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github.com/BioJulia/Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
https://github.com/BioJulia/Bio.jl

remove messages for debug

a68bb886d47962b72feda48e008e0c660d5d46ed authored almost 9 years ago by Kenta Sato <[email protected]>
fix equality syntax in tests

This patch replaces prefix equality operators with infix ones, which is more
natural in new test...

8b0ec34c282f372d2e0468f70268407d2aa13e6f authored almost 9 years ago by Kenta Sato <[email protected]>
Bio file changes and empty files

36c5a876b880bcd166a41638a45e3c8a8ec274f1 authored almost 9 years ago by Joe Greener <[email protected]>
drop FactCheck dependency

2d1789e73f85d944fdf088850c1853e6f1c50552 authored almost 9 years ago by Kenta Sato <[email protected]>
replace FactCheck with BaseTestNext

d949e5e93d50fb9559c572be73a42ee902c6ea68 authored almost 9 years ago by Kenta Sato <[email protected]>
allow to pass test targets as command-line arguments

The test/runtests.jl script can take command-line arguments to specify test
targets, which saves...

fe2eaba11485d4837d1eac7be927560079c03f11 authored almost 9 years ago by Kenta Sato <[email protected]>
require v0.4

0db18e889994bb690555f0ddf1fa86b50d9021b3 authored almost 9 years ago by Kenta Sato <[email protected]>
Merge pull request #111 from BioJulia/pairalign

Pairwise-alignment algorithms

013373f597520d807b46d79071e97ef8d66d61d8 authored almost 9 years ago by Ben J. Ward <[email protected]>
add docstrings for pairwise alignment

97a50e0df063807f2141decea0c2c16df83cb24b authored almost 9 years ago by Kenta Sato <[email protected]>
add count and count_<op> functions in place of nmatching etc.

782a23d2635c0c7097576d9c9cef1534ea08e923 authored almost 9 years ago by Kenta Sato <[email protected]>
add nmatching/nmismatching/naligned methods

8b04ed7e196d15b762438a7931385e3b0c7dcf21 authored almost 9 years ago by Kenta Sato <[email protected]>
add the local alignment

dc0ef90e0bf454ead9681789858994cc561ef7d3 authored almost 9 years ago by Kenta Sato <[email protected]>
remove an unnecessary macro

50351d2bcb4a4a9fbb9ad11bcfceb572d525ac2c authored almost 9 years ago by Kenta Sato <[email protected]>
many tweaks

5dba2f44dbc4953d010b9299d5d002d0ef30448f authored almost 9 years ago by Kenta Sato <[email protected]>
add PairwiseAlignment type

6c10e70e43c0a632b0e75ad441dc845c30de5d05 authored almost 9 years ago by Kenta Sato <[email protected]>
fix wording

857adb33cc562e16c90f3b1c067def9ef201516f authored almost 9 years ago by Kenta Sato <[email protected]>
minor performance improvement of findanchor

ff3c1ced19dc6a79fcc4a1b8433a1e6e66757355 authored almost 9 years ago by Kenta Sato <[email protected]>
add position mapping between seq and ref

efba0da6c62bf27888f8c157fbcc2299ef537da5 authored almost 9 years ago by Kenta Sato <[email protected]>
performance optimization for banded Needleman-Wunsch

529558da0b400be904ddafdb0bb3d0a05985acc6 authored almost 9 years ago by Kenta Sato <[email protected]>
add a docstring for pairalign

9f8a14d81c0217f8ae5909b6f10d5abf8236e7ee authored almost 9 years ago by Kenta Sato <[email protected]>
redesign the substitution matrix

a7e355d95e21999c9167e79377e7847e494a2e98 authored almost 9 years ago by Kenta Sato <[email protected]>
fix the interfaces of CostModel like affine gap

3955ba3380cd51c5e7fb29a6a75231af5ad799b4 authored almost 9 years ago by Kenta Sato <[email protected]>
clean up the interfaces of AffineGapScoreModel

7e93cd98187617d4d032c54e5d5c4a9a46bcc7d0 authored almost 9 years ago by Kenta Sato <[email protected]>
add the overlap alignment

2e2a56929cde2b8a98916344e1ef73838bf77c2f authored almost 9 years ago by Kenta Sato <[email protected]>
remove old files and refactoring

1ac2f7497eda08199f35e91bcae1993113268554 authored almost 9 years ago by Kenta Sato <[email protected]>
fix global alignment algorithms

5bcdada084d496390eba543a8c21d2f993ac04b1 authored almost 9 years ago by Kenta Sato <[email protected]>
add minimum and maximum for SubstitutionMatrix

b102f70047c567eb03887c650f77628ef88e0156 authored almost 9 years ago by Kenta Sato <[email protected]>
add pretty printer for substitution matrices

1c1b790c6ff0cac5c11bea8363741234d3e7612c authored almost 9 years ago by Kenta Sato <[email protected]>
delete some macros

24e6b6bc0f3be6f48353f81ddf280d07000cd898 authored almost 9 years ago by Kenta Sato <[email protected]>
break a long line

7831c445a6c52a80c789c3035f7214a9a198631a authored almost 9 years ago by Kenta Sato <[email protected]>
rename a field

016773f9c5ec2220a93b460443ba98883015eaed authored almost 9 years ago by Kenta Sato <[email protected]>
minor performance improvement of banded global alignment

9ad37dc94fad9161088c6032a86dfbddf3db828b authored almost 9 years ago by Kenta Sato <[email protected]>
minor performance improvement of semi-global alignment

f6abd51f620330266e74de9fce7d1a372eb638fa authored almost 9 years ago by Kenta Sato <[email protected]>
minor performance improvement of local alignment

328b7ceff8da917c84d062cc6c88c702446794aa authored almost 9 years ago by Kenta Sato <[email protected]>
add a few accessors for pairwise alignment

a384582ed011a03a5349d3ae9cb0707e24e32ae3 authored almost 9 years ago by Kenta Sato <[email protected]>
add some submat conversions

66f5280639dd12074a200926d09cd174fbe0c23e authored almost 9 years ago by Kenta Sato <[email protected]>
fix AffineGapScoreModel constructors

64a94290836a489741aa90914bb82eafd38dcaa1 authored almost 9 years ago by Kenta Sato <[email protected]>
add a few tests for the banded global

147b8f2783c7f65298fcd331a043b99c77c7831e authored almost 9 years ago by Kenta Sato <[email protected]>
remove unnecessary `esc`s

0e1571acd84a4e4de985cbaa2d8511047cafb931 authored almost 9 years ago by Kenta Sato <[email protected]>
add more substitution matrices

02596e323f9715db3e1372252ef0be9316ceb8e0 authored almost 9 years ago by Kenta Sato <[email protected]>
fix Smith-Waterman

d618f4d4617787a601adf35d2a6321d57e64dae5 authored almost 9 years ago by Kenta Sato <[email protected]>
add some tests for pairwise alignment

a2ea72d00c232f459dfba600834974276c53bb33 authored almost 9 years ago by Kenta Sato <[email protected]>
add the hamming distance

badc6a38abd32b95f336feb3bc441ed6f2701c79 authored almost 9 years ago by Kenta Sato <[email protected]>
add the edit distance

841513a260906eb2d06a9a4e60fca4779255e8fa authored almost 9 years ago by Kenta Sato <[email protected]>
add the semi-global alignment

0597906a39f4ec21a15966e81694e227dec64bd8 authored almost 9 years ago by Kenta Sato <[email protected]>
add the banded global alignment

d644806facafe4d4901ba7c79a7a2812a932205f authored almost 9 years ago by Kenta Sato <[email protected]>
export names

47c1ca4d7b12f74556c186ba81eafcbf171f5c84 authored almost 9 years ago by Kenta Sato <[email protected]>
add the global alignment

3dc4f3fd78d4b10890f5b5691029394844a5aadc authored almost 9 years ago by Kenta Sato <[email protected]>
clean up tests

6406b1f5c68fd14453d84c59abdba12d1ff60ca9 authored almost 9 years ago by Kenta Sato <[email protected]>
fix traceback and test alignment

24473633de568bf5100304669cd431db2ca833a1 authored almost 9 years ago by Kenta Sato <[email protected]>
minor performance improvement of global alignment

662f20d65b88dd36d8c915c47582455b390fd792 authored almost 9 years ago by Kenta Sato <[email protected]>
removed horizontal rules

938916481606ea255b9ab7fe650578f3e5f33304 authored almost 9 years ago by Ben J. Ward <[email protected]>
changed size of headings

dba73f3e211a8438bf2ccd4973c0a8dece7c6a52 authored almost 9 years ago by Ben J. Ward <[email protected]>
Added documentation badge

08f8de20e5e1c9cad9e837892a2901b48bc4b3df authored almost 9 years ago by Ben J. Ward <[email protected]>
Annotated badges

c5d0dbbc6b7537b00b00fa96c74c15ff4c3895eb authored almost 9 years ago by Ben J. Ward <[email protected]>
Merge pull request #127 from BioJulia/Ward9250-appveyor-patch

Update appveyor.yml

adec84502cc439af6db18fa5fa510c90ff63442a authored almost 9 years ago by Ben J. Ward <[email protected]>
Update appveyor.yml

Removing 32 bit support. Most computers are 64 bit now anyway.

4f83f6c5f1a8ce1ce53193f0f11addab6490390e authored almost 9 years ago by Ben J. Ward <[email protected]>
Merge pull request #116 from Ward9250/sliding-windows

Sliding windows - redux

d8df29109f05eaa4565fe3fba17715e40b4adc6b authored almost 9 years ago by Ben J. Ward <[email protected]>
Made testintervals cross platform with DevNull

da32c6e44fa20372111ce831cb7adcb29b3d6401 authored almost 9 years ago by Ward9250 <[email protected]>
Added typealias statement

569c3ac005fea1b6ec33466d281f70d1d6485e2b authored almost 9 years ago by Ward9250 <[email protected]>
src/util/Util.jl

e7168e349e7a429f2eb7ba97b24a23da57a61af1 authored almost 9 years ago by Ward9250 <[email protected]>
Added string and sequences to tests

70cc854f46a4f98be830f36bb0c742fcc6c9123a authored almost 9 years ago by Ward9250 <[email protected]>
Edited assertion in constructor and added string and sequences cases to some tests

0e03ce1228d939c460b1cdea28eb606b61ebd16c authored almost 9 years ago by Ward9250 <[email protected]>
Edited constructor function.

80dd88dc8c1629716dbf0ebd408e53d18204bbe1 authored almost 9 years ago by Ward9250 <[email protected]>
Added corrections and suggestions by bicycle1885

5795d714346ebca408bc8e0a2823e1311d91126d authored almost 9 years ago by Ben Ward (TGAC) <[email protected]>
Added next method for strings.

008efac5075dfbaedc9b812cf52b9d78ef244179 authored almost 9 years ago by Ward9250 <[email protected]>
A revival and improvement on the previous sliding window PR.

817b1c2b2193ee13c13df98bc363234e39c96a52 authored almost 9 years ago by Ward9250 <[email protected]>
Inline window iterator functions

7068d2f682cbd6d0c9dfd4e46f0259563d2d097d authored almost 9 years ago by Kevin Murray <[email protected]>
Remove import Base in windows.jl, it's in Util.jl

Also minor refactoring for a more illustrative name

9cae6e944d7c060b269f7b96613b027cc3808b59 authored almost 9 years ago by Kevin Murray <[email protected]>
Add window iterator under Bio.Util module

dcab992a811a29c014370406ccafa994b689ee9e authored almost 9 years ago by Kevin Murray <[email protected]>
Add window iterator under Bio.Util module

ac365eb1e81a708e399cca54e16d38f2f651942e authored almost 9 years ago by Kevin Murray <[email protected]>
Inline window iterator functions

114273d48915f9cdcb42e76c6d6581f4566a7909 authored almost 9 years ago by Kevin Murray <[email protected]>
Remove import Base in windows.jl, it's in Util.jl

Also minor refactoring for a more illustrative name

02de7a4307e41c9d6021dcfb307c9173c9f349c8 authored almost 9 years ago by Kevin Murray <[email protected]>
Edited test to take into account if on a windows system when opening the null stream.

e735be7513916f680abda7eb9c1bdeec444be641 authored almost 9 years ago by Ward9250 <[email protected]>
Update README.md

4212e76f3c61593f0e6aa281c44b7d9e22ca0939 authored about 9 years ago by Ben J. Ward <[email protected]>
Update README.md

ab251cd0d6605606e5525efdfdec13e5275865f9 authored about 9 years ago by Ben J. Ward <[email protected]>
Update README.md

5c0897bae505a50e8be2226d7df385f39bf116c5 authored about 9 years ago by Ben J. Ward <[email protected]>
Merge pull request #125 from Ward9250/master

Added Appveyor

93f353eea8c1c1e9286355fbcee95a831beb21af authored about 9 years ago by Ben J. Ward <[email protected]>
Added Appveyor

f1cb03a9275f6393257a7b9444131ab0a677b844 authored about 9 years ago by Ward9250 <[email protected]>
Merge pull request #120 from BioJulia/char-like

define arithmetic on nucleotides and amino acids

f6e2568f0c9a47dbc7e59a6aeab7baa7d2644e24 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
define arithmetic for Kmer

4c3a5c379c3e5f96ddefe40b2f229686b6834c76 authored about 9 years ago by Kenta Sato <[email protected]>
fix the docstring of mismatches

7d801284e71525a8443952f9338047d1f6eb9f95 authored about 9 years ago by Kenta Sato <[email protected]>
define arithmetic on nucleotides and amino acids

dc3b669ba04fbfe5592b394612c2f54726d9d5f5 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #123 from BioJulia/kmer

Kmer Overhaul

443340ebc9f948fb72898ed52a73eb810250b90e authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add hash(kmer)

d6e7a04c4cb69751f9d3aab87cc52b213d1d2285 authored about 9 years ago by Kenta Sato <[email protected]>
Kmer: the first nucleotide is at the MSBs

c42424d999ca227be9a14730c8113cf57f0f6e6a authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #119 from BioJulia/intvl-constr

Modify Interval constructors.

41bb5e6d5ab98c66bd15caea4a96db78d2469744 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add seqname accessor for interval type

4d04145ad234b3ce65f576ea4740f71bbac05f41 authored about 9 years ago by Kenta Sato <[email protected]>
Add logo

c0126d3a478c1d43965b70437f56ce0116f299a6 authored about 9 years ago by Richard Smith-Unna <[email protected]>
add strand accessor

b9f35afb258fb3f1bbb55a93a8966ab98ced9521 authored about 9 years ago by Kenta Sato <[email protected]>
make Interval constructors accept a strand char

be8b5fcf6e0c83e12ab033a7cda707afe02b3a09 authored about 9 years ago by Kenta Sato <[email protected]>
Merge pull request #113 from BioJulia/fix-alignment

fix firstref and lastref

d3f2fbf2ec45528522d31d4459609ad43d9ef38c authored about 9 years ago by Daniel C. Jones <[email protected]>
Merge pull request #115 from BioJulia/more-aa

Add more amino acids

963f853a719cef011359a858405e5c4da43f50a8 authored about 9 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix the order of amino acids

as the order of common substitution matrices downloaded from NCBI

b71e501d34f0f2c983569c4f771049f048b97800 authored about 9 years ago by Kenta Sato <[email protected]>
check ambiguous protein specimens

55d66d05bb11ea896de97934bd53f2e2caa6873f authored about 9 years ago by Kenta Sato <[email protected]>
add 'J' amino acid

Leucine or Isoleucine

199d311d0fcdbb8e2c2accd6dc0f4db2d96d3a4a authored about 9 years ago by Kenta Sato <[email protected]>
add 'O' and 'U' amino acids

'O' stands for pyrrolysine, and 'U' stands for selenocysteine.

5bf305c968e932e13908ff050746c22ab54554da authored about 9 years ago by Kenta Sato <[email protected]>
add 'B' and 'Z' amino acids

'B' stands for aspartic acid or asparagine, and 'Z' stands for glutamine
or glutamic acid.

57ab4c433031cb6dd3511a00bcc65b5c30950ea4 authored about 9 years ago by Kenta Sato <[email protected]>
fix firstref and lastref

d90cc3a78c064f39512d86212088f787c1924f30 authored about 9 years ago by Kenta Sato <[email protected]>
move anchor's test

93a83c11edcff057849ea84e41d5aa82ce308131 authored about 9 years ago by Kenta Sato <[email protected]>