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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

minor stylistic tweaks

github.com/BioJulia/IntervalTrees.jl - d3b59a289f4524288ced911b7bef635d207c668a authored over 8 years ago by Kenta Sato <[email protected]>
Added more tests for phylogeny types. (#193)

* Added more tests for phylogeny types.

* Added == method for phylogenies

* More tests add...

github.com/BioJulia/Bio.jl - f477d42696e1999616499bb38deed89cb896a41d authored over 8 years ago by Ben J. Ward <[email protected]>
make show(strand) more informative (#195)

github.com/BioJulia/Bio.jl - 7dd8aff132962993f8fde9bab94eba4c865e1f43 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
turn on precompilation

github.com/BioJulia/IntervalTrees.jl - 61f300341c337e3640f3628cc98b10b02dfb6fea authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #15 from bicycle1885/modernize

Modernize package

github.com/BioJulia/IntervalTrees.jl - 7cd940d2ed0307228c807eb0e34140a7bbb8896e authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
implement iteratorsize trait

github.com/BioJulia/IntervalTrees.jl - 28abbfc0416370ee9104c6fe33976d4b400848dc authored over 8 years ago by Kenta Sato <[email protected]>
fix a test of slice

github.com/BioJulia/IntervalTrees.jl - 916dab35cd78a47eab0d37158f72c9b31e022e1b authored over 8 years ago by Kenta Sato <[email protected]>
fix syntax of throwing exception

github.com/BioJulia/IntervalTrees.jl - 8c3954f0465e1a24486269c5da3248e8157aa4a4 authored over 8 years ago by Kenta Sato <[email protected]>
use Base.Test instead of FactCheck

github.com/BioJulia/IntervalTrees.jl - ecffc4565bc657876796a30d8dbf45afa0096341 authored over 8 years ago by Kenta Sato <[email protected]>
drop Docile dependency

github.com/BioJulia/IntervalTrees.jl - 7272525ab0d5af7685aafd054bfeee677d635f62 authored over 8 years ago by Kenta Sato <[email protected]>
require Julia 0.4

github.com/BioJulia/IntervalTrees.jl - 5ee0f83f52c823aa0d4bf14593e3665d468e8774 authored over 8 years ago by Kenta Sato <[email protected]>
Squashed Previous Phylo rework commits (#157)

edited Phylo, phylogeny, runtests.

Added a few more methods for new phylogenies.

Added som...

github.com/BioJulia/Bio.jl - ee57251b8325b3b9e9e4e4fdb0de712ac599524b authored over 8 years ago by Ben J. Ward <[email protected]>
SymbolRange, cyclic arithmetic, and more informative `show` method. (#190)

* add SymbolRange type

* make symbol arithmetic cyclic

* make show(nucleotide|amino acid) ...

github.com/BioJulia/Bio.jl - 1688351d0b689227b5c661e6d73496e6d8d3b53f authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
tweak spacing of HTML docs (#192)

github.com/BioJulia/Bio.jl - bc2fe439620e9644efe1e553a37af1d06b7fae60 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Updates for Documenter.jl syntax changes (#189)

See https://github.com/MichaelHatherly/Documenter.jl/pull/51 for details.

github.com/BioJulia/Bio.jl - ff0f66cc6ab2b29ae63a13b749f7e67f65709e9d authored over 8 years ago by Michael Hatherly <[email protected]>
use cinder theme for web docs (#181)

github.com/BioJulia/Bio.jl - 86a6c10ecdc87692581c729e3d443aef38d1115f authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix a docstring of KmerCounts (and potential bug) (#188)

github.com/BioJulia/Bio.jl - 345dedbddd9813da2440a4a41b3264063caa4374 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add exact search functions (#152)

github.com/BioJulia/Bio.jl - 999f2be26618ef4fa0aba91a83ab2b51d1449fc7 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
rename internal macros to avoid overwriting others (#187)

github.com/BioJulia/Bio.jl - 0dbae4fa41d3db614adffb478b6c334a214399de authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add iscompatible (#186)

github.com/BioJulia/Bio.jl - 1beeb0037d7532ed96a23604d1a5163235f12186 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
define eltype for Kmers (#185)

github.com/BioJulia/Bio.jl - 83f27bab863ebbffc23cd08d2f4c58729ad76833 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix deprecated (#183)

* replace symbol with Symbol

* fix deprecated types and syntaxes

github.com/BioJulia/Bio.jl - eaced8cc4991a5c5f639e48a320ae4cdf0414883 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix coding style (#182)

* remove intrinsics calls (box/unbox)

* fix style of method extensions (Seq.Intervals)

* f...

github.com/BioJulia/Bio.jl - 49251334917b3db186faf77feb9b4d0b33968cad authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added png BioJulia design

github.com/BioJulia/assets - a20fdd35a5d86f3ec37bae9ab3330bece2308b1a authored over 8 years ago by Ward9250 <[email protected]>
Changed logo for manpages

github.com/BioJulia/Bio.jl - fac931209e8bb24e7d961d45725715a5b47e472d authored over 8 years ago by Ward9250 <[email protected]>
Update code_style.md

github.com/BioJulia/Contributing - 4d9f7ca9c4b6b9e0caafc9f7003a15942fc66f2f authored over 8 years ago by Ben J. Ward <[email protected]>
Update make.jl

github.com/BioJulia/Bio.jl - 6a0c1271bab53dcc19f981f6ebf29eae1c344ff9 authored over 8 years ago by Ben J. Ward <[email protected]>
Updated makefile to bypass OS X error temporarily.

In accordance with issue 45 of Documenter.jl

github.com/BioJulia/Bio.jl - 037e80a47933b7e9b60909bf00ecc3e1f3733107 authored over 8 years ago by Ben J. Ward <[email protected]>
Updated res of png logo

github.com/BioJulia/assets - ffa9b7f033d616bd3492e0583d5ba04863ca9ec4 authored over 8 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/Bio.jl - 89040bf741b5c0691252f0b8320f42903d536329 authored over 8 years ago by Ben J. Ward <[email protected]>
Added png of logo

github.com/BioJulia/assets - 19ea38344265710ed3ead42959c8031ec7e6cc8b authored over 8 years ago by Ben J. Ward <[email protected]>
Merge pull request #1 from BioJulia/modified_logos

Modified logos

github.com/BioJulia/assets - bfc784ba56048cda51a318d5eea419a2c2ff7f7a authored over 8 years ago by Ben J. Ward <[email protected]>
Reverted change of order of after_success operations.

github.com/BioJulia/Bio.jl - 03543f40e3b74bba95762fc0e6b2e0aea3473652 authored over 8 years ago by Ben J. Ward <[email protected]>
Testing if order of after_success: operations affects OSX build.

github.com/BioJulia/Bio.jl - 8b1fa334437fa04d1ca61a15913707969e0c5176 authored over 8 years ago by Ben J. Ward <[email protected]>
Corrected spelling error in documentation

github.com/BioJulia/Bio.jl - 1db81e9aa4b5edd67691b2ee634251405a0f00c8 authored over 8 years ago by Ward9250 <[email protected]>
Merge pull request #180 from bicycle1885/precompile

Precompile

github.com/BioJulia/Bio.jl - 05c992d65457cfc8f6ba61d969cf7b33d958afee authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
precompile parsers

github.com/BioJulia/Bio.jl - 140097ee925a07c592146a5052033b30a84ce75b authored over 8 years ago by Kenta Sato <[email protected]>
switch precompile on

github.com/BioJulia/Bio.jl - 46e46cc1828514b5eb11864d10afd87c7470323f authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #179 from bicycle1885/fasta-type

FASTA type

github.com/BioJulia/Bio.jl - ff70a44cf4ed0de85a2f2aeba36c4635d6c1c2d7 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix sequence type classifier

github.com/BioJulia/Bio.jl - 35f8b1a47369c88a2e8a4c73c9223ca14594939f authored over 8 years ago by Kenta Sato <[email protected]>
make the FASTQ parser take a sequence type argument

github.com/BioJulia/Bio.jl - eeece6797751b238a0566f30b89e3f1bfa8263fb authored over 8 years ago by Kenta Sato <[email protected]>
make the FASTA parser take a sequence type argument

github.com/BioJulia/Bio.jl - 1b7e4afefc42529f6e1b5261859cb5bf7e6c3db8 authored over 8 years ago by Kenta Sato <[email protected]>
add more tests on exceptions (#28)

github.com/BioJulia/Libz.jl - f0b408970942803420ba8881dbd7b12e7ad14cca authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add VoidAlphabet

github.com/BioJulia/Bio.jl - 8430aee54fecd300d1b764788ca0fe97a3a2fa9e authored over 8 years ago by Kenta Sato <[email protected]>
Corrected an error in runtests.jl

github.com/BioJulia/Bio.jl - 9b34ca035e6953d29351f53dc172a611fb01d1d1 authored over 8 years ago by Ben J. Ward <[email protected]>
Merge pull request #26 from bicycle1885/precompile

Precompile

github.com/BioJulia/Libz.jl - f970c685db78377d67ba97604be161ba6c25fe2d authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix for 161 error. (#176)

* Fix for 161 error.

* Edited testing module names.

github.com/BioJulia/Bio.jl - 8ff06b599585137eb1e834a96d9cb26036101164 authored over 8 years ago by Ben J. Ward <[email protected]>
add vector-sink tests

github.com/BioJulia/Libz.jl - df379d28a9fcede11e5acece876a4e4e65917703 authored over 8 years ago by Kenta Sato <[email protected]>
switch __precompile__ on

github.com/BioJulia/Libz.jl - e958122472a5237e77a8cfb3eace9c8d985b4504 authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #140 from BioJulia/refactor-ragel

Refactor ragel

github.com/BioJulia/Bio.jl - dc9aca2aad186b3ad195b2e26f25812ad9e2c3b4 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fixed tools man

github.com/BioJulia/Bio.jl - a2bcc993de2b565997aaa9287d1ec1140223a902 authored over 8 years ago by Ben J. Ward <[email protected]>
Edited an error in the metablock for this manpage.

github.com/BioJulia/Bio.jl - 0ff875f36462db3e553ff7ba71557ef0d69ffdc7 authored over 8 years ago by Ben J. Ward <[email protected]>
Fixed makedocs yaml file.

The tools documentation (which contains docs for blast utilities) was not included in the mkdocs...

github.com/BioJulia/Bio.jl - ac40464b69feb51f576d9a991dfc779896408fc4 authored over 8 years ago by Ben J. Ward <[email protected]>
Indexes (#161)

* Added indexing types to a module Bio.Indexing

* Reorganised util folder a bit, and added th...

github.com/BioJulia/Bio.jl - 631dded6958ff20bbd95660365c1b8a748e3e89f authored over 8 years ago by Ben J. Ward <[email protected]>
refactor Ragel

github.com/BioJulia/Bio.jl - 4f023bd3609bec6e757ecae8d22c6254b83bf77c authored over 8 years ago by Kenta Sato <[email protected]>
remove writing FASTA tests

this is tested when parsing FASTA

github.com/BioJulia/Bio.jl - b64f7ed273db91f0f506dbf72e16f6f478dadf0d authored over 8 years ago by Kenta Sato <[email protected]>
replace deprecated Base.ttysize with displaysize (#172)

github.com/BioJulia/Bio.jl - 6f53b069093d11e913d91382cd548c8a6328aaa6 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #170 from kdmurray91/separate-ragel

[RTR] Separate ragel from julia source

github.com/BioJulia/Bio.jl - cb21c0e8c5b4494a12fa2879b39edb87bfb64665 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
bigbed: rename bigbeddata -> bigbed-parser

Makes it consisent with all the other parsers

github.com/BioJulia/Bio.jl - dae72afd78a29b21c0b075a9637bb7ddabceea39 authored over 8 years ago by Kevin Murray <[email protected]>
bed: split ragel from julia source

github.com/BioJulia/Bio.jl - 98845b7cfac30bf4d652da206029c6c3138c4c73 authored over 8 years ago by Kevin Murray <[email protected]>
fasta: separate parser from source

github.com/BioJulia/Bio.jl - cdba79b101135bdd2001eaf4267409fc4a99cf9d authored over 8 years ago by Kevin Murray <[email protected]>
fastq: rename ragel parser file

fastq-parse -> fastq-parser

github.com/BioJulia/Bio.jl - 2ce3409a6ab744c6e0b6dc2e97879a042799cc9c authored over 8 years ago by Kevin Murray <[email protected]>
Fastq: Split ragel and julia sources

github.com/BioJulia/Bio.jl - 105442ee2d057112bf172321025c5edfbae63a8a authored over 8 years ago by Kevin Murray <[email protected]>
regenerate ragel Bio.Seq sources

github.com/BioJulia/Bio.jl - 3dfa5b88900a4b37458b946618ca7994c126e822 authored over 8 years ago by Kevin Murray <[email protected]>
remove encode_seq macro (#169)

github.com/BioJulia/Bio.jl - 505c41793465a1b2b612e5fe2f8b390d845f31f8 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
clean getindex

github.com/BioJulia/ReferenceSequences.jl - f275cbf3a5b8dcbcc90be4472d106b945015d30d authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #163 from bicycle1885/fix-intervals

fix BigBed parser

github.com/BioJulia/Bio.jl - ae6e6c161ab96e8f8fd06d09f7db97bc3d4ced29 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix BigBed parser

github.com/BioJulia/Bio.jl - c14b9ada859ed9145bc209fceaab5fe015ea2cce authored over 8 years ago by Kenta Sato <[email protected]>
rename EmptyStreamSource

github.com/BioJulia/Bio.jl - a33e59e3d1b38270c53703eeee973832bd35dcb6 authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #168 from bicycle1885/install-blast

install NCBI BLAST+ before running Travis CI

github.com/BioJulia/Bio.jl - ccc5eab520c12cdaf83e3b1de3823b355fdc25c1 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
install NCBI BLAST+ before running Travis CI

github.com/BioJulia/Bio.jl - 6843f836b275888b5e9143cdbaa74e07877456db authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #24 from bicycle1885/docs

Clean up documents and a few touch-ups.

github.com/BioJulia/Libz.jl - e072678a7ed64ed8761d5e7b7b231bff4c24d127 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove ZError

github.com/BioJulia/Libz.jl - 1ba67dcc0ec1b145e81101a66ba1623a3aaafa33 authored over 8 years ago by Kenta Sato <[email protected]>
normalize documents

github.com/BioJulia/Libz.jl - 256c215c6626b76e2160b422b9bbaedf149adfb3 authored over 8 years ago by Kenta Sato <[email protected]>
update README.md

github.com/BioJulia/Libz.jl - ef54f47f74f089be3cf3dfee21148e72486d0de9 authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #23 from bicycle1885/more-tests

More tests

github.com/BioJulia/Libz.jl - abc3aeb444926afbb6b3f650e93e21f666d0596d authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
test state transitions and fix behavior of close

github.com/BioJulia/Libz.jl - 7ce96856e7dd0455f66036967956aec843391fbd authored over 8 years ago by Kenta Sato <[email protected]>
strict check of return values of crc32 and adler32

github.com/BioJulia/Libz.jl - 377b68bc0be853c546af17d2777716601da1925c authored over 8 years ago by Kenta Sato <[email protected]>
fix random seed for tests

github.com/BioJulia/Libz.jl - 8e961ca6e0466d0b2f86cac118b48772d43faa90 authored over 8 years ago by Kenta Sato <[email protected]>
remove utils introduced in #12 (#19)

github.com/BioJulia/Libz.jl - dc6fa4f424b91a4e812ef75d2f4f6000248c9779 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Refactoring and bug fixes. (#21)

* refactoring

* replace deprecated functions

github.com/BioJulia/Libz.jl - d26b9e1df53236486694c813327cac1c358bf1be authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Corrected README

github.com/BioJulia/Bio.jl - 55f87dcba7015048ea39b3d9e1a652778b5d8e9f authored over 8 years ago by Ben J. Ward <[email protected]>
Corrected badge urls in README

github.com/BioJulia/Bio.jl - 8f170bc41cf4ea3195b3dbbb8b3ca533a4bcf862 authored over 8 years ago by Ben J. Ward <[email protected]>
Merge pull request #162 from kdmurray91/vimswp

Add a bunch of temp files to gitignore

github.com/BioJulia/Bio.jl - bab535b5b96800542c5a8da043b6ff06276624b2 authored over 8 years ago by Ben J. Ward <[email protected]>
Remove misc temp/unwanted files

- Cloned BioFmtSpecimens
- KDE directory files
- Vim swap & misc temp files

github.com/BioJulia/Bio.jl - 6306f7fd09ab1a94df61a1363ae0b0a167d03ce5 authored over 8 years ago by Kevin Murray <[email protected]>
Merge pull request #158 from kescobo/blastdocs

add documentation for blast module

github.com/BioJulia/Bio.jl - 0b9bcabc3cc6027229a218a1c2082d4ae5e58e50 authored over 8 years ago by Ben J. Ward <[email protected]>
update index.md

github.com/BioJulia/Bio.jl - b1c718c9ec0958c56302f0c2ad68967c0fc50039 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>
add documentation for blast module

github.com/BioJulia/Bio.jl - deede4eb9fa17c5f0912ca17c36a3dcbc3f3968a authored over 8 years ago by Kevin Bonham, PhD <[email protected]>
Merge pull request #65 from kescobo/blastwrapper

Blastwrapper

github.com/BioJulia/Bio.jl - 234e769ba0ef047f082d431d6d831e11d990a444 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #20 from BioJulia/fix

use BaseTestNext instead of FactCheck

github.com/BioJulia/Libz.jl - bb2fc1a2c549a73bb956f2779da00ba41a643930 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
use BaseTestNext instead of FactCheck

github.com/BioJulia/Libz.jl - 33cb6c3c52005b09a2d1712c533b71d4f1a64a45 authored over 8 years ago by Kenta Sato <[email protected]>
rename type parameter

github.com/BioJulia/Libz.jl - 5898e4f67bef55d7c9067afd1e16ec16dd9a7706 authored over 8 years ago by Kenta Sato <[email protected]>
Merge pull request #18 from BioJulia/reset

set reset_on_end on by default

github.com/BioJulia/Libz.jl - c8be1dd6b44390df0057d62ff489dfe263173abb authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
set reset_on_end on by default

github.com/BioJulia/Libz.jl - c6fb3e38d9a5903639840c63a249930584c581ec authored over 8 years ago by Kenta Sato <[email protected]>
address line comments for previous commit

- remove docstrings for non-exported functions (replace with comments)
- remove unnecessary type...

github.com/BioJulia/Bio.jl - f25b173a60a381a700fc19ef80eb90f64b37d7c8 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>
Update code_style.md

github.com/BioJulia/Contributing - 2f4abd7270c7ef4853f3fe9e80488484fd0bb028 authored over 8 years ago by Ben J. Ward <[email protected]>
Update package_submission.md

github.com/BioJulia/Contributing - 0439c0d158f02c41dc1092b3bc52c03bc3ae918f authored over 8 years ago by Ben J. Ward <[email protected]>
made tests evaluate to Boolean

github.com/BioJulia/Bio.jl - ce5edfe21efe63b36d00f80fa2b1cef574ffb516 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>
Forgot to add package to Bio.jl

github.com/BioJulia/Bio.jl - 992a7a53aea97cdaa662af858fdc472035bb9f50 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>
add tests for blastn and blastp

github.com/BioJulia/Bio.jl - faf17d3e430a2f6ecc96eab775245f8ef6bc193c authored over 8 years ago by Kevin Bonham, PhD <[email protected]>