bebop/poly

Issues

• Genbank parser needs heavy refactor or a rewrite

  #434 opened a year ago by carreter
  10

• Implement Gibson Assembly

  #359 opened a year ago by carreter
  5

• Proposal: create a distance package for Mash, Geometric string distance, and other distance metrics.

  #400 opened 8 months ago by TimothyStiles
  4

• Turn on `revive` linter in golangci config

  #442 opened a year ago by carreter
  1

• Refactor `clone` package

  #367 opened a year ago by carreter
  5

• Tutorial and example tests for refactored golden gate cloning

  #399 opened a year ago by TimothyStiles
  1

• Proposal: Create a biological reviewers group

  #422 opened a year ago by TimothyStiles
  2

• Proposal - New external package - rebased

  #426 opened a year ago by TimothyStiles
  2

• Genbank parser doesn't handle feature attributes with colliding names.

  #383 opened a year ago by TimothyStiles
  5

• Each fragment in a PCR amplification should have a circular tag

  #413 opened a year ago by Koeng101
  1

• Implement Burrows-Wheeler transform

  #360 opened a year ago by carreter
  5

• `Gff.AddFeature()` code is misleading and mutates `Feature` state

  #342 opened a year ago by carreter
  5

• Common Genbank `Feature.Type` values should be enumerated

  #351 opened a year ago by carreter
  4

• slow5 doesn't detect newline

  #327 opened a year ago by Koeng101
  4

• Failed to parse Saccharomyces cerevisiae S288C chromosome IX

  #313 opened 2 years ago by Koeng101
  8

• `Feature.GetSequence()` always returns a nil error value

  #352 opened a year ago by carreter
  7

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

  #347 opened a year ago by carreter
  6

• Improvements to issue/PR labeling/management

  #346 opened a year ago by carreter
  16

• Create nightly, dev, and stable build channels

  #423 opened a year ago by carreter
  1

• Move pipelines to more reproducible platform with less YAML

  #365 opened a year ago by TimothyStiles
  14

• Reduce number of reviewers necessary for merge

  #372 opened a year ago by carreter
  5

• Genbank import and export from JSON should include feature sequences

  #388 opened a year ago by Koeng101
  2

• Add example test to MASH

  #403 opened a year ago by TimothyStiles
  1

• Remove start codon check

  #412 opened a year ago by Koeng101
  1

• Implement LinearFold for prediction of RNA secondary structure

  #361 opened a year ago by carreter
  6

• Simulate enzyme methylation through lowercasing

  #390 opened a year ago by Koeng101
  0

• MASH template matching

  #356 opened a year ago by Koeng101
  2

• Compressed Seqhash

  #397 opened a year ago by Koeng101
  0

• Poly n Plannotate

  #396 opened a year ago by Koeng101
  5

• Biowasm minimap2/samtools integration

  #349 opened a year ago by Koeng101
  3

• Concurrent mashing

  #380 opened a year ago by Koeng101
  2

• Create a tutorial series around a real-world, working example

  #362 opened a year ago by carreter
  4

• Create Automated Benchmarking Suite

  #366 opened a year ago by TimothyStiles
  5

• Pileup parsing deletion with .

  #355 opened a year ago by Koeng101
  4

• Write more thorough explanation of alignment algorithms in align.go

  #363 opened a year ago by carreter
  1

• Improve and standardize parsing API

  #364 opened a year ago by carreter
  1

• `CODE_OF_CONDUCT.md` missing contact under Enforcement section

  #345 opened a year ago by carreter
  8

• Simplifying codon table interface

  #392 opened a year ago by cachemoi
  2

• Genbank location parser breaks on parsing this location.

  #384 opened a year ago by TimothyStiles
  1

• Enable line-length linter `lll` for comments

  #348 opened a year ago by carreter
  1

• Document all these workflow changes in `CONTRIBUTING.md`

  #375 opened a year ago by carreter
  1

• This project should have a `CHANGELOG.md`

  #369 opened a year ago by carreter
  1

• Fail to parse Saccharomyces cerevisiae S288C chromosome I

  #310 opened a year ago by Koeng101
  4

• fastq de-aligned

  #325 opened a year ago by Koeng101
  2

• fastq doesnt handle optionals well

  #323 opened a year ago by Koeng101
  0

• fastq write gz

  #324 opened a year ago by Koeng101
  0

• Translate should have a setting to set first codon to M

  #305 opened a year ago by Koeng101
  2

• JCVI-Syn3a fails to read

  #303 opened a year ago by Koeng101
  1

• JCVI codon table generation is flat-out-wrong

  #306 opened a year ago by Koeng101
  2

• Functions for split sequence for scarless assembly using optimal overhangs

  #317 opened 2 years ago by isaacguerreir
  3