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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

add REQUIRE

github.com/BioJulia/FMIndexes.jl - ae32894733cb2689a819aa69b8809352a289cbeb authored about 9 years ago by Kenta Sato <[email protected]>
support pSAscan for suffix array construction

download and install pSAscan from:
https://www.cs.helsinki.fi/group/pads/pSAscan.html

github.com/BioJulia/FMIndexes.jl - 3d94b4ed297c3f2861fbd91767ab083e106ee19c authored about 9 years ago by Kenta Sato <[email protected]>
Oh, forgot to add text

github.com/BioJulia/FMIndexes.jl - 297962a5c5b08e3310c6d3130248992d70ecdea6 authored about 9 years ago by Kenta Sato <[email protected]>
Change next method for aminoacid

github.com/BioJulia/Bio.jl - 37427035d68fa3e98b437ca050485603b857ccd8 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
fix a bug for large bit vectors

github.com/BioJulia/IndexableBitVectors.jl - 295e8922cb69c52edeb2c1d0e6c1a80f7f38c3c9 authored about 9 years ago by Kenta Sato <[email protected]>
add some tests

github.com/BioJulia/FMIndexes.jl - bcb1c5d5c4fa59a00f393c46ff6e03c3e8f1d8de authored about 9 years ago by Kenta Sato <[email protected]>
use an anonymous mmap for long sequence

github.com/BioJulia/FMIndexes.jl - c41f93924bfb7f606231b370acf7ae960e78ba75 authored about 9 years ago by Kenta Sato <[email protected]>
rename type parameter `n` to `w`

github.com/BioJulia/FMIndexes.jl - 292d349fb052a5abd81f09c8acfa59d3ad5ef48c authored about 9 years ago by Kenta Sato <[email protected]>
add tests for full-text search

github.com/BioJulia/FMIndexes.jl - 890197ff8564d6f6091497ee4d78697f13ddeb45 authored about 9 years ago by Kenta Sato <[email protected]>
`sa_range` accepts an initial range

github.com/BioJulia/FMIndexes.jl - 7d178eda0f7ad17a732e0bc69379c66421b0778d authored about 9 years ago by Kenta Sato <[email protected]>
add __precompile__

github.com/BioJulia/FMIndexes.jl - f1733406ec4fa5d29938aa896b04ae7c1eeede6e authored about 9 years ago by Kenta Sato <[email protected]>
update README.md [skip ci]

github.com/BioJulia/WaveletMatrices.jl - f4a85f173ef45a87580a44c61d84b9369320a845 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove Requirements section in README [skip ci]

github.com/BioJulia/WaveletMatrices.jl - c3903645b687203c55194462338a2c4e19bf6bb5 authored about 9 years ago by Kenta Sato <[email protected]>
do not run tests on release for now

github.com/BioJulia/WaveletMatrices.jl - e2be1cca2175c450e5a1c4e93c02fac8f7d259fb authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
update the build status badge

github.com/BioJulia/WaveletMatrices.jl - ffe9bc30716b579d288bb807c1f6d8b8ee23daf0 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
remove Compat from dependencies

github.com/BioJulia/IndexableBitVectors.jl - a1a2b07fea472adbeec5a0df8f33805bacc9f062 authored about 9 years ago by Kenta Sato <[email protected]>
speed up tests

github.com/BioJulia/IndexableBitVectors.jl - cfbc333fb5c7a1472c7e870ae8975f6bac11a891 authored about 9 years ago by Kenta Sato <[email protected]>
add requirements

github.com/BioJulia/WaveletMatrices.jl - 2c9440ab6f379882997b960ed8ff0f723d735074 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #1 from BioJulia/badges

Update README badges.

github.com/BioJulia/IndexableBitVectors.jl - 3d27297d8be980dd196b54d9aeb76ac1d3fb1dac authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Update README badges.

github.com/BioJulia/IndexableBitVectors.jl - 2b495f1c7a25422182f50651bae9ef5b19aedfef authored about 9 years ago by Daniel Jones <[email protected]>
remove sucvector written in C

github.com/BioJulia/IndexableBitVectors.jl - d5c179fa1de6554fa8c1f4ce7d4be609736a147b authored about 9 years ago by Kenta Sato <[email protected]>
add test/REQUIRE

github.com/BioJulia/WaveletMatrices.jl - 8a769ed0c9143403d6db95373a1bb5ad3e6f8cec authored about 9 years ago by Kenta Sato <[email protected]>
add help (and rename variables)

github.com/BioJulia/WaveletMatrices.jl - f5e5082dacc7392e1eda11ae51048340be42365c authored about 9 years ago by Kenta Sato <[email protected]>
generalize conversion

github.com/BioJulia/IndexableBitVectors.jl - b5439d25a62501d730241b64fd2728e51624bc6e authored about 9 years ago by Kenta Sato <[email protected]>
add __precompile__

github.com/BioJulia/WaveletMatrices.jl - 0fae019a216595be8d2ae2533c646258ede51d03 authored about 9 years ago by Kenta Sato <[email protected]>
move FactCheck requirement

github.com/BioJulia/IndexableBitVectors.jl - c1a951b645bb2711ab58c8f251d09b8bf6742f19 authored about 9 years ago by Kenta Sato <[email protected]>
update README.md

github.com/BioJulia/IndexableBitVectors.jl - de13ec81b14f5d39a2d631984011a06886941efa authored about 9 years ago by Kenta Sato <[email protected]>
add help

github.com/BioJulia/IndexableBitVectors.jl - 00cc9e0b6ea13330974afcd87860f5f105520ded authored about 9 years ago by Kenta Sato <[email protected]>
remove dead code

github.com/BioJulia/IndexableBitVectors.jl - 90651dc562ac669cf56e084c3b7a60601bf5efe1 authored about 9 years ago by Kenta Sato <[email protected]>
add tests for SucVector of length >2^32

github.com/BioJulia/IndexableBitVectors.jl - 72ccd396f119c73b12ed32183164341dfb262c21 authored about 9 years ago by Kenta Sato <[email protected]>
hide CompactBitVector and LargeRRR

github.com/BioJulia/IndexableBitVectors.jl - e4f5db3cf69781ae4d30b3b46ceb47183d510b11 authored about 9 years ago by Kenta Sato <[email protected]>
make AbstractIndexableBitVector a subtype of AbstractVector{Bool}

github.com/BioJulia/IndexableBitVectors.jl - 1e5a97663cee64fe7ef4dc419ad36798f00c9f90 authored about 9 years ago by Kenta Sato <[email protected]>
README update.

github.com/BioJulia/Libz.jl - 81d376dcd5fa12d414d27af4981ff23307cd9c1d authored about 9 years ago by Daniel Jones <[email protected]>
Add LICENSE and .travil.yml.

github.com/BioJulia/Libz.jl - 768345fdf3f432692c453f5aa7069ca54631a701 authored about 9 years ago by Daniel Jones <[email protected]>
Remove julia 0.3 compat. Add REQUIRE files.

github.com/BioJulia/Libz.jl - b76f1e7088604d03a58ba442f26cbc7ae9f35992 authored about 9 years ago by Daniel Jones <[email protected]>
Fix up checksum interface.

github.com/BioJulia/Libz.jl - 2e3a2d1bd404a6880586334d6c68c32919c49e69 authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #18 from timholy/pull-request/38627c0a

Add precompile directive

github.com/BioJulia/Codecs.jl - c64cea8030fbd72a53113cb8bba9192d176a6906 authored about 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #51 from dcjones/bigbed

BigBed/BigWig reading and writing

github.com/BioJulia/Bio.jl - 7e1e9ec90149e9b2524ae5abd080c4f5b94a90d6 authored about 9 years ago by Daniel C. Jones <[email protected]>
Add Zlib to REQUIRE.

github.com/BioJulia/Bio.jl - a283eea994afc19f86a8075d44930676b24af9bc authored about 9 years ago by Daniel Jones <[email protected]>
Add precompile directive

github.com/BioJulia/Codecs.jl - 38627c0aef48d45f743a863da2d2ef4bc147285a authored about 9 years ago by Tim Holy <[email protected]>
Remove more junk from merging.

github.com/BioJulia/Bio.jl - 71c9c00dddff6e48fa396eaf007d68a72e51a9e6 authored about 9 years ago by Daniel Jones <[email protected]>
updated documentation build

github.com/BioJulia/mkdocs-biojulia - e8961cfe45e620b60961205b8fdbbd57680a0874 authored about 9 years ago by Chris Simpkins <[email protected]>
updated documentation

github.com/BioJulia/mkdocs-biojulia - 0cb77e9399d4780962f422e8cbe08058a071043c authored about 9 years ago by Chris Simpkins <[email protected]>
new site build for v0.9.1

github.com/BioJulia/mkdocs-biojulia - 287ad037d547998ca33c1207cfd4a7054e36778c authored about 9 years ago by Chris Simpkins <[email protected]>
added a changelog

github.com/BioJulia/mkdocs-biojulia - 52a2f38b6edd01857cca2037fd558fe4b374aaf9 authored about 9 years ago by Chris Simpkins <[email protected]>
updates for version 0.9.1

github.com/BioJulia/mkdocs-biojulia - b9bfab356ed01cf33a21bcec7f5e750bc461415c authored about 9 years ago by Chris Simpkins <[email protected]>
updated theme

github.com/BioJulia/mkdocs-biojulia - 7a4ba7a94848f2f026de66583f4a16b687838a44 authored about 9 years ago by Chris Simpkins <[email protected]>
added image link to the docs

github.com/BioJulia/mkdocs-biojulia - c5c926222ad5ffb2aaf35397d6727c5de5b011f6 authored about 9 years ago by Chris Simpkins <[email protected]>
updated README

github.com/BioJulia/mkdocs-biojulia - 92edec5866b0d3e38c5e904560502438cc03ac72 authored about 9 years ago by Chris Simpkins <[email protected]>
updated documentation site build

github.com/BioJulia/mkdocs-biojulia - 8d4dae03422d2b675f03f8ce145a25b07aca10f6 authored about 9 years ago by Chris Simpkins <[email protected]>
updated link to theme archive, added font links to specimen

github.com/BioJulia/mkdocs-biojulia - 4d95ca8c5b0d82183b4be09d24c74def495421de authored about 9 years ago by Chris Simpkins <[email protected]>
updated cinder home page

github.com/BioJulia/mkdocs-biojulia - 4926ccf76874a11a7043003f630948842bc1f98c authored about 9 years ago by Chris Simpkins <[email protected]>
added license to cinder css file

github.com/BioJulia/mkdocs-biojulia - 98c3e42da95014f37c6abc0b54be3cfab6e07db1 authored about 9 years ago by Chris Simpkins <[email protected]>
updated README

github.com/BioJulia/mkdocs-biojulia - 5b091e9d7e7690128cb30265c4a01b480003bd1f authored about 9 years ago by Chris Simpkins <[email protected]>
updated README

github.com/BioJulia/mkdocs-biojulia - b6586128541d327adab44be33a9ab8301ebb5efb authored about 9 years ago by Chris Simpkins <[email protected]>
added license, updated headers style

github.com/BioJulia/mkdocs-biojulia - b4aff2ae19b851dfe76db1b9bc20586a415d6678 authored about 9 years ago by Chris Simpkins <[email protected]>
added setup.py file

github.com/BioJulia/mkdocs-biojulia - e24346382d766b722a47461dda5cdbbff886de68 authored about 9 years ago by Chris Simpkins <[email protected]>
added MANIFEST.in file

github.com/BioJulia/mkdocs-biojulia - 1db73e5809b918d3bf7f866120ece3cb79c13a5b authored about 9 years ago by Chris Simpkins <[email protected]>
added __init__.py to the top level of the cinder theme dir

github.com/BioJulia/mkdocs-biojulia - 0268b73cbeb4c000b8fb5f5bbfe5a897dd2cbe8b authored about 9 years ago by Chris Simpkins <[email protected]>
initial commit

github.com/BioJulia/mkdocs-biojulia - 1e31c0ca32151b4b47ff813ab6c979c8b3d1ba3e authored about 9 years ago by Chris Simpkins <[email protected]>
Initial commit

github.com/BioJulia/mkdocs-biojulia - 30ce767cfe9fd1fc3e7da176220bc4e98947b060 authored about 9 years ago by Chris Simpkins <[email protected]>
Merge pull request #83 from BioJulia/fix-subseq

Fix subseq

github.com/BioJulia/Bio.jl - f6e89dcf201658b826493527e713cc765c9f3453 authored about 9 years ago by Daniel C. Jones <[email protected]>
add tests for subsequence of subsequence

github.com/BioJulia/Bio.jl - 6401a54d6f42ad888a505850cc40d1a87cec026f authored about 9 years ago by Kenta Sato <[email protected]>
fix #82

github.com/BioJulia/Bio.jl - cb595c6c8baf4b7acd1ee4024ff3fc0f281bc432 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #81 from Ward9250/update-travis

Update travis

github.com/BioJulia/Bio.jl - bb189ce139b06719812f22003f08ce04589c9e1b authored about 9 years ago by Daniel C. Jones <[email protected]>
Trying the setting in travis.yml for the new container architecture they say is better

github.com/BioJulia/Bio.jl - e1392cdc51082df3a426d4485e168fc52f26b950 authored about 9 years ago by Ward9250 <[email protected]>
README update

github.com/BioJulia/Libz.jl - f5292c882437838710be09b2c4e4c5dd2b8b11e5 authored about 9 years ago by Daniel Jones <[email protected]>
Document ZlibDeflateOutputStream ad ZlibDeflateInputStream

github.com/BioJulia/Libz.jl - b2450a3b046a4bd74a0a20cc714b0b0c3c0673f0 authored about 9 years ago by Daniel Jones <[email protected]>
Remove perf. This lives with BufferedStreams now.

github.com/BioJulia/Libz.jl - 0bc62ebaa2906eb4c65c11785d0f34fd4ec55a23 authored about 9 years ago by Daniel Jones <[email protected]>
Implement sinks.

github.com/BioJulia/Libz.jl - 82dc90f8704e7449da7ecdc956a7b84fab13f165 authored about 9 years ago by Daniel Jones <[email protected]>
Start generalizing source and sink concept.

github.com/BioJulia/Libz.jl - e9d6a7a3525661b1c538241c1556e9ae43942cff authored about 9 years ago by Daniel Jones <[email protected]>
Tests and fixes.

github.com/BioJulia/Libz.jl - fac2ef9307a2779630e1c43eb6de291bfac73a29 authored about 9 years ago by Daniel Jones <[email protected]>
Bindings for checksum functions.

github.com/BioJulia/Libz.jl - 6f16ef3aa97fb309425af5dcfcebd1f291f79a1a authored about 9 years ago by Daniel Jones <[email protected]>
Rewrite ZlibOutputStream using BufferedStreams.

github.com/BioJulia/Libz.jl - ea05710eaa5523d6bc5ded25d6cb2fd877631a0b authored about 9 years ago by Daniel Jones <[email protected]>
add __precompile__()

github.com/BioJulia/IndexableBitVectors.jl - 7fa48ebf4977952227369bbef93b6d5b3cbf81c9 authored about 9 years ago by Kenta Sato <[email protected]>
faster conversion from BitVector

github.com/BioJulia/IndexableBitVectors.jl - a838e23f33e81eedec3c10dbeb14a11335b388c7 authored about 9 years ago by Kenta Sato <[email protected]>
slightly simplify SucVector

github.com/BioJulia/IndexableBitVectors.jl - 2ad64aed67a2f9d1016b639995489884f860e553 authored about 9 years ago by Kenta Sato <[email protected]>
Start switching over to BufferedStreams.

github.com/BioJulia/Libz.jl - 647c1288cc625471635f431b9eaceb1f265146e6 authored about 9 years ago by Daniel Jones <[email protected]>
add document

github.com/BioJulia/FMIndexes.jl - 16adc9d23137e5b958ae869431541c45dd3b4727 authored about 9 years ago by Kenta Sato <[email protected]>
fix type params

github.com/BioJulia/FMIndexes.jl - 49d4d7aa2b96a7fa33db2551182bbf9c4bbd080c authored about 9 years ago by Kenta Sato <[email protected]>
Remove some left over merge junk.

github.com/BioJulia/Bio.jl - e88ea5eb5b0b461a06695601840ee66cfe22a8c7 authored about 9 years ago by Daniel Jones <[email protected]>
Fix fillbuffer! logic.

github.com/BioJulia/Bio.jl - 34ed8988961a11477ef0fbe2af4f6485f05d5fd1 authored about 9 years ago by Daniel Jones <[email protected]>
Start adding BigBed tests. Fix some bugs.

github.com/BioJulia/Bio.jl - 0c050e8f8bb3a0690ed726059c6369f4b4a86483 authored about 9 years ago by Daniel Jones <[email protected]>
Test BigBed intersection. A couple fixes.

github.com/BioJulia/Bio.jl - 354aa7b906c8d487ea57d2855032f07ce8b6d69b authored about 9 years ago by Daniel Jones <[email protected]>
Fixes for BigBed iteration.

github.com/BioJulia/Bio.jl - 63c2c70c0113a4895247fe1ac7eaa97eec0e9fa2 authored about 9 years ago by Daniel Jones <[email protected]>
Fix a couple BigBed output bugs.

github.com/BioJulia/Bio.jl - 31c4fab289bdde4492ff78b1f00bc18ddbff4faf authored about 9 years ago by Daniel Jones <[email protected]>
Update mmap and docstring syntax.

github.com/BioJulia/Bio.jl - 7c898acf77a66c41d05de9704ac897389071ee85 authored about 9 years ago by Daniel Jones <[email protected]>
Fix some type instabilities.

github.com/BioJulia/Bio.jl - 6b7187961521e102f7eea706622724d8027d99eb authored about 9 years ago by Daniel Jones <[email protected]>
Iteration over all entries in a BigBed file.

github.com/BioJulia/Bio.jl - 2a16921500e174dbbbafe4521cf32e2a0ddc528e authored about 9 years ago by Daniel Jones <[email protected]>
Julia 0.4 compat.

github.com/BioJulia/Bio.jl - e296a4e0a06e4e49d7762a16bdcd8c93050b725e authored about 9 years ago by Daniel Jones <[email protected]>
BigBed: Writing headers. Various fixes.

github.com/BioJulia/Bio.jl - 2e6e53c89ab5e6470e586641de8b200ad7c6a23e authored about 9 years ago by Daniel Jones <[email protected]>
Fix a couple BED read/write bugs.

github.com/BioJulia/Bio.jl - 1bfc3ba8b260a0d6bb41328b46842dd3e4fc6fef authored about 9 years ago by Daniel Jones <[email protected]>
Work on generating BigBed summarization/zoom data.

github.com/BioJulia/Bio.jl - b2b5b859a4bbdebe8724e91310475fe1b828b84b authored about 9 years ago by Daniel Jones <[email protected]>
BigWig write support.

github.com/BioJulia/Bio.jl - 90a49ad0e6090b554d714bf6accdb0e396fb4509 authored about 9 years ago by Daniel Jones <[email protected]>
Build and writing BigBed r-tree index.

github.com/BioJulia/Bio.jl - 9f1b8688d5dd7851ae61bc98e6457a459aec0bcc authored about 9 years ago by Daniel Jones <[email protected]>
WIP writing BigBed files.

github.com/BioJulia/Bio.jl - 71bf51ffe4cb34cc22cf8859acfe3c06d6efea7f authored about 9 years ago by Daniel Jones <[email protected]>
Working BigBed searching and reading.

github.com/BioJulia/Bio.jl - 58992ae0c4754fdac7f34fd2577ed8c547041256 authored about 9 years ago by Daniel Jones <[email protected]>
Initial work on reading/searching bigbed files.

github.com/BioJulia/Bio.jl - 4775527e81ff08f6620fde9e1ac0b355fe3cc0ba authored about 9 years ago by Daniel Jones <[email protected]>
Refactor Ragel. Split out reading code into BufferedReader.

github.com/BioJulia/Bio.jl - bd68454b94d6a739c427ee12481fe50c3e46c20f authored about 9 years ago by Daniel Jones <[email protected]>
Optimizations to eachkmer.

github.com/BioJulia/Bio.jl - b20c3cb5df30e0294ea7ab7391279706dc824ed5 authored about 9 years ago by Daniel Jones <[email protected]>