump version

github.com/BioJulia/BioStructures.jl - 21de6534495b0b5da37fd9ca3deaf361df36d16f authored over 3 years ago by Joe Greener <[email protected]>

atom selectors before expanding disorder

github.com/BioJulia/BioStructures.jl - 39d30a15be842f0a132c7c1e0112271ca47fc447 authored over 3 years ago by Joe Greener <[email protected]>

Merge pull request #66 from jakobnissen/simddocs

Add docs for :simd generator

github.com/BioJulia/Automa.jl - d1b047eb96827114315ffdb7d24ab0eb0f0fd24f authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #69 from jakobnissen/nodata

Remove DataStructures dependency

github.com/BioJulia/Automa.jl - 5282d7e66a3c294f0909d100997e6d4d7315f577 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove DataStructures dependency

github.com/BioJulia/Automa.jl - c62b58ac014586d2be55d8f7a702f69ee8c46d50 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #68 from jakobnissen/github

Fix CI

github.com/BioJulia/Automa.jl - 77b49c5e3b8e6f2b3935c5bd65fe2e2efb7f204e authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove old files

github.com/BioJulia/Automa.jl - 8c3bb9375c002a7f64c14f2d0921b057aeac9271 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Change CI to github

github.com/BioJulia/Automa.jl - 358bfd5aa8f6c12f1d066be1ab54a58aae1bec7f authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Add docs for :simd generator

github.com/BioJulia/Automa.jl - 680163261427ed341094e0cc47f7bb8ef3cff3f4 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #65 from jakobnissen/egal

Change equal to egal for nothing

github.com/BioJulia/Automa.jl - 55885c0d8c556a674db9222b9ff6bca748e8e54b authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Change equal to egal for nothing

github.com/BioJulia/Automa.jl - ba85056c3c19654d6a9cc0ed9313d8f2c038c02b authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #60 from jakobnissen/simd

SIMD code generator

github.com/BioJulia/Automa.jl - 8f90ba443d12792d8a1b54a18d84dc3fe11a8b0e authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

not kwarg

github.com/BioJulia/BioStructures.jl - e1d539d749689253a3368c10f0f5d60805ef509c authored over 3 years ago by Joe Greener <[email protected]>

don't skip Linux tests

github.com/BioJulia/BioStructures.jl - 83fecf82742b69bddf1ee7c122fa68433400e82f authored over 3 years ago by Joe Greener <[email protected]>

file format specimens checkout

github.com/BioJulia/BioStructures.jl - 032fdc5ffba3034d1cb8bed374b487631baa3ff1 authored over 3 years ago by Joe Greener <[email protected]>

Merge branch 'dev' of https://github.com/pdimens/PopGen.jl into dev

github.com/BioJulia/PopGen.jl - 95e17eaf64266508e91158287790ef1e8c04b6e5 authored over 3 years ago by Pavel Dimens <[email protected]>

Update README.md

github.com/BioJulia/PopGen.jl - d703863332ce5a73a235da388e06718cb0a85a3a authored over 3 years ago by Pavel V. Dimens <[email protected]>

perms

github.com/BioJulia/PopGen.jl - b42e461ad2ffda53f42605f9eca893207975e00b authored over 3 years ago by Pavel Dimens <[email protected]>

Cut down on repetitive testing

Excessive repetitive testing loops have been reduced.
Longsequence test suit cut from 4559 to 26...

github.com/BioJulia/BioSequences.jl - c67ec957e6ddd80f173714e68bce56301b98800d authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Removed VoidAlphabet

github.com/BioJulia/BioSequences.jl - d0416903428ca2c6daa9ef18c8adac4450d1e95d authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove CharAlphabet

github.com/BioJulia/BioSequences.jl - 56d6960b4d941e19fd2070716097ae87aac4b709 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

begin alternative matrix implementation for perms

github.com/BioJulia/PopGen.jl - 92ec51c33cbb280b95e77812eef4d22f8e771d7b authored over 3 years ago by Pavel Dimens <[email protected]>

Merge pull request #150 from jakobnissen/removeconditer

Remove ConditionIterator

github.com/BioJulia/BioSequences.jl - d85c8143d00badc63f45a80ed82b9eda1a52f6a5 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove ConditionIterator

github.com/BioJulia/BioSequences.jl - 929bb059bd222a48f5d1961c049d1bde4e36a67e authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #149 from jakobnissen/v3

Re-add construction between integer/kmer

github.com/BioJulia/BioSequences.jl - 347c8773bbbd9ec02e69ca3ed226f1fc37e9e44e authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Re-add construction between integer/kmer

* Conversion is still not permitted
* Construction of kmers from integers checks for overflow
* ...

github.com/BioJulia/BioSequences.jl - c0e19b664d1c87c63f7c4b6f6fad41e42d9cebd9 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #147 from jakobnissen/kmer_integers

Remove conversion to/from integers and kmers, and direct instantiatio…

github.com/BioJulia/BioSequences.jl - b506b4bfb164d3c627168d9ddfb35d178be39a87 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge branch 'v3' into kmer_integers

github.com/BioJulia/BioSequences.jl - 8016691c8bc563baef37c8d02aea7b5f779f375c authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove conversion to/from integers and kmers, and direct instantiation of kmers from integers.

Users should instead use `masked(::Type{T}, x::Unsigned)` to create kmers from integers, and `re...

github.com/BioJulia/BioSequences.jl - 19ae11331ef848240a5d2ccf7e60963d5d8a2701 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #146 from jakobnissen/undefinit

Remove the constructor `LongSequence{A}(::Integer)`

github.com/BioJulia/BioSequences.jl - 40a6a59925fa2f97912407caec7445d33f24d95e authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove the constructor `LongSequence{A}(::Integer)`

See issue # 142. Users should use `LongSequence{A}(undef, ::Integer)` instead.

github.com/BioJulia/BioSequences.jl - 44fbecd671aa796176ac0a09c2e63d6febf8a6f0 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #144 from jakobnissen/findsemantics

Change semantics of find to match Base

github.com/BioJulia/BioSequences.jl - c0bf0ec2498c5a5ee7031333a7d0bf115c90c3cf authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove find methods with single biosymbols

See issue #141. Users are adviced to use `findfirst(isequal(x), seq)` instead.

github.com/BioJulia/BioSequences.jl - e9f5b2006afb2881c4c05182c9692807c78e8536 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove bitpar compiler info messages

github.com/BioJulia/BioSequences.jl - 955b02da2b27a8a253da5af6c81227d1b25c2d1c authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Switch to CodecBGZF

github.com/BioJulia/Indexes.jl - 2403731c3381fc38ec0d4dc3a868d5e46f0165bb authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Removed demultiplexer

github.com/BioJulia/BioSequences.jl - dd268c9562866fefd1a24b8133f373ef47814c2e authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Removed ReferenceSequence

github.com/BioJulia/BioSequences.jl - b2bbcd5c8b598ee79a8512da7dc1e61e1a8d3e95 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove composition

github.com/BioJulia/BioSequences.jl - aa2895365c7fbcccd0c76d2b5da2c532fe016516 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove minhash

github.com/BioJulia/BioSequences.jl - 8325644cc839027bd8b3ecb6344c70b2a9e34925 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #133 from jakobnissen/multiindex

Move some indexing logic from LongSequence to BioSequence

github.com/BioJulia/BioSequences.jl - 0ba3d4b2e1dab04b77e244141501e6b33d53b975 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

add fstats to module

github.com/BioJulia/PopGen.jl - bd7281eacb0e31932990c10ebcd92d2f3319b5c8 authored over 3 years ago by Pavel Dimens <[email protected]>

housekeeping and speed improvements

github.com/BioJulia/PopGen.jl - fd59a33e8aa303824b82a9b2717b137b035f5416 authored over 3 years ago by Pavel Dimens <[email protected]>

slightly cleaner written

github.com/BioJulia/PopGen.jl - b743831e7d6ce99cabee1694bb956f0a1ea9465c authored over 3 years ago by Pavel Dimens <[email protected]>

Merge pull request #136 from jakobnissen/fixcodeshow

Fix typo in genetic code show

github.com/BioJulia/BioSequences.jl - 90b4df3589d54401eed2e46de4fe65e0e59baccd authored over 3 years ago by Jakob Nybo Nissen <[email protected]>