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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

group tests

github.com/BioJulia/BGZFStreams.jl - 6c0c91eaabf3e124f6bb9038bef08cab19302ea6 authored over 8 years ago by Kenta Sato <[email protected]>
add tests on Tabix

github.com/BioJulia/BGZFStreams.jl - e320456ecea9ee439cd297b48cb1f23b46c901ee authored over 8 years ago by Kenta Sato <[email protected]>
add PseudoBin

github.com/BioJulia/BGZFStreams.jl - 087bcc689d07f8192ceec1ea07d58667e474311e authored over 8 years ago by Kenta Sato <[email protected]>
fix Tabix fields

github.com/BioJulia/BGZFStreams.jl - c6cb97e5be6ae72f53f06c0289992f175072429f authored over 8 years ago by Kenta Sato <[email protected]>
add reducer of chunks to minimize seek operations

github.com/BioJulia/BGZFStreams.jl - 69a1e1faf9b9c591d3800e72734ee7fd7ad94045 authored over 8 years ago by Kenta Sato <[email protected]>
add a docstring for overlapchunks

github.com/BioJulia/BGZFStreams.jl - 4b6082f7fd0079ffff23ce82f34c727eeacc51f6 authored over 8 years ago by Kenta Sato <[email protected]>
add (limited) implementation of Tabix

github.com/BioJulia/BGZFStreams.jl - 8bc76bab4001c0a4513e0e5970e6a511fb556400 authored over 8 years ago by Kenta Sato <[email protected]>
small renaming and refactoring

github.com/BioJulia/BGZFStreams.jl - 27a32727fac2613f8046926a3a15bfbc47c69704 authored over 8 years ago by Kenta Sato <[email protected]>
fix maximum block size

github.com/BioJulia/BGZFStreams.jl - e6152472aaa52d394a1184e1ed6a1f48b2ebd441 authored over 8 years ago by Kenta Sato <[email protected]>
Initial commit

github.com/BioJulia/CWL.jl - ab47f7f1a02bbf9d4a1db8beaa8fe853f2e9f177 authored over 8 years ago by Ward9250 <[email protected]>
Initial commit

github.com/BioJulia/CWL.jl - 240d57081052f0c83305547f929fcbe7ddc220fb authored over 8 years ago by Ben J. Ward <[email protected]>
remove a type annotation

github.com/BioJulia/BGZFStreams.jl - d4220e00086b4ba634926dc8e9c9cc538e2dc266 authored over 8 years ago by Kenta Sato <[email protected]>
do not wrap ZStream in RefValue (#30)

github.com/BioJulia/Libz.jl - 67f5f3ccce4b7c3bb3a67250195c9df1b3aa2c49 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update mkdocs.yml

github.com/BioJulia/Bio.jl - 73fd7aa216924cf02ffca714125de515052772c3 authored over 8 years ago by Ben J. Ward <[email protected]>
Merge pull request #217 from BioJulia/mkdocs-biojulia

Edited docs to use mkdocs-biojulia

github.com/BioJulia/Bio.jl - 5a6eb5a00d1d61d9ea2bc3be1eef05fc08f281bd authored over 8 years ago by Ben J. Ward <[email protected]>
Edited docs to use mkdocs-biojulia

github.com/BioJulia/Bio.jl - d42b7bfbe940d4265ef9482bea096f37bd2520e9 authored over 8 years ago by Ben J. Ward <[email protected]>
Deleted unessecery folders/files

github.com/BioJulia/mkdocs-biojulia - bf168c5122ddfe360d0ea02cd9b082ba7262c208 authored over 8 years ago by Ben J. Ward <[email protected]>
biojulia modifications and customizations to cinder

github.com/BioJulia/mkdocs-biojulia - e2971cdb5f173b44197d3e02c38243ab95d5be55 authored over 8 years ago by Ben J. Ward <[email protected]>
Renamed cinder.css to biojulia.css

github.com/BioJulia/mkdocs-biojulia - 56c515664fb9e90a8377d718d531ef7a9f161bf1 authored over 8 years ago by Ben J. Ward <[email protected]>
Changed cinder to biojulia

github.com/BioJulia/mkdocs-biojulia - 5624202d42defa5ee4eece721c94302dc4045857 authored over 8 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/mkdocs-biojulia - da6e622661f791fb4d993cd081fba528a6a67aa4 authored over 8 years ago by Ben J. Ward <[email protected]>
Update README.md

github.com/BioJulia/mkdocs-biojulia - eeccb08c17140cc533ae2bdd3024d2a9ad980a84 authored over 8 years ago by Ben J. Ward <[email protected]>
remove static macro (#32)

github.com/BioJulia/Libz.jl - bdb18b84b673d9c6e558cc0f25f2cbe5f0ab41b2 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update custom.css

github.com/BioJulia/Bio.jl - 04d52e28ea00653091a011ae0427546a6858f9d9 authored over 8 years ago by Ben J. Ward <[email protected]>
Update custom.css

github.com/BioJulia/Bio.jl - faee3fd674bd3625d4d13bf4651f32a43e7cb03d authored over 8 years ago by Ben J. Ward <[email protected]>
Update mkdocs.yml

github.com/BioJulia/Bio.jl - cb36e7cbe103671846b4625afd8f2aa7623d4a40 authored over 8 years ago by Ben J. Ward <[email protected]>
Merge pull request #216 from BioJulia/sidecar

Added sidecar to docs

github.com/BioJulia/Bio.jl - 0d85b1c17d861bc081990592c9506132cc0e7a2b authored over 8 years ago by Ben J. Ward <[email protected]>
Added sidecar to docs

github.com/BioJulia/Bio.jl - 3c45e414428ac3a09c0f0f1ddf72bdeec14e1465 authored over 8 years ago by Ben J. Ward <[email protected]>
fix Compat version

github.com/BioJulia/Codecs.jl - 82a5d8bc714020b4177bd57faf118094b37c49db authored over 8 years ago by Abhijith <[email protected]>
pin Compat version

github.com/BioJulia/Codecs.jl - 80c897f4050998bfd064c58bf7270f943ea695e8 authored over 8 years ago by Abhijith <[email protected]>
fix deprecation

github.com/BioJulia/Codecs.jl - b5d21e3f79dece53bc0da2bf4f28464a7eef9ff2 authored over 8 years ago by Abhijith <[email protected]>
Fix deprecation errors (#31)

github.com/BioJulia/Libz.jl - d62791a4257d69c8e4418e864fc4bb08a9215ad9 authored over 8 years ago by Jon Malmaud <[email protected]>
Merge pull request #16 from bicycle1885/tweaks

Precompilation and small tweaks.

github.com/BioJulia/IntervalTrees.jl - cd1acbb348db8faef1ceacfaf9f89af69ca3648c authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
improve read(x, UInt8) performance

github.com/BioJulia/BGZFStreams.jl - 0ddf04bf62b3cdd8b42d6fe6b042a2080e0f1e07 authored over 8 years ago by Kenta Sato <[email protected]>
refactor virtual offset functions

github.com/BioJulia/BGZFStreams.jl - 84f03e640f3f9a198becf3da68f8159a8aea8aee authored over 8 years ago by Kenta Sato <[email protected]>
fix threading

github.com/BioJulia/BGZFStreams.jl - 1c0bbf141951c71b66c3d74f837423b59267bf04 authored over 8 years ago by Kenta Sato <[email protected]>
Added nightly builds as an allowed failiure (#215)

github.com/BioJulia/Bio.jl - 50da08ac9b79015acbfc3a1d8a468a52170f835e authored over 8 years ago by Ben J. Ward <[email protected]>
fix virtualoffset

github.com/BioJulia/BGZFStreams.jl - 1a54e350fefca90eaf4c49a8e142ede7be219d5a authored over 8 years ago by Kenta Sato <[email protected]>
clean up

github.com/BioJulia/BGZFStreams.jl - 1fe10f27802563181cda90dcfe7a0f3611252555 authored over 8 years ago by Kenta Sato <[email protected]>
support multi-threading (disable seek tests for a while)

github.com/BioJulia/BGZFStreams.jl - 2f6d9f9b1ec69419ab925e69d393eda00115f0d8 authored over 8 years ago by Kenta Sato <[email protected]>
add pretty show method

github.com/BioJulia/BGZFStreams.jl - 293f5174822dbbbbf643035d291d3b6fe0151bf5 authored over 8 years ago by Kenta Sato <[email protected]>
test byte-by-byte read/write

github.com/BioJulia/BGZFStreams.jl - e14a98a1bba61802bfae17ac7c17fed659f98f8f authored over 8 years ago by Kenta Sato <[email protected]>
improve performance of reading

github.com/BioJulia/BGZFStreams.jl - 5e4ddfae7ac827916b65ef340216dde8ce4c64d5 authored over 8 years ago by Kenta Sato <[email protected]>
check stream is open

github.com/BioJulia/BGZFStreams.jl - 28199ad053d049128c6dcdbbf5ca8978865c8bbc authored over 8 years ago by Kenta Sato <[email protected]>
check open mode

github.com/BioJulia/BGZFStreams.jl - 9e5047c76deab075367ec2556fd47651d6a46a0f authored over 8 years ago by Kenta Sato <[email protected]>
add tests for empty blocks

github.com/BioJulia/BGZFStreams.jl - 254a908da3039c09c60ba6191bba69e4f015bab2 authored over 8 years ago by Kenta Sato <[email protected]>
fix read

github.com/BioJulia/BGZFStreams.jl - 39d162bb6f37017bdb4331ddba85f2e56aabfbcb authored over 8 years ago by Kenta Sato <[email protected]>
fix write and unsafe_write

github.com/BioJulia/BGZFStreams.jl - 318b74d6e3250854ba6c76741bc0eb8c13d6f509 authored over 8 years ago by Kenta Sato <[email protected]>
do not use temporary files in round-trip tests

github.com/BioJulia/BGZFStreams.jl - 2da15672452be97489edabbaf3bbeefc869bd98f authored over 8 years ago by Kenta Sato <[email protected]>
add onclose

github.com/BioJulia/BGZFStreams.jl - e157739eaa7143d0bcf842bd79abb8b8bdd4f04b authored over 8 years ago by Kenta Sato <[email protected]>
clean up things

github.com/BioJulia/BGZFStreams.jl - c5fa98fc344e9d4287e753e8114d22c3eba0e5b5 authored over 8 years ago by Kenta Sato <[email protected]>
add an ASCII figure on internals

github.com/BioJulia/BGZFStreams.jl - 44e9cb23a24a43df1687272e752885da3f82cc49 authored over 8 years ago by Kenta Sato <[email protected]>
add unsafe_write

github.com/BioJulia/BGZFStreams.jl - 8c4c2add35b8b8546f34340bf02d7ca3dc5ea647 authored over 8 years ago by Kenta Sato <[email protected]>
implement unsafe_read

github.com/BioJulia/BGZFStreams.jl - 161764614ca4cd33cefd82c9818e9b6c2b8827af authored over 8 years ago by Kenta Sato <[email protected]>
test zero-length BGZF block

github.com/BioJulia/BGZFStreams.jl - dfe824c8fc5d4eaac46b5f781b033aeea5e6a1b0 authored over 8 years ago by Kenta Sato <[email protected]>
fix deprecated warnings

github.com/BioJulia/BGZFStreams.jl - bc68541806c476e4045f6862b914deda7ab48614 authored over 8 years ago by Kenta Sato <[email protected]>
remove the == definition for virtual offset

github.com/BioJulia/BGZFStreams.jl - 274f90c5b824029e32b949e8fb2381c84cc1eba0 authored over 8 years ago by Kenta Sato <[email protected]>
fix zstream initialization

github.com/BioJulia/BGZFStreams.jl - a5f893fd9ae41b496f33de1c23d3b47321e6cc79 authored over 8 years ago by Kenta Sato <[email protected]>
allow compression level = 0 (no compression) and = -1 (default)

github.com/BioJulia/Libz.jl - 73238dcd5ba51611e8ac09ba9bb1b031c1317fef authored over 8 years ago by Kenta Sato <[email protected]>
clean up indents

github.com/BioJulia/Libz.jl - 31c570f8e3720d1210afc0be53065c665cee6423 authored over 8 years ago by Kenta Sato <[email protected]>
rename init_deflate_stream to init_deflate_zstream

github.com/BioJulia/Libz.jl - fb8b2be038f449182e1dbd00951747ebcfc8fe2e authored over 8 years ago by Kenta Sato <[email protected]>
refactor

github.com/BioJulia/BGZFStreams.jl - 66fd1d0b4b9eba52be200c1f3f7984109aa24c6c authored over 8 years ago by Kenta Sato <[email protected]>
fix a serious data corruption bug

github.com/BioJulia/BGZFStreams.jl - bc8adf94b088127e93287595b90e2221e593b29d authored over 8 years ago by Kenta Sato <[email protected]>
add virtualoffset(stream)

github.com/BioJulia/BGZFStreams.jl - 869174499bb706c53d6e3cb2c556992aa7bc2751 authored over 8 years ago by Kenta Sato <[email protected]>
add a docstring for BGZFStream

github.com/BioJulia/BGZFStreams.jl - db5f46076fb5782f69818de1ad5d4b72ef5b3d36 authored over 8 years ago by Kenta Sato <[email protected]>
add a docstring for virtual offset

github.com/BioJulia/BGZFStreams.jl - 99b45b9e57365bdd02d600e0bb12faeda2714912 authored over 8 years ago by Kenta Sato <[email protected]>
fix README

github.com/BioJulia/BGZFStreams.jl - c1742d429cbeea53765e99d154a91703f3c14945 authored over 8 years ago by Kenta Sato <[email protected]>
add README

github.com/BioJulia/BGZFStreams.jl - 57c9b03e6f9d301deac63be8fb672f0dc71b9399 authored over 8 years ago by Kenta Sato <[email protected]>
add contents

github.com/BioJulia/BGZFStreams.jl - 929e0554318535447d82f5da9c89cac7b493c972 authored over 8 years ago by Kenta Sato <[email protected]>
BGZFStreams.jl generated files.

license: MIT
authors: Kenta Sato
years: 2016
user: bicycle1885

Julia V...

github.com/BioJulia/BGZFStreams.jl - 9bace1a6ddc9a7bbaa5134a4b080770b6111e953 authored over 8 years ago by Kenta Sato <[email protected]>
initial empty commit

github.com/BioJulia/BGZFStreams.jl - d61d3abc7b939122cdcaaf1bbfcc13ed20be5eb6 authored over 8 years ago by Kenta Sato <[email protected]>
add BEDWriter (#214)

github.com/BioJulia/Bio.jl - 0e0664cce05e10efc1351898f41443c7360e65d4 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add convert(Char, ::Strand) (#213)

github.com/BioJulia/Bio.jl - 2a1866903452016f6e6eb3e91079224feb21af01 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Replaced makedocs line as Documenter.jl is still awkward on OS X

github.com/BioJulia/Bio.jl - 5e5c61f5306e0901deb1eaf089095ddfc61321f4 authored over 8 years ago by Ben J. Ward <[email protected]>
Update make.jl

github.com/BioJulia/Bio.jl - f62a5343c916ac38cfa25d30be85ef1bd0fe9fbb authored over 8 years ago by Ben J. Ward <[email protected]>
Sliding windows return their start and ends. (#212)

* Sliding windows return their start and ends.

* Windows return the start position and view
...

github.com/BioJulia/Bio.jl - 0e5cf4ef1db6821d130ee7021eb67663e8751c0c authored over 8 years ago by Ben J. Ward <[email protected]>
fix FASTQ writer interfaces (#211)

github.com/BioJulia/Bio.jl - ace22ccc7bfb66b668c1f558161c9f4646c8f33d authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix FASTA writer interfaces (#210)

github.com/BioJulia/Bio.jl - bcc023e0eeaa0109dbeebb26d3b4ff167a548e76 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #209 from bicycle1885/writer

Writer interfaces for FASTA and FASTQ file formats.

github.com/BioJulia/Bio.jl - 2f084808a4d5d0203c3cfbd00c8b6f28cc596c97 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add FASTQWriter

github.com/BioJulia/Bio.jl - 2cc3b2b6e3604b46a716628cc165ce877ebe5da8 authored over 8 years ago by Kenta Sato <[email protected]>
add FASTAWriter

github.com/BioJulia/Bio.jl - 0020b77366420e09d83e57f3d746620dea52cc16 authored over 8 years ago by Kenta Sato <[email protected]>
Added length method for winter, which is essential for array comprehensions.

github.com/BioJulia/Bio.jl - d879f3256b67396953c3574556ddaa4b78fdeca1 authored over 8 years ago by Ben J. Ward <[email protected]>
add Bio.IO (and clean up)

github.com/BioJulia/Bio.jl - 58783c354ef77073587cb6cca3eafa7c7f990320 authored over 8 years ago by Kenta Sato <[email protected]>
SeqRecords exported (#207)

* Export SeqRecord and FASTAMETAdata

* exported FASTASeqRecord alias

github.com/BioJulia/Bio.jl - 6501b56a8756c44e331fdd03bbf09fffdba05fb9 authored over 8 years ago by Ben J. Ward <[email protected]>
Remove nightlies from appveryor

github.com/BioJulia/Bio.jl - 3d4d8a512efa8667d7b6b4dc8e1980ccc17fbabf authored over 8 years ago by Ben J. Ward <[email protected]>
Removed nightly build from travis.

github.com/BioJulia/Bio.jl - d9eeb729c41148a509354be56c77b758623243fa authored over 8 years ago by Ben J. Ward <[email protected]>
Add ReferenceSequence (#198)

* add ReferenceSequence

* add docs on ReferenceSequence

github.com/BioJulia/Bio.jl - 1d06139c2a35b19495c9e3739c2275248ce15e07 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
define DNACodon and RNACodon (#204)

github.com/BioJulia/Bio.jl - d829603f386186b1aa3c241d93111cfad319db33 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
define eltype for KmerNeighborIterator (and add tests) (#203)

github.com/BioJulia/Bio.jl - 0e8c6f72c9ff71ed41eb95c4facfc7e8afa2b63c authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #202 from bicycle1885/fix-kmer

Fix kmer

github.com/BioJulia/Bio.jl - 891f384c5a860a1cf030d9d733e37d900fcfd621 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
export Codon

github.com/BioJulia/Bio.jl - 1212dac7c7fb3652241635772bac9ffe89f7cad9 authored over 8 years ago by Kenta Sato <[email protected]>
deprecate kmer, dnakmer and rnakmer

github.com/BioJulia/Bio.jl - b43d1aa3da78a8179860894ac3692918c3b62f8e authored over 8 years ago by Kenta Sato <[email protected]>
fix k-mer arithmetic

github.com/BioJulia/Bio.jl - 360214c849b8c5a116242c99f3c0c8f7bcaad276 authored over 8 years ago by Kenta Sato <[email protected]>
move deprecated definitions

github.com/BioJulia/Bio.jl - 14eaab2b24f84cabab87f87c406314250d58c892 authored over 8 years ago by Kenta Sato <[email protected]>
fix LICENSE.md

github.com/BioJulia/IndexableBitVectors.jl - 1ce6e0847ecdb3d63faf9b2b8330a392c75e7a1a authored over 8 years ago by Kenta Sato <[email protected]>
remove switch (#3)

github.com/BioJulia/IndexableBitVectors.jl - bbda3b697f595e3234d961ab0f53edfbac196919 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
rename Blast to BLAST (take 2) (#199)

github.com/BioJulia/Bio.jl - 3ad22d8af45b0dec22ba913eee2ee9f2efd1146b authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Approximate search/rsearch for sequences. (#153)

* add alphabet methods for BioSequence and Kmer

* add approximate sequence searches

* fixu...

github.com/BioJulia/Bio.jl - 58cd5b8a4a3d87003064b849a3ae77c05fc97795 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add Base.copy (#2)

github.com/BioJulia/IndexableBitVectors.jl - 7b3c33fa370cf64eae502ef99376fb2f2871272d authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
rename Blast to BLAST (#196)

github.com/BioJulia/Bio.jl - e49a01a9e4cb72bfab690f68897d143d555f97b0 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>