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

Update user manual (#160)

87f806c70a9fa861b7dc3a17f95dcc90654d2019 authored over 3 years ago by Ben J. Ward <[email protected]>

Update interface to version 3. (#161)

* Refactor internals: Part 1

* Refactor internals 2: Add Alphabet tests

* Refactor interna...

9d40795e7ed188e2257d0f455b908b523aedf2ab authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #153 from jakobnissen/readme

Remove financial backing and Gitter from README

08a67d75d9e2005caa32a6f300c20092d521c431 authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove IndexableBitVector dependency (#159)

d95fa67b6f4d4e3400bd4f19e4e33e6218e00f5d authored over 3 years ago by Ben J. Ward <[email protected]>

Remove Combinatorics dependency (#158)

80a1c3567d95eb09fb760368511cb9d7fd8410d3 authored over 3 years ago by Ben J. Ward <[email protected]>

Remove BioGenerics dependency (#157)

* Remove BioGenerics dependency

* Remove kmer string literals from documentation

1bc7932c58724a78f6afd3dba3e096dca431bdb6 authored over 3 years ago by Ben J. Ward <[email protected]>

Remove sprintf (#156)

287c0b7ee47449604910c25e30be126dccd589ac authored over 3 years ago by Ben J. Ward <[email protected]>

Remove kmer documentation

0f0a2921643fa8910141bbce9439edc4d40e14a8 authored over 3 years ago by Ben J. Ward <[email protected]>

Remove Kmers (#121)

* Remove Kmers

* Get all tests to pass without RNACodon or DNACodon

8cf14bcb2bcba8af1c8e6c624df3c8517e3b53e2 authored over 3 years ago by Ben J. Ward <[email protected]>

Add join and join! for BioSequence (#134)

* Allow indexing with all integers

* Move some indexing logic from LongSequence to BioSequenc...

c92a5f4773a2296826f131e03dc7e3faf2c02e3d authored over 3 years ago by Jakob Nybo Nissen <[email protected]>

Remove financial backing and Gitter from README

d51a551ad6478c7f3596b1cc8825315f6996357c authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Cut down on repetitive testing

Excessive repetitive testing loops have been reduced.
Longsequence test suit cut from 4559 to 26...

c67ec957e6ddd80f173714e68bce56301b98800d authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Removed VoidAlphabet

d0416903428ca2c6daa9ef18c8adac4450d1e95d authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove CharAlphabet

56d6960b4d941e19fd2070716097ae87aac4b709 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #150 from jakobnissen/removeconditer

Remove ConditionIterator

d85c8143d00badc63f45a80ed82b9eda1a52f6a5 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove ConditionIterator

929bb059bd222a48f5d1961c049d1bde4e36a67e authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #149 from jakobnissen/v3

Re-add construction between integer/kmer

347c8773bbbd9ec02e69ca3ed226f1fc37e9e44e authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Re-add construction between integer/kmer

* Conversion is still not permitted
* Construction of kmers from integers checks for overflow
* ...

c0e19b664d1c87c63f7c4b6f6fad41e42d9cebd9 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #147 from jakobnissen/kmer_integers

Remove conversion to/from integers and kmers, and direct instantiatio…

b506b4bfb164d3c627168d9ddfb35d178be39a87 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge branch 'v3' into kmer_integers

8016691c8bc563baef37c8d02aea7b5f779f375c authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove conversion to/from integers and kmers, and direct instantiation of kmers from integers.

Users should instead use `masked(::Type{T}, x::Unsigned)` to create kmers from integers, and `re...

19ae11331ef848240a5d2ccf7e60963d5d8a2701 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #146 from jakobnissen/undefinit

Remove the constructor `LongSequence{A}(::Integer)`

40a6a59925fa2f97912407caec7445d33f24d95e authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove the constructor `LongSequence{A}(::Integer)`

See issue # 142. Users should use `LongSequence{A}(undef, ::Integer)` instead.

44fbecd671aa796176ac0a09c2e63d6febf8a6f0 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #144 from jakobnissen/findsemantics

Change semantics of find to match Base

c0bf0ec2498c5a5ee7031333a7d0bf115c90c3cf authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove find methods with single biosymbols

See issue #141. Users are adviced to use `findfirst(isequal(x), seq)` instead.

e9f5b2006afb2881c4c05182c9692807c78e8536 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove bitpar compiler info messages

955b02da2b27a8a253da5af6c81227d1b25c2d1c authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Removed demultiplexer

dd268c9562866fefd1a24b8133f373ef47814c2e authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Removed ReferenceSequence

b2bbcd5c8b598ee79a8512da7dc1e61e1a8d3e95 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove composition

aa2895365c7fbcccd0c76d2b5da2c532fe016516 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove minhash

8325644cc839027bd8b3ecb6344c70b2a9e34925 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #133 from jakobnissen/multiindex

Move some indexing logic from LongSequence to BioSequence

0ba3d4b2e1dab04b77e244141501e6b33d53b975 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #136 from jakobnissen/fixcodeshow

Fix typo in genetic code show

90b4df3589d54401eed2e46de4fe65e0e59baccd authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Fix typo in genetic code show

218ba72d9e7aa19ef4a6459a67b470bf5a8a0788 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Fix dispatch

6b693c81eea96130d7a74014df727909bf65cf9c authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Move some indexing logic from LongSequence to BioSequence

09aef8fb72af0c427bd51399dad9704bd1829570 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Allow indexing with all integers

aeebe9a6b547e2b1ac3e98479b8a26f23821fd41 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #120 from jakobnissen/seqview

Add sequence view

252720879620716f5f33a54e53ffcd9716706636 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Fix tests for subseq

09d7e92cb9100df61b819a8e098439bbac7cae91 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #132 from jakobnissen/deprminhash

Deprecate minhash

ff6b93bd2e106f892c5f7c20627c3c5cb9e163a6 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #131 from jakobnissen/optimtranslate

Refactor translation

e1743d7836cd44c4df1c61f0bf20fda3e5a4d581 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Deprecate minhash

a85f6481cf64c64d6027d479db277fec4baac60a authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Optimize translation

0b2128db6b3664f51a58aeed0bace072b2dc2c99 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge branch 'master' into seqview

c5b475b1d18dc0f1f0e725351d4e8415081e0423 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Rename SeqView to LongSubSeq

7b83950f97171cb42c2093d6974b488e4d6d0a99 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Fix RC for seq with unused data (#128)

1cfc0aa5eecd38ee02bbd23ec9b24d1832223fe3 authored almost 4 years ago by Jakob Nybo Nissen <[email protected]>

Fix `ReferenceSequence` slicing bug (#125)

1617206bc5c35934b790ef28c86e96906b3e77f8 authored about 4 years ago by lhnguyen-vn <[email protected]>

Allow hamming circle around N (#126)

Allow hamming circle around N & add more tests

5c14f3f363c6a36f069ace10b352013da4cae501 authored about 4 years ago by Thomas Poulsen <[email protected]>

CompatHelper: bump compat for "StableRNGs" to "1.0" (#122)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

6f0e437e8a2382a68be845486539f8596eb874ab authored about 4 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Make same-type conversion noop (#123)

6d99f5e9cacd67d6c2284fa9e04ffc941c7d6c31 authored about 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge branch 'master' into seqview

c96ae89caaf4f4742d61048173bd42b090e2fa5a authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Add documentation; improve tests

5abe69d4bc5f447efc2fc864c00508ffbdc22463 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove LongSequence copy-on-write (#119)

* Remove COW from LongSequence

* Improve LongSequence hashing

* Simplify code further

*...

c4ad650e6b3bce5e8fe54043d045b27f772b7deb authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Improve tests

edb4b04e9590a99eff51ce940242077a3420261f authored over 4 years ago by Jakob Nissen <[email protected]>

Added SeqView

60fc0d983fa9ea3e2c4d9a3d6cc5c354daeb6259 authored over 4 years ago by Jakob Nissen <[email protected]>

Fix ambiguity error on Julia 1.0

d6907b6f758eb7774e7032cd46e6915ea7b41768 authored over 4 years ago by Jakob Nissen <[email protected]>

Amend docs, simplify hashing code

07890da9885f11f745c34720dccc6274986eff1a authored over 4 years ago by Jakob Nissen <[email protected]>

Simplify code further

aa20e87bdc4215f6bf3afb248d2d949cec15a54c authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Improve LongSequence hashing

000b96eed888c4d06c218c98023252ff7ada1f40 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #112 from cjprybol/cjp-kmer-range

Implement range slices over kmers

a13753f709b32cc7f7e04a11735eb90ae659b96a authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Remove COW from LongSequence

bfa1f49383e83784b5d2f29d1f26972892892896 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #117 from jakobnissen/master

Fix StackOverflow error on Kmer instatiation

57e85d799f3dfb45c19e24dd70856509b59e075a authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Fix StackOverflow error on Kmer instatiation

044cd848c1ba43b63b8fe864a4b38a5215f18fc5 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #116 from jakobnissen/master

Fix push!

47040c215598d985d34df6ec67e84881c8ea2249 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Fix push!

e51dd070437526e780612be1938f5a34ddbc11e7 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Update links (#113)

fd7250be20d8a56239f51d4c37637e8f34143298 authored over 4 years ago by cjprybol <[email protected]>

Update changelog and put @test macro in front of tests

7743fb5e00cdd1c4f67a8faaa060c319e64e6a6d authored over 4 years ago by Cameron Prybol <[email protected]>

Add an `end` range test

a8339df52c975a087bf8295a0f49ff6ed2006b1b authored over 4 years ago by Cameron Prybol <[email protected]>

Cleanup module names

01ba3f8b34996945488bbcbf0795ab1894124479 authored over 4 years ago by Cameron Prybol <[email protected]>

Add slicing capabilities to mers

251c42682f51db362956dce58d741f3b55403978 authored over 4 years ago by Cameron Prybol <[email protected]>

Update Project.toml

93d9462a73a4c156b7069705d0441828dcd2663f authored over 4 years ago by Ben J. Ward <[email protected]>

hotfix for reverse_complementing a slice of a longseq (#111)

* hotfix for reverse_complementing a slice of a longseq

* Implement shallow copy fix proposed...

312e27434e68f1db6b429466b29877323c12ea1c authored over 4 years ago by cjprybol <[email protected]>

Update Project.toml

01fbc26dc6209e86ec13cdee5f8598469e98ff35 authored over 4 years ago by Ben J. Ward <[email protected]>

Update copying.jl (#109)

29d77d9f9a78c04703419090d7f92c4412a91b86 authored over 4 years ago by Ben J. Ward <[email protected]>

Update Project.toml

f0848340fdcbb65ab65eb414a7d833d5f258ab4a authored over 4 years ago by Ben J. Ward <[email protected]>

Fixup addition with a BitIndex (#108)

fb8b3a7e17c4b47f807206b3be129d1357aa08fc authored over 4 years ago by Ben J. Ward <[email protected]>

Add StableRNGs Compat entry (#107)

ref https://github.com/BioJulia/BioSequences.jl/pull/106#issuecomment-638985043

f8274b062999717042f1de9cc80b9fe1e46f7251 authored over 4 years ago by Kevin Bonham <[email protected]>

Update Project.toml

aef7d6689f9109be59a3070ffd2a0a3791508110 authored over 4 years ago by Ben J. Ward <[email protected]>

Use stable RNG (#106)

07ffb8c07c75b8a2bf7505cda2e84d06995764b9 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Fix reverse_complement orphan bug (#104)

22d54a99bd6592c18f6456b2c9c37fcf28286225 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Support LTS (#101)

83adaefcbba6da8fcf367d6f763088a20f5af241 authored over 4 years ago by Ciarán O'Mara <[email protected]>

Update CompatHelper.yml

902f8bbd92d3805eb8741dda0717939f19fe4a3f authored over 4 years ago by Ben J. Ward <[email protected]>

Update index.md

96c0bbfb64980a8c5a5ee684a6a11acff7d057a8 authored over 4 years ago by Ben J. Ward <[email protected]>

Update README.md

b33f6555d18302a0e954fde5040c646260fb37bf authored over 4 years ago by Ben J. Ward <[email protected]>

Update TagBot.yml

3323c185bd82678272813074edde704bcd978bea authored over 4 years ago by Ben J. Ward <[email protected]>

Merge pull request #95 from jakobnissen/copy_interface

Revamb copy! and copyto! interface

48a05407f7bf37a4289fd3fab7885beaefc4d34e authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Bugfix copyto!

8387ce86842a13d1b6caf1f408f827aedfde6083 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #99 from jakobnissen/fasthash

Added fast hashing for kmers

260aa4b063a4bbe935c1e10251ed9e8b41b5aab7 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Added fast hashing

a662f8a4c00b26c921471dba7f046b7ba2b42be4 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Fixed tests

741834724364a8b13187d6a3a59858b1161f42b5 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Merge branch 'master' into copy_interface

db67546551776a460f3fe80e4200d31307414ef4 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Revamb copy inferface

56da9b7f6ae69023a7c6c2cf6e6581275290456a authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #97 from jakobnissen/fastrevcomp

Faster reverse and reverse complement

35e7f085c0a0b89c288f45476a474e743659c46f authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Added tests

6ddfc896a573b6c7f7bf34bcd223027560a99cea authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Merge pull request #98 from BioJulia/benjward/patch

Syntax error fix

a5654f2654d179dd6b523a288c496830b6903d28 authored almost 5 years ago by Ben J. Ward <[email protected]>

Merge branch 'master' into benjward/patch

a99c4db280a0cd31b464c26cd060641fd696a251 authored almost 5 years ago by Ben J. Ward <[email protected]>

Update change-log and add Compat entries to Project file

ef486fe1a85d980a5ba1edd754290ab335556133 authored almost 5 years ago by Ben J. Ward <[email protected]>

Have travis ci test on v1.3

f673b0690a1d801633dabb99a915c91410da6f5b authored almost 5 years ago by Ben J. Ward <[email protected]>

Increase version number

2cb9037973c4f55dd596b21399a4ba769051d8cc authored almost 5 years ago by Ben J. Ward <[email protected]>

Fix syntax error

bcaad8563a101410a25204587f22833b20391eda authored almost 5 years ago by Ben J. Ward <[email protected]>

Improve performance of bit-parallel counting methods (#96)

cf26ba9524d3a4bf3cdac5ac3a8a92adda380b07 authored almost 5 years ago by Ben J. Ward <[email protected]>