BioJulia commits | Ecosyste.ms: OpenCollective

More reorganization of nucleotides tests

github.com/BioJulia/Bio.jl - 7207523f74481ccedaf5429dede9f4e524653556 authored over 9 years ago by brk00 <[email protected]>

Solved bug with nested facts, reorganization of Transformations and Aminoacid Sequences tests, added some more tests

github.com/BioJulia/Bio.jl - b8f4fdec38d309a3be230d607ab4b996ed55c5de authored over 9 years ago by brk00 <[email protected]>

Simplified kmer conversions

github.com/BioJulia/Bio.jl - 08aa72af1f5403320da12ae5f3f7a118d2150297 authored over 9 years ago by brk00 <[email protected]>

Added more tests and introduced BoundsError() on NucleotideSequence next method

github.com/BioJulia/Bio.jl - 0c87448fe45300903b6677137e925ec4f4830577 authored over 9 years ago by brk00 <[email protected]>

Added tests and solved bug with rnakmer construction from RNASequence

github.com/BioJulia/Bio.jl - cb91a2caa9a029f028eda49133d0e0e4f8799458 authored over 9 years ago by Paulo R. O. Castro <[email protected]>

Add test/REQUIRE

github.com/BioJulia/IntervalTrees.jl - 804413e772b0cadf86cd5782ac72f54d65283cbd authored over 9 years ago by Daniel Jones <[email protected]>

Modernize travis.yml

github.com/BioJulia/IntervalTrees.jl - 879acdb3bfb66f18434e50461a6b09a7fb8ebdcc authored over 9 years ago by Daniel Jones <[email protected]>

A few more tests.

github.com/BioJulia/IntervalTrees.jl - fc4bf94f14138059462d212fe987ae6b2c7c33bb authored over 9 years ago by Daniel Jones <[email protected]>

Modernize travis.yml.

github.com/BioJulia/Bio.jl - a984e8d077e1ff5a152b62be2707013751ed0fe3 authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #33 from brk00/master

Added 26 tests for Nucleotide Sequences

github.com/BioJulia/Bio.jl - 515e77c7a57fd67d0bf1c66ca47360c2cc70f130 authored over 9 years ago by Daniel C. Jones <[email protected]>

Added 26 tests for Nucleotide Sequences

github.com/BioJulia/Bio.jl - 8936fd0bf77f68a7b791a3dfc5dbe7c6110427f4 authored over 9 years ago by Paulo R. O. Castro <[email protected]>

Merge branch 'master' of https://github.com/brk00/Bio.jl into brk00-master

github.com/BioJulia/Bio.jl - 6d4734149424d92cac7417714a38b4fb8d6f64ca authored over 9 years ago by Daniel Jones <[email protected]>

[Seq] Reduced the number of files

github.com/BioJulia/Bio.jl - 0bdabcc86af992fd6b125467187a76787453374a authored over 9 years ago by Paulo R. O. Castro <[email protected]>

Tag weird fastq examples.

github.com/BioJulia/BioFmtSpecimens - eee67782fd97357c54b62b3fa43ded725eb699ac authored over 9 years ago by Daniel Jones <[email protected]>

Fix julia 0.4 deprecation warnings.

github.com/BioJulia/Bio.jl - bb06cc5995fd224a796ef1951aea0b2364f1e7dd authored over 9 years ago by Daniel Jones <[email protected]>

Fix julia 0.4 deprecation warnings.

github.com/BioJulia/IntervalTrees.jl - 63c37d5d898518b07b7e3337f4fddc1031f5b949 authored over 9 years ago by Daniel Jones <[email protected]>

Merge pull request #5 from julian-gehring/patch-1

Consistent variable names in readme examples

github.com/BioJulia/IntervalTrees.jl - 6ae5bfb23f1e330e9a6283a0b8bc41c7f3660b73 authored over 9 years ago by Daniel C. Jones <[email protected]>

Merge branch 'brk00-master'

github.com/BioJulia/Bio.jl - 144290623eee26f9e9cf9bf5dc4bed1b343855c5 authored over 9 years ago by Daniel Jones <[email protected]>

Merge branch 'master' of https://github.com/brk00/Bio.jl into brk00-master

github.com/BioJulia/Bio.jl - 965d59390de207c42243005570450d8a496a26be authored over 9 years ago by Daniel Jones <[email protected]>

Concrete string type for compatibility with julia 0.3

Using the abstract type String fails with julia versions 0.3.* and before.

github.com/BioJulia/IntervalTrees.jl - 5d49fb807bc3caae8e9429a9a37043486eaf4183 authored over 9 years ago by Julian Gehring <[email protected]>

Consistent variable names in readme examples

The example uses both `x` and `xs` as variable names, which lets the code fail. Use `xs` consist...

github.com/BioJulia/IntervalTrees.jl - d35ff2cb240db3eed20a67ee05f967b088e16425 authored over 9 years ago by Julian Gehring <[email protected]>

Merge pull request #30 from julian-gehring/patch-show-nt

Fix show methods for nucleotide input

github.com/BioJulia/Bio.jl - 6910e9bef5d81e7c29574f55aec91d2449811051 authored almost 10 years ago by Daniel C. Jones <[email protected]>

Fix show methods for nucleotide input

Has referred to the non-existing variable 'aa', should refer to the input 'nt'

github.com/BioJulia/Bio.jl - 61ee874371af6df2f46c6d94c501f0e70edc6c89 authored almost 10 years ago by Julian Gehring <[email protected]>

Improved kmer nucleotide counting + tests + fixed tests regressions ('Transforms')

github.com/BioJulia/Bio.jl - f6ce2125982c59160ff2300f3e6dd1f26d79c177 authored almost 10 years ago by brk00 <[email protected]>

aminoacid => amino acid

github.com/BioJulia/Bio.jl - 2512a82a7077ab95a526e2fc21826efad0b866ff authored almost 10 years ago by brk00 <[email protected]>

Fixed regressions and tests

github.com/BioJulia/Bio.jl - 630c5cbeefc3915d48b2022209f2b4675ff5ec66 authored almost 10 years ago by brk00 <[email protected]>

[Seq] geneticcode.jl bug and formatting

github.com/BioJulia/Bio.jl - c6e20299abeda86b678a7b7d2052b2fb575ee966 authored almost 10 years ago by brk00 <[email protected]>

[Seq] Code refactor and bug solving

github.com/BioJulia/Bio.jl - 825a35bb1211f1d1ab62f260880227cc844969d1 authored almost 10 years ago by brk00 <[email protected]>

Merge pull request #9 from analyzere/travis-for-canonical-repo

Add Travis configuration

github.com/BioJulia/Codecs.jl - 6d7659f47fbeba8345225afcf4c3e4ff3e6155f4 authored almost 10 years ago by Tim Holy <[email protected]>

Merge pull request #11 from michele-zaffalon/master

base64 decoding displays sentinel instead of incorrect character

github.com/BioJulia/Codecs.jl - 975e47ee0635d0e7709a77bb26dbf94a27aae8aa authored almost 10 years ago by Tim Holy <[email protected]>

Displays invalid char during base64 decoding..., take II

github.com/BioJulia/Codecs.jl - f57855f2f938f6e713b0de73765e095d0891f99c authored almost 10 years ago by zaf <[email protected]>

cosmetic changes

github.com/BioJulia/Codecs.jl - 5881968446f09a03b4d94f5c6d287cfe5b8206ed authored almost 10 years ago by zaf <[email protected]>

displays invalid char during base64 decoding instead of sentinel

also makes base64lookup Uint8 and removes the need to add 1 for the
decoding

github.com/BioJulia/Codecs.jl - 70c83b38786adaf1ead3f218e472d6dd3c233ab2 authored almost 10 years ago by zaf <[email protected]>

delete .DS_Store

github.com/BioJulia/assets - e72841ea473d0defe1abeea5ca024b8da5791ce8 authored about 10 years ago by Richard Smith-Unna <[email protected]>

gitignore

github.com/BioJulia/assets - ef02cce030316ca112babd20e3c74774efc2ad07 authored about 10 years ago by Richard Smith-Unna <[email protected]>

add logos

github.com/BioJulia/assets - 640a2e7c76242029ec6ba8022b281cef446386fe authored about 10 years ago by Richard Smith-Unna <[email protected]>

Initial commit

github.com/BioJulia/assets - 1aa7946f25cebd572d8db4777104fd66394e0e64 authored about 10 years ago by Richard Smith-Unna <[email protected]>

FASTQ files from Biopython.

github.com/BioJulia/BioFmtSpecimens - b2afd6823cc3f08160ee62b1facf52c563b975b0 authored about 10 years ago by Daniel Jones <[email protected]>

Add a boolean valid field to the index so we can include negative examples.

github.com/BioJulia/BioFmtSpecimens - 72c6c04d64ecfa785f6bca00492f0a13c04a59e1 authored about 10 years ago by Daniel Jones <[email protected]>

Fix a few filenames.

github.com/BioJulia/BioFmtSpecimens - d8709bd8666aa41143a5b07618c7c99e8c953edd authored about 10 years ago by Daniel Jones <[email protected]>

add Bioruby fasta files

github.com/BioJulia/BioFmtSpecimens - 7419ddf0e589dc7cd800325f6c4b6aca78be34ec authored about 10 years ago by Richard Smith-Unna <[email protected]>

Add FASTA specimens from Biopython and BioPerl.

github.com/BioJulia/BioFmtSpecimens - e2e67761c8510a8d4d8d514ba783c34f93440ad7 authored about 10 years ago by Daniel Jones <[email protected]>

Equality operations for sequences and kmers. Fixes #21.

github.com/BioJulia/Bio.jl - a7ecba5d52709d2c8b89e4a6e4e003358b002eab authored about 10 years ago by Daniel Jones <[email protected]>

Faster nucleotide_count with large numbers of Ns.

github.com/BioJulia/Bio.jl - 974015a3f5eaa5f7792bb4a879ff017cd0fc6247 authored about 10 years ago by Daniel Jones <[email protected]>

Enable coveralls. SVG badges.

github.com/BioJulia/Bio.jl - 9d70e78aa417bb3467b4781c4faa1c5eddad1fa2 authored about 10 years ago by Daniel Jones <[email protected]>

Merge branch 'seq'

github.com/BioJulia/Bio.jl - 98cd657ebc6a77300d2fde6ca020cbf3f881d425 authored about 10 years ago by Daniel Jones <[email protected]>

Make printing of sequence types a little nicer.

github.com/BioJulia/Bio.jl - 3236134ba6740d28912b5da428f99a5da0664b38 authored about 10 years ago by Daniel Jones <[email protected]>

Merge pull request #15 from dcjones/seq

WIP: Sequences

github.com/BioJulia/Bio.jl - 29a11dba3afba71483a97880d57ba2d3ea29922a authored about 10 years ago by Daniel Jones <[email protected]>

Kmer tests.

github.com/BioJulia/Bio.jl - aa1fd9c2afa0189bfd3fc347ca58aafae15b4226 authored about 10 years ago by Daniel Jones <[email protected]>

Handle translatable ambiguity in translate.

github.com/BioJulia/Bio.jl - c4c8a5250a304055236c178ae96fce0f3b7c9131 authored about 10 years ago by Daniel Jones <[email protected]>

Test . Fix a few things.

github.com/BioJulia/Bio.jl - c8335d09b71f2844c72ee817bc899af234e2e2c1 authored about 10 years ago by Daniel Jones <[email protected]>

Alternative genetic codes for .

github.com/BioJulia/Bio.jl - eb044105b463921a816c5a98a26d4fe2f27d307b authored about 10 years ago by Daniel Jones <[email protected]>

Translation.

github.com/BioJulia/Bio.jl - 43a293aab61499b2092c4e4e7ddee33d4e059a0b authored about 10 years ago by Daniel Jones <[email protected]>

Amino acid sequences, and eachkmer improvements.

github.com/BioJulia/Bio.jl - d5a012ff64baa5f0fdd71d7bdd6aea6aec01cb13 authored about 10 years ago by Daniel Jones <[email protected]>

Add Travis configuration

github.com/BioJulia/Codecs.jl - 69d6bad0924f973159440333115adb134e4fbf29 authored about 10 years ago by Ken Crowell <[email protected]>

Workaround for Julia 0.2.1 range iteration bug (fixes #8)

github.com/BioJulia/Codecs.jl - 40f53cf63d3686f57222af9b6d4bd7e598cd42b2 authored about 10 years ago by timholy <[email protected]>

Yet more speedups by manual inlining and branch-point consolidation

github.com/BioJulia/Codecs.jl - 2de709784ed10c4ffab20ce2495b382e163f2c00 authored about 10 years ago by timholy <[email protected]>

Fast kmer manipulation.

github.com/BioJulia/Bio.jl - 419ca7c080d5a31e98bd57c6a99cd64d54985000 authored about 10 years ago by Daniel Jones <[email protected]>

Merge pull request #7 from timholy/pull-request/874247f0

Pull request/874247f0

github.com/BioJulia/Codecs.jl - 6596ffe16b58d6011c6efa68960e0a00745464e4 authored about 10 years ago by Tim Holy <[email protected]>

Merge remote-tracking branch 'origin/master' into HEAD

Conflicts:
src/Codecs.jl

github.com/BioJulia/Codecs.jl - d232c6c9fde05beb266704395a23566e41970df3 authored about 10 years ago by timholy <[email protected]>

Cache the results of base64dec

This does not help as much as the previous commits, but it shaves another
40% off execution time.

github.com/BioJulia/Codecs.jl - 89fabf25673eda67794ba894a14f3ef1e50bc896 authored about 10 years ago by timholy <[email protected]>

Merge branch 'compact_output' of https://github.com/ssfrr/FactCheck.jl into ssfrr2

Conflicts:
.travis.yml

github.com/BioJulia/FactCheck.jl - 8e64298cdab10daa5798356e122dd2e180401a0e authored about 10 years ago by Daniel Jones <[email protected]>

Speed up base64 encoding/decoding by avoiding use of Iterators

github.com/BioJulia/Codecs.jl - 874247f0d98ce721ab6e0aa95d9a364cfcac4005 authored about 10 years ago by timholy <[email protected]>

Add base64 test

github.com/BioJulia/Codecs.jl - 0ddcd5aa263051d6ab89642bac499dc2368af39f authored about 10 years ago by timholy <[email protected]>

Fix type-stability of base64dec

github.com/BioJulia/Codecs.jl - 9aa0aebb20e211c17d8caa07c04a8add6f0bccb3 authored about 10 years ago by timholy <[email protected]>

Separate seq code into multiple files.

github.com/BioJulia/Bio.jl - cbd20c762884ae4e87b43f14b02e62224f184f9b authored about 10 years ago by Daniel Jones <[email protected]>

Nucleotide composition, iterating through kmers, better show.

github.com/BioJulia/Bio.jl - 124e77273e3fc8aa4cae20abc863a174ab715c93 authored over 10 years ago by Daniel Jones <[email protected]>

Mismatches.

github.com/BioJulia/Bio.jl - cac4dbceb75d0d312ddc6461a09ee00c609ad0a1 authored over 10 years ago by Daniel Jones <[email protected]>

Fix RNASequence constructor.

github.com/BioJulia/Bio.jl - d542e454c94201179ba1d713ba4a69fddccdfddc authored over 10 years ago by Daniel Jones <[email protected]>

Work on optimizing sequence construction.

github.com/BioJulia/Bio.jl - 732a5705b9a2bd67bfd4a9c7c28b03e079738efd authored over 10 years ago by Daniel Jones <[email protected]>

Complement, reverse, reverse complement.

github.com/BioJulia/Bio.jl - 771e4b643d2f5233b67fe82fb526e2096ff04a2f authored over 10 years ago by Daniel Jones <[email protected]>

Use bulk insertion for N mask. Better iterator.

github.com/BioJulia/Bio.jl - e52cf2de374948d76082315eea3d5de510987326 authored over 10 years ago by Daniel Jones <[email protected]>

Fix an issue with bulk insertion.

github.com/BioJulia/IntervalTrees.jl - 220913f793b2431b8c3b3e3b750312071a54e08f authored over 10 years ago by Daniel Jones <[email protected]>

Implement a iterator.

github.com/BioJulia/IntervalTrees.jl - 9be8d4915c0e9c192cba542240f64599162e83c8 authored over 10 years ago by Daniel Jones <[email protected]>

Implement bulk insertion. Fixes #1

github.com/BioJulia/IntervalTrees.jl - 292f9e83c195a6e8a83f57eba5cab23958a876dd authored over 10 years ago by Daniel Jones <[email protected]>

Optimzations to iteration.

Iterating through keys is about 3x faster now.

github.com/BioJulia/IntervalTrees.jl - 96bb022baf4b8a28765f9cbe22051ac9f8ec553c authored over 10 years ago by Daniel Jones <[email protected]>

A few tests. Copying subsequences.

github.com/BioJulia/Bio.jl - cbecfced05209ed341181585b48f9e71cf27edf8 authored over 10 years ago by Daniel Jones <[email protected]>

Sequences and subsequences are the same thing.

github.com/BioJulia/Bio.jl - e4c5555326a70d3ff3e5d654bb27b8c124d25138 authored over 10 years ago by Daniel Jones <[email protected]>

Implement efficient function for point queries.

github.com/BioJulia/IntervalTrees.jl - 92e7e28e50de9ad1a4683b9b438a36a3b90c00e6 authored over 10 years ago by Daniel Jones <[email protected]>

Initial sequence work.

github.com/BioJulia/Bio.jl - 70fe2c7c97928807cec35ad8c713eaf8a6977949 authored over 10 years ago by Daniel Jones <[email protected]>

Fix broken splice! on some platforms.

github.com/BioJulia/IntervalTrees.jl - 206de39342b349f8d6ab86ba86ad4e034e69ad74 authored over 10 years ago by Daniel Jones <[email protected]>

Correctly report exit status of tests.

github.com/BioJulia/IntervalTrees.jl - 74eb80c3575191b184b313696288a3d602d2011d authored over 10 years ago by Daniel Jones <[email protected]>

More tests.

github.com/BioJulia/IntervalTrees.jl - b94682e3a5b567f64e43274a5307c30fc49fbcad authored over 10 years ago by Daniel Jones <[email protected]>

Test that Slice correctly throws.

github.com/BioJulia/IntervalTrees.jl - ddaa23e279a96bcf1bd7396fb1acebc908a8b292 authored over 10 years ago by Daniel Jones <[email protected]>

Julia: declare data const.

github.com/BioJulia/ragel - 577d39336fc7bb2f6abe9e69e2670b406e9a8402 authored over 10 years ago by Daniel Jones <[email protected]>

Fix issue with fbreak and goto parsers.

github.com/BioJulia/ragel - 19070ab55c9da325ef294fe99d42634e433fba0c authored over 10 years ago by Daniel Jones <[email protected]>

Minor julia fixes. All tests now pass.

github.com/BioJulia/ragel - 6691625cd8c683405fca84ce8ab757846a70b704 authored over 10 years ago by Daniel Jones <[email protected]>

Add Julia support in tests

github.com/BioJulia/ragel - 8e1234c24204bcb50341b2dab756f864b2cc4ea3 authored over 10 years ago by Daniel Jones <[email protected]>

Merge julia code generator.

github.com/BioJulia/ragel - 73e9ddb21b28e76a462927df1d20fc04ad7b90f7 authored over 10 years ago by Daniel Jones <[email protected]>

Fix configure colm check for older sed versions.

github.com/BioJulia/ragel - e9b228cfc71ac1a02a4e9222540ccd301b9ed5e2 authored over 10 years ago by Daniel Jones <[email protected]>

switched to using 'Pkg.test' instead of manually running the test script

github.com/BioJulia/FactCheck.jl - 82405e9c4924a9693650b7698fdfc1248c98861d authored over 10 years ago by Spencer Russell <[email protected]>

updates julia package dir in .travis.yml

github.com/BioJulia/FactCheck.jl - fd97962f2b62742594ef309feed12781300e98c0 authored over 10 years ago by Spencer Russell <[email protected]>

changed travis config to use the current commit instead of cloning

github.com/BioJulia/FactCheck.jl - dacd67159ff9f2eba4917c6fcbaa93d1fdf838d8 authored over 10 years ago by Spencer Russell <[email protected]>

adds lock to README about compact option

github.com/BioJulia/FactCheck.jl - f000932285aeccbf073192dd239de2ae1c375484 authored over 10 years ago by Spencer Russell <[email protected]>

fixes failure printing in compact view

github.com/BioJulia/FactCheck.jl - b656f852bb516cd71abca4399efdbfc7e50d3b4b authored over 10 years ago by Spencer Russell <[email protected]>

enables compact output

github.com/BioJulia/FactCheck.jl - 511df9aac5575e6dc78df31b8e0256cbc41a993c authored over 10 years ago by Spencer Russell <[email protected]>

fixes test script name in .travis.yml

github.com/BioJulia/FactCheck.jl - e2163f66a406443ae007431cf6c870542c953a94 authored over 10 years ago by Spencer Russell <[email protected]>

renames test file to runtests.jl to follow newish julia convention

github.com/BioJulia/FactCheck.jl - 1adccfe683eb0fb09889406662cda5a4078dd47f authored over 10 years ago by Spencer Russell <[email protected]>

improved syntax for embedded host

github.com/BioJulia/ragel - 2e69d40cb5f41191d0c5f350381876336dcc2f96 authored over 10 years ago by Adrian Thurston <[email protected]>

added IlOpts for wrapping up Inline list args

Using with the ACTION funciton. Not yet propagated through the INLINE_LIST
calls.

github.com/BioJulia/ragel - 4e11f8931cd104ab388a03217c28b6590b56dee9 authored over 10 years ago by Adrian Thurston <[email protected]>