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Bebop

Create rock solid scientific software and the tools to maintain them.
Collective - Host: opensource - https://opencollective.com/bebop - Code: https://github.com/bebop

Update CHANGELOG.md

github.com/bebop/poly - 5fdb0fd75cbf1c5f60503e20d72bc7517d26d9dd authored 11 months ago by Tim <[email protected]>
Update CHANGELOG.md

github.com/bebop/poly - 86b814cf2afee535e927812640f17ab47b12618f authored 11 months ago by Tim <[email protected]>
added package level doc strings. (#441)

* added package level doc strings.

github.com/bebop/poly - f18c391f6df9fa622daa0247ec3214161b7f2423 authored 11 months ago by Tim <[email protected]>
updated CHANGELOG.

github.com/bebop/poly - 2328911d7a7967195651416faed56adb36eae8a6 authored 11 months ago by Timothy Stiles <[email protected]>
Run length bwt (#440)

* run length bwt

* better clarify mapping from original sequnce space to run space

-------...

github.com/bebop/poly - 05169d236d0ba859e846217cebb2573483cf4f61 authored 11 months ago by Trenton w Fleming <[email protected]>
Update CHANGELOG.md (#439)

github.com/bebop/poly - 324877612022ed826ce42d7b7dea11a513541799 authored 11 months ago by Tim <[email protected]>
moved align, bwt, and mash into new search package. (#438)

* moved align, bwt, and mash into new search package.

* updated import paths.

github.com/bebop/poly - b76edb9f3d4b8d599f39f6a07e3aa78f2379dac7 authored 11 months ago by Tim <[email protected]>
#360 Bwt (#411)

* basic bitvector

* jacobsons start and refactor to uint for accurate machine words

* conf...

github.com/bebop/poly - 176dd5b6c57f24f63d4ef23a57cd6483f1fef395 authored 11 months ago by Trenton w Fleming <[email protected]>
added some more test coverage to fold subpackage. (#436)

github.com/bebop/poly - 27c7d28897b8795c153f6f8504d45dfeaeff5a17 authored 12 months ago by Tim <[email protected]>
Fixing updateweights example (#435)

* generate codon table in constructor rather than at buildtime

* update tests to handle const...

github.com/bebop/poly - 43c015bd48e72e4b294492dc3373326181e86853 authored 12 months ago by Maximilien Rothier Bautzer <[email protected]>
vendored justfiles in .gitattributes. (#433)

github.com/bebop/poly - efd45404ea4d47bf6942312c8ff544d756037d31 authored about 1 year ago by Tim <[email protected]>
Ensure lint workflow uses .golangci.yml (#432)

github.com/bebop/poly - 2f26da8f7729255eec728bbdf456343314693131 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Add issue management info to CONTRIBUTING (#431)

github.com/bebop/poly - c6aec493cffed094ddf5ecdadcd768307ed0f410 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Fix coverage action (#430)

github.com/bebop/poly - b7e3a8e0231e062ed76009b0e2e575474764b70e authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Migrate to the `just` build system and add automated release tooling (#429)

* Create justfile with documentation on how to use it
* Add GitHub action to automatically make...

github.com/bebop/poly - e52eeea3491278ca60fa9ad3524371391dc9ba0d authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Fix help wanted discord webhook (#428)

github.com/bebop/poly - 74ac92bebe524dd45ba76032954981c814041529 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Comment out info lines of pull request template (#420)

github.com/bebop/poly - 80eada650a413cc72d90f6126bfd01416cba9174 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Grant blocking issues bot write access to PRs (#424)

github.com/bebop/poly - a5e8269abcf7cdaaf87dc6eb0305bc71f0a242ab authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Update tutorials no gitpod (#425)

* removed gitpod references from tutorials

* fixed typos

github.com/bebop/poly - 4a0840b36d244297e976e8be165994c45d9e60f5 authored about 1 year ago by Tim <[email protected]>
Notify on issue being labeled with help wanted (#421)

github.com/bebop/poly - 3066391fd1fc52735ea1b5f9288eaf330b2ecc26 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
removed excessive recommended extensions for vscode.

github.com/bebop/poly - e5af415c3225e2e9a8e466a694d41468bc11c2b1 authored about 1 year ago by Timothy Stiles <[email protected]>
Devops cleanup (#419)

* deprecated gitpod service.

* deprecated codeclimate workflow.

* removed excessive extens...

github.com/bebop/poly - 906dc7ed13842b889c60b1fbfafe96ce6390f83f authored about 1 year ago by Tim <[email protected]>
Bump Golang version (#401)

* Bump Golang version

* Replace ioutil references

* Update random to use new rand approach...

github.com/bebop/poly - 7b3bb48a00ef58bb741952efa6f84f8449e97c07 authored about 1 year ago by Matias Insaurralde <[email protected]>
changed parameters in .goreleaser.yml (#418)

github.com/bebop/poly - 2193867a9dbed7823d07a8fc30cbf3a291508868 authored about 1 year ago by Tim <[email protected]>
migrated namespace from TimothyStiles/poly to bebop/poly (#416)

github.com/bebop/poly - 4460c3b89a3db01dc4540372a723174d150b6114 authored about 1 year ago by Tim <[email protected]>
patched start codon regression (#414)

github.com/bebop/poly - 8ea0d047115be495f5ff178118243e8c62e3a8fc authored about 1 year ago by Tim <[email protected]>
fixed bug where linear, non-directional, single cuts were copying and not just moving overhangs from the fragment sequence. (#409)

github.com/bebop/poly - f76bf05497cb89d5a48ab0a2ac41db9cfc425d12 authored about 1 year ago by Tim <[email protected]>
fixed bug that produced wrong overhang in linear, non-directional, single cut reactions. (#408)

* fixed bug that produced wrong overhang in linear, non-directional, single cut reactions.

github.com/bebop/poly - d0f6ab370d5e0dd953567692cbb755d6fb4732ea authored about 1 year ago by Tim <[email protected]>
renamed OptimizeSequence to just Optimize. (#407)

* renamed OptimizeSequence to just Optimize.

github.com/bebop/poly - 916c92d90123b1c6171895ed947ef602ed22370b authored about 1 year ago by Tim <[email protected]>
added example test for mash usage. (#404)

github.com/bebop/poly - c9ba7f337f491956599ac3fdd10cbe83275135cf authored about 1 year ago by Tim <[email protected]>
Add FragmentWithOverhangs (#387)

* Add FragmentWithOverhangs

* Fragment naming updated

---------

Co-authored-by: Tim <Ti...

github.com/bebop/poly - 489cf9747618835d0aa9eea7f751d3ab8ab7ab50 authored about 1 year ago by Koeng101 <[email protected]>
Add stats to codon tables (#350)

* add stats to codon tables

* separate stats into its own codon analyzer struct

* stats st...

github.com/bebop/poly - 96b5cff167667ceb1f1eadb48b301ca189243706 authored about 1 year ago by Maximilien Rothier Bautzer <[email protected]>
Update README.md

github.com/bebop/poly - d87246c3d42d92b5554237abdc174fcb158851d1 authored about 1 year ago by Tim <[email protected]>
Cloning refactor and data race fix (#393)

* enzyme manager to avoid managing global state over the lifetime of a program

* clone_test -...

github.com/bebop/poly - e96a63e419525529b8408bbac5d433ab55aed18b authored about 1 year ago by Trenton w Fleming <[email protected]>
mash: optimize mash similarity function, add benchmark (#395)

* mash: optimize mash similarity function, add benchmark

Signed-off-by: Matias Insaurralde <m...

github.com/bebop/poly - 58f8699e0590e30af84e9abe857b986f26f8d3a2 authored about 1 year ago by Matias Insaurralde <[email protected]>
Add the poly Google group email as a method of contact. (#358)

* Add the poly Google group email as a method of contact.

* Update CODE_OF_CONDUCT.md

* Up...

github.com/bebop/poly - db703c301d30b27b342895379065600992abdd98 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
patched genbank parser and builder to handle BASE COUNT. (#386)

github.com/bebop/poly - 2d5d8c4551121fca4c394835efd89bffb0c3c5ca authored about 1 year ago by Tim <[email protected]>
created parser regression test for nested sublocations. (#385)

* created parser regression test for nested sublocations.

* integrating @abondrn's fix to gen...

github.com/bebop/poly - f2310dba2c5e395e747b36daa135704f8f4ecdf6 authored about 1 year ago by Tim <[email protected]>
fixed mash.NewMash to mash.New.

github.com/bebop/poly - 5bd6a5de5ff88da5b68f12b8f05591ed0b537d0c authored about 1 year ago by Timothy Stiles <[email protected]>
created mash function for sketching sequences. (#344)

github.com/bebop/poly - 2271b5d979cbad1a1f85873a0a1c79333bbde74b authored about 1 year ago by Tim <[email protected]>
Fix YAML syntax error in take.yml (#379)

github.com/bebop/poly - eacc86980baa4b5bac20944294c5d40b5131c824 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Allow non-contributors to take an issue with .take (#377)

github.com/bebop/poly - 8a9b36f68636aeb9d29ab3e544cef594e2f994bb authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Fix PCR bug (issue #279). (#378)

github.com/bebop/poly - 41a9515b164d3a1a4a062c33946adb26b065ef21 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Add CHANGELOG.md with current unreleased changes. (#371)

github.com/bebop/poly - d2ae0de98310f8b47deed62a055600c829ff507d authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Add a pull request template. (#370)

* Add a pull request template.

github.com/bebop/poly - b29c5ffe459143631fbfad71718c75396f8784e6 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Update issue templates and disable blank issues. (#368)

github.com/bebop/poly - fd4ee74967315155acf2be7eb8f59cbff0216288 authored about 1 year ago by Willow Carretero Chavez <[email protected]>
Mark issues and PRs as stale after 2 months (#354)

github.com/bebop/poly - 8e5396700a9a726ed7e4222ccaa8426956ad18a2 authored over 1 year ago by Willow Carretero Chavez <[email protected]>
Add "blocked by" relationships between issues/PRs (#353)

https://github.com/marketplace/actions/blocking-issues

github.com/bebop/poly - 1a814087acd7bd326933197ace1f955d10c0f8be authored over 1 year ago by Willow Carretero Chavez <[email protected]>
Re-enable golangci-lint.yml, turn on linters, and lint. (#343)

github.com/bebop/poly - 10b8f398c4272700dd27a177af244d6b531d2582 authored over 1 year ago by Willow Carretero Chavez <[email protected]>
fixed dev container to use most recent version of Go. (#336)

github.com/bebop/poly - ad662c741528bbb5bcaa7a3107991a86426c1e55 authored over 1 year ago by Tim <[email protected]>
add parser.line++ so error messages make sense (#332)

github.com/bebop/poly - 4049e84766aa9431af40b9863c652146c3621b62 authored over 1 year ago by Koeng101 <[email protected]>
Pileup parser (#329)

github.com/bebop/poly - 2fcf06056e7705be9d9f410ac8c03f9b649cadc9 authored over 1 year ago by Koeng101 <[email protected]>
add bit comparing alignment techniques (#330)

github.com/bebop/poly - ac04d5a01397fcc3794590dfaa091af0fd5ebd1f authored over 1 year ago by Koeng101 <[email protected]>
Ensure Non-Met start codons map to Met on translation (#322)

Also makes Translate() return an error if an invalid start codon is received

github.com/bebop/poly - 18c8a6947dac45ff66d2b4d32b2b9a0eb978626c authored over 1 year ago by Willow Carretero Chavez <[email protected]>
Update devcontainer.json

github.com/bebop/poly - b5e7023239690e65b7e5b7e8df2df6cdeb652fdb authored over 1 year ago by Tim <[email protected]>
Updated fastq to solve #325 and #323 (#326)

github.com/bebop/poly - 7ca0dcb66cf0ad63b69cc839f897755236e4cb63 authored over 1 year ago by Koeng101 <[email protected]>
Improve fragment interface (#316)

* Add checks for reverse sequence

* Add reverseComplement checker

* add comments

* Upda...

github.com/bebop/poly - f587e72731bdfebe2e452604707a4efe8906672a authored over 1 year ago by Koeng101 <[email protected]>
Seqfold (#295)

* feat: add seqfold

Add seqfold package, Go port of the python project at:
https://github.co...

github.com/bebop/poly - 4b25a31739b35d74aff235d320839e3a481c25ae authored over 1 year ago by Giacomo Tartari <[email protected]>
fix consrtm (#320)

Co-authored-by: Keoni Gandall <[email protected]>

github.com/bebop/poly - c03951edb2ed4a587068013f38b870cd7c4ff74c authored over 1 year ago by Devin Riley <[email protected]>
Update README.md

github.com/bebop/poly - ae13e0aaa6490d13bcfc2a8046336e77534301dc authored over 1 year ago by Tim <[email protected]>
Add NdeI fixing plus regression (#314)

* Add NdeI fixing plus regression

* add comment in code itself

github.com/bebop/poly - 5e9d809d24a12190305053d8259b885378ed1a8d authored over 1 year ago by Koeng101 <[email protected]>
Add checks for reverse sequence in fragment (#309)

* Add checks for reverse sequence

* Add reverseComplement checker

* add comments

* Upda...

github.com/bebop/poly - 763ad3a846be96abf6e2b8484c3e9c74152ce165 authored over 1 year ago by Koeng101 <[email protected]>
bug fix amino acid capitalization (#315)

github.com/bebop/poly - 53936a527a1021eb09e6219000e19575b1316c8e authored over 1 year ago by Koeng101 <[email protected]>
CutWithRestrictionEnzyme now cuts across origins of circular sequences (#308)

github.com/bebop/poly - ea2bc16d28d54f6e84fe15c8822ea43d519fca54 authored over 1 year ago by Koeng101 <[email protected]>
Fix #303 and add regression test (#304)

* Fix #303 and add regression test

* remove some junk from testing

* added real test

* ...

github.com/bebop/poly - e2c0e21b67cfb9eaf2203a41785369fa2ca5c073 authored over 1 year ago by Koeng101 <[email protected]>
updated example optimize (#312)

* updated example optimize

* add even better check comparing stop codons to genes

github.com/bebop/poly - bf8109ba8195ebda2a4841031893f65e5ba1bfbc authored over 1 year ago by Koeng101 <[email protected]>
Delete tweet.yml

github.com/bebop/poly - 4912e88377f76ba054ee40a4035b949f2332cbf8 authored over 1 year ago by Tim <[email protected]>
Remove redundant Linear struct member (#319)

github.com/bebop/poly - 6c9c79450d2447bb9eef8043f12e51320fc34857 authored over 1 year ago by Willow Carretero Chavez <[email protected]>
Fix spelling errors (#318)

github.com/bebop/poly - e275f86e64155dd4b91348691a5791b1f665bdeb authored over 1 year ago by Mehul Kar <[email protected]>
Update alphabet.go

github.com/bebop/poly - 039f48688f7e3e6845f4c49509b996786247225e authored over 1 year ago by Tim <[email protected]>
Alphabets and Substitution Matrices (#294)

* Add alphabet package

* Add matrix package

* improve tests

* use default matrix

* m...

github.com/bebop/poly - 7674eead88aa27f89de298d4b94d105163fe7bb5 authored over 1 year ago by Ragnor Comerford <[email protected]>
Add fastq parser (#300)

* Add fastq parser

* thank you matiasinsaurralde for speedups!

* 100% test coverage

---...

github.com/bebop/poly - 38519880dc9feb866f9ff1051b30c12c5346e8e3 authored over 1 year ago by Koeng101 <[email protected]>
Slow5 (#298)

* Added slow5 parser

* add package docs

* add better flow as suggested by matiasinsaurral...

github.com/bebop/poly - 931e546a5d19e1f021e7b50bc727c3811e78f2b1 authored over 1 year ago by Koeng101 <[email protected]>
Fix GFF parser (#302)

* fixed #152
---------

Co-authored-by: Timothy Stiles <[email protected]>

github.com/bebop/poly - 22b6bfa2ac79a93ce9d632b4b4827b7c6d72cf5c authored over 1 year ago by Toothsy <[email protected]>
fix comment typos (#296)

github.com/bebop/poly - 09599af852c2b2b7f4c7f77239022b6a876e70a3 authored almost 2 years ago by Youngsoo Sung <[email protected]>
removed gitpod badge that didn't render properly in go docs.

github.com/bebop/poly - 30b48f77dcc7fddc8649cf289d3e793a70e037a6 authored almost 2 years ago by Timothy Stiles <[email protected]>
fixed typo in documentation.

github.com/bebop/poly - 43088480443d339f09ba63899840d3aa47d80176 authored almost 2 years ago by Timothy Stiles <[email protected]>
Smith-Waterman Algorithm (#292)

Co-authored-by: Timothy Stiles <[email protected]>

github.com/bebop/poly - 94f185b7b67c4c543d27e29e59a30beffa5771ca authored almost 2 years ago by Ragnor Comerford <[email protected]>
Update LICENSE

github.com/bebop/poly - a2d8083d6ad7e88cfc7831f4b17af183bf2926e7 authored almost 2 years ago by Tim <[email protected]>
adding new alignment package and global alignment via Needleman-Wunsch (#288)

* initial implementation of global alignment via NeedlemanWunsch

* test coverage 100%

* added ...

github.com/bebop/poly - 9723a2ee595f3e1b3e4f6cd208f4b0b20831c100 authored almost 2 years ago by Tim <[email protected]>
update copyright year.

github.com/bebop/poly - f058b7b776392fbf741000dd28e7d582fe2c1030 authored almost 2 years ago by Tim <[email protected]>
Support multiple references separated by newline in rebase file (#285)

github.com/bebop/poly - e93b669647a2ea5f7b46e315926d9918fe412f35 authored about 2 years ago by palmerito0 <[email protected]>
fasta rework (#284)

* add more fasta.Parser API

* add uniprot fasta creation

* add maxLineSize argument to Par...

github.com/bebop/poly - 9fbdee21fda475cbe509dd77174a078d26dd8be6 authored about 2 years ago by Patricio Whittingslow <[email protected]>
transform: performance and test upgrades (#283)

* added transform tests
* added benchmarks
* runs 8-10X faster than previous implementation

...

github.com/bebop/poly - 07821a70c1040e66d240dbfcf7a90d8584dd29c3 authored about 2 years ago by Patricio Whittingslow <[email protected]>
Update README.md

github.com/bebop/poly - f96ebe0cdf4a237458d0854ea283cce434649d7b authored about 2 years ago by Tim <[email protected]>
Fix README installation method (#282)

New go modules requires version.

github.com/bebop/poly - fdb46d9eed05a77d11efa30d0652f98fa1a392a7 authored about 2 years ago by Patricio Whittingslow <[email protected]>
Typo in tutorial (#281)

github.com/bebop/poly - d4fcbe1d26f323591aee31f1cbdfbc38974337f8 authored about 2 years ago by jxilt <[email protected]>
fixed typo in comments.

github.com/bebop/poly - f2dcf099fea761c9d00d7fadbe50e3d92652e71c authored about 2 years ago by Tim <[email protected]>
fixed typo.

github.com/bebop/poly - b8d75a969fda6a706aa4363d9b9a69dae4e61dde authored about 2 years ago by Tim <[email protected]>
Move enzymeMap to package level, compile regular expressions only once (#273)

github.com/bebop/poly - ab57dd01d3fffea48c27859df5d4bf9c6f75883a authored about 2 years ago by Matias Insaurralde <[email protected]>
Remove unnecessary conversions (#275)

github.com/bebop/poly - 8ed8b56f78d301c024f07b07fc154f7dbd366404 authored about 2 years ago by Matias Insaurralde <[email protected]>
Precompile most of the regular expressions (#274)

github.com/bebop/poly - cff6f9ffd4c298e104d874c6a7ed9f74e2f67b6a authored about 2 years ago by Matias Insaurralde <[email protected]>
Verify JSON output in first tutorial (#272)

github.com/bebop/poly - ca24abbc04bd85d94eea5df5787c7083efdc6421 authored about 2 years ago by Leonhard Gruenschloss <[email protected]>
Open tutorial README in Gitpod (#271)

* Open tutorial README in Gitpod

* Install godef

github.com/bebop/poly - 18f9879f39ddc65e47f7309f235a723e86120350 authored about 2 years ago by Leonhard Gruenschloss <[email protected]>
Install Go Analysis Tools in Gitpod workspace (#270)

* Install Go Analysis Tools

Co-authored-by: Tim <[email protected]>

github.com/bebop/poly - d1c49c54715e87cc5c1a4013c458fd6fddde60b9 authored about 2 years ago by Leonhard Gruenschloss <[email protected]>
Rename 005-primer_design_test.go to 005_primer_design_test.go

github.com/bebop/poly - 1b342e9f12b19f3d9691b636428cf251bae8585b authored over 2 years ago by Tim <[email protected]>
Rename 005-primer-design_test.go to 005-primer_design_test.go

github.com/bebop/poly - ecea283fa059b25b8a0d61d0524e6af4f0c07779 authored over 2 years ago by Tim <[email protected]>
Update .gitpod.yml

github.com/bebop/poly - e0ed1e0993d710f3cbe13f11adf0d0bdfbb15023 authored over 2 years ago by Tim <[email protected]>
gitpod tutorial commands on startup. (#269)

* added explicit wait for tutorial startup

* added comment with issue explaining vscode -r bug.

github.com/bebop/poly - 90cc05d0fa72c3d83d1a21cc962a393bf93128a3 authored over 2 years ago by Tim <[email protected]>
fixed yml error in gitpod.yml

github.com/bebop/poly - d65de86025ae5605adfd18e9f6802862d7297bed authored over 2 years ago by Tim <[email protected]>