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

Refactor low-level parsing and hashing #29

Open
wants to merge 4 commits into
base: main
Choose a base branch
from
Open

Conversation

camillescott
Copy link
Owner

@camillescott camillescott commented Apr 1, 2022

  • Add a kmer iterator compliant with STL InputIterator
  • Add a kmer iterator that skips invalid positions
  • Add a parser that does not validate on initial sequence read
  • Maybe: once-again remove exceptions from low level validation, in favor of std::variant with error codes.
  • Clean up and centralize exception handling
  • Remove all raw C-strings from hashshifter and extenders

For the latter: exceptions in the validation and hashing code introduces approximately 20% overhead! I removed them at one point, but added them back in because of some edge cases.

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

Successfully merging this pull request may close these issues.

1 participant