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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

search for closed issues

github.com/BioJulia/attobot - 0f8ec352d78d876e376c85011a54f5e03d1bf3e3 authored almost 8 years ago by Simon Byrne <[email protected]>
Changes to Phylo documentation. (#365)

* Changes to Phylo documentation.

* Minor edit to solve interpolation error

* Fixes

* F...

github.com/BioJulia/Bio.jl - 159b3d92dd6ac2001a5831f5cb0758a89ecb533c authored almost 8 years ago by Ben J. Ward <[email protected]>
Added more to divergence time estimation (#361)

github.com/BioJulia/Bio.jl - 6dd5bf9f3e60b84de8fcba3748534835861cc292 authored almost 8 years ago by Ben J. Ward <[email protected]>
consistent capitalisation

github.com/BioJulia/attobot - 955f92451a4b08afd1ab3e6bfd76ef690c914492 authored almost 8 years ago by Simon Byrne <[email protected]>
privacy statement

github.com/BioJulia/attobot - c2238e29b7df58999f7311f6a6503dfbacfa69eb authored almost 8 years ago by Simon Byrne <[email protected]>
use full name in repo link

github.com/BioJulia/attobot - fbaf114ba73665ce21f661296ac8b2909cf35d94 authored almost 8 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/attobot - 73d340f740020efa003cbed2e3ee784f136b9e99 authored almost 8 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/attobot - 0c9c875a8a1bf816f71e01b617bebf9104b94d73 authored almost 8 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/attobot - 968835c4a48b5b79fad6a4f8edac1d6018fb8cff authored almost 8 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/attobot - 026778b484f110c14e7dd38ccf7413783aeaba27 authored almost 8 years ago by Simon Byrne <[email protected]>
open issues on certain errors

github.com/BioJulia/attobot - 7084081cbd7ed93ab20c9208fe5d384f70fc0184 authored almost 8 years ago by Simon Byrne <[email protected]>
Merge branch 'master' of github.com:attobot/attobot

github.com/BioJulia/attobot - 856552a1b9e1de3103ffb2797f5e674028f2a10a authored almost 8 years ago by Simon Byrne <[email protected]>
allow users to update releases

github.com/BioJulia/attobot - 1710a1b01161384c56fc2ea37966b469c0e39666 authored almost 8 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/attobot - bf5a6509ad402868086559a77c3ea1b7b989804b authored almost 8 years ago by Simon Byrne <[email protected]>
use https url to register

github.com/BioJulia/attobot - 06f29ca15802e753e453765e8c43ab93d9b7e3fa authored almost 8 years ago by Simon Byrne <[email protected]>
fix some syntax and other errors

github.com/BioJulia/attobot - 0f55be6c3892f8ddd58e7f903449def944792376 authored almost 8 years ago by Simon Byrne <[email protected]>
add travis link to pr

github.com/BioJulia/attobot - 9d76af271bba3aa8647022971d6e85804ac8e2cb authored almost 8 years ago by Simon Byrne <[email protected]>
display REQUIRE diff

github.com/BioJulia/attobot - 09066677efd88d157d87a879a93a9280351f22b8 authored almost 8 years ago by Simon Byrne <[email protected]>
allow package registrations

github.com/BioJulia/attobot - d27da9bcc401a82bd166fcae1b1718126eff79f2 authored almost 8 years ago by Simon Byrne <[email protected]>
fix issue with annotated tags (#3 & #4)

github.com/BioJulia/attobot - 515f6eae08545c76ea2b626f5c91d29b98f78823 authored almost 8 years ago by Simon Byrne <[email protected]>
Fix trans macro (#38)

github.com/BioJulia/Libz.jl - 1838a247a1402b01d9987a729e609b942e7b7120 authored almost 8 years ago by Andreas Noack <[email protected]>
change branch name to be pkg/ver

github.com/BioJulia/attobot - 787aa0b7e543ba1389302b6e0763a9dad48a58b9 authored almost 8 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/attobot - cb1d208ecd5968ac6104c7b06c3b265d442ce038 authored almost 8 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/attobot - d7c3d4c6afb71346c3d310a80f52e7b97d42a33b authored almost 8 years ago by Simon Byrne <[email protected]>
Add images to README

github.com/BioJulia/attobot - 7973961978baa69cdc3329fe6e8c5da6ef666fcd authored almost 8 years ago by Simon Byrne <[email protected]>
add images

github.com/BioJulia/attobot - d088b3861dbb1fbdbebdbeb1ab9c7813a9aebbe7 authored almost 8 years ago by Simon Byrne <[email protected]>
Update README.md

github.com/BioJulia/attobot - f75f0bb9af5d6a54ab706f2b0ae05f3060b1c763 authored almost 8 years ago by Simon Byrne <[email protected]>
fix reverse(BioSequence) (#357)

* fix reverse(BioSequence)

* fix test

github.com/BioJulia/Bio.jl - 403a9c96ac3c79a1c8ccbaeb76e90e042a538a2f authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
create diff links in PR

github.com/BioJulia/attobot - 7126a51121048314ff7525014051e4dc044400b4 authored almost 8 years ago by Simon Byrne <[email protected]>
add license

github.com/BioJulia/attobot - df470bfab4eacb30160a07de977d4fee2348390b authored almost 8 years ago by Simon Byrne <[email protected]>
minor formatting and return value

github.com/BioJulia/attobot - 956d023f7bd682bbd7b35e2652f5cc02924f88b5 authored almost 8 years ago by Simon Byrne <[email protected]>
formatting

github.com/BioJulia/attobot - 5b2ca1928974f86157b69fbba9e64c0221a1647e authored almost 8 years ago by Simon Byrne <[email protected]>
alignment

github.com/BioJulia/attobot - e80ac15bb5f276cc4d901927fa13c027e6d25bf6 authored almost 8 years ago by Simon Byrne <[email protected]>
update README

github.com/BioJulia/attobot - c4c9d817153326a07bd34a90002a67a7bacfcfd2 authored almost 8 years ago by Simon Byrne <[email protected]>
initial commit

github.com/BioJulia/attobot - f50e27521fb0edbd2117f07ef6a5cd6a219a0173 authored almost 8 years ago by Simon Byrne <[email protected]>
Blast xml fix (#355)

* switch XML parser from EzXML

* update REQUIRE to add EzXML

* fixes to address @bicycle18...

github.com/BioJulia/Bio.jl - 41b7a5fe2c508f9edd778fffdfca26342b33b4fa authored almost 8 years ago by Kevin Bonham <[email protected]>
Added methods for bitcursor

github.com/BioJulia/WAHVectors.jl - 871b078c5d5101ea31d98e6ee1e518f8f0eb25fd authored almost 8 years ago by Ben J. Ward <[email protected]>
Added bitcursor.jl

github.com/BioJulia/WAHVectors.jl - de82b6586102a865d2965177b2ed39e6061f0a9d authored almost 8 years ago by Ward9250 <[email protected]>
Added source file bitcursor.jl

github.com/BioJulia/WAHVectors.jl - 03f2f203b7b3375194c200d65b279714fe38ac55 authored almost 8 years ago by Ward9250 <[email protected]>
Edited manpages

github.com/BioJulia/WAHVectors.jl - c4c6d62168b846609ebc62ec6101765b07643bbd authored almost 8 years ago by Ben J. Ward <[email protected]>
Fixed an error

github.com/BioJulia/WAHVectors.jl - fe9e5ffcad14d53624e855348f8442795b78c605 authored almost 8 years ago by Ben J. Ward <[email protected]>
Added 31 bit iteration and conversion from BitVectors

github.com/BioJulia/WAHVectors.jl - 4be1015ccc3dbe75cde67780f8094392dfac7326 authored almost 8 years ago by Ben J. Ward <[email protected]>
Merge pull request #16 from marciogm/abi

Add ABI files

github.com/BioJulia/BioFmtSpecimens - a97ebc555133cb6246620aed98ea1a0e8d3b6146 authored almost 8 years ago by Ben J. Ward <[email protected]>
Added first draft of map_32bits_to_31bits

github.com/BioJulia/WAHVectors.jl - b7e3984a9683c52177c3ad2d632ab1ee9d553d5c authored almost 8 years ago by Ben J. Ward <[email protected]>
Corrected show method for WAHVectors

github.com/BioJulia/WAHVectors.jl - 7ee23d021f1b3460f45f27e07c76d7fd31d5556b authored almost 8 years ago by Ward9250 <[email protected]>
Added show method for WAHVector

github.com/BioJulia/WAHVectors.jl - efe0e115b4accbc18789c9e0b91799696ad9ab97 authored almost 8 years ago by Ward9250 <[email protected]>
Edited show method for WAHElements

github.com/BioJulia/WAHVectors.jl - 036e1d870ab497e9dece4ee25c00e5017a3a5723 authored almost 8 years ago by Ward9250 <[email protected]>
Edited show method for WAHElements

github.com/BioJulia/WAHVectors.jl - e4eba34eaf52583ac037da264f18e24386150c88 authored almost 8 years ago by Ward9250 <[email protected]>
Added show method for wah elements

github.com/BioJulia/WAHVectors.jl - f84e4468f5a715143974c2adfa13a12a2b81254b authored almost 8 years ago by Ben J. Ward <[email protected]>
Changed typo in a Base.convert method

github.com/BioJulia/WAHVectors.jl - f727cad125bd57c146b5ba31f054fc9cf6d4db3e authored almost 8 years ago by Ben J. Ward <[email protected]>
Changed errors in a Base.convert method

github.com/BioJulia/WAHVectors.jl - 40a36044ca3074d45fe505a5fc5e24b07205c2b6 authored almost 8 years ago by Ben J. Ward <[email protected]>
Corrected error in round trip test line

github.com/BioJulia/WAHVectors.jl - ee2827dc55ddb893f9c8fe9e58f72e7bd46b1691 authored almost 8 years ago by Ben J. Ward <[email protected]>
Added round-trip conversion test

github.com/BioJulia/WAHVectors.jl - dc02784058ff4213fbdc9ecf8c8a81fb952c49fe authored almost 8 years ago by Ben J. Ward <[email protected]>
Added function to make random bitvectors

github.com/BioJulia/WAHVectors.jl - c9cde2616ec407f4cec2ad10421797038e08f312 authored almost 8 years ago by Ben J. Ward <[email protected]>
Refactored the branchlength setting and getting API. (#219)

* Refactored the branchlength setting and getting API.

* Created system for getting and setti...

github.com/BioJulia/Bio.jl - d7b1876d81f74592116a2c702c72b4590479d89e authored almost 8 years ago by Ben J. Ward <[email protected]>
Add ABI files

github.com/BioJulia/BioFmtSpecimens - 1373d80bcaff6f02714d8d12c5338fb66cdc3f50 authored almost 8 years ago by Marcio Giaxa Marinheiro <[email protected]>
Initial commit

github.com/BioJulia/BioBridgeR.jl - 6b47dc6fb9b21981154c0229eff2b3bc6c0b7236 authored almost 8 years ago by Ben J. Ward <[email protected]>
Corrected an error in runfill tests

github.com/BioJulia/WAHVectors.jl - 1877b31541b35a3c7531a0dd55b295326b45944c authored almost 8 years ago by Ben J. Ward <[email protected]>
Finished second draft of conversion from WAHVectors to Vector{UInt32}

github.com/BioJulia/WAHVectors.jl - 074a1e4ee69ad94e4508be89fda4d119de075210 authored almost 8 years ago by Ben J. Ward <[email protected]>
Redesign of append_literal! for decompression

github.com/BioJulia/WAHVectors.jl - 8cb0870cffe7968d0e78f4dc3d29752c8198e07b authored almost 8 years ago by Ben J. Ward <[email protected]>
Cleaning up and correcting append_literal

github.com/BioJulia/WAHVectors.jl - 752cc39eef138d655f6da6b8636986e7464bc16b authored almost 8 years ago by Ben J. Ward <[email protected]>
Draft of refactored decompression

github.com/BioJulia/WAHVectors.jl - 2cf80618c659d415c373b06f8e892b94cc3dccbb authored almost 8 years ago by Ben J. Ward <[email protected]>
Added more work to the decompression method.

github.com/BioJulia/WAHVectors.jl - 4f279445b57b63d50a1db3a252a21a1c11fe74cd authored almost 8 years ago by Ben J. Ward <[email protected]>
Merge branch 'master' of https://github.com/BioJulia/Bio.jl

github.com/BioJulia/Bio.jl - 8e19330a756461c4e040ffb0097e8f033a94c152 authored almost 8 years ago by Ward9250 <[email protected]>
Improved security of docs building.

github.com/BioJulia/Bio.jl - dca33914c4c15a9de9bb65167f124a83880f636e authored almost 8 years ago by Ward9250 <[email protected]>
Setup automated documentation site building.

github.com/BioJulia/WAHVectors.jl - 418498dbdbe778c1bdc4a6a12ec316a4b1410a3e authored almost 8 years ago by Ward9250 <[email protected]>
Add support for raw deflate streams.

github.com/BioJulia/Libz.jl - 15f0644a91d20ef4469b00f529e6816fb5a6e7bd authored almost 8 years ago by Daniel C. Jones <[email protected]>
Added first draft of decompression method

github.com/BioJulia/WAHVectors.jl - 4767108dba124ccc3583677e500f6ec294817622 authored almost 8 years ago by Ben J. Ward <[email protected]>
Added increment_nruns_unsafe tests

github.com/BioJulia/WAHVectors.jl - 60edb6e6ae145de119b7b377cab9fefd83773c2f authored almost 8 years ago by Ben J. Ward <[email protected]>
Piloting removing Base operators as they are not really needed.

github.com/BioJulia/WAHVectors.jl - a2b6436fc3ccfe723d45156612a6d1a60bc93b9d authored almost 8 years ago by Ben J. Ward <[email protected]>
Piloting removing Base operators as they are not really needed.

github.com/BioJulia/WAHVectors.jl - c43e1917618833a3ff9c931ba04db81d610651fb authored almost 8 years ago by Ben J. Ward <[email protected]>
Fixed issue in matchingfills

github.com/BioJulia/WAHVectors.jl - 34484df0fe2665676c92f90f488f5103525957cd authored almost 8 years ago by Ben J. Ward <[email protected]>
Removed exports of internal stuff like WAHElements

github.com/BioJulia/WAHVectors.jl - 53472d600d3cf56935e8ff6c2b7f1bb7b7d971d0 authored almost 8 years ago by Ben J. Ward <[email protected]>
Removed a subtraction method that was not needed

github.com/BioJulia/WAHVectors.jl - dadd14dc68319bd067316562eac7d1badecffa1b authored almost 8 years ago by Ben J. Ward <[email protected]>
Minor changes and additions to test suite

github.com/BioJulia/WAHVectors.jl - 05bf7e617e7d94c372ff5202d70f036e9603fb3d authored almost 8 years ago by Ben J. Ward <[email protected]>
Added tests for hasroom and fillandmatch

github.com/BioJulia/WAHVectors.jl - 7e629efc400dd1a70ce93fb46ab528fb607b59c0 authored almost 8 years ago by Ward9250 <[email protected]>
Implemented AND operation for WAHVectors

github.com/BioJulia/WAHVectors.jl - c5e787bfac13afd7272bf0ed757d4d7ba0924362 authored almost 8 years ago by Ben J. Ward <[email protected]>
Added documentation files

github.com/BioJulia/WAHVectors.jl - f9d8e07fe1a70bd806991ea48aff76345124e080 authored almost 8 years ago by Ben J. Ward <[email protected]>
First implementation of compression algorithm.

github.com/BioJulia/WAHVectors.jl - bea513eaafb447eb03c5b3425183ac761e3c3b8e authored almost 8 years ago by Ben J. Ward <[email protected]>
Minor fixes, add docstrings, add tests.

github.com/BioJulia/Bio.jl - 129c129dc5c1288c3a93603b23e5e452c9aea5e6 authored almost 8 years ago by Daniel C. Jones <[email protected]>
Deal with FASTA directives.

github.com/BioJulia/Bio.jl - 2fab7c94cc50a463d6ac25b8645ed7a2836bef53 authored almost 8 years ago by Daniel C. Jones <[email protected]>
Unescape percent-encoded values.

github.com/BioJulia/Bio.jl - 6a48ca8b3c16ccb42055e93b965bdb2339cf1be9 authored almost 8 years ago by Daniel C. Jones <[email protected]>
Fix change that breaks other parsers.

github.com/BioJulia/Bio.jl - ef5766f0c706f85ad4c911671eb8be03c8369822 authored almost 8 years ago by Daniel C. Jones <[email protected]>
Handle fasta without the directive.

github.com/BioJulia/Bio.jl - 33dcdba1e590042f6a12c521e81e9b6e13fab47d authored almost 8 years ago by Daniel C. Jones <[email protected]>
Optionally save directives.

github.com/BioJulia/Bio.jl - 00fadb40b162e5f18a98036d7d582ef424533b53 authored almost 8 years ago by Daniel C. Jones <[email protected]>
Optimizations.

github.com/BioJulia/Bio.jl - c64cf1083223f1abc5779164593ffaabe65b2122 authored almost 8 years ago by Daniel C. Jones <[email protected]>
Fix some attributes issues.

github.com/BioJulia/Bio.jl - 17a9faa9118f4fca2360bdeab3857238128e35bb authored almost 8 years ago by Daniel C. Jones <[email protected]>
Get basic GFF3 parsing working.

github.com/BioJulia/Bio.jl - aacd37dfcb2d8148a12e7a634044b16d56052bb0 authored almost 8 years ago by Daniel C. Jones <[email protected]>
add docs on GFF3 (#351)

github.com/BioJulia/Bio.jl - cf2ff8546e648372b7d2f5a8efe82626823d9dad authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Store gff attributes in a custom data structure.

github.com/BioJulia/Bio.jl - 17077d7fcc65bb5ba1f92e1690e8f1afd80138ac authored almost 8 years ago by Daniel C. Jones <[email protected]>
Move gff3 files for consistency.

github.com/BioJulia/Bio.jl - 939eb04e54555448be0e54546a9ad39503f2c9e1 authored almost 8 years ago by Daniel C. Jones <[email protected]>
add GFF3 parser

github.com/BioJulia/Bio.jl - 44239c906ca6b10f74349612c31b43d0e900acb3 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Rearrange GFF3 to match other parsers.

github.com/BioJulia/Bio.jl - e48772bdfe77377129864ac725ee921317cca425 authored almost 8 years ago by Daniel C. Jones <[email protected]>
Add some tests. Fix obvious issues.

github.com/BioJulia/Bio.jl - 93440e947e8dd5c9580cb4bcfcc88758c01ba6a0 authored almost 8 years ago by Daniel C. Jones <[email protected]>
Altered logo url in readme as it was broken.

github.com/BioJulia/Bio.jl - f297d766c7756bbb9fdda86d0d3db402ed5e9a6b authored about 8 years ago by Ben J. Ward <[email protected]>
Added png Biojl logo

github.com/BioJulia/assets - 5f333204c476a5dea4f871c5bf94d7f1259c08df authored about 8 years ago by Ben J. Ward <[email protected]>
Edited and optimised SVG icons

github.com/BioJulia/assets - 49818dd126b547d81d4d0d6be2f33de99e413543 authored about 8 years ago by Ward9250 <[email protected]>
Updated assets with new icons

github.com/BioJulia/assets - 782003f61385ff35eee604fc3fcfbc0a2914dd0e authored about 8 years ago by Ward9250 <[email protected]>
Fix of Non-standard string literals (#349)

* Initial commit

* Removed return

* Incorporated both static and dynamic behaviour into th...

github.com/BioJulia/Bio.jl - fde871237fcd57bc9f5054bb8c96ba2897ccf956 authored about 8 years ago by Ben J. Ward <[email protected]>
require Julia 0.5 or later (#346)

github.com/BioJulia/Bio.jl - 17b084d49102a468ed5e11e8e679f6567bf9b3b0 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>