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

SIMD reverse!

8d791c00e69ce6b0e80674d0075aed3ce80afd6e authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Faster reverse and reverse complement

ee06cfcce5fa08572ed970ff48bc3d49134cd155 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Document and improve performance of resize! (#92)

* Document copy! and resize, improve resize! perf

* More tests of copy

762e309b872c5994be90ca1c3715c1d6882e1af3 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Revamb copy! and copyto! interface

6a80f8e8cb603337a7efd1e14629c3bee0fc7cc1 authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Misc fixes (#93)

bd7dd9bfc3228303ac8700dc81a7cb0c4d7f6d1c authored over 4 years ago by Jakob Nybo Nissen <[email protected]>

Faster printing (#91)

1f6706a6b04ffb070b03a0b0268206c83573512e authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

CompatHelper: add new compat entry for "Combinatorics" at version "1.0" (#89)

5beeaeaf89f321fbc6a8a75fef818c52ab859b82 authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

CompatHelper: add new compat entry for "BioGenerics" at version "0.1" (#90)

9329b55625a9d340431f19447f3ee5acc9f303ba authored almost 5 years ago by github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Add the CompatHelper

59b3f7d86746b3ec9bef19cb993d5561e771c6a3 authored almost 5 years ago by Ben J. Ward <[email protected]>

Fix orphan! bug (#88)

* Fix orphan! bug

* Optimize resize! of LongSequence

dad9fa8c1e8a219750031d62e72a8ed65f089c7a authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Add TagBot

83ef24489f36c7a214b7a0f7ecb1bfd3492c94d4 authored almost 5 years ago by Ben J. Ward <[email protected]>

Faster reverse! of LongSequence (#84)

* Faster, simpler sequence reversion

* Review 1: Faster reversion

* SIMD reversion, remove...

9d6decb0c2ba5d437cdbb5b48f93c72413131e3d authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Add copy! method to LongSequence (#87)

* Add copy! method to LongSequence

* Add seq to seq copy! method

2c84165b937c16b05380e0797d66e834349f41c0 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

More efficient ASCII/LongSequence conversion (#83)

* Move codetype trait to alphabet.jl

* Specialize constructors and encode_copy! for ascii lon...

7fc618e2f4d0c65398468623025425b4476c2309 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Faster copying of LongSeq (#85)

962958e2fa780535529f951520b9fabe5890bab4 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Update readme badges

61b8faeddb954317a1dbe67f07fd15c592fbd91d authored almost 5 years ago by Ben J. Ward <[email protected]>

Don't build docs on travis

22c1d94df386574b1e86848d0cf6e4f653db3de7 authored almost 5 years ago by Ben J. Ward <[email protected]>

Add GitHub Action for building the docs

813c8e93e9dd6cd942f81dd9d326f79eb5c9702c authored almost 5 years ago by Ben J. Ward <[email protected]>

Faster conversion to String #80

18f540d7f0eae670acf9da2e9b5f5d0f3fd6c58a authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Faster and more general kmer reverting #79

ca93ee3ed9d49c6efb455faed65897932ee38f79 authored almost 5 years ago by Jakob Nybo Nissen <[email protected]>

Add occursin method for exact searching (#76)

9bc2ba5e1072a31b45ec1c4c0fb52f0e4a6089ed authored almost 5 years ago by Peter Haverty <[email protected]>

Test on julia 1.2 in travis (#72)

a9b44f9b7e924acb92fc3d66e8c6b723bc55aa6b authored about 5 years ago by Ben J. Ward <[email protected]>

#73: rename the search page in docs to sequence_search (#74)

bb50837e86a4d65ed35c5ec1b59bb0ca75d36467 authored about 5 years ago by tanhevg <[email protected]>

Update the changelog

325cc1c56b389b9bc45ae5325d7393af8a10a884 authored about 5 years ago by Ben J. Ward <[email protected]>

Performance improvement by preallocating memory for the sketch (#67)

2a6d179e26ef1b4e2bd638d40f402217860c8a2d authored about 5 years ago by Harry Scholes <[email protected]>

Fixup some docs for Documenter jl

244b6c0326c0f3cd597df2e710586efe1a1dd803 authored about 5 years ago by Ben J. Ward <[email protected]>

Version 2 Changes (#69)

* Rename types in BioSequences (#53)

* Add unsafe_setindex for more Base.setindex methods (#5...

52652c8271926eae5a32b1640f4665555875868f authored about 5 years ago by Ben J. Ward <[email protected]>

Fix sequence search docs (#51)

* Fix search doc page

* Fix deprecated docs format specification

e54ee6b7652e64647bb326fe321be206649aaf4a authored almost 6 years ago by Isaac Virshup <[email protected]>

Prepare the changelog for release

3c12124952d26f85df9de88307e24ee5a93b4dab authored almost 6 years ago by Ben J. Ward <[email protected]>

Fixed directory indexing. (#48)

a42a40bb12d7387a79fcc4f6c74751c7b736fedb authored almost 6 years ago by Dave T. Johnson <[email protected]>

Allow translate(seq) to take a DNASequence (#47)

4de51b9f3bac83b4ab22513235b9d986fb463296 authored almost 6 years ago by kdyrhage <[email protected]>

Cap Documenter.jl to 0.19 on Travis (#50)

Documenter 0.20 will introduce breaking changes that will invalidate
existing make.jl setups. T...

7e686d93656ab48e220c51b3efd45a56fb50adb2 authored about 6 years ago by Morten Piibeleht <[email protected]>

Type specialization for faster kmer iteration (#49)

* Changed internals of kmeriterators for improved speed

Added type AbstractKmerIterator
Adde...

64fdae6e82ad9ee0f7170d1c5d0e4d525f3fe5e2 authored about 6 years ago by Jakob Nybo Nissen <[email protected]>

Correct a typo in .travis.yml

95d64dc58c034cb2a0af54f179478d585e970796 authored about 6 years ago by Ben J. Ward <[email protected]>

Update appveyor (#44)

75e664fc0a8869f3bca077e1428c249cb7e7355c authored about 6 years ago by Ben J. Ward <[email protected]>

Fixup documentation

19a8dfab5875cee937cbb34c94aeaee28e7a8d12 authored about 6 years ago by Ben J. Ward <[email protected]>

Version 1.0 changes (#42)

f4fcf6368f9157d7393436d3689bc1f11d4054da authored about 6 years ago by Ben J. Ward <[email protected]>

Fix deprecations (#38)

df2ed6f0d05e8637e03bcd57789f177f78b93347 authored over 6 years ago by femtocleaner[bot] <femtocleaner[bot]@users.noreply.github.com>

Contributing files rollout (#37)

* Rollout file CONTRIBUTING.md

* Rollout file CODE_OF_CONDUCT.md

* Rollout file .github/PU...

6622f2513f15876f68dd506510777bf40f25aed0 authored over 6 years ago by Ben J. Ward <[email protected]>

Added BioCore.sequence with ability to specify type (#34)

35c6414ac7792c40d6886927900ce9cbbf7dbb1b authored over 6 years ago by Ben J. Ward <[email protected]>

Add changelog

ff52b992003117edd5b2f35b00fdbada16147174 authored over 6 years ago by Ben J. Ward <[email protected]>

Bugfix: Writing FASTA sequences when width <= 0 (#33)

* Bugfix: Writing FASTA sequences when with <= 0

A typo / bracket error prevented writing seq...

0c3a698c178cbf79f2fd2fa45bd4a46e8e051a99 authored over 6 years ago by Ben J. Ward <[email protected]>

Message printed when sequence is empty. (#31)

8bffb31d747a04206479704919a754e3b097c8e3 authored almost 7 years ago by Ben J. Ward <[email protected]>

implement bit-parallel GC counter (#29)

f42bf8c8fac2468a6927d18a12c714f40ec0f357 authored almost 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

fix type definition keywords (#28)

bec2ae2001c5fc943214d0ceafd2519d11dcd865 authored almost 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

Update documentation generation (#26)

57c2810ccd36f6d0beb411603759f96851832404 authored about 7 years ago by Ben J. Ward <[email protected]>

Syntax change and News File addition.

Syntax change and News File addition.

097299644055033a9f2df174f23e170ee30a6de1 authored about 7 years ago by Ben J. Ward <[email protected]>

add position weight matrix search (#16)

501fce82de6e368b3aff84f8d8a1a0fbbd0eeba4 authored about 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

[WIP] Add unique sequence counting function (#22)

* Add unique sequence counting function

* Changed method to a generalised composition method....

45e5533d9f5305bc9016d5e9cd2cb20119667318 authored about 7 years ago by Ben J. Ward <[email protected]>

use Dict to store counts in Composition (#21)

This is a little bit slower than using Vector but it is able to store
counts of long k-mers wit...

33288b34b3ccb9992a930901fe646f7a98a6f807 authored about 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

Make minhash function for generic reader (#19)

* add fastq reader to minhash

* Use AbstractReader

08793354ba0950fe7c38d1d61dc4b687bd74fb93 authored about 7 years ago by Kevin Bonham <[email protected]>

add typemin and typemax for Kmer (#20)

e419533daf8334c9b4e84cbf83095278229c3c91 authored about 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

update doctests for Julia 0.6 (#18)

c1eaf0fd27f2e142ee32d838f9a6d1fb9b113817 authored about 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

Drop Julia 0.5 (#17)

* Julia 0.6 edits to files

* Update the CI configs

* Update syntax in alphabet.jl

* Rem...

da650d5a5e8303f8b7540925ccd7f09e30653ad9 authored about 7 years ago by Ben J. Ward <[email protected]>

[Review] Drop Julia 0.5 (#17)

* Julia 0.6 edits to files

* Update the CI configs

* Update syntax in alphabet.jl

* Rem...

6e8a2f8697f73cb25e70bdc647d212dd4e84624f authored about 7 years ago by Ben J. Ward <[email protected]>

Use IterTools instead of Iterators (#13)

f7f4d882f1c8475a06b264fc4a10bf8f14d16c7a authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

README update

37ee404877a53c7948f808624ea5dc9c113cbd74 authored over 7 years ago by Ben J. Ward <[email protected]>

Added diag_val

3c02bfe7cf8999ce191adcc93f4a7aaf6beb88ce authored over 7 years ago by Ben J. Ward <[email protected]>

Site counting hotfix

3904c46d6f513dae3cb13c533c46251e09adff5a authored over 7 years ago by Ben J. Ward <[email protected]>

Added codecov badge

9dadb5e21848c39066af36b903abb636f8419ff2 authored over 7 years ago by Ben J. Ward <[email protected]>

An eachkmer iterator fix (#8)

* eachkmer alterations

* use iscertain

* Added test for gap excluding.

* A simplificati...

992a8108e1025d9093790453aa9e8972b84878aa authored over 7 years ago by Ben J. Ward <[email protected]>

print info only when interactive (#9)

729191ebbbe5f01282df1ab3deabb7beb4d399eb authored over 7 years ago by Kenta Sato (佐藤建太) <[email protected]>

Added convenience method for removing gaps from a sequence. (#7)

* Added conveinience method for removing gaps from a sequence.

* test alterations

78b39b15393bea472ad3abc96376f2b54cc6417d authored over 7 years ago by Ben J. Ward <[email protected]>

require Compat 0.18

42ddf3880a20ca41df75edbe9d667b003c5db641 authored over 7 years ago by Kenta Sato <[email protected]>

drop dependency on PairwiseListMatices.jl

634cb3d65fc13cf38b5fc1d08710c2ccc032981c authored over 7 years ago by Kenta Sato <[email protected]>

replace takebuf_string

67d34f823476e772f2fc2e8a7638e42591b03117 authored over 7 years ago by Kenta Sato <[email protected]>

fixup! fix inner constructors of parametric types

4dc89f5f9e6314228338e0bb4db347ef0218ab30 authored over 7 years ago by Kenta Sato <[email protected]>

fixup! fixup! fix inner constructors of parametric types

1d8c666519046ca964163e6196be9b4bccacffc8 authored over 7 years ago by Kenta Sato <[email protected]>

fix deprecated type declarations

0527308eea772278619994fbc1c008f5e04a5bc0 authored over 7 years ago by Kenta Sato <[email protected]>

use Vector{T} syntax

4b1a26dcd1fd774e6dd8438cbe71dd33d8f5066c authored over 7 years ago by Kenta Sato <[email protected]>

replace takebuf_array

a169a985c1d821b854d128621aa895332b571082 authored over 7 years ago by Kenta Sato <[email protected]>

replace repeated with fill

dd1159ddbb0b0ae459974fc69a664c60ef1296a2 authored over 7 years ago by Kenta Sato <[email protected]>

test on Julia 0.6 as well

0e3c236e8de1e7d5a14e1c85e3d9f2961aa96bd3 authored over 7 years ago by Kenta Sato <[email protected]>

escape a macro

cae7eee6c9bb2756f7d0f8c18a182ebe3e13c4fa authored over 7 years ago by Kenta Sato <[email protected]>

run appveyor on Julia 0.6 as well

5b228ea37609b55f7465242b86a73cd25a87818d authored over 7 years ago by Kenta Sato <[email protected]>

replace $ with \xor

076cb37430c75326637c8b8e3369f71b9eaf8492 authored over 7 years ago by Kenta Sato <[email protected]>

fix inner constructors of parametric types

a345ec8575bfebcff0d782b4a01899107770b5c4 authored over 7 years ago by Kenta Sato <[email protected]>

Merge branch 'release-0.5'

53f86d0e49cd5fbc52607367b89b05f9619cb2ea authored over 7 years ago by Ben J. Ward <[email protected]>

use dirname(@__FILE__) instead of Pkg.dir in one more location

missed this one

9707e3b3545184ba9303f5da1fc991a3ed4996f5 authored over 7 years ago by Tony Kelman <[email protected]>

check gap existence before making a kmer

175b615ab992f584167b896525b0688e0e21ab56 authored over 7 years ago by Kenta Sato <[email protected]>

use dirname(@__FILE__) instead of Pkg.dir (#2)

* use dirname(@__FILE__) instead of Pkg.dir

this allows the package to be installed and loade...

8bcf4a068bb42417a279387ae7ad172db2c7aebe authored over 7 years ago by Tony Kelman <[email protected]>

Added a contributing page to the docs

b9196104fc119486b15b9c9ea865f84c0e144885 authored over 7 years ago by Ben J. Ward <[email protected]>

edited mkdocs file

1e3828cd42f316ac54bd74ae85fe1439df659e7b authored over 7 years ago by Ben J. Ward <[email protected]>

added twobit manpage

77a28391a7d939863613c7d4621359713b870e79 authored over 7 years ago by Ben J. Ward <[email protected]>

Added docstring to source

cd1d70f51a0990ce2f35bfface4f021a831d2267 authored over 7 years ago by Ben J. Ward <[email protected]>

Added FASTQ documentation

8f2f4320a69816c947861222e1130af45f0fb37b authored over 7 years ago by Ben J. Ward <[email protected]>

Added doc lines to source

d5446d9811b95c441428aaf25311aea5fbcf3a3e authored over 7 years ago by Ben J. Ward <[email protected]>

Added FASTA to documentation

411a518e9b285e4b468bad97db7f51705e949233 authored over 7 years ago by Ben J. Ward <[email protected]>

Documentation changes

9b824e15ca25f8bc626397e27065581955264f05 authored over 7 years ago by Ben J. Ward <[email protected]>

Added doc src files

cdb56cb8ac6be65e62f9b246c13a44fa409f524c authored over 7 years ago by Ben J. Ward <[email protected]>

added appveyor.yml

cb038f3ccbb7e391d8abe7c30a47cbe1e5dae918 authored over 7 years ago by Ben J. Ward <[email protected]>

Moved quality string tests to FASTQ tests.

5d48462cf8a2da70348ccbb951d2c46398719f16 authored over 7 years ago by Ben J. Ward <[email protected]>

Added WriteRecord to 2bit

fe4f567479e266d7ad4a311a64a76d132e08d9d1 authored over 7 years ago by Ben J. Ward <[email protected]>

test fixups

4f56b4c73b81540f36c28803f07001d9bf9189a5 authored over 7 years ago by Ben J. Ward <[email protected]>

Added quality string tests

e823f4b728283e3fefbccf4569f5401157c4a73f authored over 7 years ago by Ben J. Ward <[email protected]>

Added organised IO tests

8d8a94d52aa91898a604b89df36470b79d834957 authored over 7 years ago by Ben J. Ward <[email protected]>

Added demultiplexer tests

2f032813b7afce035728694016e4686c74e58746 authored over 7 years ago by Ben J. Ward <[email protected]>

Added translation tests

939701eb65bb0c4f4e49dd1bc4c7b485d5de6a0d authored over 7 years ago by Ben J. Ward <[email protected]>

Added organised search tests

0bc0e7ac41675dc33d97c57e2847102f3679f0ba authored over 7 years ago by Ben J. Ward <[email protected]>

Added organised kmer tests

e506bf128df540a9afa1cd557ba04dcb012af8dc authored over 7 years ago by Ben J. Ward <[email protected]>