Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Use bio crate to represent genomes #18

Open
2 tasks
sebschmi opened this issue Jul 20, 2020 · 0 comments
Open
2 tasks

Use bio crate to represent genomes #18

sebschmi opened this issue Jul 20, 2020 · 0 comments
Labels
enhancement New feature or request

Comments

@sebschmi
Copy link
Collaborator

sebschmi commented Jul 20, 2020

Apparently the bio crate contains all the functionality to store sequences compactly, so no reason to do that myself.

Clarification: The compact-genome crate should stay, as it contains the traits for genomes, but it should be enhanced with a compact representation using bio, as well as an abstraction from concrete alphabets using bio.

  • make plan
  • add SimpleGenome, CompactGenome and DefaultGenome type aliases where: Simple is the fastest, compact the smallest, and default a good compromise between both.
@sebschmi sebschmi added the enhancement New feature or request label Jul 20, 2020
@sebschmi sebschmi added this to the Load bigraph from bcalm2 milestone Jul 20, 2020
@sebschmi sebschmi removed this from the Load bigraph from bcalm2 milestone Jul 21, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

No branches or pull requests

1 participant