bebop/poly issues and pull requests

#444 - Update README.md

Pull Request - State: closed - Opened by TimothyStiles 20 days ago

#443 - Tutorial refactor

Pull Request - State: open - Opened by TimothyStiles 20 days ago

#442 - Turn on `revive` linter in golangci config

Issue - State: open - Opened by carreter 4 months ago - 1 comment
Labels: enhancement, help wanted, good first issue, devops, low priority, stale

#441 - added package level doc strings.

Pull Request - State: closed - Opened by TimothyStiles 4 months ago

#440 - Run length bwt

Pull Request - State: closed - Opened by TwFlem 4 months ago

#439 - Update CHANGELOG.md

Pull Request - State: closed - Opened by TimothyStiles 4 months ago

#438 - moved align, bwt, and mash into new search package.

Pull Request - State: closed - Opened by TimothyStiles 4 months ago

#437 - Genbank parser rewrite

Pull Request - State: open - Opened by carreter 4 months ago - 1 comment

#436 - added some more test coverage to fold subpackage.

Pull Request - State: closed - Opened by TimothyStiles 4 months ago

#435 - Fixing updateweights example

Pull Request - State: closed - Opened by cachemoi 5 months ago

#434 - Genbank parser needs heavy refactor or a rewrite

Issue - State: open - Opened by carreter 5 months ago - 8 comments
Labels: enhancement, medium priority, hard, stale

#429 - Migrate to the `just` build system and add release tooling

Pull Request - State: open - Opened by carreter 5 months ago - 1 comment

#428 - Fix help wanted discord webhook

Pull Request - State: closed - Opened by carreter 5 months ago

#427 - Fix discord help wanted notifications

Pull Request - State: closed - Opened by carreter 5 months ago

#426 - Proposal - New external package - rebased

Issue - State: open - Opened by TimothyStiles 5 months ago - 2 comments
Labels: enhancement, help wanted, medium priority, intermediate, stale

#425 - Update tutorials no gitpod

Pull Request - State: closed - Opened by TimothyStiles 5 months ago

#424 - Grant blocking issues bot write access to PRs

Pull Request - State: closed - Opened by carreter 5 months ago

#423 - Create nightly, dev, and stable build channels

Issue - State: open - Opened by carreter 5 months ago
Labels: enhancement, help wanted, high priority, devops, intermediate

#422 - Proposal: Create a biological reviewers group

Issue - State: open - Opened by TimothyStiles 5 months ago - 2 comments
Labels: needs-triage, proposal, stale

#421 - Notify on issue being labeled with help wanted

Pull Request - State: closed - Opened by carreter 5 months ago

#420 - Comment out info lines of pull request template

Pull Request - State: closed - Opened by carreter 5 months ago

#419 - Devops cleanup

Pull Request - State: closed - Opened by TimothyStiles 5 months ago

#418 - changed parameters in .goreleaser.yml

Pull Request - State: closed - Opened by TimothyStiles 5 months ago

#416 - migrated namespace from TimothyStiles/poly to bebop/poly

Pull Request - State: closed - Opened by TimothyStiles 5 months ago

#415 - more permanent fix to start codon regression

Pull Request - State: open - Opened by TimothyStiles 5 months ago - 2 comments

#414 - patched start codon regression

Pull Request - State: closed - Opened by TimothyStiles 5 months ago

#413 - Each fragment in a PCR amplification should have a circular tag

Issue - State: open - Opened by Koeng101 6 months ago - 1 comment
Labels: proposal, stale

#412 - Remove start codon check

Issue - State: closed - Opened by Koeng101 6 months ago - 1 comment

#411 - #360 Bwt

Pull Request - State: closed - Opened by TwFlem 6 months ago - 8 comments

#410 - Removed update weights

Pull Request - State: closed - Opened by Koeng101 6 months ago

#409 - fixed bug where linear, non-directional, single cuts were copying and not just moving overhangs from the fragment sequence.

Pull Request - State: closed - Opened by TimothyStiles 6 months ago

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

Pull Request - State: closed - Opened by TimothyStiles 6 months ago - 1 comment

#407 - renamed OptimizeSequence to just Optimize.

Pull Request - State: closed - Opened by TimothyStiles 6 months ago

#404 - added example test for mash usage.

Pull Request - State: closed - Opened by TimothyStiles 6 months ago

#403 - Add example test to MASH

Issue - State: closed - Opened by TimothyStiles 6 months ago - 1 comment
Labels: bug, needs-triage

#402 - Improve Hash2Fragment by using a map to validate allowed sequence characters

Pull Request - State: closed - Opened by matiasinsaurralde 6 months ago - 5 comments

#401 - Bump Golang version

Pull Request - State: closed - Opened by matiasinsaurralde 6 months ago - 2 comments

#400 - Proposal: create a distance package for Mash, Geometric string distance, and other distance metrics.

Issue - State: closed - Opened by TimothyStiles 6 months ago - 4 comments
Labels: proposal, stale

#399 - Tutorial and example tests for refactored golden gate cloning

Issue - State: open - Opened by TimothyStiles 6 months ago - 1 comment
Labels: needs-triage, stale

#398 - Add seqhash v2

Pull Request - State: closed - Opened by Koeng101 6 months ago - 4 comments

#397 - Compressed Seqhash

Issue - State: closed - Opened by Koeng101 6 months ago
Labels: enhancement, good first issue, wontfix, easy, low priority

#396 - Poly n Plannotate

Issue - State: closed - Opened by Koeng101 6 months ago - 5 comments
Labels: enhancement, help wanted, intermediate

#395 - mash: optimize mash similarity function, add benchmark

Pull Request - State: closed - Opened by matiasinsaurralde 7 months ago

#394 - Io to bio with genbank fixes

Pull Request - State: closed - Opened by abondrn 7 months ago

#393 - Cloning refactor and data race fix

Pull Request - State: closed - Opened by TwFlem 7 months ago - 3 comments

#392 - Simplifying codon table interface

Issue - State: closed - Opened by cachemoi 7 months ago - 2 comments
Labels: enhancement, needs-triage

#391 - Methylated GoldenGates

Pull Request - State: closed - Opened by Koeng101 7 months ago - 4 comments

#390 - Simulate enzyme methylation through lowercasing

Issue - State: closed - Opened by Koeng101 7 months ago

#389 - Genbank parser fixes

Pull Request - State: closed - Opened by abondrn 7 months ago - 1 comment

#388 - Genbank import and export from JSON should include feature sequences

Issue - State: closed - Opened by Koeng101 7 months ago - 2 comments
Labels: enhancement, help wanted, good first issue, wontfix, easy, low priority

#387 - Add FragmentWithOverhangs

Pull Request - State: closed - Opened by Koeng101 7 months ago - 3 comments

#386 - patched genbank parser and builder to handle BASE COUNT.

Pull Request - State: closed - Opened by TimothyStiles 7 months ago

#385 - created parser regression test for nested sublocations.

Pull Request - State: closed - Opened by TimothyStiles 7 months ago

#384 - Genbank location parser breaks on parsing this location.

Issue - State: closed - Opened by TimothyStiles 7 months ago - 1 comment
Labels: bug, help wanted, high priority, hard

#383 - Genbank parser doesn't handle feature attributes with colliding names.

Issue - State: open - Opened by TimothyStiles 8 months ago - 5 comments
Labels: bug, help wanted, high priority, hard, stale

#382 - Hacktoberfest Scratchpad

Pull Request - State: closed - Opened by abondrn 8 months ago

#380 - Concurrent mashing

Issue - State: closed - Opened by Koeng101 8 months ago - 2 comments
Labels: enhancement, wontfix, easy, low priority, stale

#379 - Fix YAML syntax error in take.yml

Pull Request - State: closed - Opened by carreter 8 months ago

#378 - Fix PCR bug (issue #279).

Pull Request - State: closed - Opened by carreter 8 months ago

#377 - Allow non-contributors to take an issue with .take

Pull Request - State: closed - Opened by carreter 8 months ago

#375 - Document all these workflow changes in `CONTRIBUTING.md`

Issue - State: closed - Opened by carreter 8 months ago - 1 comment

#372 - Reduce number of reviewers necessary for merge

Issue - State: closed - Opened by carreter 8 months ago - 5 comments
Labels: easy, devops, medium priority, proposal

#371 - Add `CHANGELOG.md` with current unreleased changes.

Pull Request - State: closed - Opened by carreter 8 months ago

#370 - Add a pull request template.

Pull Request - State: closed - Opened by carreter 8 months ago

#369 - This project should have a `CHANGELOG.md`

Issue - State: closed - Opened by carreter 8 months ago - 1 comment
Labels: documentation, high priority, easy

#368 - Update issue templates and disable blank issues.

Pull Request - State: closed - Opened by carreter 8 months ago

#367 - Refactor `clone` package

Issue - State: open - Opened by carreter 8 months ago - 5 comments
Labels: enhancement, ux, high priority, intermediate, stale

#366 - Create Automated Benchmarking Suite

Issue - State: open - Opened by TimothyStiles 8 months ago - 5 comments
Labels: devops, low priority, hard, stale

#365 - Move pipelines to more reproducible platform with less YAML

Issue - State: open - Opened by TimothyStiles 8 months ago - 11 comments
Labels: devops, medium priority, intermediate

#364 - Improve and standardize parsing API

Issue - State: open - Opened by carreter 8 months ago - 1 comment
Labels: enhancement, ux, high priority, hard, stale

#363 - Write more thorough explanation of alignment algorithms in align.go

Issue - State: open - Opened by carreter 8 months ago - 1 comment
Labels: documentation, low priority, intermediate, stale

#362 - Create a tutorial series around a real-world, working example

Issue - State: open - Opened by carreter 8 months ago - 4 comments
Labels: documentation, high priority, hard, stale

#361 - Implement LinearFold for prediction of RNA secondary structure

Issue - State: open - Opened by carreter 8 months ago - 6 comments
Labels: enhancement, easy, medium priority, stale

#360 - Implement Burrows-Wheeler transform

Issue - State: closed - Opened by carreter 8 months ago - 5 comments
Labels: good first issue, proposal, stale

#359 - Implement Gibson Assembly

Issue - State: open - Opened by carreter 8 months ago - 5 comments
Labels: enhancement, high priority, easy, stale

#358 - Add the poly Google group email as a method of contact.

Pull Request - State: closed - Opened by carreter 8 months ago - 2 comments

#357 - Add a CIF parser

Pull Request - State: open - Opened by carreter 8 months ago - 1 comment

#356 - MASH template matching

Issue - State: closed - Opened by Koeng101 8 months ago - 2 comments
Labels: enhancement, help wanted, medium priority, intermediate

#355 - Pileup parsing deletion with .

Issue - State: open - Opened by Koeng101 8 months ago - 4 comments
Labels: enhancement, medium priority, hard, stale

#354 - Mark issues and PRs as stale after 2 months

Pull Request - State: closed - Opened by carreter 8 months ago

#353 - Add "blocked by" relationships between issues/PRs

Pull Request - State: closed - Opened by carreter 8 months ago

#352 - `Feature.GetSequence()` always returns a nil error value

Issue - State: open - Opened by carreter 8 months ago - 7 comments
Labels: bug, help wanted, good first issue, easy, low priority, stale

#351 - Common Genbank `Feature.Type` values should be enumerated

Issue - State: open - Opened by carreter 8 months ago - 4 comments
Labels: enhancement, help wanted, good first issue, easy, low priority, stale

#350 - Add stats to codon tables

Pull Request - State: closed - Opened by cachemoi 8 months ago - 11 comments

#349 - Biowasm minimap2/samtools integration

Issue - State: closed - Opened by Koeng101 8 months ago - 3 comments
Labels: enhancement, help wanted, medium priority, hard, stale

#348 - Enable line-length linter `lll` for comments

Issue - State: closed - Opened by carreter 8 months ago - 1 comment
Labels: wontfix

#347 - Create top-level `types.go` to define types shared across packages

Issue - State: open - Opened by carreter 8 months ago - 6 comments
Labels: question, easy, proposal

#346 - Improvements to issue/PR labeling/management

Issue - State: open - Opened by carreter 8 months ago - 15 comments
Labels: documentation, enhancement, devops, medium priority, intermediate, stale

#345 - `CODE_OF_CONDUCT.md` missing contact under Enforcement section

Issue - State: closed - Opened by carreter 8 months ago - 8 comments
Labels: documentation, easy, low priority

#344 - created a super minimal mash function for sketching sequences.

Pull Request - State: closed - Opened by TimothyStiles 8 months ago - 4 comments
Labels: help wanted

#343 - Re-enable golangci-lint.yml, turn on linters, and lint.

Pull Request - State: closed - Opened by carreter 8 months ago

#342 - `Gff.AddFeature()` code is misleading and mutates `Feature` state

Issue - State: open - Opened by carreter 8 months ago - 5 comments
Labels: bug, good first issue, easy, medium priority, stale

#341 - Add svb compression to slow5

Pull Request - State: closed - Opened by Koeng101 8 months ago - 4 comments

#340 - Add a newline normalizing wrapper for io.Readers

Pull Request - State: open - Opened by carreter 8 months ago - 10 comments
Labels: blocked, stale

#339 - io->bio

Pull Request - State: closed - Opened by Koeng101 9 months ago - 29 comments

#337 - Add fasta2 package

Pull Request - State: closed - Opened by folago 9 months ago - 6 comments
Labels: duplicate

#333 - minimally functioning sam parser

Pull Request - State: closed - Opened by Koeng101 9 months ago - 3 comments
Labels: blocked

#327 - slow5 doesn't detect newline

Issue - State: open - Opened by Koeng101 10 months ago - 4 comments
Labels: bug, easy, medium priority, stale

#322 - Ensure Non-Met start codons map to Met on translation

Pull Request - State: closed - Opened by carreter 10 months ago

#313 - Failed to parse Saccharomyces cerevisiae S288C chromosome IX

Issue - State: open - Opened by Koeng101 12 months ago - 8 comments
Labels: bug, high priority, intermediate

GitHub / bebop/poly issues and pull requests