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BioJulia

Bioinformatics and Computational Biology in Julia
Collective - Host: opensource - https://opencollective.com/biojulia - Website: https://biojulia.net - Code: https://github.com/BioJulia

add SAM and BAM to README.md (#402)

github.com/BioJulia/Bio.jl - a405c0f62d916cd21e290d3dac1e3af83f44feb9 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Only delay deletion on non-merge closings.

github.com/BioJulia/attobot - ca4fda5358068c2ea73af6c6e91aab7654ac05f4 authored over 7 years ago by Simon Byrne <[email protected]>
Improve parsing of semver, add small delay before deleting branches.

github.com/BioJulia/attobot - 0fd3c39ffc4bf2d3fc45c4242f314d6440cae332 authored over 7 years ago by Simon Byrne <[email protected]>
add some VCF (#18)

github.com/BioJulia/BioFmtSpecimens - 23d7ad05e965ecb60c7cdb856f738af3d23a2e26 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Rewrite SAM reader (#399).

github.com/BioJulia/Bio.jl - b0456c2dce758038bb2e910fbe592538b77fe00e authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
drop 0.5 prerelease support

github.com/BioJulia/BGZFStreams.jl - a2167ba32d33f119dee25288e84dc38825ccc2a1 authored over 7 years ago by Kenta Sato <[email protected]>
fix primitive type definition (#9)

github.com/BioJulia/BGZFStreams.jl - 1f1c02cad97baa12b2fa07a5dbc2e61ca423c0b2 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
tweak DOT print

github.com/BioJulia/Automa.jl - ede4e3c80494ed3882d688374de1b144f1a5df27 authored over 7 years ago by Kenta Sato <[email protected]>
fix deprecated bitstype syntax (#10)

github.com/BioJulia/Automa.jl - 916c739b645c7b63359abf68612d52f5054d02b0 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix distinct node detection. (#9)

github.com/BioJulia/Automa.jl - ab296915fe6b2a1211b541fa8c37e9bac998a0be authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
make action ordering more intuitive (#8)

github.com/BioJulia/Automa.jl - 86946cc4c8d37e51b8f39212f13d5f4273b5e27f authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix off-by-one position problem of the goto codegen (#6)

github.com/BioJulia/Automa.jl - 52ef7eac03d47564aa60045e6b5849c20f2de9fe authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
bump up code coverage

github.com/BioJulia/Automa.jl - 125dd728ffff04d79753d6696299cd8194b72e3d authored over 7 years ago by Kenta Sato <[email protected]>
Redesign internals to support more features and reduce codegen time. (#5)

github.com/BioJulia/Automa.jl - 789b615a62f8bfe8a379e97807e9d78a34d00383 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Merge pull request #24 from yuyichao/0.6

Fix depwarns on 0.6

github.com/BioJulia/Codecs.jl - 3413ecbd244dd34a04b67a95035762088588c137 authored over 7 years ago by Randy Zwitch <[email protected]>
Fix depwarns on 0.6

github.com/BioJulia/Codecs.jl - e11759141e9c357a6f90ffcb900805a6cb6b7d5e authored over 7 years ago by Yichao Yu <[email protected]>
added limit to IntervalTrees REQUIRE

github.com/BioJulia/Bio.jl - 4fe533a46f9a1ef176e0e43aa074a5451594d994 authored over 7 years ago by Ben Ward <[email protected]>
Added convert/outer constructor method (#23)

github.com/BioJulia/IntervalTrees.jl - 1f5b320d5a5260b28c88e4d57c21db8c787a80af authored over 7 years ago by Ben J. Ward <[email protected]>
fix linear index access of BAM, fundamentally (#395)

The previous commit (049ed2df1780b0218f00db63bbb73ef3c1a13249) fixes a special
case but this wi...

github.com/BioJulia/Bio.jl - a781f21e085718bb4c43f42cb11c6756c4d8f3d0 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Edited so mkdocs-biojulia nav has link to biojulia.github.io

github.com/BioJulia/mkdocs-biojulia - a843281bbb5c0b32378e9dc447323af7504e6628 authored over 7 years ago by Ben J. Ward <[email protected]>
Update nav.html

github.com/BioJulia/mkdocs-biojulia - ee8f361106f0e0a2301cc113076b8b5fac9f64db authored over 7 years ago by Ben J. Ward <[email protected]>
deprecate DNA/RNANucleotide (#393)

github.com/BioJulia/Bio.jl - 4fcda96eca376cc7417c2db11351c4de59552860 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Rename of DNANucleotide, RNANucleotide, Nucleotide (#392)

* Rename of DNANucleotide, RNANucleotide, Nucleotide

* Review suggestions implemented

github.com/BioJulia/Bio.jl - 4e6e727cd793db5070b6ceced91bff467ca1a324 authored over 7 years ago by Ben J. Ward <[email protected]>
fix label print

github.com/BioJulia/Automa.jl - 4c369b31875ffef5f31820054359519a47ad80eb authored over 7 years ago by Kenta Sato <[email protected]>
Fix 0.6 primitive type declaration depwarn (#47)

github.com/BioJulia/Libz.jl - b9f5ed514ec37917d9f20c6760edbfd837a8fda6 authored over 7 years ago by Yichao Yu <[email protected]>
Refactor (#4)

* use pairs for transition

* relocate code

* add traverser

* add DFATransition

* mor...

github.com/BioJulia/Automa.jl - d67ec74d06944cb9d50be775d012eee82e29f407 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
encourage users to use Discourse for technical questions (#389)

github.com/BioJulia/Bio.jl - f76d066e23dee74f0b9ece3fb3b0ad6dd67af955 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
replace Pkg.dir calls with joinpath(dirname(...)) (#388)

github.com/BioJulia/Bio.jl - d013b42ccdc6b3ceb01f86ceec2aad50672a6e09 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Fix trans macro for parser changes on Julia 0.6 (#45)

github.com/BioJulia/Libz.jl - 0b5d734dc3a1020f9ea2e2c0f0796e271c77959c authored over 7 years ago by Andreas Noack <[email protected]>
Tidy import (#386)

github.com/BioJulia/Bio.jl - e8db6ae0d824473ad985d3ed0b9023d8af178b3f authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
require ColorTypes.jl instead of Colors.jl (#387)

github.com/BioJulia/Bio.jl - 555299a6469eb11f507ce28bd93bedd6b284233d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
selector table in docs (#385)

github.com/BioJulia/Bio.jl - 6aa638522e7900f4e09562c38d8934a3cd3f135c authored over 7 years ago by Joe Greener <[email protected]>
update README

github.com/BioJulia/Automa.jl - be25f9a8b10ef8ba7cafc0ed2a73da5f72bb4f5f authored over 7 years ago by Kenta Sato <[email protected]>
add branch deleter

github.com/BioJulia/attobot - ebecfcf3d6449c65a721720d5db3c8d9b9556aff authored over 7 years ago by Simon Byrne <[email protected]>
refactor rewrite_special_macros

github.com/BioJulia/Automa.jl - f3de43bbf028cdf2b72b7683c3715b43f5279d31 authored over 7 years ago by Kenta Sato <[email protected]>
list more method names in declare.jl (#381)

github.com/BioJulia/Bio.jl - 7376024ccd7ada7e0be2fbf245737ac829bf79e9 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Added guideline for methods shared among submodules.

github.com/BioJulia/Contributing - 9bd6642b991a9bee290fb3b420f34a071b900181 authored over 7 years ago by Ben J. Ward <[email protected]>
declare Bio.distance to resolve the method name conflict (#379)

github.com/BioJulia/Bio.jl - 2df81a5e215a21947f0ad40363ed7c2a60d890f2 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
deactivate Coveralls (#380)

github.com/BioJulia/Bio.jl - ebf7e6c5b82b965bdb09147162ed6ec92c9aa7e1 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
Performance improvement of the compiler (#3)

* check haskey

* use vector

* limit key range

* wip: reduce_states

* check haskey se...

github.com/BioJulia/Automa.jl - 7a42d8e4ebb490f6f6ec645d6677289331610595 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
replace Ragel's FASTA parser with Automa's one (#376)

github.com/BioJulia/Bio.jl - 61d1a20ab5885ce0fefd2e7de58a3a3e67774018 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix linear index access of BAM (#360)

github.com/BioJulia/Bio.jl - f80c74414d7d79df7d07cad9efeb43fa438a0f4d authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
add a BAM file (#17)

https://github.com/BioJulia/Bio.jl/pull/360

github.com/BioJulia/BioFmtSpecimens - 0a7875f7781f629857260264e5e01119472946b4 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix the SAM header parser (#377)

github.com/BioJulia/Bio.jl - 3c6cccac1a7d886b163d431be9c5a00ced55a6d3 authored over 7 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix numbers.jl

github.com/BioJulia/Automa.jl - 85b99163533edb1a7c7ac354d085aa6f2dbbe0de authored almost 8 years ago by Kenta Sato <[email protected]>
update docs

github.com/BioJulia/Automa.jl - db1fe54e7bdb0ae9060877b948f7c08591acf323 authored almost 8 years ago by Kenta Sato <[email protected]>
fix path of figure

github.com/BioJulia/Automa.jl - 525466544397fb408521c8acfafb22bcc3b3d766 authored almost 8 years ago by Kenta Sato <[email protected]>
add more comments on example/fasta.jl

github.com/BioJulia/Automa.jl - 61ecd9791e186a832bd4ba3075d10e72bd36f9ce authored almost 8 years ago by Kenta Sato <[email protected]>
fix the style of labels

github.com/BioJulia/Automa.jl - 7809e69ec9097324c94f807aafc257b27f8e66a9 authored almost 8 years ago by Kenta Sato <[email protected]>
do not check bounds for the current state

github.com/BioJulia/Automa.jl - c5d722d193df0d3ec1ca64378d6b1c6a7a0ce6ec authored almost 8 years ago by Kenta Sato <[email protected]>
add E-Utils (#350)

github.com/BioJulia/Bio.jl - 4e53aa578f0d01228a987dd4d6ce21ec6879c051 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix dot label printer

github.com/BioJulia/Automa.jl - c4bff57835858494bdaaa774484d7252c34df8eb authored almost 8 years ago by Kenta Sato <[email protected]>
update docs

github.com/BioJulia/Automa.jl - c075ad0591a4765b68c3ae14e8435869b8b19e67 authored almost 8 years ago by Kenta Sato <[email protected]>
add clean option to the code generator

github.com/BioJulia/Automa.jl - 7a404a8d2643dce192d2e7e0a1b266e4eb7287bf authored almost 8 years ago by Kenta Sato <[email protected]>
do not emit empty action code

github.com/BioJulia/Automa.jl - b738d1c07e91c92caa6742c0ab0c79aa539388af authored almost 8 years ago by Kenta Sato <[email protected]>
remove ns variable

github.com/BioJulia/Automa.jl - 729391ee7beb71596475ab013a178805e20f9c2d authored almost 8 years ago by Kenta Sato <[email protected]>
loosen Compat requirement

github.com/BioJulia/Automa.jl - bda5112f769aabc2d0eb30da637cd3136e4d092b authored almost 8 years ago by Kenta Sato <[email protected]>
refactor the getbyte code generator

github.com/BioJulia/Automa.jl - b53d51199697b4519fae3a003826e7a03269cf6c authored almost 8 years ago by Kenta Sato <[email protected]>
generate flatter code in the goto code generator

github.com/BioJulia/Automa.jl - 346f0929d81919a151dddc8519bcfe44848e94ce authored almost 8 years ago by Kenta Sato <[email protected]>
add goto code generator

github.com/BioJulia/Automa.jl - 7d22028c1e3b6b7455d228f2000d8e8c854ec69f authored almost 8 years ago by Kenta Sato <[email protected]>
Fix tiny typo introduced with #372 (#374)

github.com/BioJulia/Bio.jl - 964c17bfca8775883a3f2b3636b718bbc84220ba authored almost 8 years ago by Kevin Murray <[email protected]>
add docs badge

github.com/BioJulia/Automa.jl - 35cd6528e6d4ff5d4a06fcacb043c3a227140bc0 authored almost 8 years ago by Kenta Sato <[email protected]>
fix deploydocs

github.com/BioJulia/Automa.jl - d1eeac13ed2ec1bed5f2bf0f9d348e08a1e8e1af authored almost 8 years ago by Kenta Sato <[email protected]>
fix julia version in .travis.yml to deploy docs

github.com/BioJulia/Automa.jl - 486c323ac576418fa966e8d7e019b54628f4a304 authored almost 8 years ago by Kenta Sato (佐藤 建太) <[email protected]>
fix deprecated xor syntax

github.com/BioJulia/Automa.jl - cb842eae9fa1b56b389c1803eae936d98ffd386d authored almost 8 years ago by Kenta Sato <[email protected]>
do not run coverall

github.com/BioJulia/Automa.jl - 4d90c1c5212247455449eab448e7870d9698b364 authored almost 8 years ago by Kenta Sato <[email protected]>
update .gitignore

github.com/BioJulia/Automa.jl - 36663a1c1dac9132a97ebfe00c79c1704bafa187 authored almost 8 years ago by Kenta Sato <[email protected]>
add docs deployment

github.com/BioJulia/Automa.jl - 3bb8bc2249ba63372d43c3a63ca2e437a42a5874 authored almost 8 years ago by Kenta Sato <[email protected]>
add more details about machine execution

github.com/BioJulia/Automa.jl - e9adce9d07eacb3ff0e2a3e0b7874f6109b8206c authored almost 8 years ago by Kenta Sato <[email protected]>
add more tests

github.com/BioJulia/Automa.jl - 08c14b2e66f447eae4a5aa1a794836013febe79e authored almost 8 years ago by Kenta Sato <[email protected]>
do not export anything

github.com/BioJulia/Automa.jl - 5ebb556c70c0257a2e3e9481f3210d1b23549a4c authored almost 8 years ago by Kenta Sato <[email protected]>
make p point at the last read byte when failed

github.com/BioJulia/Automa.jl - 3ca76e58b8977d21f36b1523d3a43976ab851712 authored almost 8 years ago by Kenta Sato <[email protected]>
do not reset the state variable after EOF

github.com/BioJulia/Automa.jl - 54c343f0cda086a3aadc6805d40e9ef7dfe3b8c4 authored almost 8 years ago by Kenta Sato <[email protected]>
do not the zero state in final states

github.com/BioJulia/Automa.jl - 41cb98ceea51431ddac004b538e7e23388205bed authored almost 8 years ago by Kenta Sato <[email protected]>
remove coverall

github.com/BioJulia/Automa.jl - 29ae89fcd25acaab99d23f25bc05375c97e82823 authored almost 8 years ago by Kenta Sato <[email protected]>
Update documentation for Bio.Var (#372)

* Change docs to use AnyMutation not DifferentMutation

* Grammar fix in count_mutations docst...

github.com/BioJulia/Bio.jl - c93a403edeacce7b90babe2581acbcbafd2b9f45 authored almost 8 years ago by Kevin Murray <[email protected]>
add more tests

github.com/BioJulia/Automa.jl - 625c448a9f71a04f6334b3a10b1955156cc0c962 authored almost 8 years ago by Kenta Sato <[email protected]>
remove an unused function

github.com/BioJulia/Automa.jl - 8fc2685c6e24b850c16f51694560f59a6592d29d authored almost 8 years ago by Kenta Sato <[email protected]>
remove dead code in label2str

github.com/BioJulia/Automa.jl - 7668b046a9c9e27f4381f152d1932f568e9798ae authored almost 8 years ago by Kenta Sato <[email protected]>
hide dot writing code in comment

github.com/BioJulia/Automa.jl - 0a01166d5e0ac1462bfa82589ff3a5351f5efb1a authored almost 8 years ago by Kenta Sato <[email protected]>
test show(machine)

github.com/BioJulia/Automa.jl - b26006b8cd95f273cf77f9637b28c3bd8788e593 authored almost 8 years ago by Kenta Sato <[email protected]>
remove sorted_action_names

github.com/BioJulia/Automa.jl - dc1a53a8c45368a68d398712ba8fd7fa78b188f1 authored almost 8 years ago by Kenta Sato <[email protected]>
fix dfa2machine

github.com/BioJulia/Automa.jl - 857cbd4b3aa57d3598d11b3927496c51c4580d65 authored almost 8 years ago by Kenta Sato <[email protected]>
rename int to dec in numbers.jl

github.com/BioJulia/Automa.jl - f4a4a4aab1f92c83adee047b14e83412db3835c6 authored almost 8 years ago by Kenta Sato <[email protected]>
use default dict in RE

github.com/BioJulia/Automa.jl - 3a2d02753764f7ca0c9d77ae4892537013496c75 authored almost 8 years ago by Kenta Sato <[email protected]>
Update dating.jl

github.com/BioJulia/Bio.jl - 3a6b9666f1004ecb2143f73cf36e2fcfeb48eacb authored almost 8 years ago by Ben J. Ward <[email protected]>
run dfa2dot in tests

github.com/BioJulia/Automa.jl - 9df475fed201fd6d30bda01b6730c3b705874e18 authored almost 8 years ago by Kenta Sato <[email protected]>
remove takebuf_string

github.com/BioJulia/Automa.jl - 499c74a1d360296cc06ba334fc406d7a3971441c authored almost 8 years ago by Kenta Sato <[email protected]>
fix deprecated syntax

github.com/BioJulia/Automa.jl - d93bc2105e57a0a95f8bae8cd4f9717edd09d3f8 authored almost 8 years ago by Kenta Sato <[email protected]>
update README

github.com/BioJulia/Automa.jl - ff04b9a9f65847c6db98070ec670c72b4f921d45 authored almost 8 years ago by Kenta Sato <[email protected]>
update example in README

github.com/BioJulia/Automa.jl - 16813482949bdd951b5c5d699361326eedb6d437 authored almost 8 years ago by Kenta Sato <[email protected]>
update examples

github.com/BioJulia/Automa.jl - 19e22859019db3ae7606829ed22fe93bb583f755 authored almost 8 years ago by Kenta Sato <[email protected]>
update LICENSE

github.com/BioJulia/Automa.jl - 446ef1ca8d150d9f524807291f486a1b6799acc2 authored almost 8 years ago by Kenta Sato <[email protected]>
fix regular expression of numbers.jl

github.com/BioJulia/Automa.jl - 9422aac17a2008f4361a449bb3250c321ff0d693 authored almost 8 years ago by Kenta Sato <[email protected]>
add docs

github.com/BioJulia/Automa.jl - 3c69c0a5bcaa99f8173f7303233cc64b261c6f2e authored almost 8 years ago by Kenta Sato <[email protected]>
add execute

github.com/BioJulia/Automa.jl - b31484fa53783f55c2d0522dcbd937849acbe8cc authored almost 8 years ago by Kenta Sato <[email protected]>
add show method for Machin

github.com/BioJulia/Automa.jl - 25a34434a27fb6fcaca16015c318fb353462b0fb authored almost 8 years ago by Kenta Sato <[email protected]>
fix example/numbers.jl

github.com/BioJulia/Automa.jl - 9cfa73448ed2fedfb3b338d73145ad21fb06876b authored almost 8 years ago by Kenta Sato <[email protected]>
Merge branch 'master' of github.com:attobot/attobot

github.com/BioJulia/attobot - 040e8abbc3887e67e5bc70469eac9cf281968f42 authored almost 8 years ago by Simon Byrne <[email protected]>
allow for missing requires files

github.com/BioJulia/attobot - 7585284f83865038fa9ca2fbf5b2729174cf4635 authored almost 8 years ago by Simon Byrne <[email protected]>