github.com/BioJulia/Bio.jl commits | Ecosyste.ms: OpenCollective

Added length method for winter, which is essential for array comprehensions.

d879f3256b67396953c3574556ddaa4b78fdeca1 authored over 8 years ago by Ben J. Ward <[email protected]>

add Bio.IO (and clean up)

58783c354ef77073587cb6cca3eafa7c7f990320 authored over 8 years ago by Kenta Sato <[email protected]>

SeqRecords exported (#207)

* Export SeqRecord and FASTAMETAdata

* exported FASTASeqRecord alias

6501b56a8756c44e331fdd03bbf09fffdba05fb9 authored over 8 years ago by Ben J. Ward <[email protected]>

Remove nightlies from appveryor

3d4d8a512efa8667d7b6b4dc8e1980ccc17fbabf authored over 8 years ago by Ben J. Ward <[email protected]>

Removed nightly build from travis.

d9eeb729c41148a509354be56c77b758623243fa authored over 8 years ago by Ben J. Ward <[email protected]>

Add ReferenceSequence (#198)

* add ReferenceSequence

* add docs on ReferenceSequence

1d06139c2a35b19495c9e3739c2275248ce15e07 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

define DNACodon and RNACodon (#204)

d829603f386186b1aa3c241d93111cfad319db33 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

define eltype for KmerNeighborIterator (and add tests) (#203)

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

891f384c5a860a1cf030d9d733e37d900fcfd621 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

export Codon

1212dac7c7fb3652241635772bac9ffe89f7cad9 authored over 8 years ago by Kenta Sato <[email protected]>

deprecate kmer, dnakmer and rnakmer

b43d1aa3da78a8179860894ac3692918c3b62f8e authored over 8 years ago by Kenta Sato <[email protected]>

fix k-mer arithmetic

360214c849b8c5a116242c99f3c0c8f7bcaad276 authored over 8 years ago by Kenta Sato <[email protected]>

move deprecated definitions

14eaab2b24f84cabab87f87c406314250d58c892 authored over 8 years ago by Kenta Sato <[email protected]>

rename Blast to BLAST (take 2) (#199)

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...

58cd5b8a4a3d87003064b849a3ae77c05fc97795 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

rename Blast to BLAST (#196)

e49a01a9e4cb72bfab690f68897d143d555f97b0 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Added more tests for phylogeny types. (#193)

* Added more tests for phylogeny types.

* Added == method for phylogenies

* More tests add...

f477d42696e1999616499bb38deed89cb896a41d authored over 8 years ago by Ben J. Ward <[email protected]>

make show(strand) more informative (#195)

7dd8aff132962993f8fde9bab94eba4c865e1f43 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Squashed Previous Phylo rework commits (#157)

edited Phylo, phylogeny, runtests.

Added a few more methods for new phylogenies.

Added som...

ee57251b8325b3b9e9e4e4fdb0de712ac599524b authored over 8 years ago by Ben J. Ward <[email protected]>

SymbolRange, cyclic arithmetic, and more informative `show` method. (#190)

* add SymbolRange type

* make symbol arithmetic cyclic

* make show(nucleotide|amino acid) ...

1688351d0b689227b5c661e6d73496e6d8d3b53f authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

tweak spacing of HTML docs (#192)

bc2fe439620e9644efe1e553a37af1d06b7fae60 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Updates for Documenter.jl syntax changes (#189)

See https://github.com/MichaelHatherly/Documenter.jl/pull/51 for details.

ff0f66cc6ab2b29ae63a13b749f7e67f65709e9d authored over 8 years ago by Michael Hatherly <[email protected]>

use cinder theme for web docs (#181)

86a6c10ecdc87692581c729e3d443aef38d1115f authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix a docstring of KmerCounts (and potential bug) (#188)

345dedbddd9813da2440a4a41b3264063caa4374 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add exact search functions (#152)

999f2be26618ef4fa0aba91a83ab2b51d1449fc7 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

rename internal macros to avoid overwriting others (#187)

0dbae4fa41d3db614adffb478b6c334a214399de authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add iscompatible (#186)

1beeb0037d7532ed96a23604d1a5163235f12186 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

define eltype for Kmers (#185)

83f27bab863ebbffc23cd08d2f4c58729ad76833 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Fix deprecated (#183)

* replace symbol with Symbol

* fix deprecated types and syntaxes

eaced8cc4991a5c5f639e48a320ae4cdf0414883 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Fix coding style (#182)

* remove intrinsics calls (box/unbox)

* fix style of method extensions (Seq.Intervals)

* f...

49251334917b3db186faf77feb9b4d0b33968cad authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Changed logo for manpages

fac931209e8bb24e7d961d45725715a5b47e472d authored over 8 years ago by Ward9250 <[email protected]>

Update make.jl

6a0c1271bab53dcc19f981f6ebf29eae1c344ff9 authored over 8 years ago by Ben J. Ward <[email protected]>

Updated makefile to bypass OS X error temporarily.

In accordance with issue 45 of Documenter.jl

037e80a47933b7e9b60909bf00ecc3e1f3733107 authored over 8 years ago by Ben J. Ward <[email protected]>

Update README.md

89040bf741b5c0691252f0b8320f42903d536329 authored over 8 years ago by Ben J. Ward <[email protected]>

Reverted change of order of after_success operations.

03543f40e3b74bba95762fc0e6b2e0aea3473652 authored over 8 years ago by Ben J. Ward <[email protected]>

Testing if order of after_success: operations affects OSX build.

8b1fa334437fa04d1ca61a15913707969e0c5176 authored over 8 years ago by Ben J. Ward <[email protected]>

Corrected spelling error in documentation

1db81e9aa4b5edd67691b2ee634251405a0f00c8 authored over 8 years ago by Ward9250 <[email protected]>

Merge pull request #180 from bicycle1885/precompile

Precompile

05c992d65457cfc8f6ba61d969cf7b33d958afee authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

precompile parsers

140097ee925a07c592146a5052033b30a84ce75b authored over 8 years ago by Kenta Sato <[email protected]>

switch precompile on

46e46cc1828514b5eb11864d10afd87c7470323f authored over 8 years ago by Kenta Sato <[email protected]>

Merge pull request #179 from bicycle1885/fasta-type

FASTA type

ff70a44cf4ed0de85a2f2aeba36c4635d6c1c2d7 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

make the FASTQ parser take a sequence type argument

eeece6797751b238a0566f30b89e3f1bfa8263fb authored over 8 years ago by Kenta Sato <[email protected]>

fix sequence type classifier

35f8b1a47369c88a2e8a4c73c9223ca14594939f authored over 8 years ago by Kenta Sato <[email protected]>

make the FASTA parser take a sequence type argument

1b7e4afefc42529f6e1b5261859cb5bf7e6c3db8 authored over 8 years ago by Kenta Sato <[email protected]>

add VoidAlphabet

8430aee54fecd300d1b764788ca0fe97a3a2fa9e authored over 8 years ago by Kenta Sato <[email protected]>

Corrected an error in runtests.jl

9b34ca035e6953d29351f53dc172a611fb01d1d1 authored over 8 years ago by Ben J. Ward <[email protected]>

Fix for 161 error. (#176)

* Fix for 161 error.

* Edited testing module names.

8ff06b599585137eb1e834a96d9cb26036101164 authored over 8 years ago by Ben J. Ward <[email protected]>

Merge pull request #140 from BioJulia/refactor-ragel

Refactor ragel

dc9aca2aad186b3ad195b2e26f25812ad9e2c3b4 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Fixed tools man

a2bcc993de2b565997aaa9287d1ec1140223a902 authored over 8 years ago by Ben J. Ward <[email protected]>

Edited an error in the metablock for this manpage.

0ff875f36462db3e553ff7ba71557ef0d69ffdc7 authored over 8 years ago by Ben J. Ward <[email protected]>

Fixed makedocs yaml file.

The tools documentation (which contains docs for blast utilities) was not included in the mkdocs...

ac40464b69feb51f576d9a991dfc779896408fc4 authored over 8 years ago by Ben J. Ward <[email protected]>

Indexes (#161)

* Added indexing types to a module Bio.Indexing

* Reorganised util folder a bit, and added th...

631dded6958ff20bbd95660365c1b8a748e3e89f authored over 8 years ago by Ben J. Ward <[email protected]>

refactor Ragel

4f023bd3609bec6e757ecae8d22c6254b83bf77c authored over 8 years ago by Kenta Sato <[email protected]>

remove writing FASTA tests

this is tested when parsing FASTA

b64f7ed273db91f0f506dbf72e16f6f478dadf0d authored over 8 years ago by Kenta Sato <[email protected]>

replace deprecated Base.ttysize with displaysize (#172)

6f53b069093d11e913d91382cd548c8a6328aaa6 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Merge pull request #170 from kdmurray91/separate-ragel

[RTR] Separate ragel from julia source

cb21c0e8c5b4494a12fa2879b39edb87bfb64665 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

bigbed: rename bigbeddata -> bigbed-parser

Makes it consisent with all the other parsers

dae72afd78a29b21c0b075a9637bb7ddabceea39 authored over 8 years ago by Kevin Murray <[email protected]>

bed: split ragel from julia source

98845b7cfac30bf4d652da206029c6c3138c4c73 authored over 8 years ago by Kevin Murray <[email protected]>

fasta: separate parser from source

cdba79b101135bdd2001eaf4267409fc4a99cf9d authored over 8 years ago by Kevin Murray <[email protected]>

fastq: rename ragel parser file

fastq-parse -> fastq-parser

2ce3409a6ab744c6e0b6dc2e97879a042799cc9c authored over 8 years ago by Kevin Murray <[email protected]>

Fastq: Split ragel and julia sources

105442ee2d057112bf172321025c5edfbae63a8a authored over 8 years ago by Kevin Murray <[email protected]>

regenerate ragel Bio.Seq sources

3dfa5b88900a4b37458b946618ca7994c126e822 authored over 8 years ago by Kevin Murray <[email protected]>

remove encode_seq macro (#169)

505c41793465a1b2b612e5fe2f8b390d845f31f8 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Merge pull request #163 from bicycle1885/fix-intervals

fix BigBed parser

ae6e6c161ab96e8f8fd06d09f7db97bc3d4ced29 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

rename EmptyStreamSource

a33e59e3d1b38270c53703eeee973832bd35dcb6 authored over 8 years ago by Kenta Sato <[email protected]>

fix BigBed parser

c14b9ada859ed9145bc209fceaab5fe015ea2cce authored over 8 years ago by Kenta Sato <[email protected]>

Merge pull request #168 from bicycle1885/install-blast

install NCBI BLAST+ before running Travis CI

ccc5eab520c12cdaf83e3b1de3823b355fdc25c1 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

install NCBI BLAST+ before running Travis CI

6843f836b275888b5e9143cdbaa74e07877456db authored over 8 years ago by Kenta Sato <[email protected]>

Corrected README

55f87dcba7015048ea39b3d9e1a652778b5d8e9f authored over 8 years ago by Ben J. Ward <[email protected]>

Corrected badge urls in README

8f170bc41cf4ea3195b3dbbb8b3ca533a4bcf862 authored over 8 years ago by Ben J. Ward <[email protected]>

Merge pull request #162 from kdmurray91/vimswp

Add a bunch of temp files to gitignore

bab535b5b96800542c5a8da043b6ff06276624b2 authored over 8 years ago by Ben J. Ward <[email protected]>

Remove misc temp/unwanted files

- Cloned BioFmtSpecimens
- KDE directory files
- Vim swap & misc temp files

6306f7fd09ab1a94df61a1363ae0b0a167d03ce5 authored over 8 years ago by Kevin Murray <[email protected]>

Merge pull request #158 from kescobo/blastdocs

add documentation for blast module

0b9bcabc3cc6027229a218a1c2082d4ae5e58e50 authored over 8 years ago by Ben J. Ward <[email protected]>

update index.md

b1c718c9ec0958c56302f0c2ad68967c0fc50039 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>

add documentation for blast module

deede4eb9fa17c5f0912ca17c36a3dcbc3f3968a authored over 8 years ago by Kevin Bonham, PhD <[email protected]>

Merge pull request #65 from kescobo/blastwrapper

Blastwrapper

234e769ba0ef047f082d431d6d831e11d990a444 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

address line comments for previous commit

- remove docstrings for non-exported functions (replace with comments)
- remove unnecessary type...

f25b173a60a381a700fc19ef80eb90f64b37d7c8 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>

made tests evaluate to Boolean

ce5edfe21efe63b36d00f80fa2b1cef574ffb516 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>

Forgot to add package to Bio.jl

992a7a53aea97cdaa662af858fdc472035bb9f50 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>

add tests for blastn and blastp

faf17d3e430a2f6ecc96eab775245f8ef6bc193c authored over 8 years ago by Kevin Bonham, PhD <[email protected]>

BLAST command line support

090764aeb1ced656e84c02bbaaa3d79db4b71866 authored over 8 years ago by Kevin Bonham, PhD <[email protected]>

Merge pull request #150 from BioJulia/findnext

add Base.findnext for BioSequence

cf915598e3fbdb5e42bbaba310be629535309f55 authored over 8 years ago by Ben J. Ward <[email protected]>

add findnext, findprev, findfirst, and findlast for sequences

87d8dbe4eec73f2277f16869c475b63b6ca14d0d authored over 8 years ago by Kenta Sato <[email protected]>

Merge pull request #146 from jgreener64/strucdocs

Documentation for Bio.Structure

63cbc8503b161c71422fb2fa1ac77dc3889a5f4c authored over 8 years ago by Ben J. Ward <[email protected]>

doctests re-added using BioFmtSpecimens

0ce4ac048afcec6b7ba17c82783bea597aac4f8b authored over 8 years ago by Joe Greener <[email protected]>

minor change to property table

684da652a9e9db7da597a4d74af424c1a66b79e6 authored over 8 years ago by Joe Greener <[email protected]>

remove doc tests

ff9c2abb3ac8726e83756d8f7a30ab7e9fd031c2 authored over 8 years ago by Joe Greener <[email protected]>

Merge branch 'master' into strucdocs

b6017a0e6d140c5897a1623ad7b0d51de5d95089 authored over 8 years ago by Joe Greener <[email protected]>

Merge pull request #148 from MichaelHatherly/mh/rename-lapidary

Rename Lapidary to Documenter.

63d5fcda86cc3804efb60ec38315f00106c4b16b authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Rename Lapidary to Documenter.

https://github.com/MichaelHatherly/Documenter.jl/issues/1

68790f10e7c430858bd722207c473adc7868ffd1 authored over 8 years ago by Michael Hatherly <[email protected]>

Merge branch 'master' into strucdocs

d359c0b03730fc797b9aeab20fe9640e249f98c6 authored over 8 years ago by Joe Greener <[email protected]>

Structure docs in Lapidary.jl format; some in-code docs

801513925ba081357294450082d8d276aaa37050 authored over 8 years ago by Joe Greener <[email protected]>

Merge pull request #145 from BioJulia/bioseq-to-aligned

add constructors of AlignedSequence from BioSequences

0ce8751ae5416f8bcb29804741173d4394200833 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add document about AlignedSequence

4fe940ccbdc4df8eff0772022254ed51eebc27cf authored over 8 years ago by Kenta Sato <[email protected]>

add tests of AlignedSequence

a413a625a251294d7610a45127e9f88f8ddad162 authored over 8 years ago by Kenta Sato <[email protected]>

add constructors of AlignedSequence from BioSequences

f0683860d5cfe285e809c8c7f1a5d7f76d543ae6 authored over 8 years ago by Kenta Sato <[email protected]>

Merge pull request #142 from BioJulia/doc-align

Add document on pairwise alignment

d9222b0f9eae083a2262cfe7945277ccc7147520 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

update docs about Bio.Align

14de59979315c7f98c4cc31118dcfae0125ce709 authored over 8 years ago by Kenta Sato <[email protected]>

add docs of `alphabet` and `gap`

6ff4cd5bf39d8674aa3e37478855bf75c28e3441 authored over 8 years ago by Kenta Sato <[email protected]>

update docs about alignments

1d7bc401e4c85a8e97b3551bf425e7950ed40dd3 authored over 8 years ago by Kenta Sato <[email protected]>