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github.com/BioJulia/Bio.jl
[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
https://github.com/BioJulia/Bio.jl
* Rename of DNANucleotide, RNANucleotide, Nucleotide
* Review suggestions implemented
4e6e727cd793db5070b6ceced91bff467ca1a324 authored almost 8 years ago by Ben J. Ward <[email protected]>f76d066e23dee74f0b9ece3fb3b0ad6dd67af955 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
d013b42ccdc6b3ceb01f86ceec2aad50672a6e09 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
e8db6ae0d824473ad985d3ed0b9023d8af178b3f authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
555299a6469eb11f507ce28bd93bedd6b284233d authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
6aa638522e7900f4e09562c38d8934a3cd3f135c authored almost 8 years ago by Joe Greener <[email protected]>
7376024ccd7ada7e0be2fbf245737ac829bf79e9 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
2df81a5e215a21947f0ad40363ed7c2a60d890f2 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
ebf7e6c5b82b965bdb09147162ed6ec92c9aa7e1 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
61d1a20ab5885ce0fefd2e7de58a3a3e67774018 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
f80c74414d7d79df7d07cad9efeb43fa438a0f4d authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
3c6cccac1a7d886b163d431be9c5a00ced55a6d3 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
4e53aa578f0d01228a987dd4d6ce21ec6879c051 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
964c17bfca8775883a3f2b3636b718bbc84220ba authored almost 8 years ago by Kevin Murray <[email protected]>
* Change docs to use AnyMutation not DifferentMutation
* Grammar fix in count_mutations docst...
c93a403edeacce7b90babe2581acbcbafd2b9f45 authored almost 8 years ago by Kevin Murray <[email protected]>3a6b9666f1004ecb2143f73cf36e2fcfeb48eacb authored almost 8 years ago by Ben J. Ward <[email protected]>
* Changed StringField from SubString constructor
* Added StringField constructor method for S...
8c7118ec1f9b009aea2cbadac3a68475c3dbeff9 authored almost 8 years ago by Ben J. Ward <[email protected]>23f209ded52dd4b4f434895a99c721a0779b9ac8 authored almost 8 years ago by Ben J. Ward <[email protected]>
79d9fbae3f4b0b6162914d4f86869617924e8b07 authored about 8 years ago by Joe Greener <[email protected]>
e4cf92270cff283325b33c861a530dca1b52df38 authored about 8 years ago by Manabu ISHII <[email protected]>
3cf8b68167e12579c740d665f418d662c5ac75ba authored about 8 years ago by Joe Greener <[email protected]>
7f0f809bb685281bc739f8708cce47aaac9b3d66 authored about 8 years ago by Daniel C. Jones <[email protected]>
* Changes to Phylo documentation.
* Minor edit to solve interpolation error
* Fixes
* F...
159b3d92dd6ac2001a5831f5cb0758a89ecb533c authored about 8 years ago by Ben J. Ward <[email protected]>6dd5bf9f3e60b84de8fcba3748534835861cc292 authored about 8 years ago by Ben J. Ward <[email protected]>
* fix reverse(BioSequence)
* fix test
403a9c96ac3c79a1c8ccbaeb76e90e042a538a2f authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>* switch XML parser from EzXML
* update REQUIRE to add EzXML
* fixes to address @bicycle18...
41b7a5fe2c508f9edd778fffdfca26342b33b4fa authored about 8 years ago by Kevin Bonham <[email protected]>* Refactored the branchlength setting and getting API.
* Created system for getting and setti...
d7b1876d81f74592116a2c702c72b4590479d89e authored about 8 years ago by Ben J. Ward <[email protected]>8e19330a756461c4e040ffb0097e8f033a94c152 authored about 8 years ago by Ward9250 <[email protected]>
dca33914c4c15a9de9bb65167f124a83880f636e authored about 8 years ago by Ward9250 <[email protected]>
93440e947e8dd5c9580cb4bcfcc88758c01ba6a0 authored about 8 years ago by Daniel C. Jones <[email protected]>
e48772bdfe77377129864ac725ee921317cca425 authored about 8 years ago by Daniel C. Jones <[email protected]>
cf2ff8546e648372b7d2f5a8efe82626823d9dad authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
44239c906ca6b10f74349612c31b43d0e900acb3 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
aacd37dfcb2d8148a12e7a634044b16d56052bb0 authored about 8 years ago by Daniel C. Jones <[email protected]>
17a9faa9118f4fca2360bdeab3857238128e35bb authored about 8 years ago by Daniel C. Jones <[email protected]>
c64cf1083223f1abc5779164593ffaabe65b2122 authored about 8 years ago by Daniel C. Jones <[email protected]>
00fadb40b162e5f18a98036d7d582ef424533b53 authored about 8 years ago by Daniel C. Jones <[email protected]>
33dcdba1e590042f6a12c521e81e9b6e13fab47d authored about 8 years ago by Daniel C. Jones <[email protected]>
ef5766f0c706f85ad4c911671eb8be03c8369822 authored about 8 years ago by Daniel C. Jones <[email protected]>
6a48ca8b3c16ccb42055e93b965bdb2339cf1be9 authored about 8 years ago by Daniel C. Jones <[email protected]>
2fab7c94cc50a463d6ac25b8645ed7a2836bef53 authored about 8 years ago by Daniel C. Jones <[email protected]>
129c129dc5c1288c3a93603b23e5e452c9aea5e6 authored about 8 years ago by Daniel C. Jones <[email protected]>
17077d7fcc65bb5ba1f92e1690e8f1afd80138ac authored about 8 years ago by Daniel C. Jones <[email protected]>
939eb04e54555448be0e54546a9ad39503f2c9e1 authored about 8 years ago by Daniel C. Jones <[email protected]>
f297d766c7756bbb9fdda86d0d3db402ed5e9a6b authored about 8 years ago by Ben J. Ward <[email protected]>
* Initial commit
* Removed return
* Incorporated both static and dynamic behaviour into th...
fde871237fcd57bc9f5054bb8c96ba2897ccf956 authored about 8 years ago by Ben J. Ward <[email protected]>17b084d49102a468ed5e11e8e679f6567bf9b3b0 authored about 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
2040ebb207c152d4a8939ec224268f87ebee1de8 authored about 8 years ago by Daniel C. Jones <[email protected]>
a0c713c13dcae5fbbd558a7c6d0f0b4156bf8a5d authored about 8 years ago by Daniel C. Jones <[email protected]>
322abb9da801e26ebb7c1a49bd4208bf06e9f7c4 authored about 8 years ago by Daniel C. Jones <[email protected]>
* large changes to model structure and parsing; sequence; spatial functions; docs
* AtomRecor...
71c3a0bd43e39c821a90d37e07aae5af185a42d5 authored about 8 years ago by Joe Greener <[email protected]>* first draft of windowed sitance computation
* Corrected typo
* Remembered to initialize ...
ad78989811179dc1fd314479f45311b90954d986 authored over 8 years ago by Ben J. Ward <[email protected]>Most of our guidelines and rules ought to be consistently applied to all of the BioJulia package...
9cda5024065575609b70869cf1d97a8e9f1815a2 authored over 8 years ago by Ben J. Ward <[email protected]>7d278601e84591d23101d9736279e472fd4b04b7 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
This change reduces the number of read/writer operations when reading/writing BAM
records from ...
84d22864b7de3c04a8fb6f9b20321843735d0769 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
e67bebecbe1176a33c598de0983ed4f5ffb31b6e authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
10cb58b3f0d200cb815ccd7b9310770863a22fae authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
6062b532ca0a1534c492417ec62b4f80d5dfc75b authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
An unmapped record may have mapped position of its mate read. This fixes the
behavior of `isove...
12a3aa35e767ba6efb1cf35529e5cc7f5d742bca authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
b878fd8b053be81f484890b2314eb298065783f4 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
3fb4e595834a351da9683918bb0247a103ad37c9 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
87bde7925704485c7306b1a8b7a82011a6706908 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
9e623b65093127d2fe7c6ce5aa1a67f743397d21 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
9310e8865f5296ebee98d96f1aa68dc4961b7250 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
7801b444dd157f8bd969b2e37f72d364546aca73 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
* update docs of complement
* do not use the generated function
* remove Seq. module prefixes
95e7f152c0c0453c51e9122ff3e5bca1ffec289d authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>4b8afbcd798d6dcb323afaf77ac3eb0309046238 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
8ae31b421a46e6a5e090d54aa16d040b6e0a1ae7 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
f244818f906a1bdc3c476152e5affdabc33a0083 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
960c815251eb396da7e90746f0f639b2d599cd7f authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
b82581601a55d151e932c32214ab2bc6c362ab7b authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
* update interval docs
* fix style of coverage's docstring
* remove docs that are not yet ...
d1a9c4c6efdb4fdea34f371fdd23875896f92def authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>* replace BBI files
* more relocation
* more fix
* rename bigbed to bbi
* rename big...
39b869b9fbf840a424391748be1f0ff543aa60ac authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>3aaf3c6a12fd967d103a326486be9349310a6f76 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
a85c285984dd48256e33339044f18ee8a3cf3137 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
4082b7c2e0a337cd53eb467dbba77420d858f7f7 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
de9efd885b94ed15792776c4f85960a8a75860b7 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
* Added draft is_mutation methods for Matrix{N}
* Corrected and error
* Finished draft of ...
67e1ef1a79a75a41ca27e2229fcabbf8ce7a259c authored over 8 years ago by Ben J. Ward <[email protected]>ec5e0359e115110d874774199ae433f18ff3d7c2 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
597ed6c36cb10c2300bf35a95dd0d401565f211c authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
* Small change to majorityvote
* Eliminated the branching and special cases in majorityvote a...
0d49b3c667e1f605234bc83d0973faa258a11c9f authored over 8 years ago by Ben J. Ward <[email protected]>* Added a new composition method for tuples of nucleotides.
* Added consensus method
* Cor...
ef634ed538bd37dae11647764b197aaa51fb10c5 authored over 8 years ago by Ben J. Ward <[email protected]>0d1e0d784f3e593aae3c96e87ec347b3ab8e05eb authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add src/Makefile
5f61dcca3d5dce858b97e90f3e3fdd6fafa9950a authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>560560c046806d1e9db99f1de8edd8edd52a8f61 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
* unify methods
* update docs [skip ci]
7e410a087dcd96d0f5ac6e482a1f5bb7a42147db authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>* rename position accessors of alignment records
* fixup! rename position accessors of alignm...
6eea972748eda494d8708465df48946905a6b7d8 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>11847c51a890f95cd53498f3430adcee35ebe529 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
* restructure alignment files
* add alignment(::BAMRecord)
* add alignment(::SAMRecord)
...
bfab27e1a18009c5d86f1d97539db0a253ad5b47 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>* implement open(::IO, BAM)
* add tests
a6a4b5493463060fbdf259027401317c0256f3e7 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>2f01fb24ba7917b45d7a403f08b3411d1cbec6db authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
* rename AbstractParser to AbstractReader
* rename *Parsers to *Readers
* fix docs
f79b09b2d1460a31a6bd808f4273cdddaf9c4e39 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>* Make tests that create files happen in temp dir
* Try closing files before test function en...
f2a19fe0c98ea2f3fa5821817bafc3e39a72bc8d authored over 8 years ago by Kevin Murray <[email protected]>* add BAM/SAM file formats
* add tests
* add tests on SAM
* add more tests
* clean u...
ec6d53f342f555097ac07d225549228a4f081752 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>* Added a new composition method for tuples of nucleotides.
* Added consensus method
* Cor...
648ac8ba60340c8abdb99977df288cdf31b10c5e authored over 8 years ago by Ben J. Ward <[email protected]>d97c42e4dbe2056b56e3a892d0465d56e66bc42b authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
1a73078ac721ea753c0c352ba426d33d612463d8 authored over 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
* Added extra to seqmatrix
* Removed major as an optional parameter, it is not just a paramet...
ad7e781bc0fc153045ae586b2d1d4c9f1415204d authored over 8 years ago by Ben J. Ward <[email protected]>