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

Rename of DNANucleotide, RNANucleotide, Nucleotide (#392)

* Rename of DNANucleotide, RNANucleotide, Nucleotide

* Review suggestions implemented

4e6e727cd793db5070b6ceced91bff467ca1a324 authored over 7 years ago by Ben J. Ward <[email protected]>

encourage users to use Discourse for technical questions (#389)

f76d066e23dee74f0b9ece3fb3b0ad6dd67af955 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

replace Pkg.dir calls with joinpath(dirname(...)) (#388)

d013b42ccdc6b3ceb01f86ceec2aad50672a6e09 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

Tidy import (#386)

e8db6ae0d824473ad985d3ed0b9023d8af178b3f authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

require ColorTypes.jl instead of Colors.jl (#387)

555299a6469eb11f507ce28bd93bedd6b284233d authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

selector table in docs (#385)

6aa638522e7900f4e09562c38d8934a3cd3f135c authored over 7 years ago by Joe Greener <[email protected]>

list more method names in declare.jl (#381)

7376024ccd7ada7e0be2fbf245737ac829bf79e9 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

declare Bio.distance to resolve the method name conflict (#379)

2df81a5e215a21947f0ad40363ed7c2a60d890f2 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

deactivate Coveralls (#380)

ebf7e6c5b82b965bdb09147162ed6ec92c9aa7e1 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

replace Ragel's FASTA parser with Automa's one (#376)

61d1a20ab5885ce0fefd2e7de58a3a3e67774018 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix linear index access of BAM (#360)

f80c74414d7d79df7d07cad9efeb43fa438a0f4d authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix the SAM header parser (#377)

3c6cccac1a7d886b163d431be9c5a00ced55a6d3 authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

add E-Utils (#350)

4e53aa578f0d01228a987dd4d6ce21ec6879c051 authored almost 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Fix tiny typo introduced with #372 (#374)

964c17bfca8775883a3f2b3636b718bbc84220ba authored almost 8 years ago by Kevin Murray <[email protected]>

Update documentation for Bio.Var (#372)

* Change docs to use AnyMutation not DifferentMutation

* Grammar fix in count_mutations docst...

c93a403edeacce7b90babe2581acbcbafd2b9f45 authored almost 8 years ago by Kevin Murray <[email protected]>

Update dating.jl

3a6b9666f1004ecb2143f73cf36e2fcfeb48eacb authored almost 8 years ago by Ben J. Ward <[email protected]>

Fix issue #369 (#370)

* Changed StringField from SubString constructor

* Added StringField constructor method for S...

8c7118ec1f9b009aea2cbadac3a68475c3dbeff9 authored almost 8 years ago by Ben J. Ward <[email protected]>

Minor urgent typo fix for dating.jl

23f209ded52dd4b4f434895a99c721a0779b9ac8 authored almost 8 years ago by Ben J. Ward <[email protected]>

fix resname spacing bug

79d9fbae3f4b0b6162914d4f86869617924e8b07 authored almost 8 years ago by Joe Greener <[email protected]>

fix typo (#367)

e4cf92270cff283325b33c861a530dca1b52df38 authored almost 8 years ago by Manabu ISHII <[email protected]>

fix resname spacing bug

3cf8b68167e12579c740d665f418d662c5ac75ba authored almost 8 years ago by Joe Greener <[email protected]>

Fix copy(::GFFAttributes). Fixes #363 (#364)

7f0f809bb685281bc739f8708cce47aaac9b3d66 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Changes to Phylo documentation. (#365)

* Changes to Phylo documentation.

* Minor edit to solve interpolation error

* Fixes

* F...

159b3d92dd6ac2001a5831f5cb0758a89ecb533c authored almost 8 years ago by Ben J. Ward <[email protected]>

Added more to divergence time estimation (#361)

6dd5bf9f3e60b84de8fcba3748534835861cc292 authored almost 8 years ago by Ben J. Ward <[email protected]>

fix reverse(BioSequence) (#357)

* fix reverse(BioSequence)

* fix test

403a9c96ac3c79a1c8ccbaeb76e90e042a538a2f authored almost 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Blast xml fix (#355)

* switch XML parser from EzXML

* update REQUIRE to add EzXML

* fixes to address @bicycle18...

41b7a5fe2c508f9edd778fffdfca26342b33b4fa authored almost 8 years ago by Kevin Bonham <[email protected]>

Refactored the branchlength setting and getting API. (#219)

* Refactored the branchlength setting and getting API.

* Created system for getting and setti...

d7b1876d81f74592116a2c702c72b4590479d89e authored almost 8 years ago by Ben J. Ward <[email protected]>

Merge branch 'master' of https://github.com/BioJulia/Bio.jl

8e19330a756461c4e040ffb0097e8f033a94c152 authored almost 8 years ago by Ward9250 <[email protected]>

Improved security of docs building.

dca33914c4c15a9de9bb65167f124a83880f636e authored almost 8 years ago by Ward9250 <[email protected]>

Add some tests. Fix obvious issues.

93440e947e8dd5c9580cb4bcfcc88758c01ba6a0 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Rearrange GFF3 to match other parsers.

e48772bdfe77377129864ac725ee921317cca425 authored almost 8 years ago by Daniel C. Jones <[email protected]>

add docs on GFF3 (#351)

cf2ff8546e648372b7d2f5a8efe82626823d9dad authored almost 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add GFF3 parser

44239c906ca6b10f74349612c31b43d0e900acb3 authored almost 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Get basic GFF3 parsing working.

aacd37dfcb2d8148a12e7a634044b16d56052bb0 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Fix some attributes issues.

17a9faa9118f4fca2360bdeab3857238128e35bb authored almost 8 years ago by Daniel C. Jones <[email protected]>

Optimizations.

c64cf1083223f1abc5779164593ffaabe65b2122 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Optionally save directives.

00fadb40b162e5f18a98036d7d582ef424533b53 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Handle fasta without the directive.

33dcdba1e590042f6a12c521e81e9b6e13fab47d authored almost 8 years ago by Daniel C. Jones <[email protected]>

Fix change that breaks other parsers.

ef5766f0c706f85ad4c911671eb8be03c8369822 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Unescape percent-encoded values.

6a48ca8b3c16ccb42055e93b965bdb2339cf1be9 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Deal with FASTA directives.

2fab7c94cc50a463d6ac25b8645ed7a2836bef53 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Minor fixes, add docstrings, add tests.

129c129dc5c1288c3a93603b23e5e452c9aea5e6 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Store gff attributes in a custom data structure.

17077d7fcc65bb5ba1f92e1690e8f1afd80138ac authored almost 8 years ago by Daniel C. Jones <[email protected]>

Move gff3 files for consistency.

939eb04e54555448be0e54546a9ad39503f2c9e1 authored almost 8 years ago by Daniel C. Jones <[email protected]>

Altered logo url in readme as it was broken.

f297d766c7756bbb9fdda86d0d3db402ed5e9a6b authored almost 8 years ago by Ben J. Ward <[email protected]>

Fix of Non-standard string literals (#349)

* Initial commit

* Removed return

* Incorporated both static and dynamic behaviour into th...

fde871237fcd57bc9f5054bb8c96ba2897ccf956 authored about 8 years ago by Ben J. Ward <[email protected]>

require Julia 0.5 or later (#346)

17b084d49102a468ed5e11e8e679f6567bf9b3b0 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Remove uninformative comment.

2040ebb207c152d4a8939ec224268f87ebee1de8 authored about 8 years ago by Daniel C. Jones <[email protected]>

Fix orphan! on certain certain sequences.

a0c713c13dcae5fbbd558a7c6d0f0b4156bf8a5d authored about 8 years ago by Daniel C. Jones <[email protected]>

Fix copy function for BioSequences.

322abb9da801e26ebb7c1a49bd4208bf06e9f7c4 authored about 8 years ago by Daniel C. Jones <[email protected]>

New features for Bio.Structure (#255)

* large changes to model structure and parsing; sequence; spatial functions; docs

* AtomRecor...

71c3a0bd43e39c821a90d37e07aae5af185a42d5 authored about 8 years ago by Joe Greener <[email protected]>

Sliding window distance computation (#338)

* first draft of windowed sitance computation

* Corrected typo

* Remembered to initialize ...

ad78989811179dc1fd314479f45311b90954d986 authored about 8 years ago by Ben J. Ward <[email protected]>

Direct people to biojulia.github.io/Contributing/latest for contribution guidelines (#339)

Most of our guidelines and rules ought to be consistently applied to all of the BioJulia package...

9cda5024065575609b70869cf1d97a8e9f1815a2 authored about 8 years ago by Ben J. Ward <[email protected]>

remove Compat from test/tools/runtests.jl (#336)

7d278601e84591d23101d9736279e472fd4b04b7 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

re-organize BAMRecord fields (#335)

This change reduces the number of read/writer operations when reading/writing BAM
records from ...

658d40f7d9c4dc39e427b4706db6e610aa3080d3 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

remove function names that no longer exist (#333)

84d22864b7de3c04a8fb6f9b20321843735d0769 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

remove old deprecated code (#332)

e67bebecbe1176a33c598de0983ed4f5ffb31b6e authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

remove v0.5 check branches (#331)

10cb58b3f0d200cb815ccd7b9310770863a22fae authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

make BAMIntersectIterator stateless (#330)

6062b532ca0a1534c492417ec62b4f80d5dfc75b authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

do not check ismapped when checking isoverlapping (#329)

An unmapped record may have mapped position of its mate read. This fixes the
behavior of `isove...

90017693810e36ede1fc62e5f2bc3f533f8f87e1 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

implement seqlength (#328)

12a3aa35e767ba6efb1cf35529e5cc7f5d742bca authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

make BAMReader type-stable (#325)

b878fd8b053be81f484890b2314eb298065783f4 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

clean up SAM/BAMRecord printing (#326)

3fb4e595834a351da9683918bb0247a103ad37c9 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add docstrings for BEDReader/Writer (#324)

87bde7925704485c7306b1a8b7a82011a6706908 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

simplify the show method of SAM/BAMReader (and fix a bug) (#323)

9e623b65093127d2fe7c6ce5aa1a67f743397d21 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

bump BGZFStreams dependency (#322)

9310e8865f5296ebee98d96f1aa68dc4961b7250 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix Base.iteratorsize for AbstractReader (#321)

7801b444dd157f8bd969b2e37f72d364546aca73 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add touch-ups to complement and complement! (#319)

* update docs of complement

* do not use the generated function

* remove Seq. module prefixes

95e7f152c0c0453c51e9122ff3e5bca1ffec289d authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix ismapped (#318)

4b8afbcd798d6dcb323afaf77ac3eb0309046238 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add docs on HTS tools (#315)

8ae31b421a46e6a5e090d54aa16d040b6e0a1ae7 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

swap argument order of seq2ref and ref2seq (#317)

f244818f906a1bdc3c476152e5affdabc33a0083 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

bump BufferedStreams (fix #305) (#316)

960c815251eb396da7e90746f0f639b2d599cd7f authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add more tests on Bio.Seq (#314)

b82581601a55d151e932c32214ab2bc6c362ab7b authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

update interval docs (#312)

* update interval docs

* fix style of coverage's docstring

* remove docs that are not yet ...

d1a9c4c6efdb4fdea34f371fdd23875896f92def authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Restructure BigBed files (#308)

* replace BBI files

* more relocation

* more fix

* rename bigbed to bbi

* rename big...

39b869b9fbf840a424391748be1f0ff543aa60ac authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

do not insert newlines in BAM sequence (#313)

3aaf3c6a12fd967d103a326486be9349310a6f76 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

make qualities(::BAMRecord) return a vector of Int8 (#311)

a85c285984dd48256e33339044f18ee8a3cf3137 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix eltype for BAMReader (#310)

4082b7c2e0a337cd53eb467dbba77420d858f7f7 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix show of SAM/BAM records (#309)

de9efd885b94ed15792776c4f85960a8a75860b7 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

`flagmutations` for seqmatrixes (#304)

* Added draft is_mutation methods for Matrix{N}

* Corrected and error

* Finished draft of ...

67e1ef1a79a75a41ca27e2229fcabbf8ce7a259c authored about 8 years ago by Ben J. Ward <[email protected]>

add more docstrings for Bio.Seq (#307)

ec5e0359e115110d874774199ae433f18ff3d7c2 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Rewrite the FASTQ reader (#303)

597ed6c36cb10c2300bf35a95dd0d401565f211c authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Majority vote improvement (#306)

* Small change to majorityvote

* Eliminated the branching and special cases in majorityvote a...

0d49b3c667e1f605234bc83d0973faa258a11c9f authored about 8 years ago by Ben J. Ward <[email protected]>

Improvements to mutation counting. (#287)

* Added a new composition method for tuples of nucleotides.

* Added consensus method

* Cor...

ef634ed538bd37dae11647764b197aaa51fb10c5 authored about 8 years ago by Ben J. Ward <[email protected]>

implement new IO interfaces (#302)

0d1e0d784f3e593aae3c96e87ec347b3ab8e05eb authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

move reader/writer files in src/seq (#300)

add src/Makefile

5f61dcca3d5dce858b97e90f3e3fdd6fafa9950a authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add left/right position accessor to Interval (#299)

560560c046806d1e9db99f1de8edd8edd52a8f61 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

unify methods definitions of seqname, sequence and metadata (#298)

* unify methods

* update docs [skip ci]

7e410a087dcd96d0f5ac6e482a1f5bb7a42147db authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

rename position accessors of alignment records (#297)

* rename position accessors of alignment records

* fixup! rename position accessors of alignm...

6eea972748eda494d8708465df48946905a6b7d8 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

remove hasop export (#296)

11847c51a890f95cd53498f3430adcee35ebe529 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add alignment(::SAM/BAMRecord) (#294)

* restructure alignment files

* add alignment(::BAMRecord)

* add alignment(::SAMRecord)

...

bfab27e1a18009c5d86f1d97539db0a253ad5b47 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

implement open(::IO, BAM) (#293)

* implement open(::IO, BAM)

* add tests

a6a4b5493463060fbdf259027401317c0256f3e7 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

add the Bio.IO.stream function (#292)

2f01fb24ba7917b45d7a403f08b3411d1cbec6db authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

rename parsers to readers (#290)

* rename AbstractParser to AbstractReader

* rename *Parsers to *Readers

* fix docs

f79b09b2d1460a31a6bd808f4273cdddaf9c4e39 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Make tests that create files happen in temp dir (#256)

* Make tests that create files happen in temp dir

* Try closing files before test function en...

f2a19fe0c98ea2f3fa5821817bafc3e39a72bc8d authored about 8 years ago by Kevin Murray <[email protected]>

BAM and SAM formats (#265)

* add BAM/SAM file formats

* add tests

* add tests on SAM

* add more tests

* clean u...

ec6d53f342f555097ac07d225549228a4f081752 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Create a majority vote sequence from a vector of sequences (#279)

* Added a new composition method for tuples of nucleotides.

* Added consensus method

* Cor...

648ac8ba60340c8abdb99977df288cdf31b10c5e authored about 8 years ago by Ben J. Ward <[email protected]>

add bit-op docs for nucleotides (#286)

d97c42e4dbe2056b56e3a892d0465d56e66bc42b authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

force inlining of sequence iterator (#285)

1a73078ac721ea753c0c352ba426d33d612463d8 authored about 8 years ago by Kenta Sato (佐藤建太) <[email protected]>

Extra refinement to `seqmatrix` (#284)

* Added extra to seqmatrix

* Removed major as an optional parameter, it is not just a paramet...

ad7e781bc0fc153045ae586b2d1d4c9f1415204d authored about 8 years ago by Ben J. Ward <[email protected]>