Allow for ignoring reverse complements when checking neighbours#43
Merged
jermp merged 1 commit intojermp:masterfrom Feb 19, 2024
Merged
Allow for ignoring reverse complements when checking neighbours#43jermp merged 1 commit intojermp:masterfrom
jermp merged 1 commit intojermp:masterfrom
Conversation
Owner
|
Hi Harun and thanks for this! The bool was indeed necessary.
The correct implementation is the one you provided, with the bool being |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Since the k-mer lookup methods allow for ignoring reverse complements when checking the dictionary, I adapted the neighbourhood search methods to also allow for this.
I'm not sure if the current way of implementing neighbourhood searches is intended behaviour or a bug since the paper mentions that you consider both orientations of a k-mer to be equivalent.
Please let me know if you have any comments or if you'd like me to adapt some unit tests to check this extra functionality.