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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

Import Ragel 7.0.0.5

github.com/BioJulia/ragel7 - b11ed0a929eb5f122c41f7c350d1a782c221c077 authored about 9 years ago by Daniel Jones <[email protected]>
fix sizeof

github.com/BioJulia/IndexableBitVectors.jl - 34a284337ae99a1eb37c612816a6a11df56c3234 authored about 9 years ago by Kenta Sato <[email protected]>
fix deprecated syntax of Union

github.com/BioJulia/IndexableBitVectors.jl - de8d4d7ccf07f9272d1a07053adacda4bd9f6a69 authored about 9 years ago by Kenta Sato <[email protected]>
Nothing -> Void

github.com/BioJulia/Bio.jl - 9545c3f7d3100dcc260f3d772373c246b1ff410e authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #19 from ssfrr/depwarn-0.4

fixes 0.4 deprecation warnings

github.com/BioJulia/Codecs.jl - e48b871557c11693a155ab7efdc3dc9ecc2b1ad8 authored about 9 years ago by Daniel C. Jones <[email protected]>
fixes 0.4 deprecation warnings

github.com/BioJulia/Codecs.jl - 62a9a37d67e465232387b857ff9803e8460a2a7e authored about 9 years ago by Spencer Russell <[email protected]>
Merge pull request #13 from bicycle1885/compat-v0.4

suppress deprecated warnings

github.com/BioJulia/IntervalTrees.jl - d86fd98dc8f5bd1d2546f5e8d16681980bef1ab9 authored about 9 years ago by Daniel C. Jones <[email protected]>
suppress deprecated warnings

github.com/BioJulia/IntervalTrees.jl - 67b3d9a557ddd0c6c559a6cf87919e53c557ea0b authored about 9 years ago by Kenta Sato <[email protected]>
rename the package name to FMIndexes.jl

just because many papers use that name

github.com/BioJulia/FMIndexes.jl - ea497eae30e9f94ff61a6b16edbfc4f67aa9fbe8 authored about 9 years ago by Kenta Sato <[email protected]>
update README.md

github.com/BioJulia/FMIndexes.jl - 8ee19957b90b1198f33f1460f2b8b6a249703b4a authored about 9 years ago by Kenta Sato <[email protected]>
add more tests and clean up

github.com/BioJulia/FMIndexes.jl - bb0ba4859ffc23aa1539ccc771074efc601ba870 authored about 9 years ago by Kenta Sato <[email protected]>
test on v0.4 and nightly

github.com/BioJulia/FMIndexes.jl - 974984ddf5d8b5be7cd5fb50823aaf50cc78dd95 authored about 9 years ago by Kenta Sato <[email protected]>
update docs

github.com/BioJulia/FMIndexes.jl - afef939362307007db5a91786787f22c6380a7d7 authored about 9 years ago by Kenta Sato <[email protected]>
fix the badge link

github.com/BioJulia/FMIndexes.jl - 6e61a2f65a72de80a735f344f05797c3b50cbf44 authored about 9 years ago by Kenta Sato <[email protected]>
clean up code about pSAscan

github.com/BioJulia/FMIndexes.jl - 1e971d12710a110d322ff70744141ba62c84ee5c authored about 9 years ago by Kenta Sato <[email protected]>
remove benchmark.sh

github.com/BioJulia/IndexableBitVectors.jl - d0d96b9695b0fd6faaf72c68244eb41fa8f5555c authored about 9 years ago by Kenta Sato <[email protected]>
add a use case

github.com/BioJulia/IndexableBitVectors.jl - 5bef4016bd540eff16a5529c1133f00d5bc247c9 authored about 9 years ago by Kenta Sato <[email protected]>
update .travis.yml and README.md

github.com/BioJulia/WaveletMatrices.jl - ed62a02f0d5b2fc8eaed23b93af9535bc6324ba9 authored about 9 years ago by Kenta Sato <[email protected]>
update the badge link

github.com/BioJulia/IndexableBitVectors.jl - d93a7d6ecddba3d500dedce8f9c4e30faa701f86 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
test on v0.4

github.com/BioJulia/IndexableBitVectors.jl - d457461e06aff7cd088e5a1ee5a4288f95482c8c authored about 9 years ago by Kenta Sato <[email protected]>
Fix a couple deprecations.

github.com/BioJulia/Bio.jl - 2224a458fa54b0964c7a039a7dae7a6f67615036 authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #93 from BioJulia/conv

add `convert` to a byte sequence from bio sequences

github.com/BioJulia/Bio.jl - a17fa523591a9d1e419d0e1fae8c05567a68b0fe authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
fix style of `Union`

github.com/BioJulia/Bio.jl - 833c6fa1503fcfab98cc0476e98647f97664e462 authored about 9 years ago by Kenta Sato <[email protected]>
use cld

github.com/BioJulia/Bio.jl - ecb7fcc14da60bc19bef79d3dc46869c1baa3952 authored about 9 years ago by Kenta Sato <[email protected]>
a few touch-ups of document strings

github.com/BioJulia/Bio.jl - 2e42203646f04cd07a23b92a1716a04995c38775 authored about 9 years ago by Kenta Sato <[email protected]>
use `falses` to make bitarrays

github.com/BioJulia/Bio.jl - cf94553abf689288704df98e78d7b18efee3aa8b authored about 9 years ago by Kenta Sato <[email protected]>
use more conversions

github.com/BioJulia/Bio.jl - aad919f660f26ff871e05e4cffb73a80e8332fa7 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #100 from BioJulia/round-trip

Round trip tests for reading/writing. And some bug fixes.

github.com/BioJulia/Bio.jl - 1114a9aa8205be91a846fa733e60e60546379b30 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Round trip tests for fastq.

github.com/BioJulia/Bio.jl - 0df77a16e5dcf72b1298468d69ccb4a0f299a498 authored about 9 years ago by Daniel Jones <[email protected]>
Round trip test for BED.

github.com/BioJulia/Bio.jl - 88f95026b141bca2c534921663b1d5119a3aa786 authored about 9 years ago by Daniel Jones <[email protected]>
Add round-trip tests for fasta. Fix a bug in AminoAcidSequence.

github.com/BioJulia/Bio.jl - b65fcbe24eccf9aabf641f891d4dd7079ab8cf36 authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #99 from BioJulia/prcastro-test-show-rna

Test show method for RNA nucleotides

github.com/BioJulia/Bio.jl - bd48fc9f1ce25354d35a861466e74a56f05a5555 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Test show method for RNA nucleotides

github.com/BioJulia/Bio.jl - 969ddd57b33ba60ab96bea9994bf3886d3405177 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Broaden FASTA write definition.

github.com/BioJulia/Bio.jl - 2a2d8413d58518a5dc0cf9df1093a9a6a50bb983 authored about 9 years ago by Daniel Jones <[email protected]>
delegate conversion of nucleotides by calling function show()

github.com/BioJulia/Bio.jl - 8160b82daf7e0b6f476ddece31b2abd679fb0c3a authored about 9 years ago by wildgarden <[email protected]>
enhanced test: 2 sequences with description

github.com/BioJulia/Bio.jl - 8e39eea890c0d4f1d607cb005aa5acb57dfc8bc6 authored about 9 years ago by wildgarden <[email protected]>
added Base.write() to support writing of FASTASeqRecords to IO-Streams

github.com/BioJulia/Bio.jl - 6081c32c52479f1f54e87da631c85e2eb6312e53 authored about 9 years ago by wildgarden <[email protected]>
Add a link to the manual.

github.com/BioJulia/Bio.jl - d0c8881f1edebf8ff6a9d44e3d3884343b2d6dca authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #92 from BioJulia/docs

Generating a manual

github.com/BioJulia/Bio.jl - df19f272ac826bfed9db0ca99fa03e1e1d9ee17c authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Merge pull request #98 from BioJulia/show-nucs

import the write method into Bio.Seq from Base

github.com/BioJulia/Bio.jl - 057041de79f91171ac9e97bc1abb8231a904f6ca authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
import the write method into Bio.Seq from Base

github.com/BioJulia/Bio.jl - 9927727a1d55b021228c5f12ce5ef667aa063db6 authored about 9 years ago by Kenta Sato <[email protected]>
Fix a docstring.

github.com/BioJulia/Bio.jl - 004c6c08827efe93b75313684df433e20781fde2 authored about 9 years ago by Daniel Jones <[email protected]>
Some documentation for Intervals.

github.com/BioJulia/Bio.jl - 1330d3d38519baaa8d66ad2839ca1a7b40a22ef3 authored about 9 years ago by Daniel Jones <[email protected]>
Work on documentation for Seq module.

github.com/BioJulia/Bio.jl - b1c6a3537aa697667590224c7f1cbecf9053b578 authored about 9 years ago by Daniel Jones <[email protected]>
More parsing docs.

github.com/BioJulia/Bio.jl - f227966a95c290ffebc03938abcc2ff9e9319f2e authored about 9 years ago by Daniel Jones <[email protected]>
Put a something in index.

github.com/BioJulia/Bio.jl - f0a3add48e9459a023d5f1542b14d6bce64fe819 authored about 9 years ago by Daniel Jones <[email protected]>
Some more parser documentation.

github.com/BioJulia/Bio.jl - c60bafaad7dd4f565c09b4d9c7e64eb4f452ad82 authored about 9 years ago by Daniel Jones <[email protected]>
Start documenting parsing.

github.com/BioJulia/Bio.jl - 2f017da4dac06d63acd904b18276010946d93f4b authored about 9 years ago by Daniel Jones <[email protected]>
Add some simple judo-style docs.

github.com/BioJulia/Bio.jl - 7dafdd1d80920133c43290dfefeb5f922d6aa25c authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #97 from prcastro/code_refactor

Code refactor

github.com/BioJulia/Bio.jl - 5ee324be74a67d1eb4bd071ac9156016650682b5 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Rename module files

github.com/BioJulia/Bio.jl - 02849132eeaee80fa328bc2299e8f98994c91628 authored about 9 years ago by prcastro <[email protected]>
Minor bug

github.com/BioJulia/Bio.jl - 4f308f387f7bb3386c5235f7acd9f3c7b4adf5a4 authored about 9 years ago by prcastro <[email protected]>
String -> AbstractString

github.com/BioJulia/Bio.jl - 3dfd144584fa5edeb0cf97f1e881a1a14e734e81 authored about 9 years ago by prcastro <[email protected]>
Remove Compat, Docile, change Uint -> UInt and split using/import/export statements into lines

github.com/BioJulia/Bio.jl - 18d1f4ab521b3907a8f57338c61ee96b1cf63297 authored about 9 years ago by prcastro <[email protected]>
Merge pull request #85 from dcjones/io2

Parsing Infrastructure Iteration

github.com/BioJulia/Bio.jl - 48c025980eb88007db0c19f5ea688c864903d1f5 authored about 9 years ago by Daniel C. Jones <[email protected]>
Remove some Base. qualifications.

github.com/BioJulia/Bio.jl - fe28ba3686cb61fcecb77c225f7fa8c6f9ee892a authored about 9 years ago by Daniel Jones <[email protected]>
Move StringField to a module. Get rid of ParseImpl modules. Import things.

github.com/BioJulia/Bio.jl - a14b2a10b9d4031ce4ab00e6957199f8c81408d0 authored about 9 years ago by Daniel Jones <[email protected]>
Automatic iterators. Better quality encoding inference.

github.com/BioJulia/Bio.jl - a6b08e4eaa99d637a1db3850a4199463747ca739 authored about 9 years ago by Daniel Jones <[email protected]>
Fix some FASTA bugs.

github.com/BioJulia/Bio.jl - 62aff433ddbd7db43db5139707be9fbb85171030 authored about 9 years ago by Daniel Jones <[email protected]>
Fix regression in IntervalCollection versus IntervalStream intersection.

github.com/BioJulia/Bio.jl - 733a06249361285d9e641e615543bbc8e5b1abfa authored about 9 years ago by Daniel Jones <[email protected]>
In-place fastq parsing. Faster NucleotideSequence encoding.

github.com/BioJulia/Bio.jl - b57e3aac5ddff63091b713771b238640f70cbe0f authored about 9 years ago by Daniel Jones <[email protected]>
Update FASTA parser to new system.

github.com/BioJulia/Bio.jl - 6f82111295ff0a496d4b2019da8ab0ffac0d5ace authored about 9 years ago by Daniel Jones <[email protected]>
Update BED parser.

github.com/BioJulia/Bio.jl - 9d22f8597ecb60ac62260dd83b267f1aae88b688 authored about 9 years ago by Daniel Jones <[email protected]>
Update BigBed parser and writer.

github.com/BioJulia/Bio.jl - 608638d5d7fefb13b209bab61d524eaf6edd8d62 authored about 9 years ago by Daniel Jones <[email protected]>
Zlib -> Libz

github.com/BioJulia/Bio.jl - 962e567b6cc834ee32ee77b97d6037fd0efe2a75 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Make intervals mutable.

github.com/BioJulia/Bio.jl - 94097699441e80642de7934fe1a7085ffc5c0874 authored about 9 years ago by Daniel Jones <[email protected]>
Fix parsing AminoAcidSequences from FASTA.

github.com/BioJulia/Bio.jl - 71ccd8cb25b151d2610c8f4c6324e1bfda8aadb2 authored about 9 years ago by Daniel Jones <[email protected]>
Some optimizations.

github.com/BioJulia/Bio.jl - 16babdd5714d1b0fac26d576a1ef60733ec1558d authored about 9 years ago by Daniel Jones <[email protected]>
Mutability for AminoAcidSequence.

github.com/BioJulia/Bio.jl - ae7b05ac7532d5ba7d01c2ce5ed923f57e19108e authored about 9 years ago by Daniel Jones <[email protected]>
Start moving parsing over to BufferedStreams.

github.com/BioJulia/Bio.jl - 55812479e64771d7af12d6349c01e9a28bfffec8 authored about 9 years ago by Daniel Jones <[email protected]>
More work on parting to BufferedStreams.

github.com/BioJulia/Bio.jl - fd22553b98243c7c2f2c0bd1cac295ac25e0a4ca authored about 9 years ago by Daniel Jones <[email protected]>
extend rank

github.com/BioJulia/IndexableBitVectors.jl - 7c0e81e2ae7f7527231b83aab862a46b17caa375 authored about 9 years ago by Kenta Sato <[email protected]>
use clamp

github.com/BioJulia/WaveletMatrices.jl - 58162f9ab5719e38978cf61740d63f4d4c11354d authored about 9 years ago by Kenta Sato <[email protected]>
Use nightly instead of 0.5 in travis.

github.com/BioJulia/Bio.jl - 2ba7d2795dfec0dcde2b338d9915992d16361c20 authored about 9 years ago by Daniel Jones <[email protected]>
Update travis to run on julia 0.4 and 0.5.

github.com/BioJulia/Bio.jl - 7eca8f050428e15adfb4fa353b3b23066846813b authored about 9 years ago by Daniel Jones <[email protected]>
accept sequences of length 1

github.com/BioJulia/FMIndexes.jl - 67c17237ef56fdd50f16b72c1e1b29559b261a2a authored about 9 years ago by Kenta Sato <[email protected]>
extend rank indexing

this will simplify many programs

github.com/BioJulia/WaveletMatrices.jl - 1aaea5dab1fc63c16a14c25d92fac91588aaf34b authored about 9 years ago by Kenta Sato <[email protected]>
fix a bug

github.com/BioJulia/FMIndexes.jl - 4f59db25ca19fd403295559efd28dba58fbc1f03 authored about 9 years ago by Kenta Sato <[email protected]>
add a note about size limit

github.com/BioJulia/IndexableBitVectors.jl - 6c22844596cd1063a596df7ea166382f1dbdd5c6 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #94 from dcjones/codecov

Add Codecov support.

github.com/BioJulia/Bio.jl - f9105fcd61ff0c4c0f20f8568ca58f4cf391297f authored about 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #37 from dcjones/mutable_seq

Mutable Sequences

github.com/BioJulia/Bio.jl - d6e07c1a3c78ae616e013246c4abe55cff55b070 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Enable Codecov.

github.com/BioJulia/IntervalTrees.jl - b1ec7ed888745912191a941e6a7d347e714d0e25 authored about 9 years ago by Daniel Jones <[email protected]>
Add some tests. Fix orhpan! functions.

github.com/BioJulia/Bio.jl - 4b9671d0c81e83b1bb5523a2bf873982e4f8c780 authored about 9 years ago by Daniel Jones <[email protected]>
Use reorphan parameter on orphan!(::AminoAcidSequence).

github.com/BioJulia/Bio.jl - 2d2b277c6934578c3cb343539c3e82ea55414dbc authored about 9 years ago by Daniel Jones <[email protected]>
Address some review comments.

github.com/BioJulia/Bio.jl - 66bd56857e876fbadbcd8a5752c5e0374a3ddbcd authored about 9 years ago by Daniel Jones <[email protected]>
Mutability for AminoAcidSequence.

github.com/BioJulia/Bio.jl - 8087d9026352d2101c7f1376d9f8dd0619fdda73 authored about 9 years ago by Daniel Jones <[email protected]>
Basic tests for mutable sequences.

github.com/BioJulia/Bio.jl - 3f099f9e2d9cdd613e6ebd2661f92824d0023c2a authored about 9 years ago by Daniel Jones <[email protected]>
Basic mutable nucleotide sequences.

github.com/BioJulia/Bio.jl - 16654a8b336f72615bf3fd9fcfe27e3cab4a43e4 authored about 9 years ago by Daniel Jones <[email protected]>
Add Codecov support.

github.com/BioJulia/Bio.jl - 59b87c1b7aaceffa51792b7959271f589347894d authored about 9 years ago by Daniel Jones <[email protected]>
Fix codecov support.

github.com/BioJulia/Libz.jl - e4ee6272dc008b2228e186a3761e7162fdb2654e authored about 9 years ago by Daniel Jones <[email protected]>
Fix README example.

github.com/BioJulia/Libz.jl - d4903d2fbe602b2df1a7788df940f314bf0b3768 authored about 9 years ago by Daniel Jones <[email protected]>
Merge pull request #89 from BioJulia/Blahah-patch-1

Add getter/setter policy (see #25)

github.com/BioJulia/Bio.jl - de004dd0789c75596c1cd4b7bd1ab0d4d6abebf9 authored about 9 years ago by Paulo Roberto de Oliveira Castro <[email protected]>
Merge pull request #88 from Ward9250/editorconfig

Added editorconfig file

github.com/BioJulia/Bio.jl - ebea5d340ed23eaebc4b3595047c7c3d6b41b709 authored about 9 years ago by Richard Smith-Unna <[email protected]>
Add getter/setter policy (see #25)

github.com/BioJulia/Bio.jl - f93eb9ade6808fa89a3f76ff2b1fe697ffff0511 authored about 9 years ago by Richard Smith-Unna <[email protected]>
Altered pattern to include julia-hosted ragel files

github.com/BioJulia/Bio.jl - e833dacc8aabfdf0584f838743ed4f30e1089047 authored about 9 years ago by Ward9250 <[email protected]>
Added editorconfig file

github.com/BioJulia/Bio.jl - 134775a466a88afede82098310572ee3ed7ed53e authored about 9 years ago by Ward9250 <[email protected]>
Add a option to support concatenated gzip data.

github.com/BioJulia/Libz.jl - 4372c1ac0d75242f7fd5ddbd2952804ffad86fc7 authored about 9 years ago by Daniel Jones <[email protected]>
do not kick off Travis CI on release for a while

github.com/BioJulia/FMIndexes.jl - 1e8129872a286b408adf09a71ff5618f2f2596cf authored about 9 years ago by Kenta Sato <[email protected]>
fix the repository name in README

github.com/BioJulia/FMIndexes.jl - ffab88cfdf5c12af47e5241a3b97ff00747451b7 authored about 9 years ago by Kenta Sato <[email protected]>
support mmap-backed array for temporary suffix array

github.com/BioJulia/FMIndexes.jl - 0c1693839aa3554780dada42fd9d223bffac8794 authored about 9 years ago by Kenta Sato <[email protected]>