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

Added seqmatrix method

* Added seqmatrix method

a04975974a433e38b88882fa6282c725de12bc49 authored about 8 years ago by Ben J. Ward <[email protected]>

fix Bio.Util docs (#281)

f6e5732a5e8f8f4a6dc781efc1d2c2254d115b75 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix Julia version requirement (#280)

26ce2060b6051423e23e8a58700914bbc606e535 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Julia v0.5 (#220)

* fix code for Julia 0.5

* address vchuravy's comments

* fixup! fix code for Julia 0.5

b3245965c7c9ead92ad5bc11f1fc31e9d5e4c1e1 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

improve the performance of reverse nucleotide sequence (#278)

c88d81c45406cdf0ab2b964acdcf3185dcada608 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Update Var.jl

04dac217d1c950d84c3e1344ff0058ed0c52516d authored about 8 years ago by Ben J. Ward <[email protected]>

Edited dating.jl (#276)

* Edited dating.jl

* Added export

97bc93cf96c540b30f73e1fd7e45b6807437d3c4 authored about 8 years ago by Ben J. Ward <[email protected]>

improve the performance of encoding ASCII string (#277)

89463b7f454650a1011c6c476d84ae1775e7ecbe authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

improve the performance of sequence type prediction (#275)

bb2c26606f9436b25e79f3b0ee13d28bb09cd3f0 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Added Base.parse for biological sequences (#273)

* Added Base.parse for biological sequences

* Added tests

* Made base parse more general

0125b2e79c0737567d5066d8f8fdbdac693ca0d7 authored about 8 years ago by Ben J. Ward <[email protected]>

improve the performance of gc_content(::Kmer) (#274)

c7a44db6d35a2234630c85ab7b5a88effba586fe authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Evolutionary distance computation for BioSequence. (#228)

* Initial commit evo_dist

First draft of raw distance

count_differences & count_difference...

b798fd62575fd011a1dc00f49a26913b48564cef authored about 8 years ago by Ben J. Ward <[email protected]>

Furthur readme edit (#270)

Forgot to ask for Bio.Phylo to be added!
Added header above badges.

061e14939338a7822690037a6a76436e05b17921 authored about 8 years ago by Ben J. Ward <[email protected]>

update README.md (#269)

66cc78c6b013e0e9335c538e8359db08232a7b1b authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

improve the performance of reverse_complement (#268)

9d8296dfecfb5a1787af0a96859de311468246b6 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add Distributions.jl to REQUIRE (#264)

10e64789b25d932c28311d9eef9e1cf29970bb6b authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

One-hot encoding of nucleotides; closes #244. (#259)

* use one-hot encoding

* fixup! use one-hot encoding

* fixup! fixup! use one-hot encoding
...

f5481feecb9dcffdfa79db2168e0dfe748230e83 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Merge pull request #234 from bicycle1885/demultiplexer

add demultiplexer

55d750505e6c1a60124d46fea3381f06d98164f3 authored about 8 years ago by Kevin Murray <[email protected]>

Update index.md

a4c7b4614e3c96622625a9e7f2f7c02acba2a164 authored about 8 years ago by Ben J. Ward <[email protected]>

Added Var to manual.

b869cfce000c715e16432a82b226c0a034c6fbd8 authored about 8 years ago by Ben J. Ward <[email protected]>

Moved mutation counting to var module. (#258)

Moved mutation counting tests.

For now just using all of the Bio.Seq module

Added debug li...

dfefd76053a4650cabfbdd152524e42fe215ef0f authored about 8 years ago by Ben J. Ward <[email protected]>

rename ispalindrome to ispalindromic (#262)

5c0c17ebd8eeee3dc7d0c4bacafe2b1550c12534 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

remove deprecated names (#261)

088c8f9561be246885bf6743df364b53d6698f99 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Add example to parsing of fastq sequences (#260)

a583119ec5ad226535fd601400db50ba2c3d4963 authored about 8 years ago by Kevin Murray <[email protected]>

add random sequence generators (#251)

* add random sequence generators

* fixup! add random sequence generators

* fixup! fixup! a...

5c7125745dc2a382d495f73fc4404e293e818822 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Add labelled square matrix parser (#253)

* Add labelled square matrix parser w/ docs & tests

* Fix file readers

* Add test of comme...

ce1ebeb9d5ad84e871e9740c19ff6c432206bf96 authored about 8 years ago by Kevin Murray <[email protected]>

remove clipboard(seq) (#257)

da5577bbcab276ff360b39e0cc4d406603c2aafe authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add docs on demultiplexer

fca3b45372acb3ee3d42ebfe5dd0a5eb0e76d36d authored about 8 years ago by Kenta Sato <[email protected]>

fixup! fixup! fixup! fixup! fixup! fixup! fixup! fixup! fixup! add StaticTrie

b665d3718e1c0a504748b0473065f58e4e4bc61f authored about 8 years ago by Kenta Sato <[email protected]>

remove redundant order check

e3c614b47ef9a8366040f323a9e747f4e23dbf70 authored about 8 years ago by Kenta Sato <[email protected]>

add demultiplexer

e5e998077a1ff62f99192dc85415c9c14d8f453f authored about 8 years ago by Kenta Sato <[email protected]>

fixup! fixup! add StaticTrie

32eae53ccde622c09f42454eef73d8e1b0e49038 authored about 8 years ago by Kenta Sato <[email protected]>

simplify branches

5941803c6400812784a86546a5035a1eedbb1905 authored about 8 years ago by Kenta Sato <[email protected]>

fixup! fixup! fixup! add StaticTrie

b2f6833bfce527b698e959c946671b1b8b640e7b authored about 8 years ago by Kenta Sato <[email protected]>

fixup! fixup! fixup! fixup! fixup! fixup! fixup! fixup! add StaticTrie

9c6c62ef733a8446dc5fad0913b56d038cf15ce4 authored about 8 years ago by Kenta Sato <[email protected]>

fixup! fixup! fixup! fixup! fixup! fixup! fixup! add StaticTrie

4e726d4d8c37159707ba03390e2253304cbbfb9b authored about 8 years ago by Kenta Sato <[email protected]>

fixup! fixup! fixup! fixup! fixup! fixup! add StaticTrie

0c7c5adcd8f61c634a2cfc4b5f5be47c2ca73077 authored about 8 years ago by Kenta Sato <[email protected]>

fixup! fixup! fixup! fixup! fixup! add StaticTrie

cedb3eaff2963a691a8f7519d72568b3ed488c77 authored about 8 years ago by Kenta Sato <[email protected]>

fixup! fixup! fixup! fixup! add StaticTrie

9d46aff5230844a68b7f1d477fe95bb9eb542b0c authored about 8 years ago by Kenta Sato <[email protected]>

fix some

d50a3ac7fb66b52072f7ee44b1ca8cbc5b815099 authored about 8 years ago by Kenta Sato <[email protected]>

fixup! add StaticTrie

ea2f7f293c110884e316e7029020982af9257811 authored about 8 years ago by Kenta Sato <[email protected]>

add StaticTrie

0ef6dae61a5c115f9c59854546e3ac46aa46e873 authored about 8 years ago by Kenta Sato <[email protected]>

use hasambiguity to check barcodes

16fb9974688e53786e50116c3471109308235eef authored about 8 years ago by Kenta Sato <[email protected]>

rename mutated barcodes

686ca48f658b9cca44d9991933b7c6bfd162e437 authored about 8 years ago by Kenta Sato <[email protected]>

Added U for ambiguous nucleotides in Seq docs (#254)

2870dfc06abf87702a57408be3e25116de57e57a authored about 8 years ago by Kevin Bonham <[email protected]>

open with a do block (#252)

so the file handle gets closed and the file can be cleaned up on Windows

e0461b21a64aa80032ae0abb60eb50c66b7e2fc1 authored about 8 years ago by Tony Kelman <[email protected]>

Rewrite Composition (#247)

* fix composition

* make Composition <: Associative

* composition(eachkmer)

* deprecate...

ea70abb72143687b6d4c5a7e1e1f82e5e4e63c3f authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add close for FASTAParser and FASTQParser (#250)

9951522b5605d7a6b8d933ad1121f12544242b84 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix a typo in intervals.md (#249)

21dcdf20dc9ff69bfc6e1c16c9bae59a53765270 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix intervals.md (#248)

d8386b0cada35ef9aa58021553b4fc829bb854a3 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Io docs (#240)

* update IO docs

* fixup! update IO docs

* fixup! fixup! update IO docs

* fixup! fixup!...

2ab90d0992312c7028d8e1b97510935d1c9200fe authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

make unexported docstrings comments (#246)

80c0b47eea26707c7cbcfc2b560bc4c753dfc9d5 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Appveyor badge in README.md displays master status only. Stops misleading red badges.

c0ad84c4221eacb1b646220de1ecd1ad62647717 authored about 8 years ago by Ben J. Ward <[email protected]>

Fix fastq quality encoding inference (#243)

* FASTQ parser actually uses given `quality_encoding` argument.

`infer_quality_encoding()` wa...

046f166544ef4bcf312849ba4366e071b89742bd authored about 8 years ago by Kemal Eren <[email protected]>

extract BigBed types from .rl (#241)

b8e991b164688b4b94e096458fa818b6a0f2523b authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

FASTA Index (#238)

d1c60712c51190dce958df422abcbfbcd06285ab authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Removed rouge println statement (#239)

9cc8990acd5547cbcebcf37998ffdb6d459ea543 authored about 8 years ago by Ben J. Ward <[email protected]>

follow the Libz change (#236)

458cbaf2a3c5322e82c3a5562916dd1276b8f323 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

ispurine and ispyrimidine for nucleotides (#235)

* Implemented ispurine and ispyrimidine for nucleotides

* Fixed functions.

* Fixed from ca...

28b2d4d1aa2c44f20a902f4e5dadc2c66b54a2c3 authored about 8 years ago by Ben J. Ward <[email protected]>

Regular expression search (#233)

3ef85d968c51499419a20ca8cba0da122a012ee3 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

define ref2seq and seq2ref for PairwiseAlignment (#232)

a69fd5916c39dcc9d4b0da4cfca361eeaa581bd5 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

support .2bit format (#155)

2606ab8e030b1ff9bb2e5de26e2bedfdf92cb11a authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Merge pull request #229 from BioJulia/Ward9250-patch-1

Export isambiguous from Seq module.

e3b8ceb17b2286f88be7d89fb15da11ed614ac34 authored about 8 years ago by Ben J. Ward <[email protected]>

Added a line to docs listing isambiguous as a usable function for biological symbols

265c500928bb01804c5af7b46ed49267d105b4b4 authored about 8 years ago by Ben J. Ward <[email protected]>

Added tests

f93a6d5b46438d0e2f61514d806d667668d65c78 authored about 8 years ago by Ben J. Ward <[email protected]>

Export isambiguous from Seq module.

Sometimes if a user is dealing with individual nucleotides, or iterating a seq nucleotide by nuc...

89c6666f047b4d6bbee53dc451b822b6bb4cf3aa authored about 8 years ago by Ben J. Ward <[email protected]>

Merge pull request #184 from BioJulia/mol_dating

Added the Dating submodule to Phylo.

cfaefd3a5b5417f18c3c020da767010d2ff60fdd authored about 8 years ago by Ben J. Ward <[email protected]>

implement filter and filter! for BioSequence (#227)

91e2c0c31ba4d4cdd73788ab618dde998f35079a authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Corrected error in coaltime SimpleEstimate method

20517fabdc4f53bcd1b672822f7d766fe1045016 authored about 8 years ago by Ben J. Ward <[email protected]>

implement map and map! for BioSequence (#226)

4583971480a204d08c1fe01f216fbe8588cdba29 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Corrected tests for dating.jl and added another method

f8ddf63be739b848d133bdf6a4632c4c142a09cf authored about 8 years ago by Ben J. Ward <[email protected]>

add ispalindrome, hasambiguity, and isrepetitive (#222)

90062946f82b34e547f8c5c3a6b21ca7a50cf751 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Shuffle BioSequence and Kmer (#225)

* add rand(::Kmer) to generate random k-mers

* add shuffle and shuffle! for BioSequence

* ...

f508aff4d9914c48d6ab1725b2384b78d4cc813f authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add gc_content (#223)

* add gc_content

* fixup! add gc_content

47c692bf19aadf907eda43c18893b20c05d9277d authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

temporarily disable BLAST tests on Windows (#221)

9676ae681fe214f40dcd5adf9b5644d8780783aa authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

clean up mismatches and docs (#194)

c198ba10c608f67add3a3cd6a6740fa404244387 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Added simple estimation method, as well as HybridCheck estimation method.

6bd7c049b5157ef3676ec2d8fce7f73440f7c1fd authored about 8 years ago by Ben J. Ward <[email protected]>

Added tests for the coaltime function

83a6cf3fba1d5d062e95cafce2f784d9fa14051e authored about 8 years ago by Ben J. Ward <[email protected]>

Added docstring and citation.

8804e463e8efaa45857c208cc081324caac28c55 authored about 8 years ago by Ben J. Ward <[email protected]>

Modified runtests.jl

a3a188f7f9a756f82828fee53ff669402d765937 authored over 8 years ago by Ben J. Ward <[email protected]>

Added the Dating submodule to Phylo.

885576a746ccab9a2f8f693da47aa44d9daaeca3 authored over 8 years ago by Ben J. Ward <[email protected]>

Update mkdocs.yml

73fd7aa216924cf02ffca714125de515052772c3 authored over 8 years ago by Ben J. Ward <[email protected]>

Merge pull request #217 from BioJulia/mkdocs-biojulia

Edited docs to use mkdocs-biojulia

5a6eb5a00d1d61d9ea2bc3be1eef05fc08f281bd authored over 8 years ago by Ben J. Ward <[email protected]>

Edited docs to use mkdocs-biojulia

d42b7bfbe940d4265ef9482bea096f37bd2520e9 authored over 8 years ago by Ben J. Ward <[email protected]>

Update custom.css

04d52e28ea00653091a011ae0427546a6858f9d9 authored over 8 years ago by Ben J. Ward <[email protected]>

Update custom.css

faee3fd674bd3625d4d13bf4651f32a43e7cb03d authored over 8 years ago by Ben J. Ward <[email protected]>

Update mkdocs.yml

cb36e7cbe103671846b4625afd8f2aa7623d4a40 authored over 8 years ago by Ben J. Ward <[email protected]>

Merge pull request #216 from BioJulia/sidecar

Added sidecar to docs

0d85b1c17d861bc081990592c9506132cc0e7a2b authored over 8 years ago by Ben J. Ward <[email protected]>

Added sidecar to docs

3c45e414428ac3a09c0f0f1ddf72bdeec14e1465 authored over 8 years ago by Ben J. Ward <[email protected]>

Added nightly builds as an allowed failiure (#215)

50da08ac9b79015acbfc3a1d8a468a52170f835e authored over 8 years ago by Ben J. Ward <[email protected]>

add BEDWriter (#214)

0e0664cce05e10efc1351898f41443c7360e65d4 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add convert(Char, ::Strand) (#213)

2a1866903452016f6e6eb3e91079224feb21af01 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Replaced makedocs line as Documenter.jl is still awkward on OS X

5e5c61f5306e0901deb1eaf089095ddfc61321f4 authored over 8 years ago by Ben J. Ward <[email protected]>

Update make.jl

f62a5343c916ac38cfa25d30be85ef1bd0fe9fbb authored over 8 years ago by Ben J. Ward <[email protected]>

Sliding windows return their start and ends. (#212)

* Sliding windows return their start and ends.

* Windows return the start position and view
...

0e5cf4ef1db6821d130ee7021eb67663e8751c0c authored over 8 years ago by Ben J. Ward <[email protected]>

fix FASTQ writer interfaces (#211)

ace22ccc7bfb66b668c1f558161c9f4646c8f33d authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix FASTA writer interfaces (#210)

bcc023e0eeaa0109dbeebb26d3b4ff167a548e76 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Merge pull request #209 from bicycle1885/writer

Writer interfaces for FASTA and FASTQ file formats.

2f084808a4d5d0203c3cfbd00c8b6f28cc596c97 authored over 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add FASTQWriter

2cc3b2b6e3604b46a716628cc165ce877ebe5da8 authored over 8 years ago by Kenta Sato <[email protected]>

add FASTAWriter

0020b77366420e09d83e57f3d746620dea52cc16 authored over 8 years ago by Kenta Sato <[email protected]>