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

Graphbuild could use optimized representation #16

Open
jakebiesinger opened this issue Oct 21, 2013 · 2 comments
Open

Graphbuild could use optimized representation #16

jakebiesinger opened this issue Oct 21, 2013 · 2 comments

Comments

@jakebiesinger
Copy link
Contributor

@JavierJia @Nan-Zhang
Currently, graphbuild uses and outputs VKmer keys and VKmer edges. They could instead use Kmer keys and a single letter for each neighbor.

@Nan-Zhang
Copy link
Collaborator

@jakebiesinger , actually the graphbuilding currently already used Kmer to represent the key of intermediate results(after keyvalueparser, and local aggregater), and the final output's key is still VKmer. So you mean we also could change the key of final results of graphbuliding to Kmer?

@jakebiesinger
Copy link
Contributor Author

By "a single letter for each neighbor", I meant that given your Kmer and a single letter and direction, you could derive your neighbor's kmer. So during intermediate stages, graphbuild could use this altered representation.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

2 participants