Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

Optimizations to eachkmer.

github.com/BioJulia/Bio.jl - b20c3cb5df30e0294ea7ab7391279706dc824ed5 authored about 9 years ago by Daniel Jones <[email protected]>
Allow construction of uninitialized (empty) IntervalIntersectionIterator.

github.com/BioJulia/IntervalTrees.jl - d35a25485e3fe80a185c0e565de9cf1443db2208 authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #76 from BioJulia/Ward9250-update-readme

Added waffle.io badges to the Bio.jl README.md

github.com/BioJulia/Bio.jl - 0d8e8cf880034cf3f11254bd7e2993012466e4e3 authored about 9 years ago by Ben J. Ward <[email protected]>
add destructive option

github.com/BioJulia/WaveletMatrices.jl - 8ad3eb08482a71e4bd6f77199ebb57730b9c37f8 authored about 9 years ago by Kenta Sato <[email protected]>
unify constructors

github.com/BioJulia/WaveletMatrices.jl - bec10db5623e7a3339b6d3ab6c3cd16da7fa870d authored about 9 years ago by Kenta Sato <[email protected]>
more efficient construction

github.com/BioJulia/WaveletMatrices.jl - 6a17ffda4bc7f7a65d16019f1a72b5a6e5907373 authored about 9 years ago by Kenta Sato <[email protected]>
Ughh, tables.

github.com/BioJulia/Libz.jl - 77f91a3106c69419aea80a5f8eef5d89d1b23bcc authored about 9 years ago by Daniel Jones <[email protected]>
How do tables work?

github.com/BioJulia/Libz.jl - 5c30bb9756bad3c23c0dcb82241d90e07e62ca99 authored about 9 years ago by Daniel Jones <[email protected]>
Add README and some benchmarking stuff.

github.com/BioJulia/Libz.jl - 15fe470b18e7f081be7ecb10bfcd64a567988e63 authored about 9 years ago by Daniel Jones <[email protected]>
ZlibOutputStream

github.com/BioJulia/Libz.jl - 57778ce87b1be407bddc6b717046e2ae9a25c6c7 authored about 9 years ago by Daniel Jones <[email protected]>
Implement ZlibInputStream

github.com/BioJulia/Libz.jl - 7c77eee66eb4efd46951c4ebdfa055dc0988e3b3 authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #78 from NPalopoli/patch-1

Minor typo correction

github.com/BioJulia/Bio.jl - 1cafc05577421cb704997f8a48f5b9e3c6d84ea5 authored about 9 years ago by Daniel C. Jones <[email protected]>
Minor typo correction

github.com/BioJulia/Bio.jl - 48e7a2f15e0dff14dc7c10230efb7fd19e07d6bc authored about 9 years ago by Nicolas Palopoli <[email protected]>
typo

github.com/BioJulia/IndexableBitVectors.jl - 2846a956d042c199d1e746f1e4c2be59045ff656 authored about 9 years ago by Kenta Sato <[email protected]>
rename Uint* to UInt*

github.com/BioJulia/IndexableBitVectors.jl - 759b2b1a2fbc6f8a494f9531a50b1ddd5346f45e authored about 9 years ago by Kenta Sato <[email protected]>
require v0.4-

github.com/BioJulia/IndexableBitVectors.jl - 0ecd8ba1a49280f23b01d02914863693cef111f6 authored about 9 years ago by Kenta Sato <[email protected]>
update benchmarks

github.com/BioJulia/IndexableBitVectors.jl - 52d6dd017a51b084da13aa2323ec377e6429f4a5 authored about 9 years ago by Kenta Sato <[email protected]>
more inlining on SucVector

github.com/BioJulia/IndexableBitVectors.jl - f52b980ee86fcf51e13152613b89fbc7d2448753 authored about 9 years ago by Kenta Sato <[email protected]>
remove old benchmarks

github.com/BioJulia/IndexableBitVectors.jl - 19d09d59f7a79ab76edc8f443e7868402c3f0bad authored about 9 years ago by Kenta Sato <[email protected]>
update benchmark

github.com/BioJulia/IndexableBitVectors.jl - 674396a94dcaaa624a261b8fbeff63a2c6019a29 authored about 9 years ago by Kenta Sato <[email protected]>
fix .gitignore

github.com/BioJulia/IndexableBitVectors.jl - 285ecf007464931d6980298ed32809bb4357ff81 authored about 9 years ago by Kenta Sato <[email protected]>
improve performance of CompactBitVector

github.com/BioJulia/IndexableBitVectors.jl - 9e64fbb1d340486f68a64f53347361f30849314d authored about 9 years ago by Kenta Sato <[email protected]>
add benchmark result

github.com/BioJulia/IndexableBitVectors.jl - 0ad3af463316fe1f4cff628626deeadffc6e8924 authored about 9 years ago by Kenta Sato <[email protected]>
add benchmark script

github.com/BioJulia/IndexableBitVectors.jl - db73edf95fdad8ed01aef1dd406728d704a7fd08 authored about 9 years ago by Kenta Sato <[email protected]>
use convert

github.com/BioJulia/IndexableBitVectors.jl - 73466187f16ae0d788b9f8b32a8aa9c364b328e5 authored about 9 years ago by Kenta Sato <[email protected]>
use --> instead of =>

github.com/BioJulia/IndexableBitVectors.jl - f457f7afe54f7363455be663a87cf32ffba7d03f authored about 9 years ago by Kenta Sato <[email protected]>
rename RRRNP to LargeRRR

github.com/BioJulia/IndexableBitVectors.jl - 40bcba57a4474d453ea58de28069956913f47efa authored about 9 years ago by Kenta Sato <[email protected]>
a few touch-ups

github.com/BioJulia/WaveletMatrices.jl - 8f97fccaf053c7071af3f9410341b8d2f482024c authored about 9 years ago by Kenta Sato <[email protected]>
add IntArrays.jl requirement to README

github.com/BioJulia/WaveletMatrices.jl - 1c8409dbf31f5e572a8ac90b6c1337dc65e737ac authored about 9 years ago by Kenta Sato <[email protected]>
use IntVector for space-efficient construction

github.com/BioJulia/WaveletMatrices.jl - bb596975aa6acb17f51f2f2034c7e3b1ee053e06 authored about 9 years ago by Kenta Sato <[email protected]>
tidy up constructors

github.com/BioJulia/WaveletMatrices.jl - ed2c7b16590e7bece666a94994474360fa833f89 authored about 9 years ago by Kenta Sato <[email protected]>
fix sizeof

github.com/BioJulia/WaveletMatrices.jl - 98a127733accab41e5c29a486571f7fb778185b8 authored about 9 years ago by Kenta Sato <[email protected]>
add lookup table for sp

github.com/BioJulia/WaveletMatrices.jl - cf0cb8f538da7c93f1fbe95c7508bbe1044ca8f2 authored about 9 years ago by Kenta Sato <[email protected]>
reduce the number of rank ops for select

github.com/BioJulia/WaveletMatrices.jl - 1a00932beb84713176a76afb76ba3dcbbba5aae6 authored about 9 years ago by Kenta Sato <[email protected]>
update README

github.com/BioJulia/WaveletMatrices.jl - 018e6a0001f83c8d18038bcd3217b72487d2d68d authored about 9 years ago by Kenta Sato <[email protected]>
implement select

github.com/BioJulia/WaveletMatrices.jl - 9f493f18fdb3d417b03ad434fca98929760fe4b4 authored about 9 years ago by Kenta Sato <[email protected]>
add REQUIRE

github.com/BioJulia/WaveletMatrices.jl - 347a635bafef3aa45b99b554df62bbe189ac123b authored about 9 years ago by Kenta Sato <[email protected]>
convert the type of index

github.com/BioJulia/WaveletMatrices.jl - 353138082c2ecc3fa3d6a0a307dfdc546ced85ce authored about 9 years ago by Kenta Sato <[email protected]>
add @inline to getindex

github.com/BioJulia/WaveletMatrices.jl - 7228dd777dccb262aecdba9be475f2543bb5ca38 authored about 9 years ago by Kenta Sato <[email protected]>
use early return for performance of getindex

github.com/BioJulia/WaveletMatrices.jl - d0c1b784374d69a046ef8f0d487350d6057e41de authored about 9 years ago by Kenta Sato <[email protected]>
preserve element type

github.com/BioJulia/WaveletMatrices.jl - e4c9626e620f10d4d484e09b4bbb99f269f3d340 authored about 9 years ago by Kenta Sato <[email protected]>
remove the `len` field

github.com/BioJulia/WaveletMatrices.jl - 55ff1e1126657ac589aa5af03964479ecdcba58f authored about 9 years ago by Kenta Sato <[email protected]>
type-stable constructor

github.com/BioJulia/WaveletMatrices.jl - 319cb65ca265b5599b939af23ae5011150a9a37b authored about 9 years ago by Kenta Sato <[email protected]>
remove an unnecessary constructor

github.com/BioJulia/WaveletMatrices.jl - f5c2623e03415f8aa2cbdf594e99e369a637ac3b authored about 9 years ago by Kenta Sato <[email protected]>
Added waffle.io badges to the Bio.jl README.md

github.com/BioJulia/Bio.jl - a2b68b8f958ebe3e8777a33497cfc3a5914ac978 authored about 9 years ago by Ben J. Ward <[email protected]>
Better EOF halding in ragel parsers. Fixes #75.

github.com/BioJulia/Bio.jl - a2e7e041f4519026c730c62faf925b8972dc4c15 authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #57 from kdmurray91/feat/fqout

Writing of FASTQ sequences

github.com/BioJulia/Bio.jl - e020e9e7249a8d6dfbcc7d16dbcddc38d8c13c3e authored about 9 years ago by Daniel C. Jones <[email protected]>
Fix all doc syntax occurances

github.com/BioJulia/Bio.jl - c8641592f84c9d655e0d506d4149860a4ead2246 authored about 9 years ago by Kevin Murray <[email protected]>
Allow 'B' in Illumina 1.5 quality scores

github.com/BioJulia/Bio.jl - 8d160daded64c0bb4d7a5caa3ec1c4ef57c86d39 authored about 9 years ago by Kevin Murray <[email protected]>
Fix FactCheck =>/-->

github.com/BioJulia/Bio.jl - 3fe723245997691e1464376e50e5bc70d998e3c4 authored about 9 years ago by Kevin Murray <[email protected]>
Add encode_quality_string, default stop/start

This adds two functions for encoding quality score vectors as
PHRED-encoded strings (in-place an...

github.com/BioJulia/Bio.jl - 691611bd79d694b07d51467e5ff7792a72dcf1d6 authored about 9 years ago by Kevin Murray <[email protected]>
Add tests of quality score en/decoding

github.com/BioJulia/Bio.jl - 27538cb4d5dee551f4e778716dadb36edb0cd93c authored about 9 years ago by Kevin Murray <[email protected]>
Fix possible issue w/ illumina1.5 phred scores

github.com/BioJulia/Bio.jl - 7a2239e750f56c61d2f5ab10ae6e00574415e9a5 authored about 9 years ago by Kevin Murray <[email protected]>
Move write(IO, FASTQSeqRecord) to ragel source

github.com/BioJulia/Bio.jl - 5da8196dc7103c34decc95e3455a5b3c3a221dad authored about 9 years ago by Kevin Murray <[email protected]>
Copy write(IO, FASTQSeqRecord) back to fastq.jl

Now with added documentation :)

github.com/BioJulia/Bio.jl - 808ccee4d7d78458177b1ea4da571dd93f42b2a2 authored about 9 years ago by Kevin Murray <[email protected]>
Add initial hacky write(IO, FASTQSeqRecord)

github.com/BioJulia/Bio.jl - fc4dddc7c3c0ad450cdc75aecdeee23030c5e50c authored about 9 years ago by Kevin Murray <[email protected]>
Add missing intervals/Makefile. Strip trailing whitespace from ragel output.

github.com/BioJulia/Bio.jl - d531283abaa4ad8ebc8c71bf63f2f84e359d41cb authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #72 from BioJulia/remove-newlines

Remove newlines

github.com/BioJulia/Bio.jl - 01f0ac70511ee2ee608ee91e0974452f838b396a authored about 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #73 from BioJulia/safe-precomp

define hash function for Alphabet to compile safely

github.com/BioJulia/Bio.jl - 6232a96e73c717d0a36dc234f48b66b2b8fed199 authored about 9 years ago by Daniel C. Jones <[email protected]>
define hash function for Alphabet to compile safely

github.com/BioJulia/Bio.jl - 12733e0ada82b165db9d38f025fc5b355071b778 authored about 9 years ago by Kenta Sato <[email protected]>
implement equality of AminoAcidSequence

github.com/BioJulia/Bio.jl - 2a5f586492517e96adead198097b116d087a0893 authored about 9 years ago by Kenta Sato <[email protected]>
remove newlines in dna/rna literal

github.com/BioJulia/Bio.jl - 706f703c2787fb311586f5ce222c911054650e94 authored about 9 years ago by Kenta Sato <[email protected]>
touch-ups

github.com/BioJulia/FMIndexes.jl - 27ef93a42edcd76cefb26305188555fa87919b61 authored about 9 years ago by Kenta Sato <[email protected]>
add content

github.com/BioJulia/FMIndexes.jl - 9c159de7b9b1060bc0550ec139c304bb2627e120 authored about 9 years ago by Kenta Sato <[email protected]>
use new syntax of FactCheck.jl

github.com/BioJulia/WaveletMatrices.jl - 901b4b6f06e527acb81a4b59c61a0ad1932c9a97 authored about 9 years ago by Kenta Sato <[email protected]>
add freq function

github.com/BioJulia/WaveletMatrices.jl - 61b2832ddeb70ff99710ccea0528dc921093ad24 authored about 9 years ago by Kenta Sato <[email protected]>
remove Char functions

github.com/BioJulia/WaveletMatrices.jl - b8c04ebe4be6adb080681d3f69dc12472344adc7 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #70 from BioJulia/prcastro-patch-1

As promised - it's Saturday and there have been no objections. Remove 0.3 from travis

github.com/BioJulia/Bio.jl - 827f3ea2b98e0778a53a450ab8065c41b4aa65d9 authored about 9 years ago by Ben J. Ward <[email protected]>
Faster intersection.

github.com/BioJulia/IntervalTrees.jl - e04fe70e981e94e6025ac0314272846a9d95b4d3 authored about 9 years ago by Daniel Jones <[email protected]>
FMIndex.jl generated files.

license: MIT
authors: Kenta Sato
years: 2015
user: bicycle1885

Julia V...

github.com/BioJulia/FMIndexes.jl - eb088eab765867509abad422c199676f908a633e authored about 9 years ago by Kenta Sato <[email protected]>
initial empty commit

github.com/BioJulia/FMIndexes.jl - 81588094568522ff6d7d835bece91e409032d5bf authored about 9 years ago by Kenta Sato <[email protected]>
Update CONTRIBUTING.md

github.com/BioJulia/Bio.jl - d62e9779cb4d33e3172c1f0e0a02008e06f39ad9 authored about 9 years ago by Ben J. Ward <[email protected]>
Update CONTRIBUTING.md

github.com/BioJulia/Bio.jl - db74d95d7f37aae6996486a7de379ff3247f95e1 authored about 9 years ago by Ben J. Ward <[email protected]>
Update CONTRIBUTING.md

github.com/BioJulia/Bio.jl - 8823fab1c6e37f32c91084ec74a81ccdac22b653 authored about 9 years ago by Ben J. Ward <[email protected]>
Merge pull request #69 from prcastro/master

New FactCheck syntax (=> / -->)

github.com/BioJulia/Bio.jl - 08f666366a8d3a575c77231a1b708401fcfec511 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Remove 0.3 from travis

github.com/BioJulia/Bio.jl - c1ae737bf7a40fda580bcfdd67713f48639b7b67 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Merge pull request #68 from BioJulia/import-ops

import operators from Base explicitly

github.com/BioJulia/Bio.jl - 0bd1bb3a37e3b747d8e160f3225c0feac2988ab3 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
New FactCheck syntax (=> / -->)

github.com/BioJulia/Bio.jl - fa64378d29ad57e40589b3628ac86c7ee9494985 authored about 9 years ago by prcastro <[email protected]>
check bounds

github.com/BioJulia/WaveletMatrices.jl - 2543271ed5ced1e0628fbd16c7cb3d3954e57651 authored about 9 years ago by Kenta Sato <[email protected]>
fix type

github.com/BioJulia/WaveletMatrices.jl - 74f448cf89ef309b1fbd1535177df868089c5d65 authored about 9 years ago by Kenta Sato <[email protected]>
add getindex

github.com/BioJulia/WaveletMatrices.jl - 0da1746fa5148ad4cac41d4575cb918daf658885 authored about 9 years ago by Kenta Sato <[email protected]>
support v0.4

github.com/BioJulia/WaveletMatrices.jl - 56c57b7ace75ffc109485b62e920fec933949687 authored about 9 years ago by Kenta Sato <[email protected]>
remove - on julia version in REQUIRE

that refers to prereleases of 0.3 and is no longer necessary

github.com/BioJulia/IntervalTrees.jl - 51cc7b6687d199bb9ffcf2468724fe6c6ddb53d5 authored about 9 years ago by Tony Kelman <[email protected]>
import operators from Base explicitly

github.com/BioJulia/Bio.jl - 3560e10b3d27e811560419667fc5afbce1efc1bc authored about 9 years ago by Kenta Sato <[email protected]>
Update syntax in test code.

github.com/BioJulia/Bio.jl - b58280f9d332fdf76f8ce3acb2abf76fc932338d authored about 9 years ago by Daniel Jones <[email protected]>
Improve intersect(::IntervalCollection, ::IntervalCollection) type stability and performance.

github.com/BioJulia/Bio.jl - b9f79549851478455340632844416b3d3fc9724a authored about 9 years ago by Daniel Jones <[email protected]>
Update runtests.jl to julia syntax changes.

github.com/BioJulia/IntervalTrees.jl - 9137e7d78c309594f49d158e33eeb2a2cdcac820 authored about 9 years ago by Daniel Jones <[email protected]>
Improve type stability of interval tree intersection.

github.com/BioJulia/IntervalTrees.jl - 71083596459785e9897697dba369d36b770fd334 authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #66 from BioJulia/opt-getnuc

speed up the getindex method with inlining

github.com/BioJulia/Bio.jl - 0c282a35f9bddc12023a564c32b64a1c88038ef0 authored about 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #67 from BioJulia/prcastro-patch-1

Typo fix by prcastro

github.com/BioJulia/Bio.jl - 3d9d75bd60ce909b1476161a2ccaff38b5e91e7b authored about 9 years ago by Ben J. Ward <[email protected]>
Typo

Fix type leading to a travis failure

github.com/BioJulia/Bio.jl - 5b4c97ea00b29f3b5ff3119812bc625dedb2e46b authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
speed up the getindex method with inlining

github.com/BioJulia/Bio.jl - 77c93e75d1a4afa4af0a982141d3e78d3b3671df authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #56 from dcjones/miscfix

WIP: Optimization/Bugfix Omnibus

github.com/BioJulia/Bio.jl - c630a52eb0c5d3cfe121bf9dd66d618b2ae79d22 authored about 9 years ago by Daniel C. Jones <[email protected]>
Remove a couple old fashioned docstrings.

github.com/BioJulia/Bio.jl - a337e2a71550913dfaf7d41cd3f68143bb74fd4d authored about 9 years ago by Daniel Jones <[email protected]>
Fix a couple broken tests.

github.com/BioJulia/Bio.jl - 8f9ec0c512a5021a29034e4f067a3d13e8709844 authored about 9 years ago by Daniel Jones <[email protected]>
Implement IntervalCollection versus IntervalStream intersection.

github.com/BioJulia/Bio.jl - 936b2fcbe5b7c80bd1714deda9994e479c240c0d authored about 9 years ago by Daniel Jones <[email protected]>
Relax sorted requirement for coverage.

github.com/BioJulia/Bio.jl - 3a204d669251a3043523d9a0096bf54deffbacf3 authored about 9 years ago by Daniel Jones <[email protected]>
IntervalCollection bulk insertion constructors.

github.com/BioJulia/Bio.jl - 61cd409e04b354d51f6ef12106f2e5800daa8e22 authored about 9 years ago by Daniel Jones <[email protected]>
Optimization to IntervalCollection iteration.

github.com/BioJulia/Bio.jl - 850bc8410506cb588836504b10dc66393c1f82fa authored about 9 years ago by Daniel Jones <[email protected]>
Fix BED parser not clearing fields between lines.

github.com/BioJulia/Bio.jl - 6d10edb82994e99016cd461fbbd9a63237b6fb93 authored about 9 years ago by Daniel Jones <[email protected]>